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Gil-Pitarch C, Serrano-Maciá M, Simon J, Mosca L, Conter C, Rejano-Gordillo CM, Zapata-Pavas LE, Peña-Sanfélix P, Azkargorta M, Rodríguez-Agudo R, Lachiondo-Ortega S, Mercado-Gómez M, Delgado TC, Porcelli M, Aurrekoetxea I, Sutherland JD, Barrio R, Xirodimas D, Aspichueta P, Elortza F, Martínez-Cruz LA, Nogueiras R, Iruzubieta P, Crespo J, Masson S, McCain MV, Reeves HL, Andrade RJ, Lucena MI, Mayor U, Goikoetxea-Usandizaga N, González-Recio I, Martínez-Chantar ML. Neddylation inhibition prevents acetaminophen-induced liver damage by enhancing the anabolic cardiolipin pathway. Cell Rep Med 2024; 5:101653. [PMID: 39019009 PMCID: PMC11293357 DOI: 10.1016/j.xcrm.2024.101653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/28/2024] [Accepted: 06/19/2024] [Indexed: 07/19/2024]
Abstract
Drug-induced liver injury (DILI) is a significant cause of acute liver failure (ALF) and liver transplantation in the Western world. Acetaminophen (APAP) overdose is a main contributor of DILI, leading to hepatocyte cell death through necrosis. Here, we identified that neddylation, an essential post-translational modification involved in the mitochondria function, was upregulated in liver biopsies from patients with APAP-induced liver injury (AILI) and in mice treated with an APAP overdose. MLN4924, an inhibitor of the neuronal precursor cell-expressed developmentally downregulated protein 8 (NEDD8)-activating enzyme (NAE-1), ameliorated necrosis and boosted liver regeneration in AILI. To understand how neddylation interferes in AILI, whole-body biotinylated NEDD8 (bioNEDD8) and ubiquitin (bioUB) transgenic mice were investigated under APAP overdose with and without MLN4924. The cytidine diphosphate diacylglycerol (CDP-DAG) synthase TAM41, responsible for producing cardiolipin essential for mitochondrial activity, was found modulated under AILI and restored its levels by inhibiting neddylation. Understanding this ubiquitin-like crosstalk in AILI is essential for developing promising targeted inhibitors for DILI treatment.
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Affiliation(s)
- Clàudia Gil-Pitarch
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain
| | - Marina Serrano-Maciá
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain
| | - Jorge Simon
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain
| | - Laura Mosca
- Department of Life Sciences, Health and Health Professions, Link University, Via del Casale di San Pio V, 44 00165 Rome, Italy
| | - Carolina Conter
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain
| | - Claudia M Rejano-Gordillo
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 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
| | - L Estefanía Zapata-Pavas
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain
| | - Patricia Peña-Sanfélix
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed-ISCIII, CIBERehd, Science and Technology Park of Bizkaia, 48160 Derio, Spain
| | - Rubén Rodríguez-Agudo
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain
| | - Sofía Lachiondo-Ortega
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain
| | - Maria Mercado-Gómez
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain
| | - Teresa C Delgado
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain
| | - Marina Porcelli
- Department of Life Sciences, Health and Health Professions, Link University, Via del Casale di San Pio V, 44 00165 Rome, Italy
| | - Igor Aurrekoetxea
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain; Biobizkaia Health Research Institute, 48903 Barakaldo, Spain
| | - 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
| | | | - Patricia Aspichueta
- Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain; Biobizkaia Health Research Institute, 48903 Barakaldo, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, 28029 Madrid, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed-ISCIII, CIBERehd, Science and Technology Park of Bizkaia, 48160 Derio, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, 28029 Madrid, Spain
| | - Luis Alfonso Martínez-Cruz
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain
| | - Rubén Nogueiras
- Department of Physiology, School of Medicine-Instituto de Investigaciones Sanitarias, University of Santiago de Compostela, 15705 Santiago de Compostela, Spain; Department of Physiology, CIMUS, 15782 University of Santiago de Compostela, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Santiago de Compostela, Spain; Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, Spain
| | - Paula Iruzubieta
- Gastroenterology and Hepatology Department, Marqués de Valdecilla University Hospital, Clinical and Translational Digestive Research Group, IDIVAL, 39011 Santander, Spain
| | - Javier Crespo
- Gastroenterology and Hepatology Department, Marqués de Valdecilla University Hospital, Clinical and Translational Digestive Research Group, IDIVAL, 39011 Santander, Spain
| | - Steven Masson
- The Liver Unit, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, NE7 7DN Newcastle upon Tyne, UK; Newcastle University Translational and Clinical Research Institute, The Medical School, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Misti Vanette McCain
- Newcastle University Translational and Clinical Research Institute, The Medical School, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Helen L Reeves
- The Liver Unit, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, NE7 7DN Newcastle upon Tyne, UK; Newcastle University Translational and Clinical Research Institute, The Medical School, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Raul J Andrade
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, 28029 Madrid, Spain; Unidad de Gestión Clínica de Enfermedades Digestivas, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, 29590 Málaga, Spain
| | - M Isabel Lucena
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, 28029 Madrid, Spain; Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, UICEC SCReN, Universidad de Málaga, 29590 Málaga, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Naroa Goikoetxea-Usandizaga
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, 28029 Madrid, Spain
| | - Irene González-Recio
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain.
| | - María L Martínez-Chantar
- Liver Disease Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Derio 48160 Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Carlos III National Health Institute, 28029 Madrid, Spain.
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Gonzalez-Rellan MJ, Fernández U, Parracho T, Novoa E, Fondevila MF, da Silva Lima N, Ramos L, Rodríguez A, Serrano-Maciá M, Perez-Mejias G, Chantada-Vazquez P, Riobello C, Veyrat-Durebex C, Tovar S, Coppari R, Woodhoo A, Schwaninger M, Prevot V, Delgado TC, Lopez M, Diaz-Quintana A, Dieguez C, Guallar D, Frühbeck G, Diaz-Moreno I, Bravo SB, Martinez-Chantar ML, Nogueiras R. Neddylation of phosphoenolpyruvate carboxykinase 1 controls glucose metabolism. Cell Metab 2023; 35:1630-1645.e5. [PMID: 37541251 PMCID: PMC10487638 DOI: 10.1016/j.cmet.2023.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/08/2023] [Accepted: 07/10/2023] [Indexed: 08/06/2023]
Abstract
Neddylation is a post-translational mechanism that adds a ubiquitin-like protein, namely neural precursor cell expressed developmentally downregulated protein 8 (NEDD8). Here, we show that neddylation in mouse liver is modulated by nutrient availability. Inhibition of neddylation in mouse liver reduces gluconeogenic capacity and the hyperglycemic actions of counter-regulatory hormones. Furthermore, people with type 2 diabetes display elevated hepatic neddylation levels. Mechanistically, fasting or caloric restriction of mice leads to neddylation of phosphoenolpyruvate carboxykinase 1 (PCK1) at three lysine residues-K278, K342, and K387. We find that mutating the three PCK1 lysines that are neddylated reduces their gluconeogenic activity rate. Molecular dynamics simulations show that neddylation of PCK1 could re-position two loops surrounding the catalytic center into an open configuration, rendering the catalytic center more accessible. Our study reveals that neddylation of PCK1 provides a finely tuned mechanism of controlling glucose metabolism by linking whole nutrient availability to metabolic homeostasis.
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Affiliation(s)
- María J Gonzalez-Rellan
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Uxía Fernández
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Tamara Parracho
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Eva Novoa
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Marcos F Fondevila
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Natalia da Silva Lima
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Lucía Ramos
- Department of Biochemistry, CIMUS, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain
| | - Amaia Rodríguez
- CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Department of Endocrinology & Nutrition, Metabolic Research Laboratory, Clínica Universidad de Navarra, University of Navarra, IdiSNA, Pamplona, Navarra, Spain
| | - Marina Serrano-Maciá
- Liver Disease Lab, BRTA CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - Gonzalo Perez-Mejias
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-CSIC. Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Pilar Chantada-Vazquez
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15705, A Coruña, Spain
| | - Cristina Riobello
- Gene Regulatory Control in Disease, CIMUS, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Christelle Veyrat-Durebex
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sulay Tovar
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Roberto Coppari
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ashwin Woodhoo
- Gene Regulatory Control in Disease, CIMUS, University of Santiago de Compostela, Santiago de Compostela, Spain; Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, Spain
| | - Markus Schwaninger
- University of Lübeck, Institute for Experimental and Clinical Pharmacology and Toxicology, Lübeck, Germany
| | - Vincent Prevot
- University of Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Neuroendocrine Brain, Lille Neuroscience & Cognition, UMR-S 1172, European Genomic Institute for Diabetes (EGID), 59000 Lille, France
| | - Teresa C Delgado
- Liver Disease Lab, BRTA CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - Miguel Lopez
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Antonio Diaz-Quintana
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-CSIC. Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Carlos Dieguez
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Diana Guallar
- Department of Biochemistry, CIMUS, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain
| | - Gema Frühbeck
- CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Department of Endocrinology & Nutrition, Metabolic Research Laboratory, Clínica Universidad de Navarra, University of Navarra, IdiSNA, Pamplona, Navarra, Spain
| | - Irene Diaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-CSIC. Avda. Americo Vespucio 49, 41092 Sevilla, Spain
| | - Susana B Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela 15705, A Coruña, Spain
| | - Maria L Martinez-Chantar
- Liver Disease Lab, BRTA CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain.
| | - Ruben Nogueiras
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain; CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), Madrid, Spain; Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, Spain.
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Kumarasinghe L, Garcia-Gimeno MA, Ramirez J, Mayor U, Zugaza JL, Sanz P. P-Rex1 is a novel substrate of the E3 ubiquitin ligase Malin associated with Lafora disease. Neurobiol Dis 2023; 177:105998. [PMID: 36638890 PMCID: PMC10682699 DOI: 10.1016/j.nbd.2023.105998] [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: 09/01/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
Laforin and Malin are two proteins that are encoded by the genes EPM2A and EPM2B, respectively. Laforin is a glucan phosphatase and Malin is an E3-ubiquitin ligase, and these two proteins function as a complex. Mutations occurring at the level of one of the two genes lead to the accumulation of an aberrant form of glycogen meant to cluster in polyglucosans that go under the name of Lafora bodies. Individuals affected by the appearance of these polyglucosans, especially at the cerebral level, experience progressive neurodegeneration and several episodes of epilepsy leading to the manifestation of a fatal form of a rare disease called Lafora disease (LD), for which, to date, no treatment is available. Despite the different dysfunctions described for this disease, many molecular aspects still demand elucidation. An effective way to unknot some of the nodes that prevent the achievement of better knowledge of LD is to focus on the substrates that are ubiquitinated by the E3-ubiquitin ligase Malin. Some substrates have already been provided by previous studies based on protein-protein interaction techniques and have been associated with some alterations that mark the disease. In this work, we have used an unbiased alternative approach based on the activity of Malin as an E3-ubiquitin ligase. We report the discovery of novel bonafide substrates of Malin and have characterized one of them more deeply, namely PIP3-dependent Rac exchanger 1 (P-Rex1). The analysis conducted upon this substrate sets the genesis of the delineation of a molecular pathway that leads to altered glucose uptake, which could be one of the origin of the accumulation of the polyglucosans present in the disease.
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Affiliation(s)
- L Kumarasinghe
- Instituto de Biomedicina de Valencia, IBV-CSIC, 46010, Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, 28029 Madrid, Spain
| | - M A Garcia-Gimeno
- Department of Biotechnology, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural (ETSIAMN), Universitat Politécnica de València, 46022, Valencia, Spain
| | - J Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, UPV/EHU, Leioa, Bizkaia, Spain
| | - U Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, UPV/EHU, Leioa, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Plaza Euskadi, 48009 Bilbao, Spain
| | - J L Zugaza
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi, 48009 Bilbao, Spain; Achucarro Basque Center for Neuroscience, Scientific Park UPV/EHU, 48940 Leioa, Bizkaia, Spain; Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, UPV/EHU, 48940 Leioa, Bizkaia, Spain
| | - P Sanz
- Instituto de Biomedicina de Valencia, IBV-CSIC, 46010, Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, 28029 Madrid, Spain.
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Serrano-Maciá M, Delgado TC, Martínez-Chantar ML. Isolation of the Hepatic Ubiquitome/NEDDylome by Streptavidin Pull-Down Assay in the Biotinylated Ubiquitin ( bioUb)/Biotinylated NEDD8 ( bioNEDD8) Transgenic Mice. Methods Mol Biol 2023; 2602:151-162. [PMID: 36446973 DOI: 10.1007/978-1-0716-2859-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the last years, our group and others have uncovered the role of ubiquitin (Ub) and ubiquitin-like proteins such as the neural precursor cell expressed, developmentally downregulated 8 (NEDD8)-mediated modifications in several types of liver disease, including nonalcoholic fatty liver disease, liver fibrosis, and hepatocellular carcinoma. For this purpose, we have taken advantage of biotinylated ubiquitin (bioUb) and biotinylated NEDD8 (bioNEDD8) mice, transgenic mouse models in which ubiquitin and NEDD8, respectively, are biotinylated in vivo. Using these genetic tools and pull-down assays that exploit the strong biotin-streptavidin interaction, denaturing lysis conditions, and stringent washing procedures, only proteins modified by Ub or NEDD8 are isolated from mammalian tissues in vivo. Here, we report a protocol of streptavidin pull-down of ubiquitinated and NEDDylated liver proteins using the bioUb and bioNEDD8 mice that can potentially be used to characterize both the hepatic ubiquitome and NEDDylome in different models of liver injury.
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Affiliation(s)
- Marina Serrano-Maciá
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia, Spain
| | - Teresa Cardoso Delgado
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia, Spain.
| | - María Luz Martínez-Chantar
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Bizkaia, Spain
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5
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Studying the ubiquitin code through biotin-based labelling methods. Semin Cell Dev Biol 2022; 132:109-119. [PMID: 35181195 DOI: 10.1016/j.semcdb.2022.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications of cellular substrates by members of the ubiquitin (Ub) and ubiquitin-like (UbL) family are crucial for regulating protein homeostasis in organisms. The term "ubiquitin code" encapsulates how this diverse family of modifications, via adding single UbLs or different types of UbL chains, leads to specific fates for substrates. Cancer, neurodegeneration and other conditions are sometimes linked to underlying errors in this code. Studying these modifications in cells is particularly challenging since they are usually transient, scarce, and compartment-specific. Advances in the use of biotin-based methods to label modified proteins, as well as their proximally-located interactors, facilitate isolation and identification of substrates, modification sites, and the enzymes responsible for writing and erasing these modifications, as well as factors recruited as a consequence of the substrate being modified. In this review, we discuss site-specific and proximity biotinylation approaches being currently applied for studying modifications by UbLs, highlighting the pros and cons, with mention of complementary methods when possible. Future improvements may come from bioengineering and chemical biology but even now, biotin-based technology is uncovering new substrates and regulators, expanding potential therapeutic targets to manipulate the Ub code.
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Ma M, Zhang C, Cao R, Tang D, Sang X, Zou S, Wang X, Xu H, Liu G, Dai L, Tian Y, Gao X, Fu X. UBE2O promotes lipid metabolic reprogramming and liver cancer progression by mediating HADHA ubiquitination. Oncogene 2022; 41:5199-5213. [PMID: 36273042 DOI: 10.1038/s41388-022-02509-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]
Abstract
Cancer cells rely on heightened protein quality control mechanisms, including the ubiquitin-proteosome system that is predominantly driven by ubiquitination comprising E1, E2, and E3 trienzyme cascades. Although E3s have been extensively studied, the implication of E2s in tumorigenesis is poorly defined. Here we reveal a critical E2 in the pathogenesis of hepatocellular carcinoma (HCC). Among all of E2s, UBE2O shows the strongest association with HCC survival prognosis, and its expression is increased in HCC tumors. Accordingly, UBE2O deficiency inhibits HCC growth and metastasis both in vitro and in vivo, while its overexpression has opposite effects. Depending on both E2 and E3 enzymatic activities, UBE2O can interact with and mediate the ubiquitination and degradation of HADHA, a mitochondrial β-oxidation enzyme, thereby modulating lipid metabolic reprogramming. HADHA is reduced in HCC tumors and inversely correlated with UBE2O levels. Importantly, HADHA acts as a tumor suppressor and primarily mediates UBE2O's function on HCC. Moreover, liver-specific deletion of Ube2o in mice are resistant to DEN-induced hepatocarcinogenesis, along with HADHA upregulation and reduced hepatic lipid accumulation. These data reveal UBE2O as a novel oncogenic driver for metabolic reprogramming and HCC development, highlighting the potential of targeting UBE2O/HADHA axis for HCC therapy.
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Affiliation(s)
- Meilin Ma
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China
| | - Changhui Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China
| | - Rong Cao
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China
| | - Dongmei Tang
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China
| | - Xiongbo Sang
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China
| | - Sailan Zou
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China
| | - Xiuxuan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China
| | - Haixia Xu
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China
| | - Geng Liu
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China
| | - Lunzhi Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China
| | - Yan Tian
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China
| | - Xiang Gao
- Department of Neurosurgery and Institute of Neurosurgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China.
| | - Xianghui Fu
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, Sichuan, China.
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7
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Kulyyassov A. Application of Skyline for Analysis of Protein-Protein Interactions In Vivo. Molecules 2021; 26:molecules26237170. [PMID: 34885753 PMCID: PMC8658920 DOI: 10.3390/molecules26237170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
Quantitative and qualitative analyses of cell protein composition using liquid chromatography/tandem mass spectrometry are now standard techniques in biological and clinical research. However, the quantitative analysis of protein–protein interactions (PPIs) in cells is also important since these interactions are the bases of many processes, such as the cell cycle and signaling pathways. This paper describes the application of Skyline software for the identification and quantification of the biotinylated form of the biotin acceptor peptide (BAP) tag, which is a marker of in vivo PPIs. The tag was used in the Proximity Utilizing Biotinylation (PUB) method, which is based on the co-expression of BAP-X and BirA-Y in mammalian cells, where X or Y are interacting proteins of interest. A high level of biotinylation was detected in the model experiments where X and Y were pluripotency transcription factors Sox2 and Oct4, or heterochromatin protein HP1γ. MRM data processed by Skyline were normalized and recalculated. Ratios of biotinylation levels in experiment versus controls were 86 ± 6 (3 h biotinylation time) and 71 ± 5 (9 h biotinylation time) for BAP-Sox2 + BirA-Oct4 and 32 ± 3 (4 h biotinylation time) for BAP-HP1γ + BirA-HP1γ experiments. Skyline can also be applied for the analysis and identification of PPIs from shotgun proteomics data downloaded from publicly available datasets and repositories.
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Affiliation(s)
- Arman Kulyyassov
- Republican State Enterprise "National Center for Biotechnology" under the Science Committee of Ministry of Education and Science of the Republic of Kazakhstan, 13/5, Kurgalzhynskoye Road, Nur-Sultan 010000, Kazakhstan
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8
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Ramirez J, Prieto G, Olazabal-Herrero A, Borràs E, Fernandez-Vigo E, Alduntzin U, Osinalde N, Beaskoetxea J, Lectez B, Aloria K, Rodriguez JA, Paradela A, Sabidó E, Muñoz J, Corrales F, Arizmendi JM, Mayor U. A Proteomic Approach for Systematic Mapping of Substrates of Human Deubiquitinating Enzymes. Int J Mol Sci 2021; 22:ijms22094851. [PMID: 34063716 PMCID: PMC8124392 DOI: 10.3390/ijms22094851] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/02/2022] Open
Abstract
The human genome contains nearly 100 deubiquitinating enzymes (DUBs) responsible for removing ubiquitin moieties from a large variety of substrates. Which DUBs are responsible for targeting which substrates remain mostly unknown. Here we implement the bioUb approach to identify DUB substrates in a systematic manner, combining gene silencing and proteomics analyses. Silencing of individual DUB enzymes is used to reduce their ubiquitin deconjugating activity, leading to an increase of the ubiquitination of their substrates, which can then be isolated and identified. We report here quantitative proteomic data of the putative substrates of 5 human DUBs. Furthermore, we have built a novel interactive database of DUB substrates to provide easy access to our data and collect DUB proteome data from other groups as a reference resource in the DUB substrates research field.
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Affiliation(s)
- Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.R.); (U.A.); (J.B.); (B.L.); (J.M.A.)
| | - Gorka Prieto
- Department of Communications Engineering, University of the Basque Country (UPV/EHU), 48013 Bilbao, Spain;
| | - Anne Olazabal-Herrero
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (A.O.-H.); (J.A.R.)
| | - Eva Borràs
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; (E.B.); (E.S.)
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Elvira Fernandez-Vigo
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain; (E.F.-V.); (J.M.)
| | - Unai Alduntzin
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.R.); (U.A.); (J.B.); (B.L.); (J.M.A.)
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain;
| | - Javier Beaskoetxea
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.R.); (U.A.); (J.B.); (B.L.); (J.M.A.)
| | - Benoit Lectez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.R.); (U.A.); (J.B.); (B.L.); (J.M.A.)
| | - Kerman Aloria
- Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (A.O.-H.); (J.A.R.)
| | - Alberto Paradela
- Functional Proteomics Facility, Centro Nacional de Biotecnología (CNB-CSIC), ProteoRed-ISCIII, 28029 Madrid, Spain; (A.P.); (F.C.)
| | - Eduard Sabidó
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; (E.B.); (E.S.)
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain; (E.F.-V.); (J.M.)
| | - Fernando Corrales
- Functional Proteomics Facility, Centro Nacional de Biotecnología (CNB-CSIC), ProteoRed-ISCIII, 28029 Madrid, Spain; (A.P.); (F.C.)
| | - Jesus M. Arizmendi
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.R.); (U.A.); (J.B.); (B.L.); (J.M.A.)
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.R.); (U.A.); (J.B.); (B.L.); (J.M.A.)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Correspondence: ; Tel.: +34-94-601-5908
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9
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Multi-Omics Integration Highlights the Role of Ubiquitination in CCl 4-Induced Liver Fibrosis. Int J Mol Sci 2020; 21:ijms21239043. [PMID: 33261190 PMCID: PMC7729774 DOI: 10.3390/ijms21239043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 01/11/2023] Open
Abstract
Liver fibrosis is the excessive accumulation of extracellular matrix proteins that occurs in chronic liver disease. Ubiquitination is a post-translational modification that is crucial for a plethora of physiological processes. Even though the ubiquitin system has been implicated in several human diseases, the role of ubiquitination in liver fibrosis remains poorly understood. Here, multi-omics approaches were used to address this. Untargeted metabolomics showed that carbon tetrachloride (CCl4)-induced liver fibrosis promotes changes in the hepatic metabolome, specifically in glycerophospholipids and sphingolipids. Gene ontology analysis of public deposited gene array-based data and validation in our mouse model showed that the biological process “protein polyubiquitination” is enriched after CCl4-induced liver fibrosis. Finally, by using transgenic mice expressing biotinylated ubiquitin (bioUb mice), the ubiquitinated proteome was isolated and characterized by mass spectrometry in order to unravel the hepatic ubiquitinated proteome fingerprint in CCl4-induced liver fibrosis. Under these conditions, ubiquitination appears to be involved in the regulation of cell death and survival, cell function, lipid metabolism, and DNA repair. Finally, ubiquitination of proliferating cell nuclear antigen (PCNA) is induced during CCl4-induced liver fibrosis and associated with the DNA damage response (DDR). Overall, hepatic ubiquitome profiling can highlight new therapeutic targets for the clinical management of liver fibrosis.
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10
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Vere G, Kealy R, Kessler BM, Pinto-Fernandez A. Ubiquitomics: An Overview and Future. Biomolecules 2020; 10:E1453. [PMID: 33080838 PMCID: PMC7603029 DOI: 10.3390/biom10101453] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Covalent attachment of ubiquitin, a small globular polypeptide, to protein substrates is a key post-translational modification that determines the fate, function, and turnover of most cellular proteins. Ubiquitin modification exists as mono- or polyubiquitin chains involving multiple ways how ubiquitin C-termini are connected to lysine, perhaps other amino acid side chains, and N-termini of proteins, often including branching of the ubiquitin chains. Understanding this enormous complexity in protein ubiquitination, the so-called 'ubiquitin code', in combination with the ∼1000 enzymes involved in controlling ubiquitin recognition, conjugation, and deconjugation, calls for novel developments in analytical techniques. Here, we review different headways in the field mainly driven by mass spectrometry and chemical biology, referred to as "ubiquitomics", aiming to understand this system's biological diversity.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
| | - Rachel Kealy
- St Anne’s College, University of Oxford, Oxford OX2 6HS, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Chinese Academy of Medical Sciences Oxford Institute (CAMS), Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
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11
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Gillen J, Bridgwater C, Nita-Lazar A. Approaching complexity: systems biology and ms-based techniques to address immune signaling. Expert Rev Proteomics 2020; 17:341-354. [PMID: 32552048 DOI: 10.1080/14789450.2020.1780920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Studying immune signaling has been critical for our understanding of immunology, pathogenesis, cancer, and homeostasis. To enhance the breadth of the analysis, high throughput methods have been developed to survey multiple areas simultaneously, including transcriptomics, reporter assays, and ELISAs. While these techniques have been extremely informative, mass-spectrometry-based technologies have been gaining momentum and starting to be widely used in the studies of immune signaling and systems immunology. AREAS COVERED We present established proteomic methods that have been used to address immune signaling and discuss the new mass-spectrometry- based techniques of interest to the expanding field of systems immunology. Established and new proteomic methods and their applications discussed here include post-translational modification analysis, protein quantification, secretome analysis, and interactomics. In addition, we present developments in small molecule and metabolite analysis, mass spectrometry imaging, and single cell analysis. Finally, we discuss the role of multi-omic integration in aiding leading edge investigation. EXPERT OPINION In science, available techniques enhance the breadth and depth of the studies. By incorporating proteomic techniques and their innovative use, it will be possible to expand the current studies and to address novel questions at the forefront of scientific discovery.
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Affiliation(s)
- Joseph Gillen
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
| | - Caleb Bridgwater
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
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12
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Kliza K, Husnjak K. Resolving the Complexity of Ubiquitin Networks. Front Mol Biosci 2020; 7:21. [PMID: 32175328 PMCID: PMC7056813 DOI: 10.3389/fmolb.2020.00021] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/04/2020] [Indexed: 12/22/2022] Open
Abstract
Ubiquitination regulates nearly all cellular processes by coordinated activity of ubiquitin writers (E1, E2, and E3 enzymes), erasers (deubiquitinating enzymes) and readers (proteins that recognize ubiquitinated proteins by their ubiquitin-binding domains). By differentially modifying cellular proteome and by recognizing these ubiquitin modifications, ubiquitination machinery tightly regulates execution of specific cellular events in space and time. Dynamic and complex ubiquitin architecture, ranging from monoubiquitination, multiple monoubiquitination, eight different modes of homotypic and numerous types of heterogeneous polyubiquitin linkages, enables highly dynamic and complex regulation of cellular processes. We discuss available tools and approaches to study ubiquitin networks, including methods for the identification and quantification of ubiquitin-modified substrates, as well as approaches to quantify the length, abundance, linkage type and architecture of different ubiquitin chains. Furthermore, we also summarize the available approaches for the discovery of novel ubiquitin readers and ubiquitin-binding domains, as well as approaches to monitor and visualize activity of ubiquitin conjugation and deconjugation machineries. We also discuss benefits, drawbacks and limitations of available techniques, as well as what is still needed for detailed spatiotemporal dissection of cellular ubiquitination networks.
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Affiliation(s)
- Katarzyna Kliza
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
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13
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Huang Q, Zhang X. Emerging Roles and Research Tools of Atypical Ubiquitination. Proteomics 2020; 20:e1900100. [PMID: 31930661 DOI: 10.1002/pmic.201900100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/02/2019] [Indexed: 12/19/2022]
Abstract
Ubiquitination is a posttranslational modification characterized by the covalent attachment of ubiquitin molecules to protein substrates. The ubiquitination modification process is reversible, dynamic, and involved in the regulation of various biological processes, such as autophagy, inflammatory responses, and DNA damage responses. The forms of ubiquitin modification are very diverse, incorporating either a single ubiquitin molecule or a complicated ubiquitin polymer, and different types of ubiquitination usually elicit corresponding cellular responses. The development of research tools and strategies has afforded more detailed insight into atypical ubiquitin signaling pathways that were previously poorly understood. Here, an update on the understanding of atypical ubiquitin chain signaling pathways is provided and the recent development of representative research tools for ubiquitin systems is discussed. In addition, the future challenges in ubiquitin research are reflected on and summarized.
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Affiliation(s)
- Qiuling Huang
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaofei Zhang
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510530, China
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14
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Dittmar G, Winklhofer KF. Linear Ubiquitin Chains: Cellular Functions and Strategies for Detection and Quantification. Front Chem 2020; 7:915. [PMID: 31998699 PMCID: PMC6966713 DOI: 10.3389/fchem.2019.00915] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/16/2019] [Indexed: 01/06/2023] Open
Abstract
Ubiquitination of proteins is a sophisticated post-translational modification implicated in the regulation of an ever-growing abundance of cellular processes. Recent insights into different layers of complexity have shaped the concept of the ubiquitin code. Key players in determining this code are the number of ubiquitin moieties attached to a substrate, the architecture of polyubiquitin chains, and post-translational modifications of ubiquitin itself. Ubiquitination can induce conformational changes of substrates and alter their interactive profile, resulting in the formation of signaling complexes. Here we focus on a distinct type of ubiquitination that is characterized by an inter-ubiquitin linkage through the N-terminal methionine, called M1-linked or linear ubiquitination. Formation, recognition, and disassembly of linear ubiquitin chains are highly specific processes that are implicated in immune signaling, cell death regulation and protein quality control. Consistent with their role in influencing signaling events, linear ubiquitin chains are formed in a transient and spatially regulated manner, making their detection and quantification challenging.
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Affiliation(s)
- Gunnar Dittmar
- Proteomics of Cellular Signalling, Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Konstanze F Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
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15
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Mendes ML, Fougeras MR, Dittmar G. Analysis of ubiquitin signaling and chain topology cross-talk. J Proteomics 2020; 215:103634. [PMID: 31918034 DOI: 10.1016/j.jprot.2020.103634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/13/2019] [Accepted: 01/05/2020] [Indexed: 12/12/2022]
Abstract
Protein ubiquitination is a powerful post-translational modification implicated in many cellular processes. Although ubiquitination is associated with protein degradation, depending on the topology of polyubiquitin chains, protein ubiquitination is connected to non-degradative events in DNA damage response, cell cycle control, immune response, trafficking, intracellular localization, and vesicle fusion events. It has been shown that a ubiquitin chain can contain two or more topologies at the same time. These branched chains add another level of complexity to ubiquitin signaling, increasing its versatility and specificity. Mass spectrometry-based proteomics has been playing an important role in the identification of all types of ubiquitin chains and linkages. This review aims to provide an overview of ubiquitin chain topology and associated signaling pathways and discusses the MS-based proteomic methodologies used to determine such topologies. SIGNIFICANCE: Ubiquitination plays important roles in many cellular processes. Proteins can be monoubiquitinated or polyubiquitinated forming non-branched or branched chains in a high number of possible combinations, each associated with different cellular processes. The detection and the topology of ubiquitin chains is thus of extreme importance in order to explain such processes. Advances in mass spectrometry based proteomics allowed for the discovery and topology mapping of many ubiquitin chains. This review revisits the state of the art in ubiquitin chain identification by mass spectrometry and gives an insight on the implication of such chains in many cellular processes.
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Affiliation(s)
- Marta L Mendes
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Miriam R Fougeras
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Faculty of Science, Technology and Communication, University of Luxembourg, 2 avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Faculty of Science, Technology and Communication, University of Luxembourg, 2 avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg.
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16
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Lachiondo-Ortega S, Mercado-Gómez M, Serrano-Maciá M, Lopitz-Otsoa F, Salas-Villalobos TB, Varela-Rey M, Delgado TC, Martínez-Chantar ML. Ubiquitin-Like Post-Translational Modifications (Ubl-PTMs): Small Peptides with Huge Impact in Liver Fibrosis. Cells 2019; 8:cells8121575. [PMID: 31817258 PMCID: PMC6953033 DOI: 10.3390/cells8121575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 02/06/2023] Open
Abstract
Liver fibrosis is characterized by the excessive deposition of extracellular matrix proteins including collagen that occurs in most types of chronic liver disease. Even though our knowledge of the cellular and molecular mechanisms of liver fibrosis has deeply improved in the last years, therapeutic approaches for liver fibrosis remain limited. Profiling and characterization of the post-translational modifications (PTMs) of proteins, and more specifically NEDDylation and SUMOylation ubiquitin-like (Ubls) modifications, can provide a better understanding of the liver fibrosis pathology as well as novel and more effective therapeutic approaches. On this basis, in the last years, several studies have described how changes in the intermediates of the Ubl cascades are altered during liver fibrosis and how specific targeting of particular enzymes mediating these ubiquitin-like modifications can improve liver fibrosis, mainly in in vitro models of hepatic stellate cells, the main fibrogenic cell type, and in pre-clinical mouse models of liver fibrosis. The development of novel inhibitors of the Ubl modifications as well as novel strategies to assess the modified proteome can provide new insights into the overall role of Ubl modifications in liver fibrosis.
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Affiliation(s)
- Sofia Lachiondo-Ortega
- Liver Disease Lab, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Spain; (S.L.-O.); (M.M.-G.); (M.S.-M.); (M.V.-R.); (M.L.M.-C.)
| | - Maria Mercado-Gómez
- Liver Disease Lab, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Spain; (S.L.-O.); (M.M.-G.); (M.S.-M.); (M.V.-R.); (M.L.M.-C.)
| | - Marina Serrano-Maciá
- Liver Disease Lab, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Spain; (S.L.-O.); (M.M.-G.); (M.S.-M.); (M.V.-R.); (M.L.M.-C.)
| | | | - Tanya B Salas-Villalobos
- Department of Biochemistry and Molecular Medicine, School of Medicine, Autonomous University of Nuevo León, Monterrey, Nuevo León 66450, Mexico;
| | - Marta Varela-Rey
- Liver Disease Lab, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Spain; (S.L.-O.); (M.M.-G.); (M.S.-M.); (M.V.-R.); (M.L.M.-C.)
| | - Teresa C. Delgado
- Liver Disease Lab, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Spain; (S.L.-O.); (M.M.-G.); (M.S.-M.); (M.V.-R.); (M.L.M.-C.)
- Correspondence: ; Tel.: +34-944-061318; Fax: +34-944-061301
| | - María Luz Martínez-Chantar
- Liver Disease Lab, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Spain; (S.L.-O.); (M.M.-G.); (M.S.-M.); (M.V.-R.); (M.L.M.-C.)
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17
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Mattern M, Sutherland J, Kadimisetty K, Barrio R, Rodriguez MS. Using Ubiquitin Binders to Decipher the Ubiquitin Code. Trends Biochem Sci 2019; 44:599-615. [PMID: 30819414 DOI: 10.1016/j.tibs.2019.01.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
Abstract
Post-translational modifications (PTMs) by ubiquitin (Ub) are versatile, highly dynamic, and involved in nearly all aspects of eukaryote biological function. The reversibility and heterogeneity of Ub chains attached to protein substrates have complicated their isolation, quantification, and characterization. Strategies have emerged to isolate endogenous ubiquitylated targets, including technologies based on the use of Ub-binding peptides, such as tandem-repeated Ub-binding entities (TUBEs). TUBEs allow the identification and characterization of Ub chains, and novel substrates for deubiquitylases (DUBs) and Ub ligases (E3s). Here we review their impact on purification, analysis of pan or chain-selective polyubiquitylated proteins and underline the biological relevance of this information. Together with peptide aptamers and other Ub affinity-based approaches, TUBEs will contribute to unraveling the secrets of the Ub code.
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Affiliation(s)
- Michael Mattern
- Progenra Inc., 277 Great Valley Parkway, Malvern 19355, Pennsylvania, USA; These authors contributed equally
| | - James Sutherland
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain; These authors contributed equally
| | - Karteek Kadimisetty
- LifeSensors Inc., 271 Great Valley Parkway, Malvern 19355, Pennsylvania, USA
| | - Rosa Barrio
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain
| | - Manuel S Rodriguez
- ITAV-IPBS-UPS CNRS USR3505, 1 place Pierre Potier, Oncopole entrée B, 31106 Toulouse, France.
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Neuronal Proteomic Analysis of the Ubiquitinated Substrates of the Disease-Linked E3 Ligases Parkin and Ube3a. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3180413. [PMID: 29693004 PMCID: PMC5859835 DOI: 10.1155/2018/3180413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/15/2018] [Indexed: 01/09/2023]
Abstract
Both Parkin and UBE3A are E3 ubiquitin ligases whose mutations result in severe brain dysfunction. Several of their substrates have been identified using cell culture models in combination with proteasome inhibitors, but not in more physiological settings. We recently developed the bioUb strategy to isolate ubiquitinated proteins in flies and have now identified by mass spectrometry analysis the neuronal proteins differentially ubiquitinated by those ligases. This is an example of how flies can be used to provide biological material in order to reveal steady state substrates of disease causing genes. Collectively our results provide new leads to the possible physiological functions of the activity of those two disease causing E3 ligases. Particularly, in the case of Parkin the novelty of our data originates from the experimental setup, which is not overtly biased by acute mitochondrial depolarisation. In the case of UBE3A, it is the first time that a nonbiased screen for its neuronal substrates has been reported.
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Matunis MJ, Rodriguez MS. Concepts and Methodologies to Study Protein SUMOylation: An Overview. Methods Mol Biol 2018; 1475:3-22. [PMID: 27631794 DOI: 10.1007/978-1-4939-6358-4_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein modification by the small ubiquitin-related modifier (SUMO) was simultaneously discovered by several groups at the middle of the 1990s. Although distinct names were proposed including Sentrin, GMP1, PIC1, or SMT3, SUMO became the most popular. Early studies on the functions of SUMOylation focused on activities in the nucleus, including transcription activation, chromatin structure, and DNA repair. However, it is now recognized that SUMOylation affects a large diversity of cellular processes both in the nucleus and the cytoplasm and functions of SUMOylation appear to have undefined limits. SUMO-conjugating enzymes and specific proteases actively regulate the modification status of target proteins. The recent discoveries of ubiquitin-SUMO hybrid chains, multiple SUMO-interacting motifs, and macromolecular complexes regulated by SUMOylation underscore the high complexity of this dynamic reversible system. New conceptual frameworks suggested by these findings have motivated the development of new methodologies to study pre- and post-SUMOylation events in vitro and in vivo, using distinct model organisms. Here we summarize some of the new developments and methodologies in the field, particularly those that will be further elaborated on in the chapters integrating this book.
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Affiliation(s)
- Michael J Matunis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe St., Room W8118, Baltimore, MD, 21205, USA.
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20
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Ramberger E, Dittmar G. Tissue Specific Labeling in Proteomics. Proteomes 2017; 5:proteomes5030017. [PMID: 28718811 PMCID: PMC5620534 DOI: 10.3390/proteomes5030017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 01/08/2023] Open
Abstract
Mass spectrometry-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples. While it is routinely used for the characterization of simple cell line systems, the analysis of the cell specific proteome in multicellular organisms and tissues poses a significant challenge. Isolating a subset of cells from tissues requires mechanical and biochemical separation or sorting, a process which can alter cellular signaling, and thus, the composition of the proteome. Recently, several approaches for cell selective labeling of proteins, that include bioorthogonal amino acids, biotinylating enzymes, and genetic tools, have been developed. These tools facilitate the selective labeling of proteins, their interactome, or of specific cell types within a tissue or an organism, while avoiding the difficult and contamination-prone biochemical separation of cells from the tissue. In this review, we give an overview of existing techniques and their application in cell culture models and whole animals.
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Affiliation(s)
- Evelyn Ramberger
- Mass-Spectrometry Core Unit, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
- Berlin School of Integrative Oncology (BSIO), Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.
| | - Gunnar Dittmar
- Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1272 Strassen, Luxembourg.
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21
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Martinez A, Mayor U, Clague MJ. Multi-story Parkin. Oncotarget 2017; 8:50327-50328. [PMID: 28881561 PMCID: PMC5584130 DOI: 10.18632/oncotarget.18318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 05/28/2017] [Indexed: 11/25/2022] Open
Affiliation(s)
- Aitor Martinez
- Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK
| | - Ugo Mayor
- Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK
| | - Michael J Clague
- Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK
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22
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Martinez A, Lectez B, Ramirez J, Popp O, Sutherland JD, Urbé S, Dittmar G, Clague MJ, Mayor U. Quantitative proteomic analysis of Parkin substrates in Drosophila neurons. Mol Neurodegener 2017; 12:29. [PMID: 28399880 PMCID: PMC5387213 DOI: 10.1186/s13024-017-0170-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/30/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Parkin (PARK2) is an E3 ubiquitin ligase that is commonly mutated in Familial Parkinson's Disease (PD). In cell culture models, Parkin is recruited to acutely depolarised mitochondria by PINK1. PINK1 activates Parkin activity leading to ubiquitination of multiple proteins, which in turn promotes clearance of mitochondria by mitophagy. Many substrates have been identified using cell culture models in combination with depolarising drugs or proteasome inhibitors, but not in more physiological settings. METHODS Here we utilized the recently introduced BioUb strategy to isolate ubiquitinated proteins in flies. Following Parkin Wild-Type (WT) and Parkin Ligase dead (LD) expression we analysed by mass spectrometry and stringent bioinformatics analysis those proteins differentially ubiquitinated to provide the first survey of steady state Parkin substrates using an in vivo model. We further used an in vivo ubiquitination assay to validate one of those substrates in SH-SY5Y cells. RESULTS We identified 35 proteins that are more prominently ubiquitinated following Parkin over-expression. These include several mitochondrial proteins and a number of endosomal trafficking regulators such as v-ATPase sub-units, Syx5/STX5, ALiX/PDCD6IP and Vps4. We also identified the retromer component, Vps35, another PD-associated gene that has recently been shown to interact genetically with parkin. Importantly, we validated Parkin-dependent ubiquitination of VPS35 in human neuroblastoma cells. CONCLUSIONS Collectively our results provide new leads to the possible physiological functions of Parkin activity that are not overtly biased by acute mitochondrial depolarisation.
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Affiliation(s)
- Aitor Martinez
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain.,Functional Genomics Unit, CIC bioGUNE, Derio, Spain.,Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Benoit Lectez
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain.,Functional Genomics Unit, CIC bioGUNE, Derio, Spain
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Sylvie Urbé
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Gunnar Dittmar
- Department of Oncology, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Michael J Clague
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK.
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain. .,Functional Genomics Unit, CIC bioGUNE, Derio, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain.
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23
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Pirone L, Xolalpa W, Sigurðsson JO, Ramirez J, Pérez C, González M, de Sabando AR, Elortza F, Rodriguez MS, Mayor U, Olsen JV, Barrio R, Sutherland JD. A comprehensive platform for the analysis of ubiquitin-like protein modifications using in vivo biotinylation. Sci Rep 2017; 7:40756. [PMID: 28098257 PMCID: PMC5241687 DOI: 10.1038/srep40756] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/09/2016] [Indexed: 12/19/2022] Open
Abstract
Post-translational modification by ubiquitin and ubiquitin-like proteins (UbLs) is fundamental for maintaining protein homeostasis. Efficient isolation of UbL conjugates is hampered by multiple factors, including cost and specificity of reagents, removal of UbLs by proteases, distinguishing UbL conjugates from interactors, and low quantities of modified substrates. Here we describe bioUbLs, a comprehensive set of tools for studying modifications in Drosophila and mammals, based on multicistronic expression and in vivo biotinylation using the E. coli biotin protein ligase BirA. While the bioUbLs allow rapid validation of UbL conjugation for exogenous or endogenous proteins, the single vector approach can facilitate biotinylation of most proteins of interest. Purification under denaturing conditions inactivates deconjugating enzymes and stringent washes remove UbL interactors and non-specific background. We demonstrate the utility of the method in Drosophila cells and transgenic flies, identifying an extensive set of putative SUMOylated proteins in both cases. For mammalian cells, we show conjugation and localization for many different UbLs, with the identification of novel potential substrates for UFM1. Ease of use and the flexibility to modify existing vectors will make the bioUbL system a powerful complement to existing strategies for studying this important mode of protein regulation.
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Affiliation(s)
- Lucia Pirone
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | - Wendy Xolalpa
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | - Jón Otti Sigurðsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Juanma Ramirez
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Coralia Pérez
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | - Monika González
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | | | - Félix Elortza
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | - Manuel S Rodriguez
- ITAV, IPBS, Université de Toulouse, CNRS, UPS, 1 Place Pierre Potier Oncopole entrée B, BP 50624, 31106 Toulouse Cedex 1, France
| | - Ugo Mayor
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain.,Ikerbasque, Basque Foundation for Science, Alameda Urquijo, 36-5 Plaza Bizkaia, 48011 Bilbao, Spain
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Rosa Barrio
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | - James D Sutherland
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
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24
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Ramirez J, Elu N, Martinez A, Lectez B, Mayor U. In Vivo Strategies to Isolate and Characterize the Neuronal Ubiquitinated Proteome. NEUROMETHODS 2017. [DOI: 10.1007/978-1-4939-7119-0_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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25
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Ramirez J, Min M, Barrio R, Lindon C, Mayor U. Isolation of Ubiquitinated Proteins to High Purity from In Vivo Samples. Methods Mol Biol 2016; 1449:193-202. [PMID: 27613036 DOI: 10.1007/978-1-4939-3756-1_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Ubiquitination pathways are widely used within eukaryotic cells. The complexity of ubiquitin signaling gives rise to a number of problems in the study of specific pathways. One problem is that not all processes regulated by ubiquitin are shared among the different cells of an organism (e.g., neurotransmitter release is only carried out in neuronal cells). Moreover, these processes are often highly temporally dynamic. It is essential therefore to use the right system for each biological question, so that we can characterize pathways specifically in the tissue or cells of interest. However, low stoichiometry, and the unstable nature of many ubiquitin conjugates, presents a technical barrier to studying this modification in vivo. Here, we describe two approaches to isolate ubiquitinated proteins to high purity. The first one favors isolation of the whole mixture of ubiquitinated material from a given tissue or cell type, generating a survey of the ubiquitome landscape for a specific condition. The second one favors the isolation of just one specific protein, in order to facilitate the characterization of its ubiquitinated fraction. In both cases, highly stringent denaturing buffers are used to minimize the presence of contaminating material in the sample.
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Affiliation(s)
- Juanma Ramirez
- Biokimika eta Biologia Molekularra Saila, Zientzia eta Teknologia Fakultatea, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
| | - Mingwei Min
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Catherine Lindon
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
| | - Ugo Mayor
- Biokimika eta Biologia Molekularra Saila, Zientzia eta Teknologia Fakultatea, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain.
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26
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Abstract
Mass spectrometry (MS) has become the method of choice for the large-scale analysis of protein ubiquitylation. There exist a number of proposed methods for mapping ubiquitin sites, each with different pros and cons. We present here a protocol for the MS analysis of the ubiquitin-proteome captured by TUBEs and subsequent data analysis. Using dedicated software and algorithms, specific information on the presence of ubiquitylated peptides can be obtained from the MS search results. In addition, a quantitative and functional analysis of the ubiquitylated proteins and their interacting partners helps to unravel the biological and molecular processes they are involved in.
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27
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Pirone L, Xolalpa W, Mayor U, Barrio R, Sutherland JD. Analysis of SUMOylated Proteins in Cells and In Vivo Using the bioSUMO Strategy. Methods Mol Biol 2016; 1475:161-9. [PMID: 27631805 DOI: 10.1007/978-1-4939-6358-4_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Posttranslational regulation of proteins by conjugation of ubiquitin- and ubiquitin-like molecules is a common theme in almost every known biological pathway. SUMO (small ubiquitin-related modifier) is dynamically added and deleted from many cellular substrates to control activity, localization, and recruitment of other SUMO-recognizing protein complexes. The dynamic nature of this modification and its low abundance in resting cells make it challenging to study, with susceptibility to deSUMOylases further complicating its analysis. Here we describe bioSUMO, a general method to isolate and analyze SUMOylated proteins from cultured cells, using Drosophila as a highlighted example. The method also has been validated in transgenic flies, as well as human cells. SUMOylated substrates are labeled by in vivo biotinylation, which facilitates their subsequent purification using streptavidin-based affinity chromatography under stringent conditions and with very low background. The bioSUMO approach can be used to validate whether a specific protein is modified, or used to analyze an entire SUMO subproteome. If coupled to quantitative proteomics methods, it may reveal how the SUMO landscape changes with different stimuli, or in diverse cell or tissue types. This technique offers a complementary approach to study SUMO biology and we expect that the strategy can be extended to other ubiquitin-like proteins.
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Affiliation(s)
- Lucia Pirone
- CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, 48160, Spain
| | - Wendy Xolalpa
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, 62100, Mexico
| | - Ugo Mayor
- Biokimika eta Biologia Molekularra Saila, Zientzia eta Teknologia Fakultatea, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, 48940, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, 48013, Spain
| | - Rosa Barrio
- CIC bioGUNE, Bizkaia Technology Park, Derio, Bizkaia, 48160, Spain.
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28
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Beaudette P, Popp O, Dittmar G. Proteomic techniques to probe the ubiquitin landscape. Proteomics 2015; 16:273-87. [PMID: 26460060 DOI: 10.1002/pmic.201500290] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/03/2015] [Accepted: 10/06/2015] [Indexed: 01/06/2023]
Abstract
Protein ubiquitination is a powerful modulator of cellular functions. Classically linked to the degradation of proteins, it also plays a role in intracellular localization, DNA damage response, vesicle fusion events, and the immune and transcriptional responses. Ubiquitin is versatile and can code for several distinct signals, either by adding a single ubiquitin or forming a chain of ubiquitins on the target protein. The enzymatic cascade associated with the cellular process determines the nature of the modification. Numerous efforts have been made for the identification of ubiquitin acceptor sites in the target proteins using genetic, biochemical or MS-based proteomic methods, such as affinity-based enrichment of ubiquitinated proteins, and antibody-based enrichment of modified peptides. Modern instrumentation enables quantitative MS strategies to identify and characterize hundreds of ubiquitin substrates in a single analysis making it the dominant method for ubiquitin site detection. Characterization of the interubiquitin connectivity in ubiquitin polymers has also moved into focus, with the field of targeted proteomics techniques proving invaluable for identifying and quantifying linkage types found in such polyubiquitin chains. This review seeks to provide an overview of the many MS-based proteomics techniques available for exploring this dynamic field.
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Affiliation(s)
- Patrick Beaudette
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Oliver Popp
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Gunnar Dittmar
- Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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29
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Ramirez J, Martinez A, Lectez B, Lee SY, Franco M, Barrio R, Dittmar G, Mayor U. Proteomic Analysis of the Ubiquitin Landscape in the Drosophila Embryonic Nervous System and the Adult Photoreceptor Cells. PLoS One 2015; 10:e0139083. [PMID: 26460970 PMCID: PMC4604154 DOI: 10.1371/journal.pone.0139083] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/09/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ubiquitination is known to regulate physiological neuronal functions as well as to be involved in a number of neuronal diseases. Several ubiquitin proteomic approaches have been developed during the last decade but, as they have been mostly applied to non-neuronal cell culture, very little is yet known about neuronal ubiquitination pathways in vivo. METHODOLOGY/PRINCIPAL FINDINGS Using an in vivo biotinylation strategy we have isolated and identified the ubiquitinated proteome in neurons both for the developing embryonic brain and for the adult eye of Drosophila melanogaster. Bioinformatic comparison of both datasets indicates a significant difference on the ubiquitin substrates, which logically correlates with the processes that are most active at each of the developmental stages. Detection within the isolated material of two ubiquitin E3 ligases, Parkin and Ube3a, indicates their ubiquitinating activity on the studied tissues. Further identification of the proteins that do accumulate upon interference with the proteasomal degradative pathway provides an indication of the proteins that are targeted for clearance in neurons. Last, we report the proof-of-principle validation of two lysine residues required for nSyb ubiquitination. CONCLUSIONS/SIGNIFICANCE These data cast light on the differential and common ubiquitination pathways between the embryonic and adult neurons, and hence will contribute to the understanding of the mechanisms by which neuronal function is regulated. The in vivo biotinylation methodology described here complements other approaches for ubiquitome study and offers unique advantages, and is poised to provide further insight into disease mechanisms related to the ubiquitin proteasome system.
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Affiliation(s)
- Juanma Ramirez
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
- Functional Genomics Unit, CIC bioGUNE, Derio, Spain
| | - Aitor Martinez
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
- Functional Genomics Unit, CIC bioGUNE, Derio, Spain
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Benoit Lectez
- Functional Genomics Unit, CIC bioGUNE, Derio, Spain
- Mollecular Cell Biology, Turku Centre for Biotechnology, Turku, Finland
| | - So Young Lee
- Functional Genomics Unit, CIC bioGUNE, Derio, Spain
| | - Maribel Franco
- Functional Genomics Unit, CIC bioGUNE, Derio, Spain
- Developmental Neurobiology, Institute of Neurosciences, CSIC/UMH, Sant Joan d’Alacant, Alicante, Spain
| | - Rosa Barrio
- Functional Genomics Unit, CIC bioGUNE, Derio, Spain
| | - Gunnar Dittmar
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain
- Functional Genomics Unit, CIC bioGUNE, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain
- * E-mail:
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