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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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Seoane R, Lama-Díaz T, Romero AM, El Motiam A, Martínez-Férriz A, Vidal S, Bouzaher YH, Blanquer M, Tolosa RM, Castillo Mewa J, Rodríguez MS, García-Sastre A, Xirodimas D, Sutherland JD, Barrio R, Alepuz P, Blanco MG, Farràs R, Rivas C. SUMOylation modulates eIF5A activities in both yeast and pancreatic ductal adenocarcinoma cells. Cell Mol Biol Lett 2024; 29:15. [PMID: 38229033 PMCID: PMC10790418 DOI: 10.1186/s11658-024-00533-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND The eukaryotic translation initiation protein eIF5A is a highly conserved and essential factor that plays a critical role in different physiological and pathological processes including stress response and cancer. Different proteomic studies suggest that eIF5A may be a small ubiquitin-like modifier (SUMO) substrate, but whether eIF5A is indeed SUMOylated and how relevant is this modification for eIF5A activities are still unknown. METHODS SUMOylation was evaluated using in vitro SUMOylation assays, Histidine-tagged proteins purification from His6-SUMO2 transfected cells, and isolation of endogenously SUMOylated proteins using SUMO-binding entities (SUBES). Mutants were engineered by site-directed mutagenesis. Protein stability was measured by a cycloheximide chase assay. Protein localization was determined using immunofluorescence and cellular fractionation assays. The ability of eIF5A1 constructs to complement the growth of Saccharomyces cerevisiae strains harboring thermosensitive mutants of a yeast EIF5A homolog gene (HYP2) was analyzed. The polysome profile and the formation of stress granules in cells expressing Pab1-GFP (a stress granule marker) by immunofluorescence were determined in yeast cells subjected to heat shock. Cell growth and migration of pancreatic ductal adenocarcinoma PANC-1 cells overexpressing different eIF5A1 constructs were evaluated using crystal violet staining and transwell inserts, respectively. Statistical analysis was performed with GraphPad Software, using unpaired Student's t-test, or one-way or two-way analysis of variance (ANOVA). RESULTS We found that eIF5A is modified by SUMO2 in vitro, in transfected cells and under endogenous conditions, revealing its physiological relevance. We identified several SUMO sites in eIF5A and found that SUMOylation modulates both the stability and the localization of eIF5A in mammalian cells. Interestingly, the SUMOylation of eIF5A responds to specific stresses, indicating that it is a regulated process. SUMOylation of eIF5A is conserved in yeast, the eIF5A SUMOylation mutants are unable to completely suppress the defects of HYP2 mutants, and SUMOylation of eIF5A is important for both stress granules formation and disassembly of polysomes induced by heat-shock. Moreover, mutation of the SUMOylation sites in eIF5A abolishes its promigratory and proproliferative activities in PANC-1 cells. CONCLUSIONS SUMO2 conjugation to eIF5A is a stress-induced response implicated in the adaptation of yeast cells to heat-shock stress and required to promote the growth and migration of pancreatic ductal adenocarcinoma cells.
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Affiliation(s)
- Rocío Seoane
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tomás Lama-Díaz
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
- Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - Antonia María Romero
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, Burjassot, 46100, Valencia, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), C/ Américo Vespucio 24, Edificio Cabimer, 41092, Seville, Spain
| | - Ahmed El Motiam
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | | | - Santiago Vidal
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yanis H Bouzaher
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
| | - María Blanquer
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
| | - Rocío M Tolosa
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
| | - Juan Castillo Mewa
- Research Department in Genomics and Proteomics, Instituto Conmemorativo Gorgas de Estudios de la Salud, 0816-02593, Panamá, Republic of Panama
| | - Manuel S Rodríguez
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31400, Toulouse, France
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dimitris Xirodimas
- Montpellier Cell Biology Research Center (CRBM), CNRS-UMR 5237 Université de Montpellier, Montpellier, France
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Paula Alepuz
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, Burjassot, 46100, Valencia, Spain
- Instituto Bio TecMed, Universitat de València, Burjassot, 46100, Valencia, Spain
| | - Miguel G Blanco
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
- Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - Rosa Farràs
- Centro de Investigación Príncipe Felipe, 46012, Valencia, Spain
| | - Carmen Rivas
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain.
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología (CNB), CSIC, Darwin 3, 28049, Madrid, Spain.
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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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4
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Espinosa-Gil S, Ivanova S, Alari-Pahissa E, Denizli M, Villafranca-Magdalena B, Viñas-Casas M, Bolinaga-Ayala I, Gámez-García A, Faundez-Vidiella C, Colas E, Lopez-Botet M, Zorzano A, Lizcano JM. MAP kinase ERK5 modulates cancer cell sensitivity to extrinsic apoptosis induced by death-receptor agonists. Cell Death Dis 2023; 14:715. [PMID: 37919293 PMCID: PMC10622508 DOI: 10.1038/s41419-023-06229-6] [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: 08/29/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
Death receptor ligand TRAIL is a promising cancer therapy due to its ability to selectively trigger extrinsic apoptosis in cancer cells. However, TRAIL-based therapies in humans have shown limitations, mainly due inherent or acquired resistance of tumor cells. To address this issue, current efforts are focussed on dissecting the intracellular signaling pathways involved in resistance to TRAIL, to identify strategies that sensitize cancer cells to TRAIL-induced cytotoxicity. In this work, we describe the oncogenic MEK5-ERK5 pathway as a critical regulator of cancer cell resistance to the apoptosis induced by death receptor ligands. Using 2D and 3D cell cultures and transcriptomic analyses, we show that ERK5 controls the proteostasis of TP53INP2, a protein necessary for full activation of caspase-8 in response to TNFα, FasL or TRAIL. Mechanistically, ERK5 phosphorylates and induces ubiquitylation and proteasomal degradation of TP53INP2, resulting in cancer cell resistance to TRAIL. Concordantly, ERK5 inhibition or genetic deletion, by stabilizing TP53INP2, sensitizes cancer cells to the apoptosis induced by recombinant TRAIL and TRAIL/FasL expressed by Natural Killer cells. The MEK5-ERK5 pathway regulates cancer cell proliferation and survival, and ERK5 inhibitors have shown anticancer activity in preclinical models of solid tumors. Using endometrial cancer patient-derived xenograft organoids, we propose ERK5 inhibition as an effective strategy to sensitize cancer cells to TRAIL-based therapies.
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Affiliation(s)
- Sergio Espinosa-Gil
- Departament de Bioquímica i Biologia Molecular and Institut de Neurociències. Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Protein Kinases in Cancer Research. Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Saska Ivanova
- IRB Institute for Research in Biomedicine, Barcelona, Spain
- CIBERDEM, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Melek Denizli
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona. CIBERONC, Barcelona, Spain
| | - Beatriz Villafranca-Magdalena
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona. CIBERONC, Barcelona, Spain
| | - Maria Viñas-Casas
- Departament de Bioquímica i Biologia Molecular and Institut de Neurociències. Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Protein Kinases in Cancer Research. Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Idoia Bolinaga-Ayala
- Departament de Bioquímica i Biologia Molecular and Institut de Neurociències. Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Protein Kinases in Cancer Research. Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Andrés Gámez-García
- Departament de Bioquímica i Biologia Molecular and Institut de Neurociències. Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Claudia Faundez-Vidiella
- Departament de Bioquímica i Biologia Molecular and Institut de Neurociències. Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Protein Kinases in Cancer Research. Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Eva Colas
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona. CIBERONC, Barcelona, Spain
| | - Miguel Lopez-Botet
- University Pompeu Fabra, Barcelona, Spain
- Immunology laboratory, Dpt. of Pathology, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Antonio Zorzano
- IRB Institute for Research in Biomedicine, Barcelona, Spain
- CIBERDEM, Instituto de Salud Carlos III, Madrid, Spain
- Departament de Bioquímica i Biomedicina Molecular, Facultat de Biología, Universitat de Barcelona, Barcelona, Spain
| | - José Miguel Lizcano
- Departament de Bioquímica i Biologia Molecular and Institut de Neurociències. Facultat de Medicina, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.
- Protein Kinases in Cancer Research. Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.
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Li K, Xia Y, He J, Wang J, Li J, Ye M, Jin X. The SUMOylation and ubiquitination crosstalk in cancer. J Cancer Res Clin Oncol 2023; 149:16123-16146. [PMID: 37640846 DOI: 10.1007/s00432-023-05310-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND The cancer occurrence and progression are largely affected by the post-translational modifications (PTMs) of proteins. Currently, it has been shown that the relationship between ubiquitination and SUMOylation is highly complex and interactive. SUMOylation affects the process of ubiquitination and degradation of substrates. Contrarily, SUMOylation-related proteins are also regulated by the ubiquitination process thus altering their protein levels or activity. Emerging evidence suggests that the abnormal regulation between this crosstalk may lead to tumorigenesis. PURPOSE In this review, we have discussed the study of the relationship between ubiquitination and SUMOylation, as well as the possibility of a corresponding application in tumor therapy. METHODS The relevant literatures from PubMed have been reviewed for this article. CONCLUSION The interaction between ubiquitination and SUMOylation is crucial for the occurrence and development of cancer. A greater understanding of the crosstalk of SUMOylation and ubiquitination may be more conducive to the development of more selective and effective SUMOylation inhibitors, as well as a promotion of synergy with other tumor treatment strategies.
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Affiliation(s)
- Kailang Li
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Yongming Xia
- Department of Oncology, Yuyao People's Hospital of Zhejiang, Yuyao, 315400, Zhejiang, China
| | - Jian He
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Jie Wang
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Jingyun Li
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Meng Ye
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China.
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
| | - Xiaofeng Jin
- Department of Oncology, The First Hospital of Ningbo University, Ningbo, 315020, China.
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, China.
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6
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Alvarez-Mora MI, Garrabou G, Molina-Porcel L, Grillo-Risco R, Garcia-Garcia F, Barcos T, Cantó-Santos J, Rodriguez-Revenga L. Exploration of SUMO2/3 Expression Levels and Autophagy Process in Fragile X-Associated Tremor/Ataxia Syndrome: Addressing Study Limitations and Insights for Future Research. Cells 2023; 12:2364. [PMID: 37830578 PMCID: PMC10571773 DOI: 10.3390/cells12192364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/21/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder that appears in adult FMR1 premutation carriers. The neuropathological hallmark of FXTAS is an intranuclear inclusion in neurons and astrocytes. Nearly 200 different proteins have been identified in FXTAS inclusions, being the small ubiquitin-related modifier 2 (SUMO2), ubiquitin and p62 the most highly abundant. These proteins are components of the protein degradation machinery. This study aimed to characterize SUMO2/3 expression levels and autophagy process in human postmortem brain samples and skin fibroblast cultures from FXTAS patients. Results revealed that FXTAS postmortem brain samples are positive for SUMO2/3 conjugates and supported the idea that SUMO2/3 accumulation is involved in inclusion formation. Insights from RNA-sequencing data indicated that SUMOylation processes are significantly upregulated in FXTAS samples. In addition, the analysis of the autophagy flux showed the accumulation of p62 protein levels and autophagosomes in skin fibroblasts from FXTAS patients. Similarly, gene set analysis evidenced a significant downregulation in gene ontology terms related to autophagy in FXTAS samples. Overall, this study provides new evidence supporting the role of SUMOylation and autophagic processes in the pathogenic mechanisms underlying FXTAS.
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Affiliation(s)
- Maria Isabel Alvarez-Mora
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, 08036 Barcelona, Spain; (M.I.A.-M.); (T.B.)
- CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III, 08036 Barcelona, Spain; (G.G.)
- Fundacio de Recerca Clínic Barcelona-Institut d’Investigacions Biomediques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain;
| | - Glòria Garrabou
- CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III, 08036 Barcelona, Spain; (G.G.)
- Inherited Metabolic Diseases and Muscle Disorders’ Research Laboratory (U722), Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Internal Medicine Department––Hospital Clínic Clinic of Barcelona, 08036 Barcelona, Spain
| | - Laura Molina-Porcel
- Fundacio de Recerca Clínic Barcelona-Institut d’Investigacions Biomediques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain;
- Alzheimer’s Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clinic, 08036 Barcelona, Spain
- Neurological Tissue Bank of the Biobanc-Hospital Clinic-FCRB-IDIBAPS, 08036 Barcelona, Spain
| | - Ruben Grillo-Risco
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain; (R.G.-R.); (F.G.-G.)
| | - Francisco Garcia-Garcia
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain; (R.G.-R.); (F.G.-G.)
| | - Tamara Barcos
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, 08036 Barcelona, Spain; (M.I.A.-M.); (T.B.)
| | - Judith Cantó-Santos
- CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III, 08036 Barcelona, Spain; (G.G.)
- Inherited Metabolic Diseases and Muscle Disorders’ Research Laboratory (U722), Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Internal Medicine Department––Hospital Clínic Clinic of Barcelona, 08036 Barcelona, Spain
| | - Laia Rodriguez-Revenga
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, 08036 Barcelona, Spain; (M.I.A.-M.); (T.B.)
- CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III, 08036 Barcelona, Spain; (G.G.)
- Fundacio de Recerca Clínic Barcelona-Institut d’Investigacions Biomediques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain;
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7
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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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8
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Beyond metabolic waste: lysine lactylation and its potential roles in cancer progression and cell fate determination. Cell Oncol (Dordr) 2023; 46:465-480. [PMID: 36656507 DOI: 10.1007/s13402-023-00775-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/21/2022] [Accepted: 11/26/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Lactate is an important metabolite derived from glycolysis under physiological and pathological conditions. The Warburg effect reveals the vital role of lactate in cancer progression. Numerous studies have reported crucial roles for lactate in cancer progression and cell fate determination. Lactylation, a novel posttranslational modification (PTM), has provided a new opportunity to investigate metabolic epigenetic regulation, and studies of this process have been initiated in a wide range of cancer cells, cancer-associated immune cells, and embryonic stem cells. CONCLUSION Lactylation is a novel and interesting mechanism of lactate metabolism linked to metabolic rewiring and epigenetic remodeling. It is a potential and hopeful target for cancer therapy. Here, we summarize the discovery of lactylation, the mechanisms of site modification, and progress in research on nonhistone lactylation. We focus on the potential roles of lactylation in cancer progression and cell fate determination and the possible therapeutic strategies for targeting lysine lactylation. Finally, we suggest some future research topics on lactylation to inspire some interesting ideas.
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9
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Liang M, Cai Z, Jiang Y, Huo H, Shen L, He B. SENP2 Promotes VSMC Phenotypic Switching via Myocardin De-SUMOylation. Int J Mol Sci 2022; 23:ijms232012637. [PMID: 36293488 PMCID: PMC9603890 DOI: 10.3390/ijms232012637] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Myocardin is a master regulator of smooth muscle cell (SMC) differentiation, which induces the expression of smooth-muscle-specific genes through its direct association with serum response factor (SRF). During the past two decades, significant insights have been obtained regarding the regulatory control of myocardin expression and transcriptional activity at the transcriptional, post-transcriptional, and post-translational levels. However, whether and how SUMOylation plays important roles in modulating myocardin function remain elusive. In this study, we found that myocardin is modified by SUMO-1 at lysine 573, which can be reversibly de-conjugated by SENP2. SUMO-1 modification promotes myocardin protein stability, whereas SENP2 facilitates its proteasome-dependent degradation. Moreover, we found that PIAS4 is the SUMO E3 ligase that enhances the SUMOylation and protein stability of myocardin. Most importantly, we found that SENP2 promotes phenotypic switching of VSMC. We therefore concluded that SENP2 promotes VSMC phenotypic switching via de-SUMOylation of myocardin and regulation of its protein stability.
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Affiliation(s)
| | | | | | | | | | - Ben He
- Correspondence: (L.S.); (B.H.)
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10
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Cai Z, Wang Z, Yuan R, Cui M, Lao Y, Wang Y, Nie P, Shen L, Yi J, He B. Redox-sensitive enzyme SENP3 mediates vascular remodeling via de-SUMOylation of β-catenin and regulation of its stability. EBioMedicine 2021; 67:103386. [PMID: 34000626 PMCID: PMC8138600 DOI: 10.1016/j.ebiom.2021.103386] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 12/12/2022] Open
Abstract
Background Oxidative stress plays critical pathophysiological roles in vascular remodeling-related cardiovascular diseases, including hypertension, atherosclerosis, and restenosis. Previous studies demonstrate that SENP3, a redox-sensitive SUMO2/3-specific protease, is strongly implicated in cancer development and progression. However, the role of SENP3 in vascular remodeling remains unknown. Methods We generated three mouse models of vascular remodeling due to low shear stress, hypertension, and atherosclerosis. The expression of SENP3 was determined by western blotting and/or immunofluorescence staining in cultured vascular smooth muscle cells (VSMCs), animal models, and human samples. The biological function of SENP3 in proliferation and migration of VSMC and vascular remodeling was further investigated in vitro and in vivo models. Findings SENP3 was highly expressed in VSMCs of remodeled arteries, accompanied by elevated reactive oxygen species (ROS) levels. In cultured VSMCs, SENP3 protein levels were enhanced by oxidized low-density lipoprotein and Angiotensin II in a ROS-dependent manner. SENP3 overexpression significantly promoted and sh-RNA-mediated knockdown markedly inhibited VSMCs proliferation and migration. Immunofluorescence staining showed that SENP3 expression was correlated with intimal area in remodeled arteries. Furthermore, we demonstrated that SENP3 interacted with β-catenin and inhibited its proteasome-dependent degradation via de-SUMOylation of β-catenin. Most importantly, SENP3+/− mice exhibited alleviated vascular remodeling. Interpretation Our results highlight the important function of SENP3 as a redox sensor and mediator in vascular remodeling.
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Affiliation(s)
- Zhaohua Cai
- Heart Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zi Wang
- Heart Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ruosen Yuan
- Heart Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Mingli Cui
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou 256600, China
| | - Yimin Lao
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiaotong Universtity School of Medicine, Shanghai 200025, China
| | - Ying Wang
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiaotong Universtity School of Medicine, Shanghai 200025, China
| | - Peng Nie
- Department of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200127, China
| | - Linghong Shen
- Heart Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jing Yi
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiaotong Universtity School of Medicine, Shanghai 200025, China.
| | - Ben He
- Heart Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China.
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11
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Lork M, Lieber G, Hale BG. Proteomic Approaches to Dissect Host SUMOylation during Innate Antiviral Immune Responses. Viruses 2021; 13:528. [PMID: 33806893 PMCID: PMC8004987 DOI: 10.3390/v13030528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 12/21/2022] Open
Abstract
SUMOylation is a highly dynamic ubiquitin-like post-translational modification that is essential for cells to respond to and resolve various genotoxic and proteotoxic stresses. Virus infections also constitute a considerable stress scenario for cells, and recent research has started to uncover the diverse roles of SUMOylation in regulating virus replication, not least by impacting antiviral defenses. Here, we review some of the key findings of this virus-host interplay, and discuss the increasingly important contribution that large-scale, unbiased, proteomic methodologies are making to discoveries in this field. We highlight the latest proteomic technologies that have been specifically developed to understand SUMOylation dynamics in response to cellular stresses, and comment on how these techniques might be best applied to dissect the biology of SUMOylation during innate immunity. Furthermore, we showcase a selection of studies that have already used SUMO proteomics to reveal novel aspects of host innate defense against viruses, such as functional cross-talk between SUMO proteins and other ubiquitin-like modifiers, viral antagonism of SUMO-modified antiviral restriction factors, and an infection-triggered SUMO-switch that releases endogenous retroelement RNAs to stimulate antiviral interferon responses. Future research in this area has the potential to provide new and diverse mechanistic insights into host immune defenses.
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Affiliation(s)
| | | | - Benjamin G. Hale
- Institute of Medical Virology, University of Zürich, 8057 Zürich, Switzerland; (M.L.); (G.L.)
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12
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Juncker M, Kim C, Reed R, Haas A, Schwartzenburg J, Desai S. ISG15 attenuates post-translational modifications of mitofusins and congression of damaged mitochondria in Ataxia Telangiectasia cells. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166102. [PMID: 33617986 DOI: 10.1016/j.bbadis.2021.166102] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 10/22/2022]
Abstract
Mitophagy is defective in several neurodegenerative diseases, including Ataxia Telangiectasia (A-T). However, the molecular mechanism underlying defective mitophagy in A-T is unknown. Literature indicates that damaged mitochondria are transported to the perinuclear region prior to their removal via mitophagy. Our previous work has indicated that conjugation of SUMO2 (Small Ubiquitin-like Modifier 2) to mitofusins (Mfns) may be necessary for congression of mitochondria into SUMO2-/ubiquitin-/LC3-positive compact structures resembling mito-aggresomes at the perinuclear region in CCCP-treated HEK293 cells. Here, we demonstrate that Mfns are SUMOylated, and mitochondria are transported to the perinuclear region; however, mitochondria fail to congress into mito-aggresome-like structures in CCCP-treated A-T cells. Defect in mitochondrial congression is causally related to constitutively elevated ISG15 (Interferon-Stimulated Gene 15), an antagonist of the ubiquitin pathway, in A-T cells. Suppression of the ISG15 pathway restores mitochondrial congression, reduce oxidative stress, and level of unhealthy mitochondria, which is suggestive of restoration of mitophagy in A-T cells. ISG15 is also constitutively elevated and mitophagy is defective in Amytrophic Lateral Sclerosis (ALS). The constitutively elevated ISG15 pathway therefore appears to be a common unifying biochemical mechanism underlying defective mitophagy in neurodegenerative disorders thus, implying the broader significance of our findings, and suggest the potential role of ISG15 inhibitors in their treatment.
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Affiliation(s)
- Meredith Juncker
- Department of Biochemistry & Molecular Biology, LSU Health Sciences Center-School of Medicine, 1901 Perdido Street, New Orleans, LA 70112, USA
| | - Catherine Kim
- Department of Biochemistry & Molecular Biology, LSU Health Sciences Center-School of Medicine, 1901 Perdido Street, New Orleans, LA 70112, USA
| | - Ryan Reed
- Department of Biochemistry & Molecular Biology, LSU Health Sciences Center-School of Medicine, 1901 Perdido Street, New Orleans, LA 70112, USA
| | - Arthur Haas
- Department of Biochemistry & Molecular Biology, LSU Health Sciences Center-School of Medicine, 1901 Perdido Street, New Orleans, LA 70112, USA
| | - Joshua Schwartzenburg
- Department of Biochemistry & Molecular Biology, LSU Health Sciences Center-School of Medicine, 1901 Perdido Street, New Orleans, LA 70112, USA
| | - Shyamal Desai
- Department of Biochemistry & Molecular Biology, LSU Health Sciences Center-School of Medicine, 1901 Perdido Street, New Orleans, LA 70112, USA.
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Boulanger M, Chakraborty M, Tempé D, Piechaczyk M, Bossis G. SUMO and Transcriptional Regulation: The Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies. Molecules 2021; 26:molecules26040828. [PMID: 33562565 PMCID: PMC7915335 DOI: 10.3390/molecules26040828] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
One major role of the eukaryotic peptidic post-translational modifier SUMO in the cell is transcriptional control. This occurs via modification of virtually all classes of transcriptional actors, which include transcription factors, transcriptional coregulators, diverse chromatin components, as well as Pol I-, Pol II- and Pol III transcriptional machineries and their regulators. For many years, the role of SUMOylation has essentially been studied on individual proteins, or small groups of proteins, principally dealing with Pol II-mediated transcription. This provided only a fragmentary view of how SUMOylation controls transcription. The recent advent of large-scale proteomic, modifomic and genomic studies has however considerably refined our perception of the part played by SUMO in gene expression control. We review here these developments and the new concepts they are at the origin of, together with the limitations of our knowledge. How they illuminate the SUMO-dependent transcriptional mechanisms that have been characterized thus far and how they impact our view of SUMO-dependent chromatin organization are also considered.
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Affiliation(s)
- Mathias Boulanger
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Mehuli Chakraborty
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Denis Tempé
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Marc Piechaczyk
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
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14
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Huoh YS, Wu B, Park S, Yang D, Bansal K, Greenwald E, Wong WP, Mathis D, Hur S. Dual functions of Aire CARD multimerization in the transcriptional regulation of T cell tolerance. Nat Commun 2020; 11:1625. [PMID: 32242017 PMCID: PMC7118133 DOI: 10.1038/s41467-020-15448-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/12/2020] [Indexed: 11/20/2022] Open
Abstract
Aggregate-like biomolecular assemblies are emerging as new conformational states with functionality. Aire, a transcription factor essential for central T cell tolerance, forms large aggregate-like assemblies visualized as nuclear foci. Here we demonstrate that Aire utilizes its caspase activation recruitment domain (CARD) to form filamentous homo-multimers in vitro, and this assembly mediates foci formation and transcriptional activity. However, CARD-mediated multimerization also makes Aire susceptible to interaction with promyelocytic leukemia protein (PML) bodies, sites of many nuclear processes including protein quality control of nuclear aggregates. Several loss-of-function Aire mutants, including those causing autoimmune polyendocrine syndrome type-1, form foci with increased PML body association. Directing Aire to PML bodies impairs the transcriptional activity of Aire, while dispersing PML bodies with a viral antagonist restores this activity. Our study thus reveals a new regulatory role of PML bodies in Aire function, and highlights the interplay between nuclear aggregate-like assemblies and PML-mediated protein quality control.
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Affiliation(s)
- Yu-San Huoh
- Department of Biological Chemistry and Molecular Pharmacology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
| | - Bin Wu
- Department of Biological Chemistry and Molecular Pharmacology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
- NTU Institute of Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Sehoon Park
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
| | - Darren Yang
- Department of Biological Chemistry and Molecular Pharmacology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Kushagra Bansal
- Department of Immunology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
- Molecular Biology & Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560 064, India
| | - Emily Greenwald
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
| | - Wesley P Wong
- Department of Biological Chemistry and Molecular Pharmacology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Diane Mathis
- Department of Immunology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology Blavatnik Institute at Harvard Medical School, Boston, MA, 02115, USA.
- Program in Cellular and Molecular Medicine Boston Children's Hospital, Boston, MA, 02115, USA.
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15
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Liebelt F, Sebastian RM, Moore CL, Mulder MPC, Ovaa H, Shoulders MD, Vertegaal ACO. SUMOylation and the HSF1-Regulated Chaperone Network Converge to Promote Proteostasis in Response to Heat Shock. Cell Rep 2020; 26:236-249.e4. [PMID: 30605679 PMCID: PMC6316133 DOI: 10.1016/j.celrep.2018.12.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/22/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022] Open
Abstract
The role of stress-induced increases in SUMO2/3 conjugation during the heat shock response (HSR) has remained enigmatic. We investigated SUMO signal transduction at the proteomic and functional level during the HSR in cells depleted of proteostasis network components via chronic heat shock factor 1 inhibition. In the recovery phase post heat shock, high SUMO2/3 conjugation was prolonged in cells lacking sufficient chaperones. Similar results were obtained upon inhibiting HSP90, indicating that increased chaperone activity during the HSR is critical for recovery to normal SUMO2/3 levels post-heat shock. Proteasome inhibition likewise prolonged SUMO2/3 conjugation, indicating that stress-induced SUMO2/3 targets are subsequently degraded by the ubiquitin-proteasome system. Functionally, we suggest that SUMOylation can enhance the solubility of target proteins upon heat shock, a phenomenon that we experimentally observed in vitro. Collectively, our results implicate SUMO2/3 as a rapid response factor that coordinates proteome degradation and assists the maintenance of proteostasis upon proteotoxic stress. Chaperone depletion delays recovery of SUMOylation in response to heat shock SUMOylated proteins are targeted to the proteasome during heat shock recovery Chaperone depletion impairs clearance of Ub/SUMO co-modified proteins after stress SUMO is a rapid response factor likely increasing protein solubility under heat shock
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Affiliation(s)
- Frauke Liebelt
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RA, the Netherlands
| | - Rebecca M Sebastian
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher L Moore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Monique P C Mulder
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RA, the Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RA, the Netherlands
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RA, the Netherlands.
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16
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Pérez Berrocal DA, Witting KF, Ovaa H, Mulder MPC. Hybrid Chains: A Collaboration of Ubiquitin and Ubiquitin-Like Modifiers Introducing Cross-Functionality to the Ubiquitin Code. Front Chem 2020; 7:931. [PMID: 32039151 PMCID: PMC6987259 DOI: 10.3389/fchem.2019.00931] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/20/2019] [Indexed: 01/31/2023] Open
Abstract
The Ubiquitin CODE constitutes a unique post-translational modification language relying on the covalent attachment of Ubiquitin (Ub) to substrates, with Ub serving as the minimum entity to generate a message that is translated into different cellular pathways. The creation of this message is brought about by the dedicated action of writers, erasers, and readers of the Ubiquitin CODE. This CODE is greatly expanded through the generation of polyUb chains of different architectures on substrates thus regulating their fate. Through additional post-translational modification by Ub-like proteins (UbL), hybrid Ub/UbL chains, which either alter the originally encrypted message or encode a completely new one, are formed. Hybrid Ub/UbL chains are generated under both stress or physiological conditions and seem to confer improved specificity and affinity toward their cognate receptors. In such a manner, their formation must play a specific, yet still undefined role in cellular signaling and thus understanding the UbCODE message is crucial. Here, we discuss the evidence for the existence of hybrid Ub/UbL chains in addition to the current understanding of its biology. The modification of Ub by another UbL complicates the deciphering of the spatial and temporal order of events warranting the development of a hybrid chain toolbox. We discuss this unmet need and expand upon the creation of tailored tools adapted from our previously established toolkit for the Ubiquitin Proteasome System to specifically target these hybrid Ub/UbL chains.
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Affiliation(s)
- David A Pérez Berrocal
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
| | - Katharina F Witting
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
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17
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Kumar R, Sabapathy K. RNF4—A Paradigm for SUMOylation‐Mediated Ubiquitination. Proteomics 2019; 19:e1900185. [DOI: 10.1002/pmic.201900185] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/13/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Ramesh Kumar
- Cancer & Stem Cell Biology Program Duke–NUS Medical School 8 College Road Singapore 169857 Singapore
| | - Kanaga Sabapathy
- Cancer & Stem Cell Biology Program Duke–NUS Medical School 8 College Road Singapore 169857 Singapore
- Laboratory of Molecular Carcinogenesis Division of Cellular & Molecular Research Humphrey Oei Institute of Cancer Research National Cancer Centre Singapore 11 Hospital Drive Singapore 169610 Singapore
- Department of Biochemistry National University of Singapore 8 Medical Drive Singapore 117597 Singapore
- Institute of Molecular and Cellular Biology 61 Biopolis Drive Singapore 138673 Singapore
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18
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Marinello M, Werner A, Giannone M, Tahiri K, Alves S, Tesson C, den Dunnen W, Seeler JS, Brice A, Sittler A. SUMOylation by SUMO2 is implicated in the degradation of misfolded ataxin-7 via RNF4 in SCA7 models. Dis Model Mech 2019; 12:dmm.036145. [PMID: 30559154 PMCID: PMC6361149 DOI: 10.1242/dmm.036145] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/04/2018] [Indexed: 01/10/2023] Open
Abstract
Perturbation of protein homeostasis and aggregation of misfolded proteins is a major cause of many human diseases. A hallmark of the neurodegenerative disease spinocerebellar ataxia type 7 (SCA7) is the intranuclear accumulation of mutant, misfolded ataxin-7 (polyQ-ATXN7). Here, we show that endogenous ATXN7 is modified by SUMO proteins, thus also suggesting a physiological role for this modification under conditions of proteotoxic stress caused by the accumulation of polyQ-ATXN7. Co-immunoprecipitation experiments, immunofluorescence microscopy and proximity ligation assays confirmed the colocalization and interaction of polyQ-ATXN7 with SUMO2 in cells. Moreover, upon inhibition of the proteasome, both endogenous SUMO2/3 and the RNF4 ubiquitin ligase surround large polyQ-ATXN7 intranuclear inclusions. Overexpression of RNF4 and/or SUMO2 significantly decreased levels of polyQ-ATXN7 and, upon proteasomal inhibition, led to a marked increase in the polyubiquitination of polyQ-ATXN7. This provides a mechanism for the clearance of polyQ-ATXN7 from affected cells that involves the recruitment of RNF4 by SUMO2/3-modified polyQ-ATXN7, thus leading to its ubiquitination and proteasomal degradation. In a SCA7 knock-in mouse model, we similarly observed colocalization of SUMO2/3 with polyQ-ATXN7 inclusions in the cerebellum and retina. Furthermore, we detected accumulation of SUMO2/3 high-molecular-mass species in the cerebellum of SCA7 knock-in mice, compared with their wild-type littermates, and changes in SUMO-related transcripts. Immunohistochemical analysis showed the accumulation of SUMO proteins and RNF4 in the cerebellum of SCA7 patients. Taken together, our results show that the SUMO pathway contributes to the clearance of aggregated ATXN7 and suggest that its deregulation might be associated with SCA7 disease progression.
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Affiliation(s)
- Martina Marinello
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France.,Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences et Lettres (PSL) Research University, Neurogenetics Group, 75013 Paris, France
| | - Andreas Werner
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Mariagiovanna Giannone
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France.,Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences et Lettres (PSL) Research University, Neurogenetics Group, 75013 Paris, France
| | - Khadija Tahiri
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France
| | - Sandro Alves
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France
| | - Christelle Tesson
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France.,Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences et Lettres (PSL) Research University, Neurogenetics Group, 75013 Paris, France
| | - Wilfred den Dunnen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Jacob-S Seeler
- Nuclear Organization and Oncogenesis Unit, INSERM U.993, Department of Cell Biology and Infection, Institut Pasteur, F-75015 Paris, France
| | - Alexis Brice
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France.,AP-HP, Genetic Department, Pitié-Salpêtrière University Hospital, F-75013 Paris, France
| | - Annie Sittler
- Sorbonne Universités, UPMC, Univ Paris 06 UMRS 1127, INSERM U 1127, CNRS UMR 7225, ICM (Brain and Spine Institute) Pitié-Salpêtrière Hospital, 75013 Paris, France
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19
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Wang Z, Yang W. Impaired capacity to restore proteostasis in the aged brain after ischemia: Implications for translational brain ischemia research. Neurochem Int 2018; 127:87-93. [PMID: 30599146 DOI: 10.1016/j.neuint.2018.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/28/2018] [Accepted: 12/28/2018] [Indexed: 12/15/2022]
Abstract
Brain ischemia induced by cardiac arrest or ischemic stroke is a severe form of metabolic stress that substantially disrupts cellular homeostasis, especially protein homeostasis (proteostasis). As proteostasis is fundamental for cellular and organismal health, cells have developed a complex network to restore proteostasis impaired by stress. Many components of this network - including ubiquitination, small ubiquitin-like modifier (SUMO) conjugation, autophagy, and the unfolded protein response (UPR) - are activated in the post-ischemic brain, and play a crucial role in cell survival and recovery of neurologic function. Importantly, recent studies have shown that ischemia-induced activation of these proteostasis-related pathways in the aged brain is impaired, indicating an aging-related decline in the self-healing capacity of the brain. This impaired capacity is a significant factor for consideration in the field of brain ischemia because the vast majority of cardiac arrest and stroke patients are elderly. In this review, we focus on the effects of aging on these critical proteostasis-related pathways in the brain, and discuss their implications in translational brain ischemia research.
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Affiliation(s)
- Zhuoran Wang
- Center for Perioperative Organ Protection, Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Wei Yang
- Center for Perioperative Organ Protection, Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.
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20
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Sha Z, Schnell HM, Ruoff K, Goldberg A. Rapid induction of p62 and GABARAPL1 upon proteasome inhibition promotes survival before autophagy activation. J Cell Biol 2018. [PMID: 29535191 PMCID: PMC5940303 DOI: 10.1083/jcb.201708168] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cells are thought to adapt to proteasome inhibition by using alternative pathways for degradation such as autophagy. Sha et al. now report that cells rapidly induce GABARAPL1 and p62 upon proteasome inhibition, but this promotes cell survival by sequestering ubiquitinated and sumoylated proteins long before the cells induce other Atg genes and activate autophagy. Proteasome inhibitors are used as research tools and to treat multiple myeloma, and proteasome activity is diminished in several neurodegenerative diseases. We therefore studied how cells compensate for proteasome inhibition. In 4 h, proteasome inhibitor treatment caused dramatic and selective induction of GABARAPL1 (but not other autophagy genes) and p62, which binds ubiquitinated proteins and GABARAPL1 on autophagosomes. Knockdown of p62 or GABARAPL1 reduced cell survival upon proteasome inhibition. p62 induction requires the transcription factor nuclear factor (erythroid-derived 2)-like 1 (Nrf1), which simultaneously induces proteasome genes. After 20-h exposure to proteasome inhibitors, cells activated autophagy and expression of most autophagy genes by an Nrf1-independent mechanism. Although p62 facilitates the association of ubiquitinated proteins with autophagosomes, its knockdown in neuroblastoma cells blocked the buildup of ubiquitin conjugates in perinuclear aggresomes and of sumoylated proteins in nuclear inclusions but did not reduce the degradation of ubiquitinated proteins. Thus, upon proteasome inhibition, cells rapidly induce p62 expression, which enhances survival primarily by sequestering ubiquitinated proteins in inclusions.
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Affiliation(s)
- Zhe Sha
- Harvard Medical School, Boston, MA
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21
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Comprehensive list of SUMO targets in Caenorhabditis elegans and its implication for evolutionary conservation of SUMO signaling. Sci Rep 2018; 8:1139. [PMID: 29348603 PMCID: PMC5773548 DOI: 10.1038/s41598-018-19424-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/02/2018] [Indexed: 02/07/2023] Open
Abstract
Post-translational modification by small ubiquitin-related modifier (SUMO) is a key regulator of cell physiology, modulating protein-protein and protein-DNA interactions. Recently, SUMO modifications were postulated to be involved in response to various stress stimuli. We aimed to identify the near complete set of proteins modified by SUMO and the dynamics of the modification in stress conditions in the higher eukaryote, Caenorhabditis elegans. We identified 874 proteins modified by SUMO in the worm. We have analyzed the SUMO modification in stress conditions including heat shock, DNA damage, arsenite induced cellular stress, ER and osmotic stress. In all these conditions the global levels of SUMOylation was significantly increased. These results show the evolutionary conservation of SUMO modifications in reaction to stress. Our analysis showed that SUMO targets are highly conserved throughout species. By comparing the SUMO targets among species, we approximated the total number of proteins modified in a given proteome to be at least 15–20%. We developed a web server designed for convenient prediction of potential SUMO modification based on experimental evidences in other species.
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22
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Maurel C, Dangoumau A, Marouillat S, Brulard C, Chami A, Hergesheimer R, Corcia P, Blasco H, Andres CR, Vourc'h P. Causative Genes in Amyotrophic Lateral Sclerosis and Protein Degradation Pathways: a Link to Neurodegeneration. Mol Neurobiol 2018; 55:6480-6499. [PMID: 29322304 DOI: 10.1007/s12035-017-0856-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/20/2017] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a disease caused by the degeneration of motor neurons (MNs) leading to progressive muscle weakness and atrophy. Several molecular pathways have been implicated, such as glutamate-mediated excitotoxicity, defects in cytoskeletal dynamics and axonal transport, disruption of RNA metabolism, and impairments in proteostasis. ALS is associated with protein accumulation in the cytoplasm of cells undergoing neurodegeneration, which is a hallmark of the disease. In this review, we focus on mechanisms of proteostasis, particularly protein degradation, and discuss how they are related to the genetics of ALS. Indeed, the genetic bases of the disease with the implication of more than 30 genes associated with familial ALS to date, together with the important increase in understanding of endoplasmic reticulum (ER) stress, proteasomal degradation, and autophagy, allow researchers to better understand the mechanisms underlying the selective death of motor neurons in ALS. It is clear that defects in proteostasis are involved in this type of cellular degeneration, but whether or not these mechanisms are primary causes or merely consequential remains to be clearly demonstrated. Novel cellular and animal models allowing chronic expression of mutant proteins, for example, are required. Further studies linking genetic discoveries in ALS to mechanisms of protein clearance will certainly be crucial in order to accelerate translational and clinical research towards new therapeutic targets and strategies.
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Affiliation(s)
- C Maurel
- UMR INSERM U1253, Université de Tours, 37032, Tours, France
| | - A Dangoumau
- UMR INSERM U1253, Université de Tours, 37032, Tours, France
| | - S Marouillat
- UMR INSERM U1253, Université de Tours, 37032, Tours, France
| | - C Brulard
- UMR INSERM U1253, Université de Tours, 37032, Tours, France
| | - A Chami
- UMR INSERM U1253, Université de Tours, 37032, Tours, France
| | - R Hergesheimer
- UMR INSERM U1253, Université de Tours, 37032, Tours, France
| | - P Corcia
- UMR INSERM U1253, Université de Tours, 37032, Tours, France
- Service de Neurologie, CHRU de Tours, 37044, Tours, France
| | - H Blasco
- UMR INSERM U1253, Université de Tours, 37032, Tours, France
- Service de Biochimie et de Biologie Moléculaire, CHRU de Tours, 37044, Tours, France
| | - C R Andres
- UMR INSERM U1253, Université de Tours, 37032, Tours, France
- Service de Biochimie et de Biologie Moléculaire, CHRU de Tours, 37044, Tours, France
| | - P Vourc'h
- UMR INSERM U1253, Université de Tours, 37032, Tours, France.
- Service de Biochimie et de Biologie Moléculaire, CHRU de Tours, 37044, Tours, France.
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23
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Rytz TC, Miller MJ, Vierstra RD. Purification of SUMO Conjugates from Arabidopsis for Mass Spectrometry Analysis. Methods Mol Biol 2018; 1475:257-81. [PMID: 27631811 DOI: 10.1007/978-1-4939-6358-4_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The posttranslational modification of proteins with small ubiquitin-related modifier (SUMO) is a rapid, robust, and reversible mechanism that impacts a host of eukaryotic processes important to both normal cellular functions and survival during various abiotic and biotic challenges. Essential to defining the breadth of events impacted by SUMOylation is the development of full catalogues of protein targets. Here, we describe a stringent affinity method to purify native SUMO conjugates from the model plant Arabidopsis thaliana based on the expression of modified SUMOs bearing epitope tags. When combined with standard and quantitative mass spectrometric methods, deep datasets of SUMOylated proteins can be acquired. Functional analysis of these lists links SUMO to numerous regulatory events, with an emphasis on those associated with transcription, DNA replication and repair, and chromatin assembly/accessibility.
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Affiliation(s)
- Thérèse C Rytz
- Department of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, Wisconsin, 53706, USA.,Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, Missouri, 63130, USA
| | - Marcus J Miller
- Department of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, Wisconsin, 53706, USA
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin, 425-G Henry Mall, Madison, Wisconsin, 53706, USA. .,Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, Missouri, 63130, USA.
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24
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Paasch F, den Brave F, Psakhye I, Pfander B, Jentsch S. Failed mitochondrial import and impaired proteostasis trigger SUMOylation of mitochondrial proteins. J Biol Chem 2017; 293:599-609. [PMID: 29183993 PMCID: PMC5767865 DOI: 10.1074/jbc.m117.817833] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/16/2017] [Indexed: 11/23/2022] Open
Abstract
Modification by the ubiquitin-like protein SUMO affects hundreds of cellular substrate proteins and regulates a wide variety of physiological processes. While the SUMO system appears to predominantly target nuclear proteins and, to a lesser extent, cytosolic proteins, hardly anything is known about the SUMOylation of proteins targeted to membrane-enclosed organelles. Here, we identify a large set of structurally and functionally unrelated mitochondrial proteins as substrates of the SUMO pathway in yeast. We show that SUMO modification of mitochondrial proteins does not rely on mitochondrial targeting and, in fact, is strongly enhanced upon import failure, consistent with the modification occurring in the cytosol. Moreover, SUMOylated forms of mitochondrial proteins particularly accumulate in HSP70- and proteasome-deficient cells, suggesting that SUMOylation participates in cellular protein quality control. We therefore propose that SUMO serves as a mark for nonfunctional mitochondrial proteins, which only sporadically arise in unstressed cells but strongly accumulate upon defective mitochondrial import and impaired proteostasis. Overall, our findings provide support for a role of SUMO in the cytosolic response to aberrant proteins.
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Affiliation(s)
| | | | - Ivan Psakhye
- From the Department of Molecular Cell Biology and
| | - Boris Pfander
- the Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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25
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Morris JR, Garvin AJ. SUMO in the DNA Double-Stranded Break Response: Similarities, Differences, and Cooperation with Ubiquitin. J Mol Biol 2017; 429:3376-3387. [PMID: 28527786 DOI: 10.1016/j.jmb.2017.05.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 10/19/2022]
Abstract
In recent years, our knowledge of the varied role that ubiquitination plays in promoting signal amplification, novel protein interactions, and protein turnover has progressed rapidly. This is particularly remarkable in the examination of how DNA double-stranded breaks (DSBs) are repaired, with many components of the ubiquitin (Ub) conjugation, de-conjugation, and recognition machinery now identified as key factors in DSB repair. In addition, a member of the Ub-like family, small Ub-like modifier (SUMO), has also been recognised as integral for efficient repair. Here, we summarise our emerging understanding of SUMOylation both as a distinct modification and as a cooperative modification with Ub, using the cellular response to DNA DSBs as the primary setting to compare these modifications.
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Affiliation(s)
- Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomics, Medical and Dental School, University of Birmingham, Edgbaston, B15 2TT, UK.
| | - Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomics, Medical and Dental School, University of Birmingham, Edgbaston, B15 2TT, UK
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26
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Site-specific identification and quantitation of endogenous SUMO modifications under native conditions. Nat Commun 2017; 8:1171. [PMID: 29079793 PMCID: PMC5660086 DOI: 10.1038/s41467-017-01271-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 09/01/2017] [Indexed: 11/25/2022] Open
Abstract
Small ubiquitin-like modifier (SUMO) modification regulates numerous cellular processes. Unlike ubiquitin, detection of endogenous SUMOylated proteins is limited by the lack of naturally occurring protease sites in the C-terminal tail of SUMO proteins. Proteome-wide detection of SUMOylation sites on target proteins typically requires ectopic expression of mutant SUMOs with introduced tryptic sites. Here, we report a method for proteome-wide, site-level detection of endogenous SUMOylation that uses α-lytic protease, WaLP. WaLP digestion of SUMOylated proteins generates peptides containing SUMO-remnant diglycyl-lysine (KGG) at the site of SUMO modification. Using previously developed immuno-affinity isolation of KGG-containing peptides followed by mass spectrometry, we identified 1209 unique endogenous SUMO modification sites. We also demonstrate the impact of proteasome inhibition on ubiquitin and SUMO-modified proteomes using parallel quantitation of ubiquitylated and SUMOylated peptides. This methodological advancement enables determination of endogenous SUMOylated proteins under completely native conditions. SUMOylation is post-translational modification implicated in several biological pathways. Here the authors describe an approach for the global profiling of SUMO attachment sites under native conditions that also allows the parallel determination of SUMO and Ub attachments.
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27
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Garvin AJ, Morris JR. SUMO, a small, but powerful, regulator of double-strand break repair. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160281. [PMID: 28847818 PMCID: PMC5577459 DOI: 10.1098/rstb.2016.0281] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
The response to a DNA double-stranded break in mammalian cells is a process of sensing and signalling the lesion. It results in halting the cell cycle and local transcription and in the mediation of the DNA repair process itself. The response is launched through a series of post-translational modification signalling events coordinated by phosphorylation and ubiquitination. More recently modifications of proteins by Small Ubiquitin-like MOdifier (SUMO) isoforms have also been found to be key to coordination of the response (Morris et al. 2009 Nature462, 886-890 (doi:10.1038/nature08593); Galanty et al. 2009 Nature462, 935-939 (doi:10.1038/nature08657)). However our understanding of the role of SUMOylation is slight compared with our growing knowledge of how ubiquitin drives signal amplification and key chromatin interactions. In this review we consider our current knowledge of how SUMO isoforms, SUMO conjugation machinery, SUMO proteases and SUMO-interacting proteins contribute to directing altered chromatin states and to repair-protein kinetics at a double-stranded DNA lesion in mammalian cells. We also consider the gaps in our understanding.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental School, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental School, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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28
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Yang W, Paschen W. Is age a key factor contributing to the disparity between success of neuroprotective strategies in young animals and limited success in elderly stroke patients? Focus on protein homeostasis. J Cereb Blood Flow Metab 2017; 37:3318-3324. [PMID: 28752781 PMCID: PMC5624400 DOI: 10.1177/0271678x17723783] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Neuroprotection strategies to improve stroke outcome have been successful in the laboratory but not in clinical stroke trials, and thus have come under scrutiny by the medical community. Experimental stroke investigators are therefore under increased pressure to resolve this problem. Acute ischemic stroke represents a severe form of metabolic stress that activates many pathological processes and thereby impairs cellular functions. Traditionally, neuroprotection strategies were designed to improve stroke outcome by interfering with pathological processes triggered by ischemia. However, stroke outcome is also dependent on the brain's capacity to restore cellular functions impaired by ischemia, and this capacity declines with age. It is, therefore, conceivable that this age-dependent decline in the brain's self-healing capacity contributes to the disparity between the success of neuroprotective strategies in young animals, and limited success in elderly stroke patients. Here, prosurvival pathways that restore protein homeostasis impaired by ischemic stress should be considered, because their capacity decreases with increasing age, and maintenance of proteome fidelity is pivotal for cell survival. Boosting such prosurvival pathways pharmacologically to restore protein homeostasis and, thereby, cellular functions impaired by ischemic stress is expected to counterbalance the compromised self-healing capacity of aged brains and thereby help to improve stroke outcome.
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Affiliation(s)
- Wei Yang
- 1 Laboratory of Molecular Neurobiology, Multidisciplinary Neuroprotection Laboratories, Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - Wulf Paschen
- 1 Laboratory of Molecular Neurobiology, Multidisciplinary Neuroprotection Laboratories, Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.,2 Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
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Zilio N, Eifler-Olivi K, Ulrich HD. Functions of SUMO in the Maintenance of Genome Stability. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:51-87. [PMID: 28197906 DOI: 10.1007/978-3-319-50044-7_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Like in most other areas of cellular metabolism, the functions of the ubiquitin-like modifier SUMO in the maintenance of genome stability are manifold and varied. Perturbations of global sumoylation causes a wide spectrum of phenotypes associated with defects in DNA maintenance, such as hypersensitivity to DNA-damaging agents, gross chromosomal rearrangements and loss of entire chromosomes. Consistent with these observations, many key factors involved in various DNA repair pathways have been identified as SUMO substrates. However, establishing a functional connection between a given SUMO target, the cognate SUMO ligase and a relevant phenotype has remained a challenge, mainly because of the difficulties involved in identifying important modification sites and downstream effectors that specifically recognize the target in its sumoylated state. This review will give an overview over the major pathways of DNA repair and genome maintenance influenced by the SUMO system and discuss selected examples of SUMO's actions in these pathways where the biological consequences of the modification have been elucidated.
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Affiliation(s)
- Nicola Zilio
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany
| | | | - Helle D Ulrich
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany.
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Hochrainer K. Protein Modifications with Ubiquitin as Response to Cerebral Ischemia-Reperfusion Injury. Transl Stroke Res 2017; 9:157-173. [DOI: 10.1007/s12975-017-0567-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/11/2017] [Accepted: 08/17/2017] [Indexed: 12/12/2022]
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A Lysine Desert Protects a Novel Domain in the Slx5-Slx8 SUMO Targeted Ub Ligase To Maintain Sumoylation Levels in Saccharomyces cerevisiae. Genetics 2017; 206:1807-1821. [PMID: 28550017 DOI: 10.1534/genetics.117.202697] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/23/2017] [Indexed: 01/23/2023] Open
Abstract
Protein modification by the small ubiquitin-like modifier (SUMO) plays important roles in genome maintenance. In Saccharomyces cerevisiae, proper regulation of sumoylation is known to be essential for viability in certain DNA repair mutants. Here, we find the opposite result; proper regulation of sumoylation is lethal in certain DNA repair mutants. Yeast cells lacking the repair factors TDP1 and WSS1 are synthetically lethal due to their redundant roles in removing Top1-DNA covalent complexes (Top1ccs). A screen for suppressors of tdp1∆ wss1∆ synthetic lethality isolated mutations in genes known to control global sumoylation levels including ULP1, ULP2, SIZ2, and SLX5 The results suggest that alternative pathways of repair become available when sumoylation levels are altered. Curiously, both suppressor mutations that were isolated in the Slx5 subunit of the SUMO-targeted Ub ligase created new lysine residues. These "slx5-K" mutations localize to a 398 amino acid domain that is completely free of lysine, and they result in the auto-ubiquitination and partial proteolysis of Slx5. The decrease in Slx5-K protein leads to the accumulation of high molecular weight SUMO conjugates, and the residual Ub ligase activity is needed to suppress inviability presumably by targeting polysumoylated Top1ccs. This "lysine desert" is found in the subset of large fungal Slx5 proteins, but not its smaller orthologs such as RNF4. The lysine desert solves a problem that Ub ligases encounter when evolving novel functional domains.
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The Molecular Interface Between the SUMO and Ubiquitin Systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:99-110. [DOI: 10.1007/978-3-319-50044-7_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Digiacomo V, Gando IA, Venticinque L, Hurtado A, Meruelo D. The Transition of the 37-Kda Laminin Receptor (Rpsa) to Higher Molecular Weight Species: Sumoylation or Artifact? Cell Mol Biol Lett 2016; 20:571-85. [PMID: 26146125 DOI: 10.1515/cmble-2015-0031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 06/18/2015] [Indexed: 11/15/2022] Open
Abstract
The 37-kDa laminin receptor (37LRP or RPSA) is a remarkable, multifaceted protein that functions in processes ranging from matrix adhesion to ribosome biogenesis. Its ability to engage extracellular laminin is further thought to contribute to cellular migration and invasion. Most commonly associated with metastatic cancer, RPSA is also increasingly found to be important in other pathologies, including microbial infection, neurodegenerative disease and developmental malformations. Importantly, it is thought to have higher molecular weight forms, including a 67-kDa species (67LR), the expression of which is linked to strong laminin binding and metastatic behavior. The composition of these larger forms has remained elusive and controversial. Homo- and heterodimerization have been proposed as events capable of building the larger species from the monomeric 37-kDa precursor, but solid evidence is lacking. Here, we present data suggesting that higher molecular weight species require SUMOylation to form. We also comment on the difficulty of isolating larger RPSA species for unambiguous identification and demonstrate that cell lines stably expressing tagged RPSA for long periods of time fail to produce tagged higher molecular weight RPSA. It is possible that higher molecular weight species like 67LR are not derived from RPSA.
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Abstract
Small ubiquitin-like modifiers (SUMOs) are essential for the regulation of several cellular processes and are potential therapeutic targets owing to their involvement in diseases such as cancer and Alzheimer disease. In the past decade, we have witnessed a rapid expansion of proteomic approaches for identifying sumoylated proteins, with recent advances in detecting site-specific sumoylation. In this Analysis, we combined all human SUMO proteomics data currently available into one cohesive database. We provide proteomic evidence for sumoylation of 3,617 proteins at 7,327 sumoylation sites, and insight into SUMO group modification by clustering the sumoylated proteins into functional networks. The data support sumoylation being a frequent protein modification (on par with other major protein modifications) with multiple nuclear functions, including in transcription, mRNA processing, DNA replication and the DNA-damage response.
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Liebelt F, Vertegaal ACO. Ubiquitin-dependent and independent roles of SUMO in proteostasis. Am J Physiol Cell Physiol 2016; 311:C284-96. [PMID: 27335169 PMCID: PMC5129774 DOI: 10.1152/ajpcell.00091.2016] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/15/2016] [Indexed: 01/04/2023]
Abstract
Cellular proteomes are continuously undergoing alterations as a result of new production of proteins, protein folding, and degradation of proteins. The proper equilibrium of these processes is known as proteostasis, implying that proteomes are in homeostasis. Stress conditions can affect proteostasis due to the accumulation of misfolded proteins as a result of overloading the degradation machinery. Proteostasis is affected in neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, and multiple polyglutamine disorders including Huntington's disease. Owing to a lack of proteostasis, neuronal cells build up toxic protein aggregates in these diseases. Here, we review the role of the ubiquitin-like posttranslational modification SUMO in proteostasis. SUMO alone contributes to protein homeostasis by influencing protein signaling or solubility. However, the main contribution of SUMO to proteostasis is the ability to cooperate with, complement, and balance the ubiquitin-proteasome system at multiple levels. We discuss the identification of enzymes involved in the interplay between SUMO and ubiquitin, exploring the complexity of this crosstalk which regulates proteostasis. These enzymes include SUMO-targeted ubiquitin ligases and ubiquitin proteases counteracting these ligases. Additionally, we review the role of SUMO in brain-related diseases, where SUMO is primarily investigated because of its role during formation of aggregates, either independently or in cooperation with ubiquitin. Detailed understanding of the role of SUMO in these diseases could lead to novel treatment options.
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Affiliation(s)
- Frauke Liebelt
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
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González-Prieto R, Cuijpers SA, Kumar R, Hendriks IA, Vertegaal AC. c-Myc is targeted to the proteasome for degradation in a SUMOylation-dependent manner, regulated by PIAS1, SENP7 and RNF4. Cell Cycle 2016; 14:1859-72. [PMID: 25895136 DOI: 10.1080/15384101.2015.1040965] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
c-Myc is the most frequently overexpressed oncogene in tumors, including breast cancer, colon cancer and lung cancer. Post-translational modifications comprising phosphorylation, acetylation and ubiquitylation regulate the activity of c-Myc. Recently, it was shown that c-Myc-driven tumors are strongly dependent on the SUMO pathway. Currently, the relevant SUMO target proteins in this pathway are unknown. Here we show that c-Myc is a target protein for SUMOylation, and that SUMOylated c-Myc is subsequently ubiquitylated and degraded by the proteasome. SUMO chains appeared to be dispensable for this process, polymerization-deficient SUMO mutants supported proteolysis of SUMOylated c-Myc. These results indicate that multiple SUMO monomers conjugated to c-Myc could be sufficient to direct SUMOylated c-Myc to the ubiquitin-proteasome pathway. Knocking down the SUMO-targeted ubiquitin ligase RNF4 enhanced the levels of SUMOylated c-Myc, indicating that RNF4 could recognize a multi-SUMOylated protein as a substrate in addition to poly-SUMOylated proteins. Knocking down the SUMO E3 ligase PIAS1 resulted in reduced c-Myc SUMOylation and increased c-Myc transcriptional activity, indicating that PIAS1 mediates c-Myc SUMOylation. Increased SUMOylation of c-Myc was noted upon knockdown of the SUMO protease SENP7, indicating that it also could regulate a multi-SUMOylated protein in addition to poly-SUMOylated proteins. C-Myc lacks KxE-type SUMOylation consensus motifs. We used mass spectrometry to identify 10 SUMO acceptor lysines: K52, K148, K157, K317, K323, K326, K389, K392, K398 and K430. Intriguingly, mutating all 10 SUMO acceptor lysines did not reduce c-Myc SUMOylation, suggesting that SUMO acceptor lysines in c-Myc act promiscuously. Our results provide novel insight into the complexity of c-Myc post-translational regulation.
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Affiliation(s)
- Román González-Prieto
- a Department of Molecular Cell Biology; Leiden University Medical Center ; Leiden , The Netherlands
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37
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Park IS, Han YG, Chung HJ, Jung YW, Kim Y, Kim H. SUMOylation regulates nuclear localization and stability of TRAIP/RNF206. Biochem Biophys Res Commun 2016; 470:881-7. [DOI: 10.1016/j.bbrc.2016.01.141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 01/22/2016] [Indexed: 12/14/2022]
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Lee J, Yang DJ, Lee S, Hammer GD, Kim KW, Elmquist JK. Nutritional conditions regulate transcriptional activity of SF-1 by controlling sumoylation and ubiquitination. Sci Rep 2016; 6:19143. [PMID: 26750456 PMCID: PMC4707483 DOI: 10.1038/srep19143] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 11/20/2015] [Indexed: 12/23/2022] Open
Abstract
Steroidogenic factor 1 (SF-1) is a transcription factor expressed in the ventral medial nucleus of the hypothalamus that regulates energy homeostasis. However, the molecular mechanisms of SF-1 in the control of energy balance are largely unknown. Here, we show that nutritional conditions, such as the presence or absence of serum, affect SF-1 action. Serum starvation significantly decreased hypothalamic SF-1 levels by promoting ubiquitin-dependent degradation, and sumoylation was required for this process. SF-1 transcriptional activity was also differentially regulated by nutritional status. Under normal conditions, the transcriptional activity of hypothalamic SF-1 was activated by SUMO, but this was attenuated during starvation. Taken together, these results indicate that sumoylation and ubiquitination play crucial roles in the regulation of SF-1 function and that these effects are dependent on nutritional conditions, further supporting the importance of SF-1 in the control of energy homeostasis.
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Affiliation(s)
- Jiwon Lee
- Departments of Pharmacology and Internal Medicine, Division of Hypothalamic Research, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Dong Joo Yang
- Departments of Pharmacology and Global Medical Science, Institute of Lifestyle Medicine and Nuclear Receptor Research Consortium, Wonju College of Medicine, Yonsei University, Wonju, 26426, South Korea
| | - Syann Lee
- Departments of Pharmacology and Internal Medicine, Division of Hypothalamic Research, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Gary D Hammer
- Endocrine Oncology Program, Center for Organogenesis, University of Michigan Health System, Ann Arbor, Michigan 48109, USA
| | - Ki Woo Kim
- Departments of Pharmacology and Global Medical Science, Institute of Lifestyle Medicine and Nuclear Receptor Research Consortium, Wonju College of Medicine, Yonsei University, Wonju, 26426, South Korea
| | - Joel K Elmquist
- Departments of Pharmacology and Internal Medicine, Division of Hypothalamic Research, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Abstract
Mass spectrometry-based approaches are utilized with increasing frequency to facilitate identification of novel SUMO target proteins and to elucidate the dynamics of SUMOylation in response to cellular stresses. Here, we describe a robust method for the identification of SUMO target proteins, and the relative quantification of SUMOylation dynamics, using a label-free approach. The method relies on a decahistidine (His10)-tagged SUMO, which is expressed at a low level in a mammalian cell line or model organism. The His10-tag allows for a single-step, high-yield, and high-purity enrichment of SUMOylated proteins, which are then digested and analyzed by high-resolution mass spectrometry. Matching between runs and label-free quantification integrated in the freely available MaxQuant software allow for a high rate and accuracy of quantification, providing a strong alternative to laborious sample or cell labeling techniques. The method described here allows for identification of >1000 SUMO target proteins, and characterization of their SUMOylation dynamics, without requiring sample fractionation. The purification procedure, starting from total lysate, can be performed in ~4 days.
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Affiliation(s)
- Ivo A Hendriks
- Department of Molecular Cell Biology, Leiden University medical Center, Albinusdreef 2, 2300, Leiden, Netherlands
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University medical Center, Albinusdreef 2, 2300, Leiden, Netherlands.
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Wang M, Sang J, Ren Y, Liu K, Liu X, Zhang J, Wang H, Wang J, Orian A, Yang J, Yi J. SENP3 regulates the global protein turnover and the Sp1 level via antagonizing SUMO2/3-targeted ubiquitination and degradation. Protein Cell 2016; 7:63-77. [PMID: 26511642 PMCID: PMC4707158 DOI: 10.1007/s13238-015-0216-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 09/08/2015] [Indexed: 12/19/2022] Open
Abstract
SUMOylation is recently found to function as a targeting signal for the degradation of substrates through the ubiquitin-proteasome system. RNF4 is the most studied human SUMO-targeted ubiquitin E3 ligase. However, the relationship between SUMO proteases, SENPs, and RNF4 remains obscure. There are limited examples of the SENP regulation of SUMO2/3-targeted proteolysis mediated by RNF4. The present study investigated the role of SENP3 in the global protein turnover related to SUMO2/3-targeted ubiquitination and focused in particular on the SENP3 regulation of the stability of Sp1. Our data demonstrated that SENP3 impaired the global ubiquitination profile and promoted the accumulation of many proteins. Sp1, a cancer-associated transcription factor, was among these proteins. SENP3 increased the level of Sp1 protein via antagonizing the SUMO2/3-targeted ubiquitination and the consequent proteasome-dependent degradation that was mediated by RNF4. De-conjugation of SUMO2/3 by SENP3 attenuated the interaction of Sp1 with RNF4. In gastric cancer cell lines and specimens derived from patients and nude mice, the level of Sp1 was generally increased in parallel to the level of SENP3. These results provided a new explanation for the enrichment of the Sp1 protein in various cancers, and revealed a regulation of SUMO2/3 conjugated proteins whose levels may be tightly controlled by SENP3 and RNF4.
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Affiliation(s)
- Ming Wang
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing Sang
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yanhua Ren
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Kejia Liu
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinyi Liu
- Department of Pathophysiology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Haolu Wang
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jian Wang
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Amir Orian
- Faculty of Medicine, Cancer and Vascular Biology Research Center, Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Jie Yang
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jing Yi
- Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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PIAS1-mediated sumoylation promotes STUbL-dependent proteasomal degradation of the human telomeric protein TRF2. FEBS Lett 2015; 589:3277-86. [PMID: 26450775 DOI: 10.1016/j.febslet.2015.09.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 01/25/2023]
Abstract
The human telomeric protein TRF2 protects chromosome ends by facilitating their organization into the protective capping structure. Here we show that the stability of TRF2 is regulated via modification by the small ubiquitin-like modifiers (SUMO). TRF2 specifically interacts with and is sumoylated by PIAS1 in mammalian cells. The proteasome inhibitor stabilizes SUMO-conjugated TRF2 without affecting the level of unmodified TRF2, suggesting that SUMO conjugation is required for proteasomal degradation of TRF2. We also show that RNF4, a mammalian SUMO-targeted ubiquitin ligase, interacts with TRF2 in a SUMO-dependent manner and preferentially targets SUMO-conjugated TRF2 for ubiquitination. Collectively, our data demonstrate that the PIAS1-mediated sumoylation status of TRF2 serves as a molecular switch that controls the level of TRF2 at telomeres.
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Lee J, Chun SK, Son GH, Kim K. Sumoylation of Hes6 Regulates Protein Degradation and Hes1-Mediated Transcription. Endocrinol Metab (Seoul) 2015; 30:381-8. [PMID: 26435136 PMCID: PMC4595364 DOI: 10.3803/enm.2015.30.3.381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 11/27/2014] [Accepted: 12/01/2014] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Hes6 is a transcriptional regulator that induces transcriptional activation by binding to transcription repressor Hes1 and suppressing its activity. Hes6 is controlled by the ubiquitin-proteosome-mediated degradation system. Here we investigated the sumoylation of Hes6 and its functional role in its rhythmic expression. METHODS Hes6, SUMO, and ubiquitin were transfected into HeLa cells and the expression pattern was observed by Western blot and immunoprecipitation. To confirm the effect of sumoylation on the rhythmic expression of Hes6, we generated mouse Hes6 promoter-driven GFP-Hes6 fusion constructs and expressed these constructs in NIH 3T3 cells. RESULTS Overexpression of SUMO led to sumoylation of Hes6 at both lysine 27 and 30. Protein stability of Hes6 was decreased by sumoylation. Moreover, expression of a Hes6 sumoylation-defective mutant, the 2KR (K27/30R) mutant, or co-expression of SUMO protease SUSP1 with native Hes6, strongly reduced ubiquitination. In addition, sumoylation was associated with both the rhythmic expression and transcriptional regulation of Hes6. Wild type Hes6 showed oscillatory expression with about 2-hour periodicity, whereas the 2KR mutant displayed a longer period. Furthermore, sumoylation of Hes6 derepressed Hes1-induced transcriptional repression. CONCLUSION Hes6 sumoylation plays an important role in the regulation of its stability and Hes1-mediated transcription. These results suggest that sumoylation may be crucial for rhythmic expression of Hes6 and downstream target genes.
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Affiliation(s)
- Jiwon Lee
- Department of Brain and Cognitive Sciences, Seoul National University School of Biological Sciences, Seoul, Korea
| | - Sung Kook Chun
- Department of Brain and Cognitive Sciences, Seoul National University School of Biological Sciences, Seoul, Korea
| | - Gi Hoon Son
- Department of Legal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Kyungjin Kim
- Department of Brain and Cognitive Sciences, Seoul National University School of Biological Sciences, Seoul, Korea.
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Bish R, Cuevas-Polo N, Cheng Z, Hambardzumyan D, Munschauer M, Landthaler M, Vogel C. Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins. Biomolecules 2015; 5:1441-66. [PMID: 26184334 PMCID: PMC4598758 DOI: 10.3390/biom5031441] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/15/2015] [Indexed: 12/24/2022] Open
Abstract
DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58) of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2) and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2). We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6's multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1β, we tested for and observed a significant enrichment of sumoylation amongst DDX6's interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions-many of which are likely conserved across eukaryotes.
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Affiliation(s)
- Rebecca Bish
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
| | - Nerea Cuevas-Polo
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
| | - Zhe Cheng
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
| | - Dolores Hambardzumyan
- The Cleveland Clinic, Department of Neurosciences, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA.
| | - Mathias Munschauer
- RNA Biology and Post-Transcriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin-Buch, Robert-Rössle-Str. 10, Berlin 13092, Germany.
| | - Markus Landthaler
- RNA Biology and Post-Transcriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin-Buch, Robert-Rössle-Str. 10, Berlin 13092, Germany.
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
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Hendriks IA, D'Souza RC, Chang JG, Mann M, Vertegaal ACO. System-wide identification of wild-type SUMO-2 conjugation sites. Nat Commun 2015; 6:7289. [PMID: 26073453 PMCID: PMC4490555 DOI: 10.1038/ncomms8289] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/26/2015] [Indexed: 12/18/2022] Open
Abstract
SUMOylation is a reversible post-translational modification (PTM) regulating all nuclear processes. Identification of SUMOylation sites by mass spectrometry (MS) has been hampered by bulky tryptic fragments, which thus far necessitated the use of mutated SUMO. Here we present a SUMO-specific protease-based methodology which circumvents this problem, dubbed Protease-Reliant Identification of SUMO Modification (PRISM). PRISM allows for detection of SUMOylated proteins as well as identification of specific sites of SUMOylation while using wild-type SUMO. The method is generic and could be widely applied to study lysine PTMs. We employ PRISM in combination with high-resolution MS to identify SUMOylation sites from HeLa cells under standard growth conditions and in response to heat shock. We identified 751 wild-type SUMOylation sites on endogenous proteins, including 200 dynamic SUMO sites in response to heat shock. Thus, we have developed a method capable of quantitatively studying wild-type mammalian SUMO at the site-specific and system-wide level. Tryptic digestion of SUMOylated proteins generates large peptides, rendering proteomic characterisation of this post-translational modification particularly challenging unless mutant SUMO is used. Hendriks et al. present a method that allows the quantitative identification of wild-type SUMO sites.
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Affiliation(s)
- Ivo A Hendriks
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Rochelle C D'Souza
- Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Jer-Gung Chang
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Matthias Mann
- Department for Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
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Cui W, Sun M, Galeva N, Williams TD, Azuma Y, Staudinger JL. SUMOylation and Ubiquitylation Circuitry Controls Pregnane X Receptor Biology in Hepatocytes. Drug Metab Dispos 2015; 43:1316-25. [PMID: 26063058 DOI: 10.1124/dmd.115.065201] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/10/2015] [Indexed: 12/25/2022] Open
Abstract
Several nuclear receptor (NR) superfamily members are known to be the molecular target of either the small ubiquitin-related modifier (SUMO) or ubiquitin-signaling pathways. However, little is currently known regarding how these two post-translational modifications interact to control NR biology. We show that SUMO and ubiquitin circuitry coordinately modifies the pregnane X receptor (PXR, NR1I2) to play a key role in regulating PXR protein stability, transactivation capacity, and transcriptional repression. The SUMOylation and ubiquitylation of PXR is increased in a ligand- and tumor necrosis factor alpha -: dependent manner in hepatocytes. The SUMO-E3 ligase enzymes protein inhibitor of activated signal transducer and activator of transcription-1 (STAT1) STAT-1 (PIAS1) and protein inhibitor of activated STAT Y (PIASy) drive high levels of PXR SUMOylation. Expression of protein inhibitor of activated stat 1 selectively increases SUMO(3)ylation as well as PXR-mediated induction of cytochrome P450, family 3, subfamily A and the xenobiotic response. The PIASy-mediated SUMO(1)ylation imparts a transcriptionally repressive function by ameliorating interaction of PXR with coactivator protein peroxisome proliferator-activated receptor gamma coactivator-1-alpha. The SUMO modification of PXR is effectively antagonized by the SUMO protease sentrin protease (SENP) 2, whereas SENP3 and SENP6 proteases are highly active in the removal of SUMO2/3 chains. The PIASy-mediated SUMO(1)ylation of PXR inhibits ubiquitin-mediated degradation of this important liver-enriched NR by the 26S proteasome. Our data reveal a working model that delineates the interactive role that these two post-translational modifications play in reconciling PXR-mediated gene activation of the xenobiotic response versus transcriptional repression of the proinflammatory response in hepatocytes. Taken together, our data reveal that the SUMOylation and ubiquitylation of the PXR interface in a fundamental manner directs its biologic function in the liver in response to xenobiotic or inflammatory stress.
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Affiliation(s)
- Wenqi Cui
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
| | - Mengxi Sun
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
| | - Nadezhda Galeva
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
| | - Todd D Williams
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
| | - Yoshiaki Azuma
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
| | - Jeff L Staudinger
- Departments of Pharmacology and Toxicology (W.C., J.L.S.), Mass Spectrometry Laboratory (N.G., T.D.W.), and Molecular Biosciences, University of Kansas, Lawrence, Kansas (Y.A.); and Department of Medicine, University of California, San Diego, La Jolla, California (M.S.)
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Hendriks IA, Schimmel J, Eifler K, Olsen JV, Vertegaal ACO. Ubiquitin-specific Protease 11 (USP11) Deubiquitinates Hybrid Small Ubiquitin-like Modifier (SUMO)-Ubiquitin Chains to Counteract RING Finger Protein 4 (RNF4). J Biol Chem 2015; 290:15526-15537. [PMID: 25969536 DOI: 10.1074/jbc.m114.618132] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Indexed: 11/06/2022] Open
Abstract
Ring finger protein 4 (RNF4) is a SUMO-targeted ubiquitin E3 ligase with a pivotal function in the DNA damage response (DDR). SUMO interaction motifs (SIMs) in the N-terminal part of RNF4 tightly bind to SUMO polymers, and RNF4 can ubiquitinate these polymers in vitro. Using a proteomic approach, we identified the deubiquitinating enzyme ubiquitin-specific protease 11 (USP11), a known DDR-component, as a functional interactor of RNF4. USP11 can deubiquitinate hybrid SUMO-ubiquitin chains to counteract RNF4. SUMO-enriched nuclear bodies are stabilized by USP11, which functions downstream of RNF4 as a counterbalancing factor. In response to DNA damage induced by methyl methanesulfonate, USP11 could counteract RNF4 to inhibit the dissolution of nuclear bodies. Thus, we provide novel insight into cross-talk between ubiquitin and SUMO and uncover USP11 and RNF4 as a balanced SUMO-targeted ubiquitin ligase/protease pair with a role in the DDR.
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Affiliation(s)
- Ivo A Hendriks
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Joost Schimmel
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Karolin Eifler
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
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Analysis of PTEN ubiquitylation and SUMOylation using molecular traps. Methods 2015; 77-78:112-8. [DOI: 10.1016/j.ymeth.2014.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/29/2014] [Accepted: 09/03/2014] [Indexed: 02/02/2023] Open
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HIF-1α SUMOylation affects the stability and transcriptional activity of HIF-1α in human lens epithelial cells. Graefes Arch Clin Exp Ophthalmol 2015; 253:1279-90. [PMID: 25877955 DOI: 10.1007/s00417-015-2999-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/02/2015] [Accepted: 03/25/2015] [Indexed: 01/11/2023] Open
Abstract
PURPOSE High blood glucose can induce oxidative damage and result in diabetic cataract. Oxidative stress induces various signal pathways including HIF-1α transcriptional signal to attenuate the damage of lenses. Whether HIF-1α SUMOylation can increase the activation of HIF-1α or if high glucose can affect the SUMOylation of HIF-1α in cultured human lens epithelial cells (HLECs) is still unknown, as well as the function of HIF-1α SUMOylation in oxidative damage induced by high glucose in HLECs. In the present study, we examined SUMO and SUMO E3 (Cbx4 and PIASy) expression induced by high glucose, and investigated SUMO or SUMO E3 overexpression that enhanced HIF-1α SUMOylation in HLECs. METHODS SRA01/04 cells, one kind of human lens epithelial cell line, were addressed in media with 5.5 mmol/l (normal control group), 25 mmol/l (high glucose1 group) and 50 mmol/l (high glucose2 group) final glucose respectively. Expression of SUMO1 ~ 4, Cbx4, PIASy, HIF-1α, GLUT1, and VEGFA were detected in the mRNA and protein levels by RT-PCR and Western blot analysis. Protein expression localization and co-localization were examined by immunofluorescence and co-immunofluorescence. The effects of SUMO overexpression, SUMO E3 overexpression, and Proteasome inhibitor MG132 respectively on the stability and transcriptional activity of HIF-1α were analyzed by immunoblot. RESULTS High glucose treatment induced SUMO1-4 expression and enhanced the expression of Cbx4 and PIASy. It also increased the expression of HIF-1α, GLUT1, and VEGFA. The co-localization of HIF-1α and SUMO was mainly in the nucleus induced by high glucose. Further studies showed that SUMO overexpression or SUMO E3 overexpression could enhance HIF-1α stability and transcriptional activity in HLECs. Proteasome inhibitor MG132 protected the stability and transcriptional activity of HIF-1α in the SRA01/04 cells. CONCLUSIONS HIF-1α SUMOylation affected the stability and transcriptional activity of HIF-1α in cultured human lens epithelial cells; SUMO overexpression or SUMO E3 overexpression enhanced the expression of HIF-1α, which is involved in inhibiting cell apoptosis and protecting lens opacification, and presumably plays a key role in protecting lenses from diabetic cataract.
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Bursomanno S, McGouran JF, Kessler BM, Hickson ID, Liu Y. Regulation of SUMO2 target proteins by the proteasome in human cells exposed to replication stress. J Proteome Res 2015; 14:1687-99. [PMID: 25748227 DOI: 10.1021/pr500997p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In human cells, SUMO2 is predominantly conjugated to target proteins in response to cellular stress. Previous studies suggested that proteins conjugated to SUMO2, but not to SUMO1, could be regulated by the ubiquitin-mediated proteasome system. Hence, we set out to understand the role of the proteasome in determining the fate of proteins conjugated to SUMO2 when cells are treated with DNA replication stress conditions. We conducted a quantitative proteomic analysis in a U2OS cell line stably expressing SUMO2(Q87R) tagged with StrepHA in the presence or absence of epoxomicin (EPOX), a proteasome inhibitor. We identified subgroups of putative SUMO2 targets that were either degraded or stabilized by EPOX upon SUMO2 conjugation in response to replication stress. Interestingly, the subgroup of proteins degraded upon SUMO2 conjugation was enriched in proteins playing roles in DNA damage repair and replication, while the proteins stabilized upon SUMOylation were mainly involved in chromatin maintenance. In addition, we identified 43 SUMOylation sites in target proteins, of which 17 are located in the proximity of phosphorylated residues. Considering that DNA replication stress is a major source of genome instability, which is suggested to drive tumorigenesis and possibly aging, our data will facilitate future functional studies in the fields of DNA metabolism and cancer biology.
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Affiliation(s)
- Sara Bursomanno
- †Center for Chromosome Stability, and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Joanna F McGouran
- ‡Ubiquitin Proteolysis Group, TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, OX3 7FZ Oxford, UK
| | - Benedikt M Kessler
- ‡Ubiquitin Proteolysis Group, TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, OX3 7FZ Oxford, UK
| | - Ian D Hickson
- †Center for Chromosome Stability, and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Ying Liu
- †Center for Chromosome Stability, and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
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DiGiacomo V, Meruelo D. Looking into laminin receptor: critical discussion regarding the non-integrin 37/67-kDa laminin receptor/RPSA protein. Biol Rev Camb Philos Soc 2015; 91:288-310. [PMID: 25630983 DOI: 10.1111/brv.12170] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/04/2014] [Accepted: 12/08/2014] [Indexed: 02/06/2023]
Abstract
The 37/67-kDa laminin receptor (LAMR/RPSA) was originally identified as a 67-kDa binding protein for laminin, an extracellular matrix glycoprotein that provides cellular adhesion to the basement membrane. LAMR has evolutionary origins, however, as a 37-kDa RPS2 family ribosomal component. Expressed in all domains of life, RPS2 proteins have been shown to have remarkably diverse physiological roles that vary across species. Contributing to laminin binding, ribosome biogenesis, cytoskeletal organization, and nuclear functions, this protein governs critical cellular processes including growth, survival, migration, protein synthesis, development, and differentiation. Unsurprisingly given its purview, LAMR has been associated with metastatic cancer, neurodegenerative disease and developmental abnormalities. Functioning in a receptor capacity, this protein also confers susceptibility to bacterial and viral infection. LAMR is clearly a molecule of consequence in human disease, directly mediating pathological events that make it a prime target for therapeutic interventions. Despite decades of research, there are still a large number of open questions regarding the cellular biology of LAMR, the nature of its ability to bind laminin, the function of its intrinsically disordered C-terminal region and its conversion from 37 to 67 kDa. This review attempts to convey an in-depth description of the complexity surrounding this multifaceted protein across functional, structural and pathological aspects.
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Affiliation(s)
- Vincent DiGiacomo
- Department of Pathology, New York University School of Medicine, 180 Varick Street, New York, NY 10014, U.S.A
| | - Daniel Meruelo
- Department of Pathology, New York University School of Medicine, 180 Varick Street, New York, NY 10014, U.S.A.,NYU Cancer Institute, 550 First Avenue, New York, NY 10016, U.S.A.,NYU Gene Therapy Center, 550 First Avenue, New York, NY 10016, U.S.A
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