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Bouvier C, Lawrence R, Cavallo F, Xolalpa W, Jordan A, Hjerpe R, Rodriguez MS. Breaking Bad Proteins-Discovery Approaches and the Road to Clinic for Degraders. Cells 2024; 13:578. [PMID: 38607017 PMCID: PMC11011670 DOI: 10.3390/cells13070578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) describe compounds that bind to and induce degradation of a target by simultaneously binding to a ubiquitin ligase. More generally referred to as bifunctional degraders, PROTACs have led the way in the field of targeted protein degradation (TPD), with several compounds currently undergoing clinical testing. Alongside bifunctional degraders, single-moiety compounds, or molecular glue degraders (MGDs), are increasingly being considered as a viable approach for development of therapeutics, driven by advances in rational discovery approaches. This review focuses on drug discovery with respect to bifunctional and molecular glue degraders within the ubiquitin proteasome system, including analysis of mechanistic concepts and discovery approaches, with an overview of current clinical and pre-clinical degrader status in oncology, neurodegenerative and inflammatory disease.
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Affiliation(s)
- Corentin Bouvier
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
| | - Rachel Lawrence
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Francesca Cavallo
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Wendy Xolalpa
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62209, Morelos, Mexico;
| | - Allan Jordan
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Roland Hjerpe
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Manuel S. Rodriguez
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
- Pharmadev, UMR 152, Université de Toulouse, IRD, UT3, 31400 Toulouse, France
- B Molecular, Centre Pierre Potier, Canceropôle, 31106 Toulouse, France
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Hjerpe R, Kurz T. Cryo-EM reveals important regulatory mechanism of the workhorses of targeted protein degradation. Mol Cell 2023; 83:2159-2160. [PMID: 37419088 DOI: 10.1016/j.molcel.2023.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/09/2023]
Abstract
Most methods for targeted protein degradation (TPD) deliver targets to E3 ubiquitin ligases, leading to proteasomal degradation. In this issue of Molecular Cell, Shaaban et al.1 illuminate cullin-RING ubiquitin ligase (CRL) modulation by CAND1, which can be utilized for TPD.
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Affiliation(s)
- Roland Hjerpe
- Sygnature Discovery, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Thimo Kurz
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK; Evotec SE, Innovation Dr, Milton, Abingdon OX14 4RT, UK.
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Zhang Y, Bates J, Gourdet B, Birch L, Addis P, Hjerpe R, Jordan AM. Abstract 3429: Beyond cereblon IMIDs - biophysics-based discovery of novel molecular glue chemotypes. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Molecular glue degraders are compact, low molecular weight molecules that can efficiently induce specific and potent degradation of a target protein. This class of degraders function by inducing interactions between a target of interest and a ubiquitin-ligase, either by stabilization of weak pre-existing interactions, or by generation of entirely novel interactions. These molecules offer significant opportunity beyond heterobifunctional degraders such as PROTACs, not least in terms of improved molecular properties.
However, beyond the IMID molecular glues, typified by thalidomide, pomalidomide and lenalidomide, novel molecular glue chemotypes remain scarce.
To address this need, we have developed biophysics-based molecular glue screening platform, exploiting our internal, high quality fragment library and proximity-based screening platforms to rapidly identify promising new molecular glues for further optimization. A potential advantage of utilizing cell-free biophysical systems is the opportunity to select both the target and the desired ligase, opening up for development of degraders that capitalize upon differential expression of ligases in different tissues.
As proof of concept, we have applied this platform to find new molecular glues to degrade CK1α. This Ser/Thr kinase has been found to be over-expressed in metastatic colorectal cancer, and this over-expression correlates with poor overall survival. The kinase has also been implicated as an oncogenic driver in tumors such as B-Cell lymphomas and non-Hodgkin lymphomas, suggesting a potential therapeutic application for novel CK1α molecular glues.
Utilizing known IMID-derived molecular glues between CK1α and CRBN as benchmark controls, we identified several non-IMID derived chemotypes as tentative stabilizers of the CRBN/CK1α interaction. Further studies on these novel candidate degrader templates are now underway.
Citation Format: Yujia Zhang, Jessica Bates, Benoit Gourdet, Louise Birch, Philip Addis, Roland Hjerpe, Allan M. Jordan. Beyond cereblon IMIDs - biophysics-based discovery of novel molecular glue chemotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3429.
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Affiliation(s)
- Yujia Zhang
- 1Sygnature Discovery, Nottnigham, United Kingdom
| | | | | | - Louise Birch
- 1Sygnature Discovery, Nottnigham, United Kingdom
| | - Philip Addis
- 1Sygnature Discovery, Nottnigham, United Kingdom
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Rovira E, Moreno B, Razquin N, Hjerpe R, Gonzalez-Lopez M, Barrio R, Ruiz de los Mozos I, Ule J, Pastor F, Blazquez L, Fortes P. U1A is a positive regulator of the expression of heterologous and cellular genes involved in cell proliferation and migration. Molecular Therapy - Nucleic Acids 2022; 28:831-846. [PMID: 35664701 PMCID: PMC9136276 DOI: 10.1016/j.omtn.2022.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/07/2022] [Indexed: 11/16/2022]
Abstract
Here, we show that direct recruitment of U1A to target transcripts can increase gene expression. This is a new regulatory role, in addition to previous knowledge showing that U1A decreases the levels of U1A mRNA and other specific targets. In fact, genome-wide, U1A more often increases rather than represses gene expression and many U1A-upregulated transcripts are directly bound by U1A according to individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) studies. Interestingly, U1A-mediated positive regulation can be transferred to a heterologous system for biotechnological purposes. Finally, U1A-bound genes are enriched for those involved in cell cycle and adhesion. In agreement with this, higher U1A mRNA expression associates with lower disease-free survival and overall survival in many cancer types, and U1A mRNA levels positively correlate with those of some oncogenes involved in cell proliferation. Accordingly, U1A depletion leads to decreased expression of these genes and the migration-related gene CCN2/CTGF, which shows the strongest regulation by U1A. A decrease in U1A causes a strong drop in CCN2 expression and CTGF secretion and defects in the expression of CTGF EMT targets, cell migration, and proliferation. These results support U1A as a putative therapeutic target for cancer treatment. In addition, U1A-binding sequences should be considered in biotechnological applications.
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Affiliation(s)
- Eric Rovira
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain
| | - Beatriz Moreno
- Department of Molecular Therapy, Aptamer Unit, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain
| | - Nerea Razquin
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain
| | - Roland Hjerpe
- Department of Functional Genomics, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Monika Gonzalez-Lopez
- Department of Functional Genomics, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Rosa Barrio
- Department of Functional Genomics, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Igor Ruiz de los Mozos
- Department of Neuromuscular Diseases, Institute of Neurology, UCL, WC1B5EH London, UK
- RNA Networks Lab, The Francis Crick Institute, NW11BF London, UK
| | - Jernej Ule
- Department of Neuromuscular Diseases, Institute of Neurology, UCL, WC1B5EH London, UK
- RNA Networks Lab, The Francis Crick Institute, NW11BF London, UK
| | - Fernando Pastor
- Department of Molecular Therapy, Aptamer Unit, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Lorea Blazquez
- Department of Neuromuscular Diseases, Institute of Neurology, UCL, WC1B5EH London, UK
- RNA Networks Lab, The Francis Crick Institute, NW11BF London, UK
- Neurosciences Area, Biodonostia Health Research Institute, 20014 San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
- Corresponding author. Lorea Blazquez, Department of Neuromuscular Diseases, Institute of Neurology, UCL, WC1B5EH London, UK.
| | - Puri Fortes
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
- Corresponding author. Puri Fortes, Neurosciences Area, Biodonostia Health Research Institute, 20014 San Sebastian, Spain.
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Keuss MJ, Hjerpe R, Hsia O, Gourlay R, Burchmore R, Trost M, Kurz T. Unanchored tri-NEDD8 inhibits PARP-1 to protect from oxidative stress-induced cell death. EMBO J 2019; 38:embj.2018100024. [PMID: 30804002 PMCID: PMC6418418 DOI: 10.15252/embj.2018100024] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 01/10/2019] [Accepted: 01/28/2019] [Indexed: 12/18/2022] Open
Abstract
NEDD8 is a ubiquitin‐like protein that activates cullin‐RING E3 ubiquitin ligases (CRLs). Here, we identify a novel role for NEDD8 in regulating the activity of poly(ADP‐ribose) polymerase 1 (PARP‐1) in response to oxidative stress. We show that treatment of cells with H2O2 results in the accumulation of NEDD8 chains, likely by directly inhibiting the deneddylase NEDP1. One chain type, an unanchored NEDD8 trimer, specifically bound to the second zinc finger domain of PARP‐1 and attenuated its activation. In cells in which Nedp1 is deleted, large amounts of tri‐NEDD8 constitutively form, resulting in inhibition of PARP‐1 and protection from PARP‐1‐dependent cell death. Surprisingly, these NEDD8 trimers are additionally acetylated, as shown by mass spectrometry analysis, and their binding to PARP‐1 is reduced by the overexpression of histone de‐acetylases, which rescues PARP‐1 activation. Our data suggest that trimeric, acetylated NEDD8 attenuates PARP‐1 activation after oxidative stress, likely to delay the initiation of PARP‐1‐dependent cell death.
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Affiliation(s)
- Matthew J Keuss
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Roland Hjerpe
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Oliver Hsia
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Robert Gourlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dundee, UK
| | - Richard Burchmore
- Glasgow Polyomics, College of Veterinary, Medical and Life Sciences, University of Glasgow, Glasgow, UK
| | - Matthias Trost
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dundee, UK.,Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Thimo Kurz
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
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Hjerpe R, Bett JS, Keuss MJ, Solovyova A, McWilliams TG, Johnson C, Sahu I, Varghese J, Wood N, Wightman M, Osborne G, Bates GP, Glickman MH, Trost M, Knebel A, Marchesi F, Kurz T. UBQLN2 Mediates Autophagy-Independent Protein Aggregate Clearance by the Proteasome. Cell 2016; 166:935-949. [PMID: 27477512 PMCID: PMC5003816 DOI: 10.1016/j.cell.2016.07.001] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/18/2016] [Accepted: 07/02/2016] [Indexed: 12/14/2022]
Abstract
Clearance of misfolded and aggregated proteins is central to cell survival. Here, we describe a new pathway for maintaining protein homeostasis mediated by the proteasome shuttle factor UBQLN2. The 26S proteasome degrades polyubiquitylated substrates by recognizing them through stoichiometrically bound ubiquitin receptors, but substrates are also delivered by reversibly bound shuttles. We aimed to determine why these parallel delivery mechanisms exist and found that UBQLN2 acts with the HSP70-HSP110 disaggregase machinery to clear protein aggregates via the 26S proteasome. UBQLN2 recognizes client-bound HSP70 and links it to the proteasome to allow for the degradation of aggregated and misfolded proteins. We further show that this process is active in the cell nucleus, where another system for aggregate clearance, autophagy, does not act. Finally, we found that mutations in UBQLN2, which lead to neurodegeneration in humans, are defective in chaperone binding, impair aggregate clearance, and cause cognitive deficits in mice. UBQLN2 clears aggregates independent of autophagy via HSP70 and the proteasome A disease mutation in UBQLN2 prevents its binding to HSP70 Mutant UBQLN2 is defective in clearance of aggregates in vivo UBQLN2 knockin mice develop cognitive impairment and brain pathology
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Affiliation(s)
- Roland Hjerpe
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Davidson Building, Henry Wellcome Lab of Cell Biology, University of Glasgow, G12 8QQ Glasgow, UK; The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - John S Bett
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Davidson Building, Henry Wellcome Lab of Cell Biology, University of Glasgow, G12 8QQ Glasgow, UK; The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland.
| | - Matthew J Keuss
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Alexandra Solovyova
- Newcastle University Protein and Proteome Analysis, Devonshire Building, Devonshire Terrace, Newcastle upon Tyne NE1 7RU, UK
| | - Thomas G McWilliams
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Clare Johnson
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Indrajit Sahu
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Joby Varghese
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Nicola Wood
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Melanie Wightman
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Georgina Osborne
- Department of Medical and Molecular Genetics, King's College London, 8th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Gillian P Bates
- Department of Medical and Molecular Genetics, King's College London, 8th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Matthias Trost
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Axel Knebel
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland
| | - Francesco Marchesi
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Thimo Kurz
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Davidson Building, Henry Wellcome Lab of Cell Biology, University of Glasgow, G12 8QQ Glasgow, UK; The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland.
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Lang V, Pallara C, Zabala A, Lobato-Gil S, Lopitz-Otsoa F, Farrás R, Hjerpe R, Torres-Ramos M, Zabaleta L, Blattner C, Hay RT, Barrio R, Carracedo A, Fernandez-Recio J, Rodríguez MS, Aillet F. Tetramerization-defects of p53 result in aberrant ubiquitylation and transcriptional activity. Mol Oncol 2014; 8:1026-42. [PMID: 24816189 DOI: 10.1016/j.molonc.2014.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 03/19/2014] [Accepted: 04/02/2014] [Indexed: 11/26/2022] Open
Abstract
The tumor suppressor p53 regulates the expression of genes involved in cell cycle progression, senescence and apoptosis. Here, we investigated the effect of single point mutations in the oligomerization domain (OD) on tetramerization, transcription, ubiquitylation and stability of p53. As predicted by docking and molecular dynamics simulations, p53 OD mutants show functional defects on transcription, Mdm2-dependent ubiquitylation and 26S proteasome-mediated degradation. However, mutants unable to form tetramers are well degraded by the 20S proteasome. Unexpectedly, despite the lower structural stability compared to WT p53, p53 OD mutants form heterotetramers with WT p53 when expressed transiently or stably in cells wild type or null for p53. In consequence, p53 OD mutants interfere with the capacity of WT p53 tetramers to be properly ubiquitylated and result in changes of p53-dependent protein expression patterns, including the pro-apoptotic proteins Bax and PUMA under basal and adriamycin-induced conditions. Importantly, the patient derived p53 OD mutant L330R (OD1) showed the more severe changes in p53-dependent gene expression. Thus, in addition to the well-known effects on p53 stability, ubiquitylation defects promote changes in p53-dependent gene expression with implications on some of its functions.
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Affiliation(s)
- Valérie Lang
- Ubiquitylation and Cancer Molecular Biology Laboratory, Inbiomed, Mikeletegi 81, San Sebastián-Donostia 20009, Gipuzkoa, Spain.
| | - Chiara Pallara
- Joint BSC-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, Carrer Jordi Girona 29, 08034 Barcelona, Spain.
| | - Amaia Zabala
- CIC bioGUNE, Ed 801A Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.
| | - Sofia Lobato-Gil
- Ubiquitylation and Cancer Molecular Biology Laboratory, Inbiomed, Mikeletegi 81, San Sebastián-Donostia 20009, Gipuzkoa, Spain.
| | | | - Rosa Farrás
- Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012 Valencia, Spain.
| | - Roland Hjerpe
- CIC bioGUNE, Ed 801A Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.
| | - Monica Torres-Ramos
- CIC bioGUNE, Ed 801A Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.
| | - Lorea Zabaleta
- Ubiquitylation and Cancer Molecular Biology Laboratory, Inbiomed, Mikeletegi 81, San Sebastián-Donostia 20009, Gipuzkoa, Spain.
| | - Christine Blattner
- Karlsruher Institute of Technology, Institute of Toxicology and Genetics, Fritz-Erler-Straße 23, 76133 Karlsruhe, Germany.
| | - Ronald T Hay
- Center for Interdisciplinary Research, School of Life Sciences, University of Dundee, Dow Street, DD15EH Scotland, United Kingdom.
| | - Rosa Barrio
- CIC bioGUNE, Ed 801A Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain.
| | - Arkaitz Carracedo
- CIC bioGUNE, Ed 801A Parque Tecnológico de Bizkaia, 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain; Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, E-48080 Bilbao, Spain.
| | - Juan Fernandez-Recio
- Joint BSC-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, Carrer Jordi Girona 29, 08034 Barcelona, Spain.
| | - Manuel S Rodríguez
- Ubiquitylation and Cancer Molecular Biology Laboratory, Inbiomed, Mikeletegi 81, San Sebastián-Donostia 20009, Gipuzkoa, Spain.
| | - Fabienne Aillet
- Ubiquitylation and Cancer Molecular Biology Laboratory, Inbiomed, Mikeletegi 81, San Sebastián-Donostia 20009, Gipuzkoa, Spain.
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Aillet F, Lopitz-Otsoa F, Egaña I, Hjerpe R, Fraser P, Hay RT, Rodriguez MS, Lang V. Heterologous SUMO-2/3-ubiquitin chains optimize IκBα degradation and NF-κB activity. PLoS One 2012; 7:e51672. [PMID: 23284737 PMCID: PMC3527444 DOI: 10.1371/journal.pone.0051672] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 11/05/2012] [Indexed: 01/09/2023] Open
Abstract
The NF-κB pathway is regulated by SUMOylation at least at three levels: the inhibitory molecule IκBα, the IKK subunit γ/NEMO and the p52 precursor p100. Here we investigate the role of SUMO-2/3 in the degradation of IκBα and activation of NF-κB mediated by TNFα. We found that under conditions of deficient SUMOylation, an important delay in both TNFα-mediated proteolysis of IκBα and NF-κB dependent transcription occurs. In vitro and ex vivo approaches, including the use of ubiquitin-traps (TUBEs), revealed the formation of chains on IκBα containing SUMO-2/3 and ubiquitin after TNFα stimulation. The integration of SUMO-2/3 appears to promote the formation of ubiquitin chains on IκBα after activation of the TNFα signalling pathway. Furthermore, heterologous chains of SUMO-2/3 and ubiquitin promote a more efficient degradation of IκBα by the 26S proteasome in vitro compared to chains of either SUMO-2/3 or ubiquitin alone. Consistently, Ubc9 silencing reduced the capture of IκBα modified with SUMO-ubiquitin hybrid chains that display a defective proteasome-mediated degradation. Thus, hybrid SUMO-2/3-ubiquitin chains increase the susceptibility of modified IκBα to the action of 26S proteasome, contributing to the optimal control of NF-κB activity after TNFα-stimulation.
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Affiliation(s)
- Fabienne Aillet
- Proteomics Unit, CIC bioGUNE, CIBERehd, Derio, Bizkaia, Spain
- Ubiquitylation & Cancer Molecular Biology Laboratory, Inbiomed, San Sebastián-Donostia, Gipuzkoa, Spain
| | | | - Isabel Egaña
- Proteomics Unit, CIC bioGUNE, CIBERehd, Derio, Bizkaia, Spain
| | - Roland Hjerpe
- Proteomics Unit, CIC bioGUNE, CIBERehd, Derio, Bizkaia, Spain
| | - Paul Fraser
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Ron T. Hay
- Centre for Interdisciplinary Research, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | | | - Valérie Lang
- Proteomics Unit, CIC bioGUNE, CIBERehd, Derio, Bizkaia, Spain
- Ubiquitylation & Cancer Molecular Biology Laboratory, Inbiomed, San Sebastián-Donostia, Gipuzkoa, Spain
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Hjerpe R, Thomas Y, Kurz T. NEDD8 overexpression results in neddylation of ubiquitin substrates by the ubiquitin pathway. J Mol Biol 2012; 421:27-9. [PMID: 22608973 DOI: 10.1016/j.jmb.2012.05.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 05/09/2012] [Indexed: 10/28/2022]
Abstract
Ubiquitin and ubiquitin-like proteins use unique E1, E2, and E3 enzymes for conjugation to their substrates. We and others have recently reported that increases in the relative concentration of the ubiquitin-like protein NEDD8 over ubiquitin lead to activation of NEDD8 by the ubiquitin E1 enzyme. We now show that this results in erroneous conjugation of NEDD8 to ubiquitin substrates, such as p53, Caspase 7, and Hif1α, demonstrating that overexpression of NEDD8 is not appropriate for identification of substrates of the NEDD8 pathway.
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Affiliation(s)
- Roland Hjerpe
- Scottish Institute for Cell Signalling—Protein Ubiquitylation Unit, University of Dundee, Dow Street,Dundee DD1 5EH, UK
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Aillet F, Lopitz-Otsoa F, Hjerpe R, Torres-Ramos M, Lang V, Rodríguez MS. Isolation of ubiquitylated proteins using tandem ubiquitin-binding entities. Methods Mol Biol 2012; 832:173-183. [PMID: 22350885 DOI: 10.1007/978-1-61779-474-2_12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Studying postubiquitylation events has always been a difficult task due to the labile nature of these posttranslational modifications. When utilized in tandem, ubiquitin-binding entities (TUBEs) not only increase up to thousand times the affinity for poly-ubiquitin chains but also protect ubiquitylated proteins from the action of the proteasome and de-ubiquitylating enzymes.
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Affiliation(s)
- Fabienne Aillet
- Proteomics Unit, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, Derio, Spain
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Sánchez J, Talamillo A, Lopitz-Otsoa F, Pérez C, Hjerpe R, Sutherland JD, Herboso L, Rodríguez MS, Barrio R. Sumoylation modulates the activity of Spalt-like proteins during wing development in Drosophila. J Biol Chem 2010; 285:25841-9. [PMID: 20562097 DOI: 10.1074/jbc.m110.124024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Spalt-like family of zinc finger transcription factors is conserved throughout evolution and is involved in fundamental processes during development and during embryonic stem cell maintenance. Although human SALL1 is modified by SUMO-1 in vitro, it is not known whether this post-translational modification plays a role in regulating the activity of this family of transcription factors. Here, we show that the Drosophila Spalt transcription factors are modified by sumoylation. This modification influences their nuclear localization and capacity to induce vein formation through the regulation of target genes during wing development. Furthermore, spalt genes interact genetically with the sumoylation machinery to repress vein formation in intervein regions and to attain the wing final size. Our results suggest a new level of regulation of Sall activity in vivo during animal development through post-translational modification by sumoylation. The evolutionary conservation of this family of transcription factors suggests a functional role for sumoylation in vertebrate Sall members.
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Affiliation(s)
- Jonatan Sánchez
- CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
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Hjerpe R, Aillet F, Lopitz-Otsoa F, Lang V, Torres-Ramos M, Farrás R, Hay RT, Rodríguez MS. Oligomerization conditions Mdm2-mediated efficient p53 polyubiquitylation but not its proteasomal degradation. Int J Biochem Cell Biol 2010; 42:725-35. [PMID: 20080206 DOI: 10.1016/j.biocel.2010.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Revised: 12/22/2009] [Accepted: 01/10/2010] [Indexed: 10/19/2022]
Abstract
In normal cells p53 is maintained at low level through the action of the ubiquitin-proteasome system. As a consequence of p53 transcriptional activity, various regulators of this tumor suppressor are produced, forming a negative feedback loop tightly controlling p53 stability. One of the most prominent is the ubiquitin-ligase Mdm2. Here, we have used a transfer of signals strategy to study the p53 degradation process promoted by Mdm2 in the absence of p53 transcriptional activity. Our results show that in a p53 null background, transcriptionally silent p53-fusions require multiple N- and C-terminal signals to be optimally targeted to proteasomal degradation. As for WT p53, p53-fusions able to form tetramers are polyubiquitylated and optimally degraded by the proteasome. However, p53 molecules unable to oligomerize, show Mdm2-mediated polyubiquitylation deficiency but are still targeted to proteasome degradation in vitro and ex vivo. In the presence of Mdm2, nuclear shuttling of p53 monomeric fusions favours proteasome-dependent degradability but not its polyubiquitylation. In vitro, 26S proteasome fails to drive degradation of OD mutants in the presence of Mdm2, suggesting the contribution of additional cellular factors in this process. All together, our results indicate that Mdm2-mediated proteasome-dependent degradation of polyubiquitylation deficient p53 monomers is mechanistically possible, taking alternative pathways to better achieve their proteolysis. These results support the existence of additional levels to regulate p53 stability and activity acting on individual subunits of the functional tetramer.
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Affiliation(s)
- Roland Hjerpe
- The Proteomics Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Bizkaia, Spain
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Hjerpe R, Rodríguez MS. Alternative UPS drug targets upstream the 26S proteasome. Int J Biochem Cell Biol 2007; 40:1126-40. [PMID: 18203645 DOI: 10.1016/j.biocel.2007.11.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Revised: 11/13/2007] [Accepted: 11/20/2007] [Indexed: 10/22/2022]
Abstract
The successful use of proteasome inhibitors in anti-cancer therapy encouraged the development of new drugs targeting the activity of the ubiquitin-proteasome system (UPS) at various levels. The UPS comprises a complex set of protein adaptors whose coordinated function modulates the interaction of ubiquitin-modified proteins with protein effectors. In addition, UPS crosstalk with other post-translational modifications, complicates a sophisticated set of conjugation and de-conjugation pathways, providing a large variety of potential targets for the development of specific inhibitors. Traditionally associated with the proteasome, ubiquitin-conjugation does not always result in protein degradation. The major signal that targets proteins for degradation is the formation of ubiquitin-chains on lysine 48 (K48). Other ubiquitin features such as K63 chains or mono-ubiquitylation appear to regulate the transient formation of functional macromolecular complexes or relocate modified proteins inside the cell. The emerging idea that UPS-mediated degradation participates not only in the initiation but also in the termination step of certain functions, highlights new potential drug targets upstream the 26S proteasome. This review underlines some of these, in particular, possibilities for intervention before the recognition of substrates by the ubiquitin-conjugating enzymes and after the conjugation of target proteins with ubiquitin. To illustrate possible therapeutic targets at the level of transcription, subcellular distribution and signal transduction pathways, NF-kappaB and p53 have been used as main examples in this review.
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Affiliation(s)
- Roland Hjerpe
- Ubiquitin-Like Molecules and Cancer Laboratory, Proteomics Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
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