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Gill JK, Shaw GS. Using Förster Resonance Energy Transfer (FRET) to Understand the Ubiquitination Landscape. Chembiochem 2024; 25:e202400193. [PMID: 38632088 DOI: 10.1002/cbic.202400193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Förster resonance energy transfer (FRET) is a fluorescence technique that allows quantitative measurement of protein interactions, kinetics and dynamics. This review covers the use of FRET to study the structures and mechanisms of ubiquitination and related proteins. We survey FRET assays that have been developed where donor and acceptor fluorophores are placed on E1, E2 or E3 enzymes and ubiquitin (Ub) to monitor steady-state and real-time transfer of Ub through the ubiquitination cascade. Specialized FRET probes placed on Ub and Ub-like proteins have been developed to monitor Ub removal by deubiquitinating enzymes (DUBs) that result in a loss of a FRET signal upon cleavage of the FRET probes. FRET has also been used to understand conformational changes in large complexes such as multimeric E3 ligases and the proteasome, frequently using sophisticated single molecule methods. Overall, FRET is a powerful tool to help unravel the intricacies of the complex ubiquitination system.
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Affiliation(s)
- Jashanjot Kaur Gill
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
| | - Gary S Shaw
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
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2
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Amer-Sarsour F, Falik D, Berdichevsky Y, Kordonsky A, Eid S, Rabinski T, Ishtayeh H, Cohen-Adiv S, Braverman I, Blumen SC, Laviv T, Prag G, Vatine GD, Ashkenazi A. Disease-associated polyalanine expansion mutations impair UBA6-dependent ubiquitination. EMBO J 2024; 43:250-276. [PMID: 38177505 PMCID: PMC10897158 DOI: 10.1038/s44318-023-00018-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/23/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024] Open
Abstract
Expansion mutations in polyalanine stretches are associated with a growing number of diseases sharing a high degree of genotypic and phenotypic commonality. These similarities prompted us to query the normal function of physiological polyalanine stretches and to investigate whether a common molecular mechanism is involved in these diseases. Here, we show that UBA6, an E1 ubiquitin-activating enzyme, recognizes a polyalanine stretch within its cognate E2 ubiquitin-conjugating enzyme USE1. Aberrations in this polyalanine stretch reduce ubiquitin transfer to USE1 and, subsequently, polyubiquitination and degradation of its target, the ubiquitin ligase E6AP. Furthermore, we identify competition for the UBA6-USE1 interaction by various proteins with polyalanine expansion mutations in the disease state. The deleterious interactions of expanded polyalanine tract proteins with UBA6 in mouse primary neurons alter the levels and ubiquitination-dependent degradation of E6AP, which in turn affects the levels of the synaptic protein Arc. These effects are also observed in induced pluripotent stem cell-derived autonomic neurons from patients with polyalanine expansion mutations, where UBA6 overexpression increases neuronal resilience to cell death. Our results suggest a shared mechanism for such mutations that may contribute to the congenital malformations seen in polyalanine tract diseases.
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Affiliation(s)
- Fatima Amer-Sarsour
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Daniel Falik
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel
- The Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel
- The Zelman Center for Neuroscience, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel
| | - Yevgeny Berdichevsky
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Alina Kordonsky
- School of Neurobiology, Biochemistry and Biophysics, the George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Sharbel Eid
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Tatiana Rabinski
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel
- The Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel
| | - Hasan Ishtayeh
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Stav Cohen-Adiv
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Itzhak Braverman
- Department of Otolaryngology, Head and Neck Surgery, Hillel Yaffe Medical Center, Hadera, Israel
- Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Sergiu C Blumen
- Rappaport Faculty of Medicine, Technion, Haifa, Israel
- Department of Neurology, Hillel Yaffe Medical Center, Hadera, Israel
| | - Tal Laviv
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Gali Prag
- School of Neurobiology, Biochemistry and Biophysics, the George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Gad D Vatine
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel.
- The Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel.
- The Zelman Center for Neuroscience, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel.
| | - Avraham Ashkenazi
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel.
- Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel.
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Sewduth RN, Carai P, Ivanisevic T, Zhang M, Jang H, Lechat B, Van Haver D, Impens F, Nussinov R, Jones E, Sablina A. Spatial Mechano-Signaling Regulation of GTPases through Non-Degradative Ubiquitination. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303367. [PMID: 37946677 PMCID: PMC10754123 DOI: 10.1002/advs.202303367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/14/2023] [Indexed: 11/12/2023]
Abstract
Blood flow produces shear stress exerted on the endothelial layer of the vessels. Spatial characterization of the endothelial proteome is required to uncover the mechanisms of endothelial activation by shear stress, as blood flow varies in the vasculature. An integrative ubiquitinome and proteome analysis of shear-stressed endothelial cells demonstrated that the non-degradative ubiquitination of several GTPases is regulated by mechano-signaling. Spatial analysis reveals increased ubiquitination of the small GTPase RAP1 in the descending aorta, a region exposed to laminar shear stress. The ubiquitin ligase WWP2 is identified as a novel regulator of RAP1 ubiquitination during shear stress response. Non-degradative ubiquitination fine-tunes the function of GTPases by modifying their interacting network. Specifically, WWP2-mediated RAP1 ubiquitination at lysine 31 switches the balance from the RAP1/ Talin 1 (TLN1) toward RAP1/ Afadin (AFDN) or RAP1/ RAS Interacting Protein 1 (RASIP1) complex formation, which is essential to suppress shear stress-induced reactive oxygen species (ROS) production and maintain endothelial barrier integrity. Increased ROS production in endothelial cells in the descending aorta of endothelial-specific Wwp2-knockout mice leads to increased levels of oxidized lipids and inflammation. These results highlight the importance of the spatially regulated non-degradative ubiquitination of GTPases in endothelial mechano-activation.
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Affiliation(s)
- Raj N. Sewduth
- VIB‐KU Leuven Center for Cancer BiologyVIBLeuven3000Belgium
- Department of OncologyKU LeuvenHerestraat 49Leuven3000Belgium
| | - Paolo Carai
- Department of Cardiovascular SciencesCentre for Molecular and Vascular BiologyKU LeuvenHerestraat 49Leuven3000Belgium
| | - Tonci Ivanisevic
- VIB‐KU Leuven Center for Cancer BiologyVIBLeuven3000Belgium
- Department of OncologyKU LeuvenHerestraat 49Leuven3000Belgium
| | - Mingzhen Zhang
- Computational Structural Biology SectionFrederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunoMetabolismNational Cancer InstituteFrederickMD21702USA
| | - Hyunbum Jang
- Computational Structural Biology SectionFrederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunoMetabolismNational Cancer InstituteFrederickMD21702USA
| | - Benoit Lechat
- VIB‐KU Leuven Center for Cancer BiologyVIBLeuven3000Belgium
- Department of OncologyKU LeuvenHerestraat 49Leuven3000Belgium
| | - Delphi Van Haver
- VIB‐UGent Center for Medical BiotechnologyTechnologiepark‐Zwijnaarde 75Ghent9052Belgium
- Department of Biomolecular MedicineGhent UniversityTechnologiepark‐Zwijnaarde 75Ghent9052Belgium
- VIB Proteomics CoreTechnologiepark‐Zwijnaarde 75Ghent9052Belgium
| | - Francis Impens
- VIB‐UGent Center for Medical BiotechnologyTechnologiepark‐Zwijnaarde 75Ghent9052Belgium
- Department of Biomolecular MedicineGhent UniversityTechnologiepark‐Zwijnaarde 75Ghent9052Belgium
- VIB Proteomics CoreTechnologiepark‐Zwijnaarde 75Ghent9052Belgium
| | - Ruth Nussinov
- Computational Structural Biology SectionFrederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunoMetabolismNational Cancer InstituteFrederickMD21702USA
- Department of Human Molecular Genetics and BiochemistrySackler School of MedicineTel Aviv UniversityTel Aviv69978Israel
| | - Elizabeth Jones
- Department of Cardiovascular SciencesCentre for Molecular and Vascular BiologyKU LeuvenHerestraat 49Leuven3000Belgium
- Department of CardiologyCARIM School for Cardiovascular DiseasesMaastricht UniversityUniversiteitssingel 50Maastricht6229 ERThe Netherlands
| | - Anna Sablina
- VIB‐KU Leuven Center for Cancer BiologyVIBLeuven3000Belgium
- Department of OncologyKU LeuvenHerestraat 49Leuven3000Belgium
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Zhang YF, Huang J, Zhang WX, Liu YH, Wang X, Song J, Jin CY, Zhang SY. Tubulin degradation: Principles, agents, and applications. Bioorg Chem 2023; 139:106684. [PMID: 37356337 DOI: 10.1016/j.bioorg.2023.106684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023]
Abstract
The microtubule system plays an important role in the mitosis and growth of eukaryotic cells, and it is considered as an appealing and highly successful molecular target for cancer treatment. In fact, microtubule targeting agents, such as paclitaxel and vinblastine, have been approved by FDA for tumor therapy, which have achieved significant therapeutic effects and sales performance. At present, microtubule targeting agents mainly include microtubule-destabilizing agents, microtubule-stabilizing agents, and a few tubulin degradation agents. Although there are few reports about tubulin degradation agents at present, tubulin degradation agents show great potential in overcoming multidrug resistance and reducing neurotoxicity. In addition, some natural drugs could specifically degrade tubulin in tumor cells, but have no effect in normal cells, thus showing a good biosafety profile. Therefore, tubulin degradation agents might exhibit a better application. Currently, some small molecules have been designed to promote tubulin degradation with potent antiproliferative activities, showing the potential for cancer treatment. In this work, we reviewed the reports on tubulin degradation, and focused on the degradation mechanism and important functional groups of chemically synthesized compounds, hoping to provide help for the degradation design of tubulin.
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Affiliation(s)
- Yi-Fan Zhang
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Jiao Huang
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Wei-Xin Zhang
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Yun-He Liu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Xiao Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jian Song
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Cheng-Yun Jin
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China.
| | - Sai-Yang Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
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Ji R, Chen J, Xie Y, Dou X, Qing B, Liu Z, Lu Y, Dang L, Zhu X, Sun Y, Zheng X, Zhang L, Guo D, Chen Y. Multi-omics profiling of cholangiocytes reveals sex-specific chromatin state dynamics during hepatic cystogenesis in polycystic liver disease. J Hepatol 2023; 78:754-769. [PMID: 36681161 DOI: 10.1016/j.jhep.2022.12.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 12/09/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND & AIMS Cholangiocytes transit from quiescence to hyperproliferation during cystogenesis in polycystic liver disease (PLD), the severity of which displays prominent sex differences. Epigenetic regulation plays important roles in cell state transition. We aimed to investigate the sex-specific epigenetic basis of hepatic cystogenesis and to develop therapeutic strategies targeting epigenetic modifications for PLD treatment. METHODS Normal and cystic primary cholangiocytes were isolated from wild-type and PLD mice of both sexes. Chromatin states were characterized by analyzing chromatin accessibility (ATAC sequencing) and multiple histone modifications (chromatin immunoprecipitation sequencing). Differential gene expression was determined by transcriptomic analysis (RNA sequencing). Pharmacologic inhibition of epigenetic modifying enzymes was undertaken in PLD model mice. RESULTS Through genome-wide profiling of chromatin dynamics, we revealed a profound increase of global chromatin accessibility during cystogenesis in both male and female PLD cholangiocytes. We identified a switch from H3K9me3 to H3K9ac on cis-regulatory DNA elements of cyst-associated genes and showed that inhibition of H3K9ac acetyltransferase or H3K9me3 demethylase slowed cyst growth in male, but not female, PLD mice. In contrast, we found that H3K27ac was specifically increased in female PLD mice and that genes associated with H3K27ac-gained regions were enriched for cyst-related pathways. In an integrated epigenomic and transcriptomic analysis, we identified an estrogen receptor alpha-centered transcription factor network associated with the H3K27ac-regulated cystogenic gene expression program in female PLD mice. CONCLUSIONS Our findings highlight the multi-layered sex-specific epigenetic dynamics underlying cholangiocyte state transition and reveal a potential epigenetic therapeutic strategy for male PLD patients. IMPACT AND IMPLICATIONS In the present study, we elucidate a sex-specific epigenetic mechanism underlying the cholangiocyte state transition during hepatic cystogenesis and identify epigenetic drugs that effectively slow cyst growth in male PLD mice. These findings underscore the importance of sex difference in the pathogenesis of PLD and may guide researchers and physicians to develop sex-specific personalized approaches for PLD treatment.
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Affiliation(s)
- Rongjie Ji
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Jiayuan Chen
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuyang Xie
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, China
| | - Xudan Dou
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Bo Qing
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Zhiheng Liu
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Yumei Lu
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Lin Dang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Xu Zhu
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Ying Sun
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, China
| | - Xiangjian Zheng
- Department of Pharmacology and Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Lirong Zhang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China.
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, China.
| | - Yupeng Chen
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China.
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6
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Kohler V, Andréasson C. Reversible protein assemblies in the proteostasis network in health and disease. Front Mol Biosci 2023; 10:1155521. [PMID: 37021114 PMCID: PMC10067754 DOI: 10.3389/fmolb.2023.1155521] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/09/2023] [Indexed: 04/07/2023] Open
Abstract
While proteins populating their native conformations constitute the functional entities of cells, protein aggregates are traditionally associated with cellular dysfunction, stress and disease. During recent years, it has become clear that large aggregate-like protein condensates formed via liquid-liquid phase separation age into more solid aggregate-like particles that harbor misfolded proteins and are decorated by protein quality control factors. The constituent proteins of the condensates/aggregates are disentangled by protein disaggregation systems mainly based on Hsp70 and AAA ATPase Hsp100 chaperones prior to their handover to refolding and degradation systems. Here, we discuss the functional roles that condensate formation/aggregation and disaggregation play in protein quality control to maintain proteostasis and why it matters for understanding health and disease.
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Affiliation(s)
- Verena Kohler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Claes Andréasson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
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7
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Dao TP, Yang Y, Presti MF, Cosgrove MS, Hopkins JB, Ma W, Loh SN, Castañeda CA. Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains. EMBO Rep 2022; 23:e55056. [PMID: 35762418 PMCID: PMC9346500 DOI: 10.15252/embr.202255056] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ubiquitin‐binding shuttle UBQLN2 mediates crosstalk between proteasomal degradation and autophagy, likely via interactions with K48‐ and K63‐linked polyubiquitin chains, respectively. UBQLN2 comprises self‐associating regions that drive its homotypic liquid–liquid phase separation (LLPS). Specific interactions between one of these regions and ubiquitin inhibit UBQLN2 LLPS. Here, we show that, unlike ubiquitin, the effects of multivalent polyubiquitin chains on UBQLN2 LLPS are highly dependent on chain types. Specifically, K11‐Ub4 and K48‐Ub4 chains generally inhibit UBQLN2 LLPS, whereas K63‐Ub4, M1‐Ub4 chains, and a designed tetrameric ubiquitin construct significantly enhance LLPS. We demonstrate that these opposing effects stem from differences in chain conformations but not in affinities between chains and UBQLN2. Chains with extended conformations and increased accessibility to the ubiquitin‐binding surface promote UBQLN2 LLPS by enabling a switch between homotypic to partially heterotypic LLPS that is driven by both UBQLN2 self‐interactions and interactions between multiple UBQLN2 units with each polyubiquitin chain. Our study provides mechanistic insights into how the structural and conformational properties of polyubiquitin chains contribute to heterotypic LLPS with ubiquitin‐binding shuttles and adaptors.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
| | - Yiran Yang
- Department of Chemistry Syracuse University Syracuse NY USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Weikang Ma
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
- Interdisciplinary Neuroscience Program Syracuse University Syracuse NY USA
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8
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Perry M, Ghosal G. Mechanisms and Regulation of DNA-Protein Crosslink Repair During DNA Replication by SPRTN Protease. Front Mol Biosci 2022; 9:916697. [PMID: 35782873 PMCID: PMC9240642 DOI: 10.3389/fmolb.2022.916697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
DNA-protein crosslinks (DPCs) are deleterious DNA lesions that occur when proteins are covalently crosslinked to the DNA by the action of variety of agents like reactive oxygen species, aldehydes and metabolites, radiation, and chemotherapeutic drugs. Unrepaired DPCs are blockades to all DNA metabolic processes. Specifically, during DNA replication, replication forks stall at DPCs and are vulnerable to fork collapse, causing DNA breakage leading to genome instability and cancer. Replication-coupled DPC repair involves DPC degradation by proteases such as SPRTN or the proteasome and the subsequent removal of DNA-peptide adducts by nucleases and canonical DNA repair pathways. SPRTN is a DNA-dependent metalloprotease that cleaves DPC substrates in a sequence-independent manner and is also required for translesion DNA synthesis following DPC degradation. Biallelic mutations in SPRTN cause Ruijs-Aalfs (RJALS) syndrome, characterized by hepatocellular carcinoma and segmental progeria, indicating the critical role for SPRTN and DPC repair pathway in genome maintenance. In this review, we will discuss the mechanism of replication-coupled DPC repair, regulation of SPRTN function and its implications in human disease and cancer.
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Affiliation(s)
- Megan Perry
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States,Fred and Pamela Buffett Cancer Center, Omaha, NE, United States,*Correspondence: Gargi Ghosal,
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9
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Tak YJ, Kang S. The E2 ubiquitin-conjugating enzyme HIP2 is a crucial regulator of quality control against mutant SOD1 proteotoxicity. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166316. [PMID: 34856358 DOI: 10.1016/j.bbadis.2021.166316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022]
Abstract
Mutations in superoxide dismutase 1 (SOD1) leading to the formation of intracellular protein aggregates cause amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder characterized by a selective degeneration of motor neurons. The ALS-linked mutant SOD1 emerged as a possible target for ubiquitin-proteasome system (UPS)-mediated degradation. We aimed to elucidate the role of huntingtin interaction protein 2 (HIP2), an E2 ubiquitin-conjugating enzyme, in the proteotoxicity of mutant SOD1 aggregates. We found that HIP2 interacts with mutant SOD1, but not wild-type SOD1, and is upregulated in response to mutant SOD1 expression. Upregulation of HIP2 protein was observed in the spinal cord of 16-week-old SOD1-G93A transgenic mice. HIP2 further modified mutant SOD1 proteins via K48-linked polyubiquitination and degraded mutant SOD1 proteins through the UPS. Upregulation of HIP2 protected cells from mutant SOD1-induced toxicity. Taken together, our findings demonstrate that HIP2 is a crucial regulator of quality control against the proteotoxicity of mutant SOD1. Our results suggest that modulating HIP2 may represent a novel therapeutic strategy for the treatment of ALS.
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Affiliation(s)
- Yeong Jin Tak
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Seongman Kang
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea.
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10
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Levin-Kravets O, Kordonsky A, Shusterman A, Biswas S, Persaud A, Elias S, Langut Y, Florentin A, Simpson-Lavy KJ, Yariv E, Avishid R, Sror M, Almog O, Marshanski T, Kadosh S, Ben David N, Manori B, Fischer Z, Lilly J, Borisova E, Ambrozkiewicz MC, Tarabykin V, Kupiec M, Thaker M, Rotin D, Prag G. Split Chloramphenicol Acetyl-Transferase Assay Reveals Self-Ubiquitylation-Dependent Regulation of UBE3B. J Mol Biol 2021; 433:167276. [PMID: 34599943 DOI: 10.1016/j.jmb.2021.167276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Split reporter protein-based genetic section systems are widely used to identify and characterize protein-protein interactions (PPI). The assembly of split markers that antagonize toxins, rather than required for synthesis of missing metabolites, facilitates the seeding of high density of cells and selective growth. Here we present a newly developed split chloramphenicol acetyltransferase (split-CAT) -based genetic selection system. The N terminus fragment of CAT is fused downstream of the protein of interest and the C terminus fragment is tethered upstream to its postulated partner. We demonstrate the system's advantages for the study of PPIs. Moreover, we show that co-expression of a functional ubiquitylation cascade where the target and ubiquitin are tethered to the split-CAT fragments results in ubiquitylation-dependent selective growth. Since proteins do not have to be purified from the bacteria and due to the high sensitivity of the split-CAT reporter, detection of challenging protein cascades and post-translation modifications is enabled. In addition, we demonstrate that the split-CAT system responds to small molecule inhibitors and molecular glues (GLUTACs). The absence of ubiquitylation-dependent degradation and deubiquitylation in E. coli significantly simplify the interpretation of the results. We harnessed the developed system to demonstrate that like NEDD4, UBE3B also undergoes self-ubiquitylation-dependent inactivation. We show that self-ubiquitylation of UBE3B on K665 induces oligomerization and inactivation in yeast and mammalian cells respectively. Finally, we showcase the advantages of split-CAT in the study of human diseases by demonstrating that mutations in UBE3B that cause Kaufman oculocerebrofacial syndrome exhibit clear E. coli growth phenotypes.
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Affiliation(s)
- Olga Levin-Kravets
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Alina Kordonsky
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Anna Shusterman
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Sagnik Biswas
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Avinash Persaud
- Cell Biology Program, The Hospital for Sick Children and Biochemistry Department, University of Toronto, Toronto, ON, Canada
| | - Sivan Elias
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Yael Langut
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Amir Florentin
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Kobi J Simpson-Lavy
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Elon Yariv
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Reut Avishid
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Mor Sror
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Ofir Almog
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Tal Marshanski
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel. https://twitter.com/@TalMarsh
| | - Shira Kadosh
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Nicole Ben David
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Bar Manori
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Zohar Fischer
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Jeremiah Lilly
- Novartis Institutes for Biomedical Research, 250 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Ekaterina Borisova
- Institute of Medical Genetics, Tomsk National Research Medical Center Neuroscience, Lobachevsky University of the Russian Academy of Sciences Nizhny Novgorod, pr. Gagarina 24, Nizhny Novgorod, Russia; Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Mateusz C Ambrozkiewicz
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany. https://twitter.com/@MAmbrozkiewicz
| | - Victor Tarabykin
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel
| | - Maulik Thaker
- Novartis Institutes for Biomedical Research, 250 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Daniela Rotin
- Cell Biology Program, The Hospital for Sick Children and Biochemistry Department, University of Toronto, Toronto, ON, Canada
| | - Gali Prag
- School of Neurobiology, Biochemistry & Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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11
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Wang Y, Yu J. Dissecting multiple roles of SUMOylation in prostate cancer. Cancer Lett 2021; 521:88-97. [PMID: 34464672 DOI: 10.1016/j.canlet.2021.08.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/27/2022]
Abstract
Protein modification with small ubiquitin-like modifiers (SUMOs) plays dual roles in prostate cancer (PCa) tumorigenesis and development. Any intermediary of the SUMO conjugation cycle going awry may forfeit the balance between tumorigenic potential and anticancer effects. Deregulated SUMOylation on the androgen receptor and oncoproteins also takes part in this pathological process, as exemplified by STAT3/NF-κB and tumor suppressors such as PTEN and p53. Here, we outline recent developments and discoveries of SUMOylation in PCa and present an overview of its multiple roles in PCa tumorigenesis/promotion and suppression, while elucidating its potential as a therapeutic target for PCa.
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Affiliation(s)
- Yishu Wang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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12
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Lü J, Liu ZQ, Guo W, Guo MJ, Chen SM, Yang CX, Zhang YJ, Pan HP. Oral delivery of dsHvlwr is a feasible method for managing the pest Henosepilachna vigintioctopunctata (Coleoptera: Coccinellidae). INSECT SCIENCE 2021; 28:509-520. [PMID: 32240577 DOI: 10.1111/1744-7917.12784] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/18/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
RNA interference (RNAi) techniques have emerged as powerful tools that facilitate development of novel management strategies for insect pests, such as Henosepilachna vigintioctopunctata (Coleoptera: Coccinellidae), which is a major pest of solanaceous plants in Asia. In this study, the potential of oral delivery of in vitro-synthesized and bacterially expressed double-stranded H. vigintioctopunctata lesswright (lwr) gene (dsHvlwr) to manage of H. vigintioctopunctata was investigated. Our results showed that the gene Hvlwr had a 480-bp open reading frame and encoded a 160-amino acid protein. Hvlwr expression levels were greater in the fat body than other tissue types. Hvlwr silencing led to greater H. vigintioctopunctata mortality rates and appeared to be time- and partially dose-dependent, likely as a result of the number of hemocytes increasing with dsRNA concentration, but decreasing with time. Bacterially expressed dsHvlwr that was applied to leaf discs caused 88%, 66%, and 36% mortality in 1st instars, 3rd instars, and adults after 10, 10, and 14 d, respectively; when applied to living plants, there was greater mortality in 1st and 3rd instars, but there was no effect on adults. Furthermore, dsHvlwr led to improved plant protection against H. vigintioctopunctata. Our study shows an effective dietary RNAi response in H. vigintioctopunctata and that Hvlwr is a promising RNAi target gene for control of this pest species.
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Affiliation(s)
- Jing Lü
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Zhuo-Qi Liu
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Wei Guo
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Mu-Juan Guo
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Shi-Min Chen
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Chun-Xiao Yang
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - You-Jun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui-Peng Pan
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou, China
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13
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Zhao S, Kieser A, Li HY, Reinking HK, Weickert P, Euteneuer S, Yaneva D, Acampora AC, Götz MJ, Feederle R, Stingele J. A ubiquitin switch controls autocatalytic inactivation of the DNA-protein crosslink repair protease SPRTN. Nucleic Acids Res 2021; 49:902-915. [PMID: 33348378 PMCID: PMC7826251 DOI: 10.1093/nar/gkaa1224] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022] Open
Abstract
Repair of covalent DNA–protein crosslinks (DPCs) by the metalloprotease SPRTN prevents genome instability, premature aging and carcinogenesis. SPRTN is specifically activated by DNA structures containing single- and double-stranded features, but degrades the protein components of DPCs promiscuously and independent of amino acid sequence. This lack of specificity is useful to target diverse protein adducts, however, it requires tight control in return, in order to prohibit uncontrolled proteolysis of chromatin proteins. Here, we discover the components and principles of a ubiquitin switch, which negatively regulates SPRTN. We demonstrate that monoubiquitylation is induced in an E3 ligase-independent manner and, in contrast to previous assumptions, does not control chromatin access of the enzyme. Data obtained in cells and in vitro reveal that monoubiquitylation induces inactivation of the enzyme by triggering autocatalytic cleavage in trans while also priming SPRTN for proteasomal degradation in cis. Finally, we show that the deubiquitylating enzyme USP7 antagonizes this negative control of SPRTN in the presence of DPCs.
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Affiliation(s)
- Shubo Zhao
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Anja Kieser
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Hao-Yi Li
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Hannah K Reinking
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Pedro Weickert
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Simon Euteneuer
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Denitsa Yaneva
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Aleida C Acampora
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Maximilian J Götz
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Regina Feederle
- Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Julian Stingele
- Department of Biochemistry, Ludwig-Maximilians-University, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany
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14
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Ashton NW, Valles GJ, Jaiswal N, Bezsonova I, Woodgate R. DNA Polymerase ι Interacts with Both the TRAF-like and UBL1-2 Domains of USP7. J Mol Biol 2021; 433:166733. [PMID: 33279577 PMCID: PMC7873624 DOI: 10.1016/j.jmb.2020.166733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022]
Abstract
Reversible protein ubiquitination is an essential signaling mechanism within eukaryotes. Deubiquitinating enzymes are critical to this process, as they mediate removal of ubiquitin from substrate proteins. Ubiquitin-specific protease 7 (USP7) is a prominent deubiquitinating enzyme, with an extensive network of interacting partners and established roles in cell cycle activation, immune responses and DNA replication. Characterized USP7 substrates primarily interact with one of two major binding sites outside the catalytic domain. These are located on the USP7 N-terminal TRAF-like (TRAF) domain and the first and second UBL domains (UBL1-2) within the C-terminal tail. Here, we report that DNA polymerase iota (Pol ι) is a novel USP7 substrate that interacts with both TRAF and UBL1-2. Through the use of biophysical approaches and mutational analysis, we characterize both interfaces and demonstrate that bipartite binding to both USP7 domains is required for efficient Pol ι deubiquitination. Together, these data establish a new bipartite mode of USP7 substrate binding.
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Affiliation(s)
- Nicholas W Ashton
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
| | - Gabrielle J Valles
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA.
| | - Nancy Jaiswal
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA.
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA.
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3371, USA.
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15
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Harris LD, Le Pen J, Scholz N, Mieszczanek J, Vaughan N, Davis S, Berridge G, Kessler BM, Bienz M, Licchesi JDF. The deubiquitinase TRABID stabilizes the K29/K48-specific E3 ubiquitin ligase HECTD1. J Biol Chem 2021; 296:100246. [PMID: 33853758 PMCID: PMC7948964 DOI: 10.1074/jbc.ra120.015162] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 12/18/2022] Open
Abstract
Ubiquitin is a versatile posttranslational modification, which is covalently attached to protein targets either as a single moiety or as a ubiquitin chain. In contrast to K48 and K63-linked chains, which have been extensively studied, the regulation and function of most atypical ubiquitin chains are only starting to emerge. The deubiquitinase TRABID/ZRANB1 is tuned for the recognition and cleavage of K29 and K33-linked chains. Yet, substrates of TRABID and the cellular functions of these atypical ubiquitin signals remain unclear. We determined the interactome of two TRABID constructs rendered catalytic dead either through a point mutation in the catalytic cysteine residue or through removal of the OTU catalytic domain. We identified 50 proteins trapped by both constructs and which therefore represent candidate substrates of TRABID. The E3 ubiquitin ligase HECTD1 was then validated as a substrate of TRABID and used UbiCREST and Ub-AQUA proteomics to show that HECTD1 preferentially assembles K29- and K48-linked ubiquitin chains. Further in vitro autoubiquitination assays using ubiquitin mutants established that while HECTD1 can assemble short homotypic K29 and K48-linked chains, it requires branching at K29/K48 in order to achieve its full ubiquitin ligase activity. We next used transient knockdown and genetic knockout of TRABID in mammalian cells in order to determine the functional relationship between TRABID and HECTD1. This revealed that upon TRABID depletion, HECTD1 is readily degraded. Thus, this study identifies HECTD1 as a mammalian E3 ligase that assembles branched K29/K48 chains and also establishes TRABID-HECTD1 as a DUB/E3 pair regulating K29 linkages.
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Affiliation(s)
- Lee D Harris
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Janic Le Pen
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Nico Scholz
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Juliusz Mieszczanek
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Natalie Vaughan
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Simon Davis
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Georgina Berridge
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Julien D F Licchesi
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
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16
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The dialogue between the ubiquitin-proteasome system and autophagy: Implications in ageing. Ageing Res Rev 2020; 64:101203. [PMID: 33130248 DOI: 10.1016/j.arr.2020.101203] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/09/2020] [Accepted: 10/25/2020] [Indexed: 02/06/2023]
Abstract
Dysregulated proteostasis is one of the hallmarks of ageing. Damaged proteins may impair cellular function and their accumulation may lead to tissue dysfunction and disease. This is why protective mechanisms to safeguard the cell proteome have evolved. These mechanisms consist of cellular machineries involved in protein quality control, including regulators of protein translation, folding, trafficking and degradation. In eukaryotic cells, protein degradation occurs via two main pathways: the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway. Although distinct pathways, they are not isolated systems and have a complementary nature, as evidenced by recent studies. These findings raise the question of how autophagy and the proteasome crosstalk. In this review we address how the two degradation pathways impact each other, thereby adding a new layer of regulation to protein degradation. We also analyze the implications of the UPS and autophagy in ageing.
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17
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Blount JR, Johnson SL, Todi SV. Unanchored Ubiquitin Chains, Revisited. Front Cell Dev Biol 2020; 8:582361. [PMID: 33195227 PMCID: PMC7659471 DOI: 10.3389/fcell.2020.582361] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
The small modifier protein, ubiquitin, holds a special place in eukaryotic biology because of its myriad post-translational effects that control normal cellular processes and are implicated in various diseases. By being covalently conjugated onto other proteins, ubiquitin changes their interaction landscape - fostering new interactions as well as inhibiting others - and ultimately deciding the fate of its substrates and controlling pathways that span most cell physiology. Ubiquitin can be attached onto other proteins as a monomer or as a poly-ubiquitin chain of diverse structural topologies. Among the types of poly-ubiquitin species generated are ones detached from another substrate - comprising solely ubiquitin as their constituent - referred to as unanchored, or free chains. Considered to be toxic byproducts, these species have recently emerged to have specific physiological functions in immune pathways and during cell stress. Free chains also do not appear to be detrimental to multi-cellular organisms; they can be active members of the ubiquitination process, rather than corollary species awaiting disassembly into mono-ubiquitin. Here, we summarize past and recent studies on unanchored ubiquitin chains, paying special attention to their emerging roles as second messengers in several signaling pathways. These investigations paint complex and flexible outcomes for free ubiquitin chains, and present a revised model of unanchored poly-ubiquitin biology that is in need of additional investigation.
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Affiliation(s)
- Jessica R Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Sean L Johnson
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States.,Department of Neurology, Wayne State University School of Medicine, Detroit, MI, United States
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18
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Wilkinson NA, Mnuskin KS, Ashton NW, Woodgate R. Ubiquitin and Ubiquitin-Like Proteins Are Essential Regulators of DNA Damage Bypass. Cancers (Basel) 2020; 12:cancers12102848. [PMID: 33023096 PMCID: PMC7600381 DOI: 10.3390/cancers12102848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Ubiquitin and ubiquitin-like proteins are conjugated to many other proteins within the cell, to regulate their stability, localization, and activity. These modifications are essential for normal cellular function and the disruption of these processes contributes to numerous cancer types. In this review, we discuss how ubiquitin and ubiquitin-like proteins regulate the specialized replication pathways of DNA damage bypass, as well as how the disruption of these processes can contribute to cancer development. We also discuss how cancer cell survival relies on DNA damage bypass, and how targeting the regulation of these pathways by ubiquitin and ubiquitin-like proteins might be an effective strategy in anti-cancer therapies. Abstract Many endogenous and exogenous factors can induce genomic instability in human cells, in the form of DNA damage and mutations, that predispose them to cancer development. Normal cells rely on DNA damage bypass pathways such as translesion synthesis (TLS) and template switching (TS) to replicate past lesions that might otherwise result in prolonged replication stress and lethal double-strand breaks (DSBs). However, due to the lower fidelity of the specialized polymerases involved in TLS, the activation and suppression of these pathways must be tightly regulated by post-translational modifications such as ubiquitination in order to limit the risk of mutagenesis. Many cancer cells rely on the deregulation of DNA damage bypass to promote carcinogenesis and tumor formation, often giving them heightened resistance to DNA damage from chemotherapeutic agents. In this review, we discuss the key functions of ubiquitin and ubiquitin-like proteins in regulating DNA damage bypass in human cells, and highlight ways in which these processes are both deregulated in cancer progression and might be targeted in cancer therapy.
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Affiliation(s)
| | | | - Nicholas W. Ashton
- Correspondence: (N.W.A.); (R.W.); Tel.: +1-301-435-1115 (N.W.A.); +1-301-435-0740 (R.W.)
| | - Roger Woodgate
- Correspondence: (N.W.A.); (R.W.); Tel.: +1-301-435-1115 (N.W.A.); +1-301-435-0740 (R.W.)
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19
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Mattioni A, Boldt K, Auciello G, Komada M, Rappoport JZ, Ueffing M, Castagnoli L, Cesareni G, Santonico E. Ring Finger Protein 11 acts on ligand-activated EGFR via the direct interaction with the UIM region of ANKRD13 protein family. FEBS J 2020; 287:3526-3550. [PMID: 31985874 DOI: 10.1111/febs.15226] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 11/13/2019] [Accepted: 01/22/2020] [Indexed: 01/07/2023]
Abstract
RING finger protein 11 (RNF11) is an evolutionary conserved Really Interesting New Gene E3 ligase that is overexpressed in several human tumours. Although several reports have highlighted its involvement in crucial cellular processes, the mechanistic details underlying its function are still poorly understood. Utilizing stable isotope labelling by amino acids in culture (SILAC)-based proteomics analysis, we identified 51 proteins that co-immunoprecipitate with wild-type RNF11 and/or with its catalytically inactive mutant. We focused our attention on the interaction of RNF11 with Ankyrin repeat domain-containing protein 13 (ANKRD13)s family. Members of the ANKRD13 family contain ubiquitin-interacting motifs (UIM) that recognize the Lys-63-linked ubiquitin (Ub) chains appended to Epidermal growth factor receptor (EGFR) soon after ligand binding. We show that ANKRD13A, ANKRD13B and ANKRD13D form a complex with RNF11 in vivo and that the UIMs are required for complex formation. However, at odds with the conventional UIM binding mode, Ub modification of RNF11 is not required for the interaction with ANKRD13 proteins. We also show that the interaction between ANKRD13A and RNF11 is modulated by the EGF stimulus and that a complex formed by ANKRD13A, RNF11 and activated EGFR is transiently assembled in the early phases of receptor endocytosis. Moreover, loss of function of the E3 ligases Itchy E3 ubiquitin-protein ligase (ITCH) or RNF11, respectively, abrogates or increases the ubiquitination of endogenous ANKRD13A, affecting its ability to bind activated EGFR. We propose a model whereby the ANKRD13 proteins act as molecular scaffolds that promote the transient formation of a complex between the activated EGFR and the E3 ligases ITCH and RNF11. By regulating the ubiquitination status of ANKRD13A and consequently its endocytic adaptor function, RNF11 promotes sorting of the activated EGFR for lysosomal degradation.
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Affiliation(s)
- Anna Mattioni
- Department of Biology, University of Rome Tor Vergata, Italy
| | - Karsten Boldt
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Germany
| | - Giulio Auciello
- Istituto di Ricerche di Biologia Molecolare (IRBM), Pomezia, Italy
| | - Masayuki Komada
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | | | - Marius Ueffing
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Germany
| | | | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Italy
- Fondazione Santa Lucia Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Elena Santonico
- Department of Biology, University of Rome Tor Vergata, Italy
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20
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Zeng M, Liu W, Hu Y, Fu N. Sumoylation in liver disease. Clin Chim Acta 2020; 510:347-353. [PMID: 32710938 DOI: 10.1016/j.cca.2020.07.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 02/07/2023]
Abstract
Small ubiquitin-like modifiers (SUMO) are highly conserved post-translational modification proteins that are present in eukaryotic cells. They are extensively expressed in diverse tissues, including the heart, liver, kidney, and lungs. SUMOylation, a crucial post-translational modification, exhibits a strong effect on DNA repair, transcriptional regulation, protein stability and cell cycle progression. Increasing evidence has demonstrated that SUMOylation is closely related to the development of liver disease. Therefore, the effects of SUMOylation in liver diseases, such as Hepatocellular carcinoma (HCC), viral hepatitis, non-alcoholic fatty liver disease (NAFLD), cirrhosis and primary biliary cirrhosis (PBC) were reviewed in this study. Specifically, SUMO1 was found to promote the invasion and metastasis of HCC and may promote hypoxia-mediated P65 nuclear transport while accelerating the progression of HCC. In addition, SUMO1-modified centrosomal P4.1-associated protein (CAPA) was observed to be overexpressed in Hepatitis B virus (HBV)-related HCC in response to TNF-α stimulation. Furthermore, SUMOylated CAPA was found to induce HBX-triggered NF-κB activation. Considering the diversity and significance of SUMOylation, targeting of the SUMOylation pathway may serve as an effective approach in the treatment of liver diseases.
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Affiliation(s)
- Min Zeng
- Department of Gastroenterology, Affiliated Nanhua Hospital, University of South China, Hengyang, Hunan, China
| | - Wenhui Liu
- Department of Gastroenterology, Affiliated Nanhua Hospital, University of South China, Hengyang, Hunan, China
| | - Yang Hu
- Department of Gastroenterology, Affiliated Nanhua Hospital, University of South China, Hengyang, Hunan, China.
| | - Nian Fu
- Department of Gastroenterology, Affiliated Nanhua Hospital, University of South China, Hengyang, Hunan, China.
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21
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Abstract
The catalytic activity of the protease MALT1 is required for adaptive immune responses and regulatory T (Treg)-cell development, while dysregulated MALT1 activity can lead to lymphoma. MALT1 activation requires its monoubiquitination on lysine 644 (K644) within the Ig3 domain, localized adjacent to the protease domain. The molecular requirements for MALT1 monoubiquitination and the mechanism by which monoubiquitination activates MALT1 had remained elusive. Here, we show that the Ig3 domain interacts directly with ubiquitin and that an intact Ig3-ubiquitin interaction surface is required for the conjugation of ubiquitin to K644. Moreover, by generating constitutively active MALT1 mutants that overcome the need for monoubiquitination, we reveal an allosteric communication between the ubiquitination site K644, the Ig3-protease interaction surface, and the active site of the protease domain. Finally, we show that MALT1 mutants that alter the Ig3-ubiquitin interface impact the biological response of T cells. Thus, ubiquitin binding by the Ig3 domain promotes MALT1 activation by an allosteric mechanism that is essential for its biological function.
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22
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Krajewski WA. "Direct" and "Indirect" Effects of Histone Modifications: Modulation of Sterical Bulk as a Novel Source of Functionality. Bioessays 2019; 42:e1900136. [PMID: 31805213 DOI: 10.1002/bies.201900136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/17/2019] [Indexed: 12/26/2022]
Abstract
The chromatin-regulatory principles of histone post-translational modifications (PTMs) are discussed with a focus on the potential alterations in chromatin functional state due to steric and mechanical constraints imposed by bulky histone modifications such as ubiquitin and SUMO. In the classical view, PTMs operate as recruitment platforms for histone "readers," and as determinants of chromatin array compaction. Alterations of histone charges by "small" chemical modifications (e.g., acetylation, phosphorylation) could regulate nucleosome spontaneous dynamics without globally affecting nucleosome structure. These fluctuations in nucleosome wrapping can be exploited by chromatin-processing machinery. In contrast, ubiquitin and SUMO are comparable in size to histones, and it seems logical that these PTMs could conflict with canonical nucleosome organization. An experimentally testable hypothesis that by adding sterical bulk these PTMs can robustly alter nucleosome primary structure is proposed. The model presented here stresses the diversity of mechanisms by which histone PTMs regulate chromatin dynamics, primary structure and, hence, functionality.
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Affiliation(s)
- Wladyslaw A Krajewski
- N. K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Vavilova str. 26, Moscow, 119334, Russia
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23
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Li X, Cheng G, Qin F, Liu J, Li H, Jin Y. Function of the lesswright (lwr) gene in the growth, development, and reproduction of Schistosoma japonicum. Vet Parasitol 2019; 272:31-39. [PMID: 31395202 DOI: 10.1016/j.vetpar.2019.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 01/21/2023]
Abstract
The lesswright (lwr) gene and its products are essential molecules in mitosis, DNA repair, and embryo formation in many eukaryotes. In this study, immunohistochemical analysis revealed that the Lwr protein was located in the internal tissues and the surface layer of the adult Schistosoma japonicum (Sj) worms. The mRNA expression levels of SjLwr at different points were evaluated by quantitative real-time RT-PCR. The expression of SjLwr peaked at 14 days and then decreased thereafter. SjLwr expression was relatively more stable in male worms than in female worms. The functions of SjLwr were explored by siRNA-based gene silencing with a simple soaking method. The results showed that knockdown of the SjLwr gene impaired the growth and development of S. japonicum in mice, as well as survival, morphology, reproductive capacity, and egg vitality. These observations imply that SjLwr presents a novel target for the development of immuno- and/or small molecule-based therapeutics for the control and treatment of schistosome infections.
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Affiliation(s)
- Xiaochun Li
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guifeng Cheng
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Shanxi, China
| | - Fanglin Qin
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jinming Liu
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hao Li
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yamei Jin
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.
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24
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Krajewski WA, Vassiliev OL. Analysis of histone ubiquitylation by MSL1/MSL2 proteins in vitro. Arch Biochem Biophys 2019; 666:22-30. [PMID: 30930284 DOI: 10.1016/j.abb.2019.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/24/2022]
Abstract
Histone posttranslational modifications (PTM) control gene activity by targeting chromatin-regulatory proteins. By altering histone charges PTMs could also modulate inter- and intra-nucleosomal interactions, and thus affect chromatin high-order compaction and nucleosome stochastic folding, respectively. However, recently it has been shown that histone H2BK34- ubiquitylation (which is deposited in vivo by MOF-MSL) can destabilize one of the nucleosomal H2A-H2B dimers in symmetrically and (albeit to a lesser extend) asymmetrically modified nucleosomes, and thus promote formation of a hexasome particle. Here we have studied ubiquitylation patterns by purified MSL1/MSL2 using nucleosomes and different histone substrates. We have shown that H2B-ubiquitylation by MSL1/2 depends on substrate configuration. In addition, MSL1/2 efficiently ubiquitylate histone substrates but very poorly modify nucleosomes, which implies a requirement for nucleosome structural alteration for efficient ubiquitylation of H2BK34. Nucleosome modification by MSL1/MSL2 in vitro was analyzed directly using nucleosome gel-mobility shift assay, which suggested that MSL1/2 can deposit two ubiquitin moieties in one nucleosome.
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Affiliation(s)
- Wladyslaw A Krajewski
- N.K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Oleg L Vassiliev
- Shemyakin Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, Moscow, V-437, Russia
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25
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Kelsall IR, Kristariyanto YA, Knebel A, Wood NT, Kulathu Y, Alpi AF. Coupled monoubiquitylation of the co-E3 ligase DCNL1 by Ariadne-RBR E3 ubiquitin ligases promotes cullin-RING ligase complex remodeling. J Biol Chem 2018; 294:2651-2664. [PMID: 30587576 PMCID: PMC6393609 DOI: 10.1074/jbc.ra118.005861] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/07/2018] [Indexed: 12/29/2022] Open
Abstract
Cullin-RING E3 ubiquitin ligases (CRLs) are large and diverse multisubunit protein complexes that contribute to about one-fifth of ubiquitin-dependent protein turnover in cells. CRLs are activated by the attachment of the ubiquitin-like protein neural precursor cell expressed, developmentally down-regulated 8 (NEDD8) to the cullin subunits. This cullin neddylation is essential for a plethora of CRL-regulated cellular processes and is vital for life. In mammals, neddylation is promoted by the five co-E3 ligases, defective in cullin neddylation 1 domain-containing 1–5 (DCNL1–5); however, their functional regulation within the CRL complex remains elusive. We found here that the ubiquitin-associated (UBA) domain–containing DCNL1 is monoubiquitylated when bound to CRLs and that this monoubiquitylation depends on the CRL-associated Ariadne RBR ligases TRIAD1 (ARIH2) and HHARI (ARIH1) and strictly requires the DCNL1's UBA domain. Reconstitution of DCNL1 monoubiquitylation in vitro revealed that autoubiquitylated TRIAD1 mediates binding to the UBA domain and subsequently promotes a single ubiquitin attachment to DCNL1 in a mechanism previously dubbed coupled monoubiquitylation. Moreover, we provide evidence that DCNL1 monoubiquitylation is required for efficient CRL activity, most likely by remodeling CRLs and their substrate receptors. Collectively, this work identifies DCNL1 as a critical target of Ariadne RBR ligases and coupled monoubiquitylation of DCNL1 as an integrated mechanism that affects CRL activity and client–substrate ubiquitylation at multiple levels.
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Affiliation(s)
- Ian R Kelsall
- From the MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Yosua A Kristariyanto
- From the MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Axel Knebel
- From the MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Nicola T Wood
- From the MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Yogesh Kulathu
- From the MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Arno F Alpi
- From the MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
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26
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Veggiani G, Sidhu SS. Peptides meet ubiquitin: Simple interactions regulating complex cell signaling. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research; University of Toronto; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research; University of Toronto; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
- Department of Biochemistry; University of Toronto; Toronto Ontario Canada
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27
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Peng H, Yang J, Li G, You Q, Han W, Li T, Gao D, Xie X, Lee BH, Du J, Hou J, Zhang T, Rao H, Huang Y, Li Q, Zeng R, Hui L, Wang H, Xia Q, Zhang X, He Y, Komatsu M, Dikic I, Finley D, Hu R. Ubiquitylation of p62/sequestosome1 activates its autophagy receptor function and controls selective autophagy upon ubiquitin stress. Cell Res 2017; 27:657-674. [PMID: 28322253 PMCID: PMC5520855 DOI: 10.1038/cr.2017.40] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/06/2016] [Accepted: 01/22/2017] [Indexed: 12/16/2022] Open
Abstract
Alterations in cellular ubiquitin (Ub) homeostasis, known as Ub stress, feature and affect cellular responses in multiple conditions, yet the underlying mechanisms are incompletely understood. Here we report that autophagy receptor p62/sequestosome-1 interacts with E2 Ub conjugating enzymes, UBE2D2 and UBE2D3. Endogenous p62 undergoes E2-dependent ubiquitylation during upregulation of Ub homeostasis, a condition termed as Ub+ stress, that is intrinsic to Ub overexpression, heat shock or prolonged proteasomal inhibition by bortezomib, a chemotherapeutic drug. Ubiquitylation of p62 disrupts dimerization of the UBA domain of p62, liberating its ability to recognize polyubiquitylated cargoes for selective autophagy. We further demonstrate that this mechanism might be critical for autophagy activation upon Ub+ stress conditions. Delineation of the mechanism and regulatory roles of p62 in sensing Ub stress and controlling selective autophagy could help to understand and modulate cellular responses to a variety of endogenous and environmental challenges, potentially opening a new avenue for the development of therapeutic strategies against autophagy-related maladies.
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Affiliation(s)
- Hong Peng
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
- Graduate School, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jiao Yang
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
- Graduate School, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Guangyi Li
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
- Graduate School, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Qing You
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
- Graduate School, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Wen Han
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
| | - Tianrang Li
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
| | - Daming Gao
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
| | - Xiaoduo Xie
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
| | - Byung-Hoon Lee
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - Juan Du
- Department of Hematology, Changzheng Hospital, The Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Jian Hou
- Department of Hematology, Changzheng Hospital, The Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Tao Zhang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, 12 Central Urumqi Road, Shanghai 200040, China
| | - Hai Rao
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Ying Huang
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Qinrun Li
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
| | - Rong Zeng
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
| | - Lijian Hui
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Hongyan Wang
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
| | - Qin Xia
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xuemin Zhang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Institute of Basic Medical Sciences, Beijing 100850, China
| | - Yongning He
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Masaaki Komatsu
- Department of Biochemistry, School of Medicine Niigata University, 757, Ichibancho, Asahimachidori, Chuo-ku, Niigata 951-8510, Japan
| | - Ivan Dikic
- Molecular Signaling, Institute of Biochemistry II, Goethe University School of Medicine, 60590 Frankfurt am Main, Germany
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - Ronggui Hu
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Shanghai 200031, China
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28
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E2-25K SUMOylation inhibits proteasome for cell death during cerebral ischemia/reperfusion. Cell Death Dis 2016; 7:e2573. [PMID: 28032866 PMCID: PMC5261013 DOI: 10.1038/cddis.2016.428] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 01/12/2023]
Abstract
Cerebral ischemia/reperfusion (I/R) causes brain damage accompanied by ubiquitin accumulation and impairment of proteasome activity. In this study, we report that E2-25K, an E2-conjugating enzyme, is SUMOylated during oxidative stress and regulates cerebral I/R-induced damage. Knockdown of E2-25K expression protects against oxygen/glucose deprivation and reoxygenation (OGD/R)-induced neuronal cell death, whereas ectopic expression of E2-25K stimulates it. Compared with the control mice, cerebral infarction lesions and behavioral/neurological disorders are ameliorated in E2-25K knockout mice during middle cerebral artery occlusion and reperfusion. In particular, E2-25K is SUMOylated at Lys14 under oxidative stress, OGD/R and I/R to prompt cell death. Further, E2-25K downregulates the proteasome subunit S5a to impair proteasome complex and thus restrain proteasome activity under oxidative stress. This proteasome inhibitory activity of E2-25K is dependent on its SUMOylation. These results suggest that E2-25K has a crucial role in oxidative stress and cerebral I/R-induced damage through inhibiting proteasome via its SUMOylation.
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29
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A bacterial genetic selection system for ubiquitylation cascade discovery. Nat Methods 2016; 13:945-952. [DOI: 10.1038/nmeth.4003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/01/2016] [Indexed: 12/11/2022]
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30
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Niño CA, Guet D, Gay A, Brutus S, Jourquin F, Mendiratta S, Salamero J, Géli V, Dargemont C. Posttranslational marks control architectural and functional plasticity of the nuclear pore complex basket. J Cell Biol 2016; 212:167-80. [PMID: 26783300 PMCID: PMC4738382 DOI: 10.1083/jcb.201506130] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ubiquitin modifications of the nuclear pore complex (NPC) control the architectural plasticity of the nuclear basket, contributing to its tethering to the core NPC, with consequences on the cellular response to DNA damage and telomere recombination. The nuclear pore complex (NPC) serves as both the unique gate between the nucleus and the cytoplasm and a major platform that coordinates nucleocytoplasmic exchanges, gene expression, and genome integrity. To understand how the NPC integrates these functional constraints, we dissected here the posttranslational modifications of the nuclear basket protein Nup60 and analyzed how they intervene to control the plasticity of the NPC. Combined approaches highlight the role of monoubiquitylation in regulating the association dynamics of Nup60 and its partner, Nup2, with the NPC through an interaction with Nup84, a component of the Y complex. Although major nuclear transport routes are not regulated by Nup60 modifications, monoubiquitylation of Nup60 is stimulated upon genotoxic stress and regulates the DNA-damage response and telomere repair. Together, these data reveal an original mechanism contributing to the plasticity of the NPC at a molecular-organization and functional level.
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Affiliation(s)
- Carlos A Niño
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
| | - David Guet
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
| | - Alexandre Gay
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
| | - Sergine Brutus
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
| | - Frédéric Jourquin
- Aix-Marseille University, CNRS UMR 7258, INSERM UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille, Equipe labellisée Ligue contre le cancer, 13273 Marseille, France
| | - Shweta Mendiratta
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
| | - Jean Salamero
- Institut Curie, PSL Research University, CNRS UMR 144, Pierre-and-Marie-Curie Université, Team-Space time imaging of endomembranes and organelles dynamics and PICT-IBiSA Imaging Core Facility, 75005 Paris, France
| | - Vincent Géli
- Aix-Marseille University, CNRS UMR 7258, INSERM UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille, Equipe labellisée Ligue contre le cancer, 13273 Marseille, France
| | - Catherine Dargemont
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
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Sun L, Fang J. E3-Independent Constitutive Monoubiquitination Complements Histone Methyltransferase Activity of SETDB1. Mol Cell 2016; 62:958-966. [PMID: 27237050 DOI: 10.1016/j.molcel.2016.04.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 04/01/2016] [Accepted: 04/20/2016] [Indexed: 12/27/2022]
Abstract
Ubiquitination typically occurs through the sequential action of three enzymes catalyzing ubiquitin activation (E1), conjugation (E2), and ligation (E3) and regulates diverse eukaryotic cellular processes. Although monoubiquitination commonly confers nondegradative activities, mechanisms underlying its temporal and spatial regulation and functional plasticity still remain largely unknown. Here we demonstrate that SETDB1, a major histone H3K9 methyltransferase is monoubiquitinated at the evolutionarily conserved lysine-867 in its SET-Insertion domain. This ubiquitination is directly catalyzed by UBE2E family of E2 enzymes in an E3-independent manner while the conjugated-ubiquitin (Ub) is protected from active deubiquitination. The resulting constitutive lysine-867 monoubiquitination is essential for SETDB1's enzymatic activity and endogenous retrovirus silencing in murine embryonic stem cells. Furthermore, the canonical hydrophobic patch on the conjugated-Ub is critical for Ub protection and function. Together, our findings highlight an E3-independent mechanism for monoubiquitination and reveal mechanistic details of SETDB1's enzymatic activity and the functional significance of its SET-Insertion.
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Affiliation(s)
- Lidong Sun
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jia Fang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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32
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García-Rodríguez N, Wong RP, Ulrich HD. Functions of Ubiquitin and SUMO in DNA Replication and Replication Stress. Front Genet 2016; 7:87. [PMID: 27242895 PMCID: PMC4865505 DOI: 10.3389/fgene.2016.00087] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/27/2016] [Indexed: 12/14/2022] Open
Abstract
Complete and faithful duplication of its entire genetic material is one of the essential prerequisites for a proliferating cell to maintain genome stability. Yet, during replication DNA is particularly vulnerable to insults. On the one hand, lesions in replicating DNA frequently cause a stalling of the replication machinery, as most DNA polymerases cannot cope with defective templates. This situation is aggravated by the fact that strand separation in preparation for DNA synthesis prevents common repair mechanisms relying on strand complementarity, such as base and nucleotide excision repair, from working properly. On the other hand, the replication process itself subjects the DNA to a series of hazardous transformations, ranging from the exposure of single-stranded DNA to topological contortions and the generation of nicks and fragments, which all bear the risk of inducing genomic instability. Dealing with these problems requires rapid and flexible responses, for which posttranslational protein modifications that act independently of protein synthesis are particularly well suited. Hence, it is not surprising that members of the ubiquitin family, particularly ubiquitin itself and SUMO, feature prominently in controlling many of the defensive and restorative measures involved in the protection of DNA during replication. In this review we will discuss the contributions of ubiquitin and SUMO to genome maintenance specifically as they relate to DNA replication. We will consider cases where the modifiers act during regular, i.e., unperturbed stages of replication, such as initiation, fork progression, and termination, but also give an account of their functions in dealing with lesions, replication stalling and fork collapse.
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Mathew S, Abdel-Hafiz H, Raza A, Fatima K, Qadri I. Host nucleotide polymorphism in hepatitis B virus-associated hepatocellular carcinoma. World J Hepatol 2016; 8:485-498. [PMID: 27057306 PMCID: PMC4820640 DOI: 10.4254/wjh.v8.i10.485] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 12/04/2015] [Accepted: 03/09/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is etiologically linked with hepatitis B virus (HBV) and is the leading cause of death amongst 80% of HBV patients. Among HBV affected patients, genetic factors are also involved in modifying the risk factors of HCC. However, the genetic factors that regulate progression to HCC still remain to be determined. In this review, we discuss several single nucleotide polymorphisms (SNPs) which were reportedly associated with increased or reduced risk of HCC occurrence in patients with chronic HBV infection such as cyclooxygenase (COX)-2 expression specifically at COX-2 -1195G/A in Chinese, Turkish and Egyptian populations, tumor necrosis factor α and the three most commonly studied SNPs: PAT-/+, Lys939Gln (A33512C, rs2228001) and Ala499Val (C21151T, rs2228000). In genome-wide association studies, strong associations have also been found at loci 1p36.22, 11q22.3, 6p21 (rs1419881, rs3997872, rs7453920 and rs7768538), 8p12 (rs2275959 and rs37821974) and 22q11.21. The genes implicated in these studies include HLA-DQB2, HLA-DQA1, TCF19, HLA-C, UBE2L3, LTL, FDX1, MICA, UBE4B and PG. The SNPs found to be associated with the above-mentioned genes still require validation in association studies in order to be considered good prognostic candidates for HCC. Screening of these polymorphisms is very beneficial in clinical experiments to stratify the higher or lower risk for HCC and may help in designing effective and efficient HCC surveillance programs for chronic HBV-infected patients if further genetic vulnerabilities are detected.
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Regulation of TORC1 by ubiquitin through non-covalent binding. Curr Genet 2016; 62:553-5. [PMID: 26910532 DOI: 10.1007/s00294-016-0581-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 12/24/2022]
Abstract
Ubiquitin (Ub) regulates numerous cellular processes through covalent attachment to other proteins in the forms of poly- and mono-ubiquitination. A recent study in yeast shows that ubiquitin controls TORC1 through a noncovalent binding with Kog1, a regulatory subunit of TORC1. The binding stabilizes Kog1 and prevents its degradation under stress conditions. This finding unveils a novel role of Ub in TORC1 function and implicates a unique mechanism that attributes the action of Ub in cell signaling.
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35
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Shafiee SM, Rasti M, Seghatoleslam A, Azimi T, Owji AA. UBE2Q1 in a Human Breast Carcinoma Cell Line: Overexpression and Interaction with p53. Asian Pac J Cancer Prev 2016; 16:3723-7. [PMID: 25987028 DOI: 10.7314/apjcp.2015.16.9.3723] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The p53 tumor suppressor protein is a principal mediator of growth arrest, senescence, and apoptosis in response to a broad array of cellular damage. p53 is a substrate for the ubiquitin-proteasome system, however, the ubiquitin-conjugating enzymes (E2s) involved in p53 ubiquitination have not been well studied. UBE2Q1 is a novel E2 ubiquitin conjugating enzyme gene. Here, we investigated the effect of UBE2Q1 overexpression on the level of p53 in the MDA-MB-468 breast cancer cell line as well as the interaction between UBE2Q1 and p53. By using a lipofection method, the p53 mutated breast cancer cell line, MDA-MB-468, was transfected with the vector pCMV6-AN-GFP, containing UBE2Q1 ORF. Western blot analysis was employed to verify the overexpression of UBE2Q1 in MDA-MB-468 cells and to evaluate the expression level of p53 before and after cell transfection. Immunoprecipitation and GST pull-down protocols were used to investigate the binding of UBE2Q1 to p53. We established MDA-MB-468 cells that transiently expressed a GFP fusion proteins containing UBE2Q1 (GFP-UBE2Q1). Western blot analysis revealed that levels of p53 were markedly lower in UBE2Q1 transfected MDA-MB-468 cells as compared with control MDA-MB-468 cells. Both in vivo and in vitro data showed that UBE2Q1 co-precipitated with p53 protein. Our data for the first time showed that overexpression of UBE2Q1can lead to the repression of p53 in MDA-MB-468 cells. This repression of p53 may be due to its UBE2Q1 mediated ubiquitination and subsequent proteasome degradation, a process that may involve direct interaction of UBE2Q1with p53.
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Affiliation(s)
- Sayed Mohammad Shafiee
- Departments of Biochemistry- Recombinant Protein Laboratory, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran E-mail :
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36
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Yu F, Wu Y, Xie Q. Ubiquitin-Proteasome System in ABA Signaling: From Perception to Action. MOLECULAR PLANT 2016; 9:21-33. [PMID: 26455462 DOI: 10.1016/j.molp.2015.09.015] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 05/18/2023]
Abstract
Protein post-translational modification (PTM) by ubiquitination has been observed during many aspects of plant growth, development, and stress responses. The ubiquitin-proteasome system precisely regulates phytohormone signaling by affecting protein activity, localization, assembly, and interaction ability. Abscisic acid (ABA) is a major phytohormone, and plays important roles in plants under normal or stressed growth conditions. The ABA signaling pathway is composed of phosphatases, kinases, transcription factors, and membrane ion channels. It has been reported that multiple ABA signaling transducers are subjected to the regulations by ubiquitination. In particular, recent studies have identified different types of E3 ligases that mediate ubiquitination of ABA receptors in different cell compartments. This review focuses on modulation of these components by monoubiquitination or polyubiquitination that occurs in the plasma membrane, endomembranes, and from the cytosol to the nucleus; this implies the existence of retrograde and trafficking processes that are regulated by ubiquitination in ABA signaling. A number of single-unit E3 ligases, components of multi-subunit E3 ligases, E2s, and specific subunits of the 26S proteasome involved in ABA signal regulation are discussed. Dissecting the precise functions of ubiquitination in the ABA pathway may help us understand key factors in the signaling of other phytohormones regulated by ubiquitination and other types of PTMs.
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Affiliation(s)
- Feifei Yu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, P. R. China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, P. R. China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, P. R. China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China.
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37
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Wertz IE, Newton K, Seshasayee D, Kusam S, Lam C, Zhang J, Popovych N, Helgason E, Schoeffler A, Jeet S, Ramamoorthi N, Kategaya L, Newman RJ, Horikawa K, Dugger D, Sandoval W, Mukund S, Zindal A, Martin F, Quan C, Tom J, Fairbrother WJ, Townsend M, Warming S, DeVoss J, Liu J, Dueber E, Caplazi P, Lee WP, Goodnow CC, Balazs M, Yu K, Kolumam G, Dixit VM. Phosphorylation and linear ubiquitin direct A20 inhibition of inflammation. Nature 2015; 528:370-5. [PMID: 26649818 DOI: 10.1038/nature16165] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 10/11/2015] [Indexed: 12/26/2022]
Abstract
Inactivation of the TNFAIP3 gene, encoding the A20 protein, is associated with critical inflammatory diseases including multiple sclerosis, rheumatoid arthritis and Crohn's disease. However, the role of A20 in attenuating inflammatory signalling is unclear owing to paradoxical in vitro and in vivo findings. Here we utilize genetically engineered mice bearing mutations in the A20 ovarian tumour (OTU)-type deubiquitinase domain or in the zinc finger-4 (ZnF4) ubiquitin-binding motif to investigate these discrepancies. We find that phosphorylation of A20 promotes cleavage of Lys63-linked polyubiquitin chains by the OTU domain and enhances ZnF4-mediated substrate ubiquitination. Additionally, levels of linear ubiquitination dictate whether A20-deficient cells die in response to tumour necrosis factor. Mechanistically, linear ubiquitin chains preserve the architecture of the TNFR1 signalling complex by blocking A20-mediated disassembly of Lys63-linked polyubiquitin scaffolds. Collectively, our studies reveal molecular mechanisms whereby A20 deubiquitinase activity and ubiquitin binding, linear ubiquitination, and cellular kinases cooperate to regulate inflammation and cell death.
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Affiliation(s)
- Ingrid E Wertz
- Discovery Oncology, Genentech, South San Francisco, California 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Kim Newton
- Physiological Chemistry, Genentech, South San Francisco, California 94080, USA
| | - Dhaya Seshasayee
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Saritha Kusam
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Cynthia Lam
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Juan Zhang
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Nataliya Popovych
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Elizabeth Helgason
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Allyn Schoeffler
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Surinder Jeet
- Immunology, Genentech, South San Francisco, California 94080, USA
| | | | - Lorna Kategaya
- Discovery Oncology, Genentech, South San Francisco, California 94080, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Robert J Newman
- Molecular Biology, Genentech, South San Francisco, California 94080, USA
| | - Keisuke Horikawa
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Debra Dugger
- Physiological Chemistry, Genentech, South San Francisco, California 94080, USA
| | - Wendy Sandoval
- Protein Chemistry, Genentech, South San Francisco, California 94080, USA
| | - Susmith Mukund
- Structural Biology, Genentech, South San Francisco, California 94080, USA
| | - Anuradha Zindal
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Flavius Martin
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Clifford Quan
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Jeffrey Tom
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Wayne J Fairbrother
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Michael Townsend
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Søren Warming
- Molecular Biology, Genentech, South San Francisco, California 94080, USA
| | - Jason DeVoss
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Jinfeng Liu
- Bioinformatics, Genentech, South San Francisco, California 94080, USA
| | - Erin Dueber
- Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, USA
| | - Patrick Caplazi
- Pathology, Genentech, South San Francisco, California 94080, USA
| | - Wyne P Lee
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Christopher C Goodnow
- Immunogenomics Laboratory, Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Sydney, Australia
| | - Mercedesz Balazs
- Immunology, Genentech, South San Francisco, California 94080, USA
| | - Kebing Yu
- Protein Chemistry, Genentech, South San Francisco, California 94080, USA
| | - Ganesh Kolumam
- Molecular Biology, Genentech, South San Francisco, California 94080, USA
| | - Vishva M Dixit
- Physiological Chemistry, Genentech, South San Francisco, California 94080, USA
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38
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Sharma V, Sharma P, Selvapandiyan A, Salotra P. Leishmania donovani-specific Ub-related modifier-1: an early endosome-associated ubiquitin-like conjugation inLeishmania donovani. Mol Microbiol 2015; 99:597-610. [DOI: 10.1111/mmi.13253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Vanila Sharma
- National Institute of Pathology (ICMR); Safdarjang Hospital Campus; New Delhi 110029 India
- Symbiosis School of Biomedical Sciences; Symbiosis International University; Pune 412115 Maharashtra India
| | - Paresh Sharma
- National Institute of Pathology (ICMR); Safdarjang Hospital Campus; New Delhi 110029 India
| | - Angamuthu Selvapandiyan
- Institute of Molecular Medicine; 254 Okhla Industrial Estate, Phase III New Delhi 110020 India
| | - Poonam Salotra
- National Institute of Pathology (ICMR); Safdarjang Hospital Campus; New Delhi 110029 India
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Depletion of UBC9 Causes Nuclear Defects during the Vegetative and Sexual Life Cycles in Tetrahymena thermophila. EUKARYOTIC CELL 2015; 14:1240-52. [PMID: 26453653 DOI: 10.1128/ec.00115-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/03/2015] [Indexed: 11/20/2022]
Abstract
Ubc9p is the sole E2-conjugating enzyme for SUMOylation, and its proper function is required for regulating key nuclear events such as transcription, DNA repair, and mitosis. In Tetrahymena thermophila, the genome is separated into a diploid germ line micronucleus (MIC) that divides by mitosis and a polyploid somatic macronucleus (MAC) that divides amitotically. This unusual nuclear organization provides novel opportunities for the study of SUMOylation and Ubc9p function. We identified the UBC9 gene and demonstrated that its complete deletion from both MIC and MAC genomes is lethal. Rescue of the lethal phenotype with a GFP-UBC9 fusion gene driven by a metallothionein promoter generated a cell line with CdCl2-dependent expression of green fluorescent protein (GFP)-Ubc9p. Depletion of Ubc9p in vegetative cells resulted in the loss of MICs, but MACs continued to divide. In contrast, expression of catalytically inactive Ubc9p resulted in the accumulation of multiple MICs. Critical roles for Ubc9p were also identified during the sexual life cycle of Tetrahymena. Cell lines that were depleted for Ubc9p did not form mating pairs and therefore could not complete any of the subsequent stages of conjugation, including meiosis and macronuclear development. Mating between cells expressing catalytically inactive Ubc9p resulted in arrest during macronuclear development, consistent with our observation that Ubc9p accumulates in the developing macronucleus.
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McIntyre J, Woodgate R. Regulation of translesion DNA synthesis: Posttranslational modification of lysine residues in key proteins. DNA Repair (Amst) 2015; 29:166-79. [PMID: 25743599 PMCID: PMC4426011 DOI: 10.1016/j.dnarep.2015.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 01/30/2023]
Abstract
Posttranslational modification of proteins often controls various aspects of their cellular function. Indeed, over the past decade or so, it has been discovered that posttranslational modification of lysine residues plays a major role in regulating translesion DNA synthesis (TLS) and perhaps the most appreciated lysine modification is that of ubiquitination. Much of the recent interest in ubiquitination stems from the fact that proliferating cell nuclear antigen (PCNA) was previously shown to be specifically ubiquitinated at K164 and that such ubiquitination plays a key role in regulating TLS. In addition, TLS polymerases themselves are now known to be ubiquitinated. In the case of human polymerase η, ubiquitination at four lysine residues in its C-terminus appears to regulate its ability to interact with PCNA and modulate TLS. Within the past few years, advances in global proteomic research have revealed that many proteins involved in TLS are, in fact, subject to a previously underappreciated number of lysine modifications. In this review, we will summarize the known lysine modifications of several key proteins involved in TLS; PCNA and Y-family polymerases η, ι, κ and Rev1 and we will discuss the potential regulatory effects of such modification in controlling TLS in vivo.
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Affiliation(s)
- Justyna McIntyre
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
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41
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Polge C, Attaix D, Taillandier D. Role of E2-Ub-conjugating enzymes during skeletal muscle atrophy. Front Physiol 2015; 6:59. [PMID: 25805999 PMCID: PMC4354305 DOI: 10.3389/fphys.2015.00059] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/14/2015] [Indexed: 01/05/2023] Open
Abstract
The Ubiquitin Proteasome System (UPS) is a major actor of muscle wasting during various physio-pathological situations. In the past 15 years, increasing amounts of data have depicted a picture, although incomplete, of the mechanisms implicated in myofibrillar protein degradation, from the discovery of muscle-specific E3 ligases to the identification of the signaling pathways involved. The targeting specificity of the UPS relies on the capacity of the system to first recognize and then label the proteins to be degraded with a poly-ubiquitin (Ub) chain. It is fairly assumed that the recognition of the substrate is accomplished by the numerous E3 ligases present in mammalian cells. However, most E3s do not possess any catalytic activity and E2 enzymes may be more than simple Ub-providers for E3s since they are probably important actors in the ubiquitination machinery. Surprisingly, most authors have tried to characterize E3 substrates, but the exact role of E2s in muscle protein degradation is largely unknown. A very limited number of the 35 E2s described in humans have been studied in muscle protein breakdown experiments and the vast majority of studies were only descriptive. We review here the role of E2 enzymes in skeletal muscle and the difficulties linked to their study and provide future directions for the identification of muscle E2s responsible for the ubiquitination of contractile proteins.
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Affiliation(s)
- Cecile Polge
- UMR 1019 Nutrition Humaine, Institut National de la Recherche Agronomique Saint Genès Champanelle, France
| | - Didier Attaix
- UMR 1019 Nutrition Humaine, Institut National de la Recherche Agronomique Saint Genès Champanelle, France
| | - Daniel Taillandier
- UMR 1019 Nutrition Humaine, Institut National de la Recherche Agronomique Saint Genès Champanelle, France
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42
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Atherton PJ, Phillips BE, Wilkinson DJ. Exercise and Regulation of Protein Metabolism. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 135:75-98. [DOI: 10.1016/bs.pmbts.2015.06.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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43
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Akimov V, Henningsen J, Hallenborg P, Rigbolt KTG, Jensen SS, Nielsen MM, Kratchmarova I, Blagoev B. StUbEx: Stable tagged ubiquitin exchange system for the global investigation of cellular ubiquitination. J Proteome Res 2014; 13:4192-204. [PMID: 25093938 DOI: 10.1021/pr500549h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Post-translational modification of proteins with the small polypeptide ubiquitin plays a pivotal role in many cellular processes, altering protein lifespan, location, and function and regulating protein-protein interactions. Ubiquitination exerts its diverse functions through complex mechanisms by formation of different polymeric chains and subsequent recognition of the ubiquitin signal by specific protein interaction domains. Despite some recent advances in the analytical tools for the analysis of ubiquitination by mass spectrometry, there is still a need for additional strategies suitable for investigation of cellular ubiquitination at the proteome level. Here, we present a stable tagged ubiquitin exchange (StUbEx) cellular system in which endogenous ubiquitin is replaced with an epitope-tagged version, thereby allowing specific and efficient affinity purification of ubiquitinated proteins for global analyses of protein ubiquitination. Importantly, the overall level of ubiquitin in the cell remains virtually unchanged, thus avoiding ubiquitination artifacts associated with overexpression. The efficiency and reproducibility of the method were assessed through unbiased analysis of epidermal growth factor (EGF) signaling by quantitative mass spectrometry, covering over 3400 potential ubiquitinated proteins. The StUbEx system is applicable to virtually any cell line and can be readily adapted to any of the ubiquitin-like post-translational modifications.
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Affiliation(s)
- Vyacheslav Akimov
- Center for Experimental Bioinformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, DK-5230 Odense, Denmark
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Budhidarmo R, Day CL. The ubiquitin-associated domain of cellular inhibitor of apoptosis proteins facilitates ubiquitylation. J Biol Chem 2014; 289:25721-36. [PMID: 25065467 DOI: 10.1074/jbc.m113.545475] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The cellular inhibitor of apoptosis (cIAP) proteins are essential RING E3 ubiquitin ligases that regulate apoptosis and inflammatory responses. cIAPs contain a ubiquitin-associated (UBA) domain that binds ubiquitin and is implicated in the regulation of cell survival and proteasomal degradation. Here we show that mutation of the MGF and LL motifs in the UBA domain of cIAP1 caused unfolding and increased cIAP1 multimonoubiquitylation. By developing a UBA mutant that disrupted ubiquitin binding but not the structure of the UBA domain, we found that the UBA domain enhances cIAP1 and cIAP2 ubiquitylation. We demonstrate that the UBA domain binds to the UbcH5b∼Ub conjugate, and this promotes RING domain-dependent monoubiquitylation. This study establishes ubiquitin-binding modules, such as the UBA domain, as important regulatory modules that can fine tune the activity of E3 ligases.
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Affiliation(s)
- Rhesa Budhidarmo
- From the Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- From the Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
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45
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Ray S, Zhao Y, Jamaluddin M, Edeh CB, Lee C, Brasier AR. Inducible STAT3 NH2 terminal mono-ubiquitination promotes BRD4 complex formation to regulate apoptosis. Cell Signal 2014; 26:1445-55. [PMID: 24657799 PMCID: PMC4067092 DOI: 10.1016/j.cellsig.2014.03.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/24/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
Signal Transducers and Activator of Transcription-3 (STAT3) are latent transcription factors that are regulated by post-translational modifications (PTMs) in response to cellular activation by the IL-6 superfamily of cytokines to regulate cell cycle progression and/or apoptosis. Here we observe that STAT3 is inducibly mono-ubiquitinated and investigate its consequences. Using domain mapping and highly specific selected reaction monitoring-mass spectrometric assays, we identify lysine (K) 97 in its NH2-terminal domain as the major mono-ubiquitin conjugation site. We constructed a mono-ubiquitinated mimic consisting of a deubiquitinase-resistant monomeric ubiquitin fused to the NH2 terminus of STAT3 (ubiquitinated-STAT3 FP). In complex assays of ectopically expressed ubi-STAT3-FP, we observed enhanced complex formation with bromodomain-containing protein 4 (BRD4), a component of the activated positive transcriptional elongation factor (P-TEFb) complex. Chromatin immunoprecipitation experiments in STAT3(+/-) and STAT3(-/-) MEFs showed BRD4 recruitment to STAT3-dependent suppressor of cytokine signaling-3 gene (SOCS3). The effect of a selective small molecule inhibitor of BRD4, JQ1, to inhibit SOCS3 expression demonstrated the functional role of BRD4 for STAT3-dependent transcription. Additionally, ectopic ubiquitinated-STAT3 FP expression upregulated BCL2, BCL2L1, APEX1, SOD2, CCND1 and MYC expression indicating the role of ubiquitinated STAT3 in anti-apoptosis and cellular proliferation. Finally we observed that ubiquitinated-STAT3 FP suppressed TNFα-induced apoptotic cell death, indicating the functional importance of mono-ubiquitinated STAT3 in antiapoptotic gene expression. We conclude that STAT3 mono-ubiquitination is a key trigger in BRD4-dependent antiapoptotic and pro-proliferative gene expression programs. Thus, inhibiting the STAT3 mono-ubiquitination-BRD4 pathway may be a novel therapeutic target for the treatment of STAT3-dependent proliferative diseases.
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Affiliation(s)
- Sutapa Ray
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States; Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Yingxin Zhao
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States; Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Mohammad Jamaluddin
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Chukwudi B Edeh
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Chang Lee
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Allan R Brasier
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States; Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, United States; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, United States.
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46
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Abstract
Prokaryotes form ubiquitin (Ub)-like isopeptide bonds on the lysine residues of proteins by at least two distinct pathways that are reversible and regulated. In mycobacteria, the C-terminal Gln of Pup (prokaryotic ubiquitin-like protein) is deamidated and isopeptide linked to proteins by a mechanism distinct from ubiquitylation in enzymology yet analogous to ubiquitylation in targeting proteins for destruction by proteasomes. Ub-fold proteins of archaea (SAMPs, small archaeal modifier proteins) and Thermus (TtuB, tRNA-two-thiouridine B) that differ from Ub in amino acid sequence, yet share a common β-grasp fold, also form isopeptide bonds by a mechanism that appears streamlined compared with ubiquitylation. SAMPs and TtuB are found to be members of a small group of Ub-fold proteins that function not only in protein modification but also in sulfur-transfer pathways associated with tRNA thiolation and molybdopterin biosynthesis. These multifunctional Ub-fold proteins are thought to be some of the most ancient of Ub-like protein modifiers.
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Affiliation(s)
- Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611;
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47
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Jacobson AD, MacFadden A, Wu Z, Peng J, Liu CW. Autoregulation of the 26S proteasome by in situ ubiquitination. Mol Biol Cell 2014; 25:1824-35. [PMID: 24743594 PMCID: PMC4055262 DOI: 10.1091/mbc.e13-10-0585] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The 26S proteasome degrades ubiquitinated proteins, and proteasomal degradation controls various cellular events. Here we report that the human 26S proteasome is ubiquitinated, by which the ubiquitin receptors Adrm1 and S5a, the ATPase subunit Rpt5, and the deubiquitinating enzyme Uch37 are ubiquitinated in situ by proteasome-associating ubiquitination enzymes. Ubiquitination of these subunits significantly impairs the 26S proteasome's ability to bind, deubiquitinate, and degrade ubiquitinated proteins. Moreover, ubiquitination of the 26S proteasome can be antagonized by proteasome-residing deubiquitinating enzymes, by the binding of polyubiquitin chains, and by certain cellular stress, indicating that proteasome ubiquitination is dynamic and regulated in cells. We propose that in situ ubiquitination of the 26S proteasome regulates its activity, which could function to adjust proteasomal activity in response to the alteration of cellular ubiquitination levels.
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Affiliation(s)
- Andrew D Jacobson
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
| | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
| | - Zhiping Wu
- Structural Biology and Developmental Neurobiology, St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Junmin Peng
- Structural Biology and Developmental Neurobiology, St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Chang-Wei Liu
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
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48
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Diggin' on u(biquitin): a novel method for the identification of physiological E3 ubiquitin ligase substrates. Cell Biochem Biophys 2014; 67:127-38. [PMID: 23695782 DOI: 10.1007/s12013-013-9624-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The ubiquitin-proteasome system (UPS) plays a central role in maintaining protein homeostasis, emphasized by a myriad of diseases that are associated with altered UPS function such as cancer, muscle-wasting, and neurodegeneration. Protein ubiquitination plays a central role in both the promotion of proteasomal degradation as well as cellular signaling through regulation of the stability of transcription factors and other signaling molecules. Substrate-specificity is a critical regulatory step of ubiquitination and is mediated by ubiquitin ligases. Recent studies implicate ubiquitin ligases in multiple models of cardiac diseases such as cardiac hypertrophy, atrophy, and ischemia/reperfusion injury, both in a cardioprotective and maladaptive role. Therefore, identifying physiological substrates of cardiac ubiquitin ligases provides both mechanistic insights into heart disease as well as possible therapeutic targets. Current methods identifying substrates for ubiquitin ligases rely heavily upon non-physiologic in vitro methods, impeding the unbiased discovery of physiological substrates in relevant model systems. Here we describe a novel method for identifying ubiquitin ligase substrates utilizing tandem ubiquitin binding entities technology, two-dimensional differential in gel electrophoresis, and mass spectrometry, validated by the identification of both known and novel physiological substrates of the ubiquitin ligase MuRF1 in primary cardiomyocytes. This method can be applied to any ubiquitin ligase, both in normal and disease model systems, in order to identify relevant physiological substrates under various biological conditions, opening the door to a clearer mechanistic understanding of ubiquitin ligase function and broadening their potential as therapeutic targets.
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49
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SIM-dependent enhancement of substrate-specific SUMOylation by a ubiquitin ligase in vitro. Biochem J 2014; 457:435-40. [DOI: 10.1042/bj20131381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The present study demonstrates that the Saccharomyces cerevisiae ubiquitin ligase Rad18 can unexpectedly catalyse conjugation of SUMO to its target, PCNA, with high selectivity under in vitro conditions by means of a SUMO-interacting motif that is normally involved in substrate recognition.
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50
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Structural Characterization of a Noncovalent Complex between Ubiquitin and the Transactivation Domain of the Erythroid-Specific Factor EKLF. Structure 2013; 21:2014-24. [DOI: 10.1016/j.str.2013.08.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/14/2013] [Accepted: 08/30/2013] [Indexed: 11/20/2022]
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