1
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Wang Y, Niu K, Shi Y, Zhou F, Li X, Li Y, Chen T, Zhang Y. A review: targeting UBR5 domains to mediate emerging roles and mechanisms - chance or necessity? Int J Surg 2024; 110:4947-4964. [PMID: 38701508 PMCID: PMC11326040 DOI: 10.1097/js9.0000000000001541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024]
Abstract
Ubiquitinases are known to catalyze ubiquitin chains on target proteins to regulate various physiological functions like cell proliferation, autophagy, apoptosis, and cell cycle progression. As a member of E3 ligase, ubiquitin protein ligase E3 component n-recognin 5 (UBR5) belongs to the HECT E3 ligase and has been reported to be correlated with various pathophysiological processes. In this review, the authors give a comprehensive insight into the structure and function of UBR5. The authors discuss the specific domains of UBR5 and explore their biological functions separately. Furthermore, the authors describe the involvement of UBR5 in different pathophysiological conditions, including immune response, virus infection, DNA damage response, and protein quality control. Moreover, the authors provide a thorough summary of the important roles and regulatory mechanisms of UBR5 in cancers and other diseases. On the whole, investigating the domains and functions of UBR5, elucidating the underlying mechanisms of UBR5 with various substrates in detail may provide new theoretical basis for the treatment of diseases, including cancers, which could improve future studies to construct novel UBR5-targeted therapy strategies.
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Affiliation(s)
- Yizhu Wang
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
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2
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Hehl LA, Horn-Ghetko D, Prabu JR, Vollrath R, Vu DT, Pérez Berrocal DA, Mulder MPC, van der Heden van Noort GJ, Schulman BA. Structural snapshots along K48-linked ubiquitin chain formation by the HECT E3 UBR5. Nat Chem Biol 2024; 20:190-200. [PMID: 37620400 PMCID: PMC10830417 DOI: 10.1038/s41589-023-01414-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/30/2023] [Indexed: 08/26/2023]
Abstract
Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron microscopy (cryo-EM) to visualize stable mimics of the intermediates along K48-linked Ub chain formation by the human E3, UBR5. The structural data reveal a ≈ 620 kDa UBR5 dimer as the functional unit, comprising a scaffold with flexibly tethered Ub-associated (UBA) domains, and elaborately arranged HECT domains. Chains are forged by a UBA domain capturing an acceptor Ub, with its K48 lured into the active site by numerous interactions between the acceptor Ub, manifold UBR5 elements and the donor Ub. The cryo-EM reconstructions allow defining conserved HECT domain conformations catalyzing Ub transfer from E2 to E3 and from E3. Our data show how a full-length E3, ubiquitins to be adjoined, E2 and intermediary products guide a feed-forward HECT domain conformational cycle establishing a highly efficient, broadly targeting, K48-linked Ub chain forging machine.
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Affiliation(s)
- Laura A Hehl
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ronnald Vollrath
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - D Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David A Pérez Berrocal
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Brenda A Schulman
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany.
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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3
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Hodáková Z, Grishkovskaya I, Brunner HL, Bolhuis DL, Belačić K, Schleiffer A, Kotisch H, Brown NG, Haselbach D. Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5. EMBO J 2023; 42:e113348. [PMID: 37409633 PMCID: PMC10425842 DOI: 10.15252/embj.2022113348] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of human UBR5, revealing an α-solenoid scaffold with numerous protein-protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo-EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein-protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases.
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Affiliation(s)
- Zuzana Hodáková
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Hanna L Brunner
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Katarina Belačić
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Harald Kotisch
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
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4
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Tsai JM, Aguirre JD, Li YD, Brown J, Focht V, Kater L, Kempf G, Sandoval B, Schmitt S, Rutter JC, Galli P, Sandate CR, Cutler JA, Zou C, Donovan KA, Lumpkin RJ, Cavadini S, Park PMC, Sievers Q, Hatton C, Ener E, Regalado BD, Sperling MT, Słabicki M, Kim J, Zon R, Zhang Z, Miller PG, Belizaire R, Sperling AS, Fischer ES, Irizarry R, Armstrong SA, Thomä NH, Ebert BL. UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability. Mol Cell 2023; 83:2753-2767.e10. [PMID: 37478846 PMCID: PMC11134608 DOI: 10.1016/j.molcel.2023.06.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/23/2023]
Abstract
Nuclear hormone receptors (NRs) are ligand-binding transcription factors that are widely targeted therapeutically. Agonist binding triggers NR activation and subsequent degradation by unknown ligand-dependent ubiquitin ligase machinery. NR degradation is critical for therapeutic efficacy in malignancies that are driven by retinoic acid and estrogen receptors. Here, we demonstrate the ubiquitin ligase UBR5 drives degradation of multiple agonist-bound NRs, including the retinoic acid receptor alpha (RARA), retinoid x receptor alpha (RXRA), glucocorticoid, estrogen, liver-X, progesterone, and vitamin D receptors. We present the high-resolution cryo-EMstructure of full-length human UBR5 and a negative stain model representing its interaction with RARA/RXRA. Agonist ligands induce sequential, mutually exclusive recruitment of nuclear coactivators (NCOAs) and UBR5 to chromatin to regulate transcriptional networks. Other pharmacological ligands such as selective estrogen receptor degraders (SERDs) degrade their receptors through differential recruitment of UBR5 or RNF111. We establish the UBR5 transcriptional regulatory hub as a common mediator and regulator of NR-induced transcription.
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Affiliation(s)
- Jonathan M Tsai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob D Aguirre
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Yen-Der Li
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Jared Brown
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Vivian Focht
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lukas Kater
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Brittany Sandoval
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stefan Schmitt
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Justine C Rutter
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pius Galli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Science, University of Basel, Basel, Switzerland
| | - Colby R Sandate
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jevon A Cutler
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Charles Zou
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Paul M C Park
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Quinlan Sievers
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlie Hatton
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Ener
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Brandon D Regalado
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Micah T Sperling
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mikołaj Słabicki
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeonghyeon Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Rebecca Zon
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Zinan Zhang
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Peter G Miller
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Roger Belizaire
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Adam S Sperling
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Rafael Irizarry
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Scott A Armstrong
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Benjamin L Ebert
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA.
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5
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Hehl LA, Schulman BA. To be (in a transcriptional complex) or not to be (promoting UBR5 ubiquitylation): That is an answer to how degradation controls gene expression. Mol Cell 2023; 83:2616-2618. [PMID: 37541216 DOI: 10.1016/j.molcel.2023.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/06/2023]
Abstract
Tsai et al.1 in this issue and Mark et al.2 in Cell reveal how the E3 ligase UBR5 mediates broad regulation by selectively targeting agonist-bound nuclear hormone receptors, MYC, and other transcriptional regulators not incorporated into active gene expression complexes.
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Affiliation(s)
- Laura A Hehl
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; TUM School of Natural Sciences, Department of Chemistry, 85747 Garching, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; TUM School of Natural Sciences, Department of Chemistry, 85747 Garching, Germany.
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6
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Mihalič F, Simonetti L, Giudice G, Sander MR, Lindqvist R, Peters MBA, Benz C, Kassa E, Badgujar D, Inturi R, Ali M, Krystkowiak I, Sayadi A, Andersson E, Aronsson H, Söderberg O, Dobritzsch D, Petsalaki E, Överby AK, Jemth P, Davey NE, Ivarsson Y. Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs. Nat Commun 2023; 14:2409. [PMID: 37100772 PMCID: PMC10132805 DOI: 10.1038/s41467-023-38015-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Viruses mimic host short linear motifs (SLiMs) to hijack and deregulate cellular functions. Studies of motif-mediated interactions therefore provide insight into virus-host dependencies, and reveal targets for therapeutic intervention. Here, we describe the pan-viral discovery of 1712 SLiM-based virus-host interactions using a phage peptidome tiling the intrinsically disordered protein regions of 229 RNA viruses. We find mimicry of host SLiMs to be a ubiquitous viral strategy, reveal novel host proteins hijacked by viruses, and identify cellular pathways frequently deregulated by viral motif mimicry. Using structural and biophysical analyses, we show that viral mimicry-based interactions have similar binding strength and bound conformations as endogenous interactions. Finally, we establish polyadenylate-binding protein 1 as a potential target for broad-spectrum antiviral agent development. Our platform enables rapid discovery of mechanisms of viral interference and the identification of potential therapeutic targets which can aid in combating future epidemics and pandemics.
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Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Girolamo Giudice
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Marie Rubin Sander
- Department of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, Box 591, SE-751 24, Uppsala, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90187, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Marie Berit Akpiroro Peters
- Department of Clinical Microbiology, Umeå University, 90187, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eszter Kassa
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Dilip Badgujar
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Muhammad Ali
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Izabella Krystkowiak
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Ahmed Sayadi
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Hanna Aronsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, Box 591, SE-751 24, Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90187, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden.
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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7
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Wang F, He Q, Zhan W, Yu Z, Finkin-Groner E, Ma X, Lin G, Li H. Structure of the human UBR5 E3 ubiquitin ligase. Structure 2023; 31:541-552.e4. [PMID: 37040767 PMCID: PMC10403316 DOI: 10.1016/j.str.2023.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/02/2023] [Accepted: 03/16/2023] [Indexed: 04/13/2023]
Abstract
The human UBR5 is a single polypeptide chain homology to E6AP C terminus (HECT)-type E3 ubiquitin ligase essential for embryonic development in mammals. Dysregulated UBR5 functions like an oncoprotein to promote cancer growth and metastasis. Here, we report that UBR5 assembles into a dimer and a tetramer. Our cryoelectron microscopy (cryo-EM) structures reveal that two crescent-shaped UBR5 monomers assemble head to tail to form the dimer, and two dimers bind face to face to form the cage-like tetramer with all four catalytic HECT domains facing the central cavity. Importantly, the N-terminal region of one subunit and the HECT of the other form an "intermolecular jaw" in the dimer. We show the jaw-lining residues are important for function, suggesting that the intermolecular jaw functions to recruit ubiquitin-loaded E2 to UBR5. Further work is needed to understand how oligomerization regulates UBR5 ligase activity. This work provides a framework for structure-based anticancer drug development and contributes to a growing appreciation of E3 ligase diversity.
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Affiliation(s)
- Feng Wang
- Department of Structural Biology, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA
| | - Qing He
- Department of Structural Biology, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA
| | - Wenhu Zhan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Ziqi Yu
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Efrat Finkin-Groner
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th Street, New York, NY 10021, USA
| | - Xiaojing Ma
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Gang Lin
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA.
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8
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Zheng J, Fan W, Zhang X, Quan W, Wu Y, Shu M, Chen M, Liang M. PAIP1 regulates expression of immune and inflammatory response associated genes at transcript level in liver cancer cell. PeerJ 2023; 11:e15070. [PMID: 37101794 PMCID: PMC10124545 DOI: 10.7717/peerj.15070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/23/2023] [Indexed: 04/28/2023] Open
Abstract
Poly(A) binding protein interacting protein 1 (PAIP1) is a translation regulator and also regulate the decay of mRNA. PAIP1 has also been reported to be a marker of increased invasive potential of liver cancer. However, the roles and underlying molecular mechanism of PAIP1 in liver cancer is still unclear. Here, cell viability and the gene expression profile of liver cancer line HepG2 transfected with PAIP1 siRNA was compared with cells transfected with non-targeting control siRNA. The results showed that PAIP1 knockdown inhibited cell viability, and extensively affects expression of 893 genes at transcriptional level in HepG2 cells. Gene function analysis showed that a large number of PAIP1 up-regulated genes were enriched in term of DNA-dependent transcription and the down-regulated genes were enriched in some pathways including immune response and inflammatory response. qPCR confirmed that PAIP1 knockdown positively regulated the expression of selected immune and inflammatory factor genes in HepG2 cells. Expression analysis of TCGA revealed that PAIP1 had positive correlations with two immune associated genes IL1R2 and PTAFR in liver tumor tissue. Taken together, our results demonstrated that PAIP1 was not only a translation regulator, but also a transcription regulator in liver cancer. Moreover, PAIP1 could function as a regulatory factor of immune and inflammatory genes in liver cancer. Thus, our study provides important cues for further study on the regulatory mechanism of PAIP1 in liver cancer.
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Affiliation(s)
- Jianfeng Zheng
- Department of Laboratory Medicine, Baoan Central Hospital of Shenzhen, The Fifth Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Weiwei Fan
- Department of Infectious Medicine, Heilongjiang Provincial Hospital, Harbin, Heilongjiang, China
| | - Xiaoyu Zhang
- First Department of Infection, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Weili Quan
- Center for Genome Analysis, ABLife Inc., Wuhan, Hubei, China
- ABLife BioBigData Institute, Wuhan, Hubei, China
| | - Yunfei Wu
- Center for Genome Analysis, ABLife Inc., Wuhan, Hubei, China
| | - Mengni Shu
- First Department of Infection, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Moyang Chen
- First Department of Infection, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Ming Liang
- First Department of Infection, Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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9
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Sap KA, Geijtenbeek KW, Schipper-Krom S, Guler AT, Reits EA. Ubiquitin-modifying enzymes in Huntington's disease. Front Mol Biosci 2023; 10:1107323. [PMID: 36926679 PMCID: PMC10013475 DOI: 10.3389/fmolb.2023.1107323] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the N-terminus of the HTT gene. The CAG repeat expansion translates into a polyglutamine expansion in the mutant HTT (mHTT) protein, resulting in intracellular aggregation and neurotoxicity. Lowering the mHTT protein by reducing synthesis or improving degradation would delay or prevent the onset of HD, and the ubiquitin-proteasome system (UPS) could be an important pathway to clear the mHTT proteins prior to aggregation. The UPS is not impaired in HD, and proteasomes can degrade mHTT entirely when HTT is targeted for degradation. However, the mHTT protein is differently ubiquitinated when compared to wild-type HTT (wtHTT), suggesting that the polyQ expansion affects interaction with (de) ubiquitinating enzymes and subsequent targeting for degradation. The soluble mHTT protein is associated with several ubiquitin-modifying enzymes, and various ubiquitin-modifying enzymes have been identified that are linked to Huntington's disease, either by improving mHTT turnover or affecting overall homeostasis. Here we describe their potential mechanism of action toward improved mHTT targeting towards the proteostasis machinery.
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Affiliation(s)
- Karen A Sap
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Karlijne W Geijtenbeek
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sabine Schipper-Krom
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Arzu Tugce Guler
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eric A Reits
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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10
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Wu B, Song M, Dong Q, Xiang G, Li J, Ma X, Wei F. UBR5 promotes tumor immune evasion through enhancing IFN-γ-induced PDL1 transcription in triple negative breast cancer. Am J Cancer Res 2022; 12:5086-5102. [PMID: 35836797 PMCID: PMC9274738 DOI: 10.7150/thno.74989] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023] Open
Abstract
Background: The up-regulation of PD-L1 is recognized as an adaption of cancer cells to evade immune surveillance and attack. However, the intrinsic mechanisms of the induction of PD-L1 by interferon-γ (IFN-γ) in tumor microenvironment remain incompletely characterized. Ubiquitin ligase E3 component N-recognition protein 5 (UBR5) has a critical role in tumorigenesis of triple negative breast cancer (TNBC) by triggering specific immune responses to the tumor. Dual targeting of UBR5 and PD-L1 exhibited superior therapeutic benefits in a preclinical TNBC model in short term. Methods: The regulation of UBR5 to PD-L1 upon IFN-γ stimulation was evaluated through in UBR5 deficiency, reconstitution or overexpression cell line models by quantitative PCR, immunohistochemistry and RNA-seq. The effects of PD-L1 regulation by UBR5 and double blockade of both genes were evaluated in mouse TNBC model. Luciferase reporter assay, chromatin immunoprecipitation-qPCR and bioinformatics analysis were performed to explore the transcription factors involved in the regulation of UBR5 to PD-L1. Results: E3 ubiquitin ligase UBR5 plays a key role in IFN-γ-induced PDL1 transcription in TNBC in an E3 ubiquitination activity-independent manner. RNA-seq-based transcriptomic analyses reveal that UBR5 globally affects the genes in the IFN-γ-induced signaling pathway. Through its poly adenylate binding (PABC) domain, UBR5 enhances the transactivation of PDL1 by upregulating protein kinase RNA-activated (PKR), and PKR's downstream factors including signal transducers and activators of transcription 1 (STAT1) and interferon regulatory factor 1 (IRF1). Restoration of PD-L1 expression in UBR5-deficient tumor cells recoups their malignancy in vivo, whereas CRISPR/Cas9-mediated simultaneous abrogation of UBR5 and PD-L1 expression yields synergistic therapeutic benefits than either blockade alone, with a strong impact on the tumor microenvironment. Conclusions: This study identifies a novel regulator of PDL1 transcription, elucidates the underlying molecular mechanisms and provides a strong rationale for combination cancer immunotherapies targeting UBR5 and PD-L1.
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Affiliation(s)
- Bingbing Wu
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mei Song
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Qun Dong
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Xiang
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojing Ma
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York.,✉ Corresponding author: Fang Wei, 800 Dongchuan Road, Minghang, Shanghai 200240, China. Phone: 86-21-34205287; Fax: 86-21-34205287; E-mail: ; Xiaojing Ma,
| | - Fang Wei
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,✉ Corresponding author: Fang Wei, 800 Dongchuan Road, Minghang, Shanghai 200240, China. Phone: 86-21-34205287; Fax: 86-21-34205287; E-mail: ; Xiaojing Ma,
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11
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A MademoiseLLE domain binding platform links the key RNA transporter to endosomes. PLoS Genet 2022; 18:e1010269. [PMID: 35727840 PMCID: PMC9249222 DOI: 10.1371/journal.pgen.1010269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/01/2022] [Accepted: 05/20/2022] [Indexed: 11/19/2022] Open
Abstract
Spatiotemporal expression can be achieved by transport and translation of mRNAs at defined subcellular sites. An emerging mechanism mediating mRNA trafficking is microtubule-dependent co-transport on shuttling endosomes. Although progress has been made in identifying various components of the endosomal mRNA transport machinery, a mechanistic understanding of how these RNA-binding proteins are connected to endosomes is still lacking. Here, we demonstrate that a flexible MademoiseLLE (MLLE) domain platform within RNA-binding protein Rrm4 of Ustilago maydis is crucial for endosomal attachment. Our structure/function analysis uncovered three MLLE domains at the C-terminus of Rrm4 with a functionally defined hierarchy. MLLE3 recognises two PAM2-like sequences of the adaptor protein Upa1 and is essential for endosomal shuttling of Rrm4. MLLE1 and MLLE2 are most likely accessory domains exhibiting a variable binding mode for interaction with currently unknown partners. Thus, endosomal attachment of the mRNA transporter is orchestrated by a sophisticated MLLE domain binding platform. Eukaryotic cells rely on sophisticated intracellular logistics. Macromolecules like mRNA must be transported to defined subcellular destinations for local translation. This is mediated by active transport along the cytoskeleton. Endosomes are carrier vehicles that shuttle along microtubules by the action of molecular motors. It is currently unclear how mRNAs are attached mechanistically to these membranous units during transport. We study the model microorganism Ustilago maydis where numerous components of endosomal mRNA transport have already been identified. Previously, we found that the key RNA-binding protein Rrm4 interacts with the endosomal adaptor protein Upa1. Here, we perform a structure/function analysis and discovered that Rrm4 contains not one but three different versions of a protein-protein interaction domain, called the MademoiseLLE domain, to facilitate the attachment with transport endosomes. Importantly, they function with a strict hierarchy with one essential domain and the others play accessory roles. This is currently, the most detailed mechanistic description of how an RNA-binding protein and its bound cargo mRNAs are attached to endosomes. The usage of three similar protein-protein interaction domains forming a complex binding platform with a defined hierarchy might be operational also in other unknown protein-protein interactions.
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12
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Role of ubiquitin-protein ligase UBR5 in the disassembly of mitotic checkpoint complexes. Proc Natl Acad Sci U S A 2022; 119:2121478119. [PMID: 35217622 PMCID: PMC8892521 DOI: 10.1073/pnas.2121478119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 11/18/2022] Open
Abstract
The mitotic checkpoint system is essential for the prevention of mistakes in the segregation of chromosomes in mitosis. As long as chromosomes are not attached correctly to the mitotic spindle, a mitotic checkpoint complex (MCC) is assembled and inhibits the action of ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome) to initiate anaphase. When the checkpoint is turned off, MCC is disassembled, allowing anaphase initiation. The mechanisms of MCC disassembly have been studied, but the regulation of this process remained obscure. We found that a second ubiquitin ligase, UBR5 (ubiquitin-protein ligase N-recognin 5), ubiquitylates MCC components and stimulates the disassembly of MCC from APC/C, as well as the dissociation of a subcomplex of MCC. The mitotic (or spindle assembly) checkpoint system ensures accurate chromosome segregation in mitosis by preventing the onset of anaphase until correct bipolar attachment of sister chromosomes to the mitotic spindle is attained. It acts by promoting the assembly of a mitotic checkpoint complex (MCC), composed of mitotic checkpoint proteins BubR1, Bub3, Mad2, and Cdc20. MCC binds to and inhibits the action of ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome), which targets for degradation regulators of anaphase initiation. When the checkpoint system is satisfied, MCCs are disassembled, allowing the recovery of APC/C activity and initiation of anaphase. Many of the pathways of the disassembly of the different MCCs have been elucidated, but the mode of their regulation remained unknown. We find that UBR5 (ubiquitin-protein ligase N-recognin 5) is associated with the APC/C*MCC complex immunopurified from extracts of nocodazole-arrested HeLa cells. UBR5 binds to mitotic checkpoint proteins BubR1, Bub3, and Cdc20 and promotes their polyubiquitylation in vitro. The dissociation of a Bub3*BubR1 subcomplex of MCC is stimulated by UBR5-dependent ubiquitylation, as suggested by observations that this process in mitotic extracts requires UBR5 and α−β bond hydrolysis of adenosine triphosphate. Furthermore, a system reconstituted from purified recombinant components carries out UBR5- and ubiquitylation-dependent dissociation of Bub3*BubR1. Immunodepletion of UBR5 from mitotic extracts slows down the release of MCC components from APC/C and prolongs the lag period in the recovery of APC/C activity in the exit from mitotic checkpoint arrest. We suggest that UBR5 may be involved in the regulation of the inactivation of the mitotic checkpoint.
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13
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Galimova IA, Dorogova NV, Fedorova SA. Functions of E3 Ubiquitin Ligase Hyd in Drosophila Tissues. Mol Biol 2021. [DOI: 10.1134/s0026893321020205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Singh S, Ng J, Sivaraman J. Exploring the "Other" subfamily of HECT E3-ligases for therapeutic intervention. Pharmacol Ther 2021; 224:107809. [PMID: 33607149 DOI: 10.1016/j.pharmthera.2021.107809] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/13/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022]
Abstract
The HECT E3 ligase family regulates key cellular signaling pathways, with its 28 members divided into three subfamilies: NEDD4 subfamily (9 members), HERC subfamily (6 members) and "Other" subfamily (13 members). Here, we focus on the less-explored "Other" subfamily and discuss the recent findings pertaining to their biological roles. The N-terminal regions preceding the conserved HECT domains are significantly diverse in length and sequence composition, and are mostly unstructured, except for short regions that incorporate known substrate-binding domains. In some of the better-characterized "Other" members (e.g., HUWE1, AREL1 and UBE3C), structure analysis shows that the extended region (~ aa 50) adjacent to the HECT domain affects the stability and activity of the protein. The enzymatic activity is also influenced by interactions with different adaptor proteins and inter/intramolecular interactions. Primarily, the "Other" subfamily members assemble atypical ubiquitin linkages, with some cooperating with E3 ligases from the other subfamilies to form branched ubiquitin chains on substrates. Viruses and pathogenic bacteria target and hijack the activities of "Other" subfamily members to evade host immune responses and cause diseases. As such, these HECT E3 ligases have emerged as potential candidates for therapeutic drug development.
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Affiliation(s)
- Sunil Singh
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore
| | - Joel Ng
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore
| | - J Sivaraman
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore.
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15
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Mattijssen S, Kozlov G, Fonseca BD, Gehring K, Maraia RJ. LARP1 and LARP4: up close with PABP for mRNA 3' poly(A) protection and stabilization. RNA Biol 2021; 18:259-274. [PMID: 33522422 PMCID: PMC7928012 DOI: 10.1080/15476286.2020.1868753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
La-related proteins (LARPs) share a La motif (LaM) followed by an RNA recognition motif (RRM). Together these are termed the La-module that, in the prototypical nuclear La protein and LARP7, mediates binding to the UUU-3'OH termination motif of nascent RNA polymerase III transcripts. We briefly review La and LARP7 activities for RNA 3' end binding and protection from exonucleases before moving to the more recently uncovered poly(A)-related activities of LARP1 and LARP4. Two features shared by LARP1 and LARP4 are direct binding to poly(A) and to the cytoplasmic poly(A)-binding protein (PABP, also known as PABPC1). LARP1, LARP4 and other proteins involved in mRNA translation, deadenylation, and decay, contain PAM2 motifs with variable affinities for the MLLE domain of PABP. We discuss a model in which these PABP-interacting activities contribute to poly(A) pruning of active mRNPs. Evidence that the SARS-CoV-2 RNA virus targets PABP, LARP1, LARP 4 and LARP 4B to control mRNP activity is also briefly reviewed. Recent data suggests that LARP4 opposes deadenylation by stabilizing PABP on mRNA poly(A) tails. Other data suggest that LARP1 can protect mRNA from deadenylation. This is dependent on a PAM2 motif with unique characteristics present in its La-module. Thus, while nuclear La and LARP7 stabilize small RNAs with 3' oligo(U) from decay, LARP1 and LARP4 bind and protect mRNA 3' poly(A) tails from deadenylases through close contact with PABP.Abbreviations: 5'TOP: 5' terminal oligopyrimidine, LaM: La motif, LARP: La-related protein, LARP1: La-related protein 1, MLLE: mademoiselle, NTR: N-terminal region, PABP: cytoplasmic poly(A)-binding protein (PABPC1), Pol III: RNA polymerase III, PAM2: PABP-interacting motif 2, PB: processing body, RRM: RNA recognition motif, SG: stress granule.
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Affiliation(s)
- Sandy Mattijssen
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Guennadi Kozlov
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | | | - Kalle Gehring
- Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, Canada
| | - Richard J. Maraia
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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16
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Hughes DC, Turner DC, Baehr LM, Seaborne RA, Viggars M, Jarvis JC, Gorski PP, Stewart CE, Owens DJ, Bodine SC, Sharples AP. Knockdown of the E3 ubiquitin ligase UBR5 and its role in skeletal muscle anabolism. Am J Physiol Cell Physiol 2021; 320:C45-C56. [PMID: 33052072 DOI: 10.1152/ajpcell.00432.2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
UBR5 is an E3 ubiquitin ligase positively associated with anabolism, hypertrophy, and recovery from atrophy in skeletal muscle. The precise mechanisms underpinning UBR5's role in the regulation of skeletal muscle mass remain unknown. The present study aimed to elucidate these mechanisms by silencing the UBR5 gene in vivo. To achieve this aim, we electroporated a UBR5-RNAi plasmid into mouse tibialis anterior muscle to investigate the impact of reduced UBR5 on anabolic signaling MEK/ERK/p90RSK and Akt/GSK3β/p70S6K/4E-BP1/rpS6 pathways. Seven days after UBR5 RNAi electroporation, although reductions in overall muscle mass were not detected, the mean cross-sectional area (CSA) of green fluorescent protein (GFP)-positive fibers were reduced (-9.5%) and the number of large fibers were lower versus the control. Importantly, UBR5-RNAi significantly reduced total RNA, muscle protein synthesis, ERK1/2, Akt, and GSK3β activity. Although p90RSK phosphorylation significantly increased, total p90RSK protein levels demonstrated a 45% reduction with UBR5-RNAi. Finally, these early events after 7 days of UBR5 knockdown culminated in significant reductions in muscle mass (-4.6%) and larger reductions in fiber CSA (-18.5%) after 30 days. This was associated with increased levels of phosphatase PP2Ac and inappropriate chronic elevation of p70S6K and rpS6 between 7 and 30 days, as well as corresponding reductions in eIF4e. This study demonstrates that UBR5 plays an important role in anabolism/hypertrophy, whereby knockdown of UBR5 culminates in skeletal muscle atrophy.
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Affiliation(s)
- David C Hughes
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Daniel C Turner
- Norwegian School of Sport Sciences (NiH), Institute for Physical Performance, Oslo, Norway
- School of Pharmacy and Bioengineering, Institute for Science & Technology in Medicine (ISTM), Keele University, Staffordshire, United Kingdom
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Research Institute for Sport & Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, United Kingdom
| | - Leslie M Baehr
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Robert A Seaborne
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Research Institute for Sport & Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, United Kingdom
- Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Mark Viggars
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Research Institute for Sport & Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, United Kingdom
| | - Jonathan C Jarvis
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Research Institute for Sport & Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, United Kingdom
| | - Piotr P Gorski
- Norwegian School of Sport Sciences (NiH), Institute for Physical Performance, Oslo, Norway
- School of Pharmacy and Bioengineering, Institute for Science & Technology in Medicine (ISTM), Keele University, Staffordshire, United Kingdom
| | - Claire E Stewart
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Research Institute for Sport & Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, United Kingdom
| | - Daniel J Owens
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Research Institute for Sport & Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, United Kingdom
| | - Sue C Bodine
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Adam P Sharples
- Norwegian School of Sport Sciences (NiH), Institute for Physical Performance, Oslo, Norway
- School of Pharmacy and Bioengineering, Institute for Science & Technology in Medicine (ISTM), Keele University, Staffordshire, United Kingdom
- Stem Cells, Ageing and Molecular Physiology Unit (SCAMP), Research Institute for Sport & Exercise Sciences (RISES), Liverpool John Moores University, Liverpool, United Kingdom
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17
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Garcia-Barcena C, Osinalde N, Ramirez J, Mayor U. How to Inactivate Human Ubiquitin E3 Ligases by Mutation. Front Cell Dev Biol 2020; 8:39. [PMID: 32117970 PMCID: PMC7010608 DOI: 10.3389/fcell.2020.00039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/16/2020] [Indexed: 12/24/2022] Open
Abstract
E3 ubiquitin ligases are the ultimate enzymes involved in the transfer of ubiquitin to substrate proteins, a process that determines the fate of the modified protein. Numerous diseases are caused by defects in the ubiquitin-proteasome machinery, including when the activity of a given E3 ligase is hampered. Thus, inactivation of E3 ligases and the resulting effects at molecular or cellular level have been the focus of many studies during the last few years. For this purpose, site-specific mutation of key residues involved in either protein interaction, substrate recognition or ubiquitin transfer have been reported to successfully inactivate E3 ligases. Nevertheless, it is not always trivial to predict which mutation(s) will block the catalytic activity of a ligase. Here we review over 250 site-specific inactivating mutations that have been carried out in 120 human E3 ubiquitin ligases. We foresee that the information gathered here will be helpful for the design of future experimental strategies.
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Affiliation(s)
- Cristina Garcia-Barcena
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Ikerbasque - Basque Foundation for Science, Bilbao, Spain
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18
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Saez I, Gerbracht JV, Koyuncu S, Lee HJ, Horn M, Kroef V, Denzel MS, Dieterich C, Gehring NH, Vilchez D. The E3 ubiquitin ligase UBR5 interacts with the H/ACA ribonucleoprotein complex and regulates ribosomal RNA biogenesis in embryonic stem cells. FEBS Lett 2019; 594:175-188. [PMID: 31365120 DOI: 10.1002/1873-3468.13559] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 12/27/2022]
Abstract
UBR5 is an E3 ubiquitin ligase involved in distinct processes such as transcriptional regulation and development. UBR5 is highly upregulated in embryonic stem cells (ESCs), whereas its expression decreases with differentiation, suggesting a role for UBR5 in ESC function. However, little is known about how UBR5 regulates ESC identity. Here, we define the protein interactome of UBR5 in ESCs and find interactions with distinct components of the H/ACA ribonucleoprotein complex, which is required for proper maturation of ribosomal RNA (rRNA). Notably, loss of UBR5 induces an abnormal accumulation of rRNA processing intermediates, resulting in diminished ribosomal levels. Consequently, lack of UBR5 triggers an increase in p53 levels and a concomitant decrease in cellular proliferation rates. Thus, our results indicate a link between UBR5 and rRNA maturation.
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Affiliation(s)
- Isabel Saez
- Institute for Genetics and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | | | - Seda Koyuncu
- Institute for Genetics and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | - Hyun Ju Lee
- Institute for Genetics and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | - Moritz Horn
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Virginia Kroef
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Martin S Denzel
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus, Tschira Institute for Computational Cardiology, University Hospital, Heidelberg, Germany
| | - Niels H Gehring
- Institute for Genetics, Department of Biology, University of Cologne, Germany
| | - David Vilchez
- Institute for Genetics and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
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19
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Shen Q, Qiu Z, Wu W, Zheng J, Jia Z. Characterization of interaction and ubiquitination of phosphoenolpyruvate carboxykinase by E3 ligase UBR5. Biol Open 2018; 7:bio.037366. [PMID: 30552140 PMCID: PMC6310884 DOI: 10.1242/bio.037366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Phosphoenolpyruvate carboxykinase (PEPCK1) is ubiquitinated by E3 ubiquitin ligase UBR5, which was thought to be facilitated by the acetylation of Lys70, Lys71 and Lys594 in PEPCK1. Here, we made a series of UBR5 HECT domain truncation variants and, through pull-down assay, showed that the N-terminal lobe of the UBR5 HECT domain is largely responsible for interacting with PEPCK1. We mutated all three lysine residues thought to be acetylated in PEPCK1 but were surprised to observe no loss of binding to UBR5 HECT domain. Furthermore, two PEPCK1 truncation variants (74-622 aa and 10-560 aa) lacking these lysine residues were still able to bind with UBR5 and ubiquitinated in HEK293T cells. To discover the ubiquitination site(s) of PEPCK1, which is currently unknown, the Lys residues of PEPCK1 were mutated to Ala and the ubiquitination level of the PEPCK1 mutants was assessed. Results revealed at least two ubiquitination sites (Lys243 and Lys342), which represent the first time that ubiquitination sites of PEPCK1 have been identified. Our pull-down experiments further show that the lack of ubiquitination of PEPCK1 Lys243Ala and Lys342Ala mutants is not due to their binding to UBR5, which remained unchanged. Taken together, our work has provided new insights into UBR5 mediated ubiquitination of PEPCK1. Summary: Identification of the recruit function of the N-terminal lobe of the UBR5 HECT domain and ubiquitination site(s) of PEPCK1.
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Affiliation(s)
- Qingya Shen
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zhiyu Qiu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wenping Wu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zongchao Jia
- Department of Biochemical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
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20
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Shearer RF, Frikstad KAM, McKenna J, McCloy RA, Deng N, Burgess A, Stokke T, Patzke S, Saunders DN. The E3 ubiquitin ligase UBR5 regulates centriolar satellite stability and primary cilia. Mol Biol Cell 2018; 29:1542-1554. [PMID: 29742019 PMCID: PMC6080653 DOI: 10.1091/mbc.e17-04-0248] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Primary cilia are crucial for signal transduction in a variety of pathways, including hedgehog and Wnt. Disruption of primary cilia formation (ciliogenesis) is linked to numerous developmental disorders (known as ciliopathies) and diseases, including cancer. The ubiquitin-proteasome system (UPS) component UBR5 was previously identified as a putative positive regulator of ciliogenesis in a functional genomics screen. UBR5 is an E3 ubiquitin ligase that is frequently deregulated in tumors, but its biological role in cancer is largely uncharacterized, partly due to a lack of understanding of interacting proteins and pathways. We validated the effect of UBR5 depletion on primary cilia formation using a robust model of ciliogenesis, and identified CSPP1, a centrosomal and ciliary protein required for cilia formation, as a UBR5-interacting protein. We show that UBR5 ubiquitylates CSPP1, and that UBR5 is required for cytoplasmic organization of CSPP1-comprising centriolar satellites in centrosomal periphery, suggesting that UBR5-mediated ubiquitylation of CSPP1 or associated centriolar satellite constituents is one underlying requirement for cilia expression. Hence, we have established a key role for UBR5 in ciliogenesis that may have important implications in understanding cancer pathophysiology.
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Affiliation(s)
- Robert F Shearer
- Garvan Institute of Medical Research, Kinghorn Cancer Centre, Darlinghurst 2010, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia
| | - Kari-Anne Myrum Frikstad
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway
| | - Jessie McKenna
- Faculty of Medicine, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Rachael A McCloy
- Garvan Institute of Medical Research, Kinghorn Cancer Centre, Darlinghurst 2010, Australia
| | - Niantao Deng
- Garvan Institute of Medical Research, Kinghorn Cancer Centre, Darlinghurst 2010, Australia
| | - Andrew Burgess
- Garvan Institute of Medical Research, Kinghorn Cancer Centre, Darlinghurst 2010, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia
| | - Trond Stokke
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway
| | - Sebastian Patzke
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway
| | - Darren N Saunders
- Faculty of Medicine, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
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Lorenz S. Structural mechanisms of HECT-type ubiquitin ligases. Biol Chem 2018; 399:127-145. [PMID: 29016349 DOI: 10.1515/hsz-2017-0184] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/25/2017] [Indexed: 12/31/2022]
Abstract
Ubiquitin ligases (E3 enzymes) transfer ubiquitin from ubiquitin-conjugating (E2) enzymes to target proteins. By determining the selection of target proteins, modification sites on those target proteins, and the types of ubiquitin modifications that are formed, E3 enzymes are key specificity factors in ubiquitin signaling. Here, I summarize our knowledge of the structural mechanisms in the HECT E3 subfamily, many members of which play important roles in human disease. I discuss interactions of the conserved HECT domain with E2 enzymes, ubiquitin and target proteins, as well as macromolecular interactions with regulatory functions. While we understand individual steps in the catalytic cycle of HECT E3 enzymes on a structural level, this review also highlights key aspects that have yet to be elucidated. For instance, it remains unclear how diverse target proteins are presented to the catalytic center and how certain HECT E3 enzymes achieve specificity in ubiquitin linkage formation. The structural and functional properties of the N-terminal regions of HECT E3 enzymes that likely act as signaling hubs are also largely unknown. Structural insights into these aspects may open up routes for a therapeutic intervention with specific HECT E3 functions in distinct pathophysiological settings.
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Affiliation(s)
- Sonja Lorenz
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
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22
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Flack JE, Mieszczanek J, Novcic N, Bienz M. Wnt-Dependent Inactivation of the Groucho/TLE Co-repressor by the HECT E3 Ubiquitin Ligase Hyd/UBR5. Mol Cell 2017; 67:181-193.e5. [PMID: 28689657 PMCID: PMC5592244 DOI: 10.1016/j.molcel.2017.06.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 05/01/2017] [Accepted: 06/09/2017] [Indexed: 12/19/2022]
Abstract
Extracellular signals are transduced to the cell nucleus by effectors that bind to enhancer complexes to operate transcriptional switches. For example, the Wnt enhanceosome is a multiprotein complex associated with Wnt-responsive enhancers through T cell factors (TCF) and kept silent by Groucho/TLE co-repressors. Wnt-activated β-catenin binds to TCF to overcome this repression, but how it achieves this is unknown. Here, we discover that this process depends on the HECT E3 ubiquitin ligase Hyd/UBR5, which is required for Wnt signal responses in Drosophila and human cell lines downstream of activated Armadillo/β-catenin. We identify Groucho/TLE as a functionally relevant substrate, whose ubiquitylation by UBR5 is induced by Wnt signaling and conferred by β-catenin. Inactivation of TLE by UBR5-dependent ubiquitylation also involves VCP/p97, an AAA ATPase regulating the folding of various cellular substrates including ubiquitylated chromatin proteins. Thus, Groucho/TLE ubiquitylation by Hyd/UBR5 is a key prerequisite that enables Armadillo/β-catenin to activate transcription.
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Affiliation(s)
- Joshua E Flack
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Juliusz Mieszczanek
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nikola Novcic
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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23
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Abstract
Ubiquitin E3 ligases control every aspect of eukaryotic biology by promoting protein ubiquitination and degradation. At the end of a three-enzyme cascade, ubiquitin ligases mediate the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to specific substrate proteins. Early investigations of E3s of the RING (really interesting new gene) and HECT (homologous to the E6AP carboxyl terminus) types shed light on their enzymatic activities, general architectures, and substrate degron-binding modes. Recent studies have provided deeper mechanistic insights into their catalysis, activation, and regulation. In this review, we summarize the current progress in structure-function studies of ubiquitin ligases as well as exciting new discoveries of novel classes of E3s and diverse substrate recognition mechanisms. Our increased understanding of ubiquitin ligase function and regulation has provided the rationale for developing E3-targeting therapeutics for the treatment of human diseases.
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Affiliation(s)
- Ning Zheng
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
| | - Nitzan Shabek
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
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Sander B, Xu W, Eilers M, Popov N, Lorenz S. A conformational switch regulates the ubiquitin ligase HUWE1. eLife 2017; 6:e21036. [PMID: 28193319 PMCID: PMC5308896 DOI: 10.7554/elife.21036] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/27/2017] [Indexed: 12/27/2022] Open
Abstract
The human ubiquitin ligase HUWE1 has key roles in tumorigenesis, yet it is unkown how its activity is regulated. We present the crystal structure of a C-terminal part of HUWE1, including the catalytic domain, and reveal an asymmetric auto-inhibited dimer. We show that HUWE1 dimerizes in solution and self-associates in cells, and that both occurs through the crystallographic dimer interface. We demonstrate that HUWE1 is inhibited in cells and that it can be activated by disruption of the dimer interface. We identify a conserved segment in HUWE1 that counteracts dimer formation by associating with the dimerization region intramolecularly. Our studies reveal, intriguingly, that the tumor suppressor p14ARF binds to this segment and may thus shift the conformational equilibrium of HUWE1 toward the inactive state. We propose a model, in which the activity of HUWE1 underlies conformational control in response to physiological cues-a mechanism that may be exploited for cancer therapy.
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Affiliation(s)
- Bodo Sander
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Wenshan Xu
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
- Department of Radiation Oncology, University Hospital Würzburg, Würzburg, Germany
| | - Martin Eilers
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
- Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Nikita Popov
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
- Department of Radiation Oncology, University Hospital Würzburg, Würzburg, Germany
| | - Sonja Lorenz
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
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25
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Shearer RF, Iconomou M, Watts CKW, Saunders DN. Functional Roles of the E3 Ubiquitin Ligase UBR5 in Cancer. Mol Cancer Res 2015; 13:1523-32. [PMID: 26464214 DOI: 10.1158/1541-7786.mcr-15-0383] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/06/2015] [Indexed: 11/16/2022]
Abstract
The Ubiquitin-Proteasome System (UPS) is an important regulator of cell signaling and proteostasis, which are essential to a variety of cellular processes. The UPS is disrupted in many diseases including cancer, and targeting the UPS for cancer therapy is gaining wide interest. E3 ubiquitin ligases occupy a key position in the hierarchical UPS enzymatic cascade, largely responsible for determining substrate specificity and ubiquitin (Ub) chain topology. The E3 ligase UBR5 (aka EDD1) is emerging as a key regulator of the UPS in cancer and development. UBR5 expression is deregulated in many cancer types and UBR5 is frequently mutated in mantle cell lymphoma. UBR5 is highly conserved in metazoans, has unique structural features, and has been implicated in regulation of DNA damage response, metabolism, transcription, and apoptosis. Hence, UBR5 is a key regulator of cell signaling relevant to broad areas of cancer biology. However, the mechanism by which UBR5 may contribute to tumor initiation and progression remains poorly defined. This review synthesizes emerging insights from genetics, biochemistry, and cell biology to inform our understanding of UBR5 in cancer. These molecular insights indicate a role for UBR5 in integrating/coordinating various cellular signaling pathways. Finally, we discuss outstanding questions in UBR5 biology and highlight the need to systematically characterize substrates, and address limitations in current animal models, to better define the role of UBR5 in cancer.
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Affiliation(s)
- Robert F Shearer
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Mary Iconomou
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Colin K W Watts
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Darren N Saunders
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia.
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