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Sun Y, Tian Z, Zuo D, Wang Q, Song G. GhUBC10-2 mediates GhGSTU17 degradation to regulate salt tolerance in cotton (Gossypium hirsutum). PLANT, CELL & ENVIRONMENT 2024; 47:1606-1624. [PMID: 38282268 DOI: 10.1111/pce.14839] [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: 06/27/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 01/30/2024]
Abstract
Ubiquitin-conjugating enzyme (UBC) is a crucial component of the ubiquitin-proteasome system, which contributes to plant growth and development. While some UBCs have been identified as potential regulators of abiotic stress responses, the underlying mechanisms of this regulation remain poorly understood. Here, we report a cotton (Gossypium hirsutum) UBC gene, GhUBC10-2, which negatively regulates the salt stress response. We found that the gain of function of GhUBC10-2 in both Arabidopsis (Arabidopsis thaliana) and cotton leads to reduced salinity tolerance. Additionally, GhUBC10-2 interacts with glutathione S-transferase (GST) U17 (GhGSTU17), forming a heterodimeric complex that promotes GhGSTU17 degradation. Intriguingly, GhUBC10-2 can be self-polyubiquitinated, suggesting that it possesses E3-independent activity. Our findings provide new insights into the PTM of plant GST-mediated salt response pathways. Furthermore, we found that the WRKY transcription factor GhWRKY13 binds to the GhUBC10-2 promoter and suppresses its expression under salt conditions. Collectively, our study unveils a regulatory module encompassing GhWRKY13-GhUBC10-2-GhGSTU17, which orchestrates the modulation of reactive oxygen species homeostasis to enhance salt tolerance.
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Affiliation(s)
- Yaru Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zailong Tian
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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2
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Sakurai Y, Kubota N, Takamoto I, Wada N, Aihara M, Hayashi T, Kubota T, Hiraike Y, Sasako T, Nakao H, Aiba A, Chikaoka Y, Kawamura T, Kadowaki T, Yamauchi T. Overexpression of UBE2E2 in Mouse Pancreatic β-Cells Leads to Glucose Intolerance via Reduction of β-Cell Mass. Diabetes 2024; 73:474-489. [PMID: 38064504 DOI: 10.2337/db23-0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 12/03/2023] [Indexed: 02/22/2024]
Abstract
Genome-wide association studies have identified several gene polymorphisms, including UBE2E2, associated with type 2 diabetes. Although UBE2E2 is one of the ubiquitin-conjugating enzymes involved in the process of ubiquitin modifications, the pathophysiological roles of UBE2E2 in metabolic dysfunction are not yet understood. Here, we showed upregulated UBE2E2 expression in the islets of a mouse model of diet-induced obesity. The diabetes risk allele of UBE2E2 (rs13094957) in noncoding regions was associated with upregulation of UBE2E2 mRNA in the human pancreas. Although glucose-stimulated insulin secretion was intact in the isolated islets, pancreatic β-cell-specific UBE2E2-transgenic (TG) mice exhibited reduced insulin secretion and decreased β-cell mass. In TG mice, suppressed proliferation of β-cells before the weaning period and while receiving a high-fat diet was accompanied by elevated gene expression levels of p21, resulting in decreased postnatal β-cell mass expansion and compensatory β-cell hyperplasia, respectively. In TG islets, proteomic analysis identified enhanced formation of various types of polyubiquitin chains, accompanied by increased expression of Nedd4 E3 ubiquitin protein ligase. Ubiquitination assays showed that UBE2E2 mediated the elongation of ubiquitin chains by Nedd4. The data suggest that UBE2E2-mediated ubiquitin modifications in β-cells play an important role in regulating glucose homeostasis and β-cell mass.
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Affiliation(s)
- Yoshitaka Sakurai
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Naoto Kubota
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Department of Metabolic Medicine, Faculty of Life Science, Kumamoto University, Kumamoto, Japan
- Clinical Nutrition Program, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Iseki Takamoto
- Department of Metabolism and Endocrinology, Ibaraki Medical Center, Tokyo Medical University, Tokyo, Japan
| | - Nobuhiro Wada
- Department of Anatomy I, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Masakazu Aihara
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Takanori Hayashi
- Clinical Nutrition Program, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Tetsuya Kubota
- Clinical Nutrition Program, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Division of Diabetes and Metabolism, Institute of Medical Science, Asahi Life Foundation, Tokyo, Japan
| | - Yuta Hiraike
- Division for Health Service Promotion, The University of Tokyo, Tokyo, Japan
| | - Takayoshi Sasako
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Harumi Nakao
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Atsu Aiba
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoko Chikaoka
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | | | | | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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Yao S, Xie M, Hu M, Cui X, Wu H, Li X, Hu P, Tong C, Yu X. Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 14:1118339. [PMID: 37021309 PMCID: PMC10067767 DOI: 10.3389/fpls.2023.1118339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Ubiquitin-conjugating enzyme (UBC) is a critical part of the ubiquitin-proteasome pathway and plays crucial roles in growth, development and abiotic stress response in plants. Although UBC genes have been detected in several plant species, characterization of this gene family at the whole-genome level has not been conducted in Brassica napus. In the present study, 200 putative BnUBCs were identified in B. napus, which were clustered into 18 subgroups based on phylogenetic analysis. BnUBCs within each subgroup showed relatively conserved gene architectures and motifs. Moreover, the gene expression patterns in various tissues as well as the identification of cis-acting regulatory elements in BnUBC promoters suggested further investigation of their potential functions in plant growth and development. Furthermore, three BnUBCs were predicted as candidate genes for regulating agronomic traits related to oil content and yield through association mapping. In conclusion, this study provided a wealth of information on the UBC family in B. napus and revealed their effects on oil content and yield, which will aid future functional research and genetic breeding of B. napus.
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Affiliation(s)
- Shengli Yao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Ming Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - XiaoBo Cui
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Haoming Wu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Xiaohua Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Peng Hu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoli Yu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
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4
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Gingerich MA, Liu X, Chai B, Pearson GL, Vincent MP, Stromer T, Zhu J, Sidarala V, Renberg A, Sahu D, Klionsky DJ, Schnell S, Soleimanpour SA. An intrinsically disordered protein region encoded by the human disease gene CLEC16A regulates mitophagy. Autophagy 2023; 19:525-543. [PMID: 35604110 PMCID: PMC9851259 DOI: 10.1080/15548627.2022.2080383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
CLEC16A regulates mitochondrial health through mitophagy and is associated with over 20 human diseases. However, the key structural and functional regions of CLEC16A, and their relevance for human disease, remain unknown. Here, we report that a disease-associated CLEC16A variant lacks a C-terminal intrinsically disordered protein region (IDPR) that is critical for mitochondrial quality control. IDPRs comprise nearly half of the human proteome, yet their mechanistic roles in human disease are poorly understood. Using carbon detect NMR, we find that the CLEC16A C terminus lacks secondary structure, validating the presence of an IDPR. Loss of the CLEC16A C-terminal IDPR in vivo impairs mitophagy, mitochondrial function, and glucose-stimulated insulin secretion, ultimately causing glucose intolerance. Deletion of the CLEC16A C-terminal IDPR increases CLEC16A ubiquitination and degradation, thus impairing assembly of the mitophagy regulatory machinery. Importantly, CLEC16A stability is dependent on proline bias within the C-terminal IDPR, but not amino acid sequence order or charge. Together, we elucidate how an IDPR in CLEC16A regulates mitophagy and implicate pathogenic human gene variants that disrupt IDPRs as novel contributors to diabetes and other CLEC16A-associated diseases.Abbreviations : CAS: carbon-detect amino-acid specific; IDPR: intrinsically disordered protein region; MEFs: mouse embryonic fibroblasts; NMR: nuclear magnetic resonance.
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Affiliation(s)
- Morgan A. Gingerich
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xueying Liu
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA,Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Biaoxin Chai
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Gemma L. Pearson
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Michael P. Vincent
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Tracy Stromer
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Jie Zhu
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Vaibhav Sidarala
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Aaron Renberg
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Debashish Sahu
- BioNMR Core Facility, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Santiago Schnell
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Scott A. Soleimanpour
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Medicine Service, Endocrinology and Metabolism Section, VA Ann Arbor Health Care System, Ann Arbor, MI, USA,CONTACT Scott A. Soleimanpour Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Wall Street, Brehm Tower Room, Ann Arbor, MI, USA
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5
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Peter JJ, Magnussen HM, DaRosa PA, Millrine D, Matthews SP, Lamoliatte F, Sundaramoorthy R, Kopito RR, Kulathu Y. A non-canonical scaffold-type E3 ligase complex mediates protein UFMylation. EMBO J 2022; 41:e111015. [PMID: 36121123 DOI: 10.15252/embj.2022111015] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
Protein UFMylation, i.e., post-translational modification with ubiquitin-fold modifier 1 (UFM1), is essential for cellular and endoplasmic reticulum homeostasis. Despite its biological importance, we have a poor understanding of how UFM1 is conjugated onto substrates. Here, we use a rebuilding approach to define the minimal requirements of protein UFMylation. We find that the reported cognate E3 ligase UFL1 is inactive on its own and instead requires the adaptor protein UFBP1 to form an active E3 ligase complex. Structure predictions suggest the UFL1/UFBP1 complex to be made up of winged helix (WH) domain repeats. We show that UFL1/UFBP1 utilizes a scaffold-type E3 ligase mechanism that activates the UFM1-conjugating E2 enzyme, UFC1, for aminolysis. Further, we characterize a second adaptor protein CDK5RAP3 that binds to and forms an integral part of the ligase complex. Unexpectedly, we find that CDK5RAP3 inhibits UFL1/UFBP1 ligase activity in vitro. Results from reconstituting ribosome UFMylation suggest that CDK5RAP3 functions as a substrate adaptor that directs UFMylation to the ribosomal protein RPL26. In summary, our reconstitution approach reveals the biochemical basis of UFMylation and regulatory principles of this atypical E3 ligase complex.
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Affiliation(s)
- Joshua J Peter
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Helge M Magnussen
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Paul A DaRosa
- Department of Biology, Stanford University, Stanford, CA, USA
| | - David Millrine
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Stephen P Matthews
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
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6
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Szymanska K, Boldt K, Logan CV, Adams M, Robinson PA, Ueffing M, Zeqiraj E, Wheway G, Johnson CA. Regulation of canonical Wnt signalling by the ciliopathy protein MKS1 and the E2 ubiquitin-conjugating enzyme UBE2E1. eLife 2022; 11:57593. [PMID: 35170427 PMCID: PMC8880992 DOI: 10.7554/elife.57593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 02/10/2022] [Indexed: 11/24/2022] Open
Abstract
Primary ciliary defects cause a group of developmental conditions known as ciliopathies. Here, we provide mechanistic insight into ciliary ubiquitin processing in cells and for mouse model lacking the ciliary protein Mks1. In vivo loss of Mks1 sensitises cells to proteasomal disruption, leading to abnormal accumulation of ubiquitinated proteins. We identified UBE2E1, an E2 ubiquitin-conjugating enzyme that polyubiquitinates β-catenin, and RNF34, an E3 ligase, as novel interactants of MKS1. UBE2E1 and MKS1 colocalised, and loss of UBE2E1 recapitulates the ciliary and Wnt signalling phenotypes observed during loss of MKS1. Levels of UBE2E1 and MKS1 are co-dependent and UBE2E1 mediates both regulatory and degradative ubiquitination of MKS1. We demonstrate that processing of phosphorylated β-catenin occurs at the ciliary base through the functional interaction between UBE2E1 and MKS1. These observations suggest that correct β-catenin levels are tightly regulated at the primary cilium by a ciliary-specific E2 (UBE2E1) and a regulatory substrate-adaptor (MKS1).
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Affiliation(s)
- Katarzyna Szymanska
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Karsten Boldt
- Institute of Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | | | - Matthew Adams
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | | | - Marius Ueffing
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Colin A Johnson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
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7
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Funyu T, Kanemaru Y, Onoda H, Arita K. Preparation of the ubiquitination-triggered active form of SETDB1 in E. coli for biochemical and structural analyses. J Biochem 2021; 170:655-662. [PMID: 34324684 DOI: 10.1093/jb/mvab087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022] Open
Abstract
Trimethylation of histone H3 at K9 by the lysine methyltransferase, SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) plays a pivotal role in silencing tissue-specific genes and retrotransposable elements. In mammalian cells, SETDB1 undergoes monoubiquitination in the insertion region of the SET domain in an E3 ubiquitin ligase-independent manner. This ubiquitination has been shown to enhance the histone H3-K9 methyltransferase activity of SETDB1; however, the molecular mechanism underlying SETDB1 activation by ubiquitination is unknown. In this study, we developed an E. coli ubiquitination plasmid for the preparation of ubiquitinated SETDB1. Western blotting and mutational analyses showed that coexpression of the SET domain of SETDB1 with the proteins encoded by the ubiquitination plasmid led to site-specific monoubiquitination of the SET domain at K867. An in vitro histone H3 methylation assay demonstrated that the ubiquitinated SET domain of SETDB1 acquired enzymatic activity. Taken together, these findings demonstrate successful preparation of the active form of SETDB1 with the E. coli ubiquitination system, which will aid biochemical and structural studies of ubiquitinated SETDB1.
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Affiliation(s)
- Tomoko Funyu
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yuka Kanemaru
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroki Onoda
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kyohei Arita
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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8
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Abstract
OTUB1 is a highly expressed cysteine protease that specifically cleaves K48-linked polyubiquitin chains. This unique deubiquitinating enzyme (DUB) can bind to a subset of E2 ubiquitin conjugating enzymes, forming complexes in which the two enzymes can regulate one another's activity. OTUB1 can noncatalytically suppress the ubiquitin conjugating activity of its E2 partners by sequestering the charged E2∼Ub thioester and preventing ubiquitin transfer. The same E2 enzymes, when uncharged, can stimulate the DUB activity of OTUB1 in vitro, although the importance of OTUB1 stimulation in vivo remains unclear. To assess the potential balance between these activities that might occur in cells, we characterized the kinetics and thermodynamics governing the formation and activity of OTUB1:E2 complexes. We show that both stimulation of OTUB1 by E2 enzymes and noncatalytic inhibition of E2 enzymes by OTUB1 occur at physiologically relevant concentrations of both partners. Whereas E2 partners differ in their ability to stimulate OTUB1 activity, we find that this variability is not correlated with the affinity of each E2 for OTUB1. In addition to UBE2N and the UBE2D isoforms, we find that OTUB1 inhibits the polyubiquitination activity of all three UBE2E enzymes, UBE2E1, UBE2E2, and UBE2E3. Interestingly, although OTUB1 also inhibits the auto-monoubiquitination and autopolyubiquitination activity of UBE2E1 and UBE2E2, it is unable to suppress autoubiquitination by UBE2E3. Our quantitative analysis provides a basis for further exploring the biological roles of OTUB1:E2 complexes in cells.
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Affiliation(s)
- Lauren T. Que
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21210-2185 USA
| | - Marie E. Morrow
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21210-2185 USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21210-2185 USA
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9
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Structural and Functional Analysis of Ubiquitin-based Inhibitors That Target the Backsides of E2 Enzymes. J Mol Biol 2019; 432:952-966. [PMID: 31634471 DOI: 10.1016/j.jmb.2019.09.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 08/12/2018] [Accepted: 09/09/2019] [Indexed: 12/28/2022]
Abstract
Ubiquitin-conjugating E2 enzymes are central to the ubiquitination cascade and have been implicated in cancer and other diseases. Despite strong interest in developing specific E2 inhibitors, the shallow and exposed active site has proven recalcitrant to targeting with reversible small-molecule inhibitors. Here, we used phage display to generate highly potent and selective ubiquitin variants (UbVs) that target the E2 backside, which is located opposite to the active site. A UbV targeting Ube2D1 did not affect charging but greatly attenuated chain elongation. Likewise, a UbV targeting the E2 variant Ube2V1 did not interfere with the charging of its partner E2 enzyme but inhibited formation of diubiquitin. In contrast, a UbV that bound to the backside of Ube2G1 impeded the generation of thioester-linked ubiquitin to the active site cysteine of Ube2G1 by the E1 enzyme. Crystal structures of UbVs in complex with three E2 proteins revealed distinctive molecular interactions in each case, but they also highlighted a common backside pocket that the UbVs used for enhanced affinity and specificity. These findings validate the E2 backside as a target for inhibition and provide structural insights to aid inhibitor design and screening efforts.
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10
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Brühl J, Trautwein J, Schäfer A, Linne U, Bouazoune K. The DNA repair protein SHPRH is a nucleosome-stimulated ATPase and a nucleosome-E3 ubiquitin ligase. Epigenetics Chromatin 2019; 12:52. [PMID: 31434570 PMCID: PMC6702750 DOI: 10.1186/s13072-019-0294-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/10/2019] [Indexed: 12/22/2022] Open
Abstract
Background Maintenance of genome integrity during DNA replication is crucial to the perpetuation of all organisms. In eukaryotes, the bypass of DNA lesions by the replication machinery prevents prolonged stalling of the replication fork, which could otherwise lead to greater damages such as gross chromosomal rearrangements. Bypassing DNA lesions and subsequent repair are accomplished by the activation of DNA damage tolerance pathways such as the template switching (TS) pathway. In yeast, the RAD5 (Radiation-sensitive 5) protein plays a crucial role in initiating the TS pathway by catalyzing the polyubiquitination of PCNA (Proliferation Cell Nuclear Antigen). Likewise, one of the mammalian RAD5-homologs, SHPRH (SNF2, histone linker, PHD, RING, helicase) mediates PCNA polyubiquitination. To date, the study of SHPRH enzymatic functions has been limited to this modification. It is therefore unclear how SHPRH carries out its function in DNA repair. Moreover, how this protein regulates gene transcription at the enzymatic level is also unknown. Results Given that SHPRH harbors domains found in chromatin remodeling proteins, we investigated its biochemical properties in the presence of nucleosomal substrates. We find that SHPRH binds equally well to double-stranded (ds) DNA and to nucleosome core particles, however, like ISWI and CHD-family remodelers, SHPRH shows a strong preference for nucleosomes presenting extranucleosomal DNA. Moreover, nucleosomes but not dsDNA strongly stimulate the ATPase activity of SHPRH. Intriguingly, unlike typically observed with SNF2-family enzymes, ATPase activity does not translate into conventional nucleosome remodeling, under standard assay conditions. To test whether SHPRH can act as a ubiquitin E3 ligase for nucleosomes, we performed a screen using 26 E2-conjugating enzymes. We uncover that SHPRH is a potent nucleosome E3-ubiquitin-ligase that can function with at least 7 different E2s. Mass spectrometry analyses of products generated in the presence of the UBE2D1-conjugating enzyme reveal that SHPRH can catalyze the formation of polyubiquitin linkages that are either branched or associated with the recruitment of DNA repair factors, as well as linkages involved in proteasomal degradation. Conclusions We propose that, in addition to polyubiquitinating PCNA, SHPRH promotes DNA repair or transcriptional regulation in part through chromatin ubiquitination. Our study sets a biochemical framework for studying other RAD5- and RAD16-related protein functions through the ubiquitination of nucleosomes. Electronic supplementary material The online version of this article (10.1186/s13072-019-0294-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joanna Brühl
- Institut für Molekularbiologie und Tumorforschung (IMT), Biomedizinisches Forschungszentrum, Philipps-Universität Marburg, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Jonathan Trautwein
- Institut für Molekularbiologie und Tumorforschung (IMT), Biomedizinisches Forschungszentrum, Philipps-Universität Marburg, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Agnes Schäfer
- Institut für Molekularbiologie und Tumorforschung (IMT), Biomedizinisches Forschungszentrum, Philipps-Universität Marburg, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Uwe Linne
- Fachbereich Chemie und Synmikro, Gerätezentrum Massenspektrometrie und Elementanalaytik, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Karim Bouazoune
- Institut für Molekularbiologie und Tumorforschung (IMT), Biomedizinisches Forschungszentrum, Philipps-Universität Marburg, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany.
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11
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Abstract
Many receptor tyrosine kinases (RTKs, such as EGFR, MET) are negatively regulated by ubiquitination and degradation mediated by Cbl proteins, a family of RING finger (RF) ubiquitin ligases (E3s). Loss of Cbl protein function is associated with malignant transformation driven by increased RTK activity. RF E3s, such as the Cbl proteins, interact with a ubiquitin-conjugating enzyme (E2) to confer specificity to the ubiquitination process and direct the transfer of ubiquitin from the E2 to one or more lysines on the target proteins. Using in vitro E3 assays and yeast two-hybrid screens, we found that Ube2d, Ube2e families, Ube2n/2v1, and Ube2w catalyze autoubiquitination of the Cbl protein and Ube2d2, Ube2e1, and Ube 2n/2v1 catalyze Cbl-mediated substrate ubiquitination of the EGFR and SYK. Phosphorylation of the Cbl protein by by Src resulted in increased E3 activity compared to unphosphorylated cbl or Cbl containing a phosphomimetic Y371E mutation. Ubiquitin chain formation depended on the E2 tested with Cbl with Ube2d2 forming both K48 and K63 linked chains, Ube2n/2v1 forming only K63 linked chains, and Ube2w inducing monoubiquitination. In cells, the Ube2d family, Ube2e family, and Ube2n/2v1 contributed to EGFR ubiquitination. Our data suggest that multiple E2s can interact with Cbl and modulate its E3 activity in vitro and in cells.
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12
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Song L, Luo ZQ. Post-translational regulation of ubiquitin signaling. J Cell Biol 2019; 218:1776-1786. [PMID: 31000580 PMCID: PMC6548142 DOI: 10.1083/jcb.201902074] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/29/2019] [Accepted: 04/03/2019] [Indexed: 12/22/2022] Open
Abstract
Song and Luo review the roles of post-translational modifications in ubiquitin signaling. Ubiquitination regulates many essential cellular processes in eukaryotes. This post-translational modification (PTM) is typically achieved by E1, E2, and E3 enzymes that sequentially catalyze activation, conjugation, and ligation reactions, respectively, leading to covalent attachment of ubiquitin, usually to lysine residues of substrate proteins. Ubiquitin can also be successively linked to one of the seven lysine residues on ubiquitin to form distinctive forms of polyubiquitin chains, which, depending upon the lysine used and the length of the chains, dictate the fate of substrate proteins. Recent discoveries revealed that this ubiquitin code is further expanded by PTMs such as phosphorylation, acetylation, deamidation, and ADP-ribosylation, on ubiquitin, components of the ubiquitination machinery, or both. These PTMs provide additional regulatory nodes to integrate development or insulting signals with cellular homeostasis. Understanding the precise roles of these PTMs in the regulation of ubiquitin signaling will provide new insights into the mechanisms and treatment of various human diseases linked to ubiquitination, including neurodegenerative diseases, cancer, infection, and immune disorders.
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Affiliation(s)
- Lei Song
- Department of Respiratory Medicine and Center of Infection and Immunity, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Department of Respiratory Medicine and Center of Infection and Immunity, The First Hospital of Jilin University, Changchun, China .,Purdue Institute for Inflammation, Immunology and Infectious Diseases and Department of Biological Sciences, Purdue University, West Lafayette, IN
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13
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Analysis of the Zn-Binding Domains of TRIM32, the E3 Ubiquitin Ligase Mutated in Limb Girdle Muscular Dystrophy 2H. Cells 2019; 8:cells8030254. [PMID: 30884854 PMCID: PMC6468550 DOI: 10.3390/cells8030254] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/02/2019] [Accepted: 03/12/2019] [Indexed: 01/08/2023] Open
Abstract
Members of the tripartite motif family of E3 ubiquitin ligases are characterized by the presence of a conserved N-terminal module composed of a RING domain followed by one or two B-box domains, a coiled-coil and a variable C-terminal region. The RING and B-box are both Zn-binding domains but, while the RING is found in a large number of proteins, the B-box is exclusive to the tripartite motif (TRIM) family members in metazoans. Whereas the RING has been extensively characterized and shown to possess intrinsic E3 ligase catalytic activity, much less is known about the role of the B-box domains. In this study, we adopted an in vitro approach using recombinant point- and deletion-mutants to characterize the contribution of the TRIM32 Zn-binding domains to the activity of this E3 ligase that is altered in a genetic form of muscular dystrophy. We found that the RING domain is crucial for E3 ligase activity and E2 specificity, whereas a complete B-box domain is involved in chain assembly rate modulation. Further, in vitro, the RING domain is necessary to modulate TRIM32 oligomerization, whereas, in cells, both the RING and B-box cooperate to specify TRIM32 subcellular localization, which if altered may impact the pathogenesis of diseases.
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14
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Ma Y, Xu J, Huang P, Bai X, Gao H. Ubiquitin-independent, Proteasome-mediated targeted degradation of KRAS in pancreatic adenocarcinoma cells using an engineered ornithine decarboxylase/antizyme system. IUBMB Life 2019; 71:57-65. [PMID: 30347501 PMCID: PMC7379993 DOI: 10.1002/iub.1945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/06/2018] [Indexed: 12/21/2022]
Abstract
The oncogene KRAS not only promotes the tumorigenesis of pancreatic cancers but also is required for the malignant progression and metastasis of these cancers. Many methods have been explored to influence the malignant biological behavior of these cancers by targeting mutant KRAS. The ornithine decarboxylase/antizyme (ODC/AZ) system is another protein degradation pathway that exists in nature. The formation of an ODC and protein substrate complex through direct combination can promote its degradation by the 26S proteasome without ubiquitination, and this process can be catalyzed by AZ. In this study, we designed and reconstructed a chimeric fusion protein (named RC-ODC). The engineered fusion protein RC-ODC was confirmed to interact with the mutant KRAS oncoprotein in a co-immunoprecipitation assay, and the introduction of both RC-ODC and AZ resulted in degradation of the exogenous and endogenous mutant KRAS oncoprotein at the post-translational level independent of ubiquitination in vitro. Along with a decreased KRAS level, suppression of PANC-1 cell proliferation was detected in vitro and in vivo, and meanwhile downregulation of phosphorylated extracellular signal-regulated kinase 1/2 (ERK1/2) was also observed. Targeted degradation of the KRAS oncoprotein through the ODC/AZ pathway at the post-translational level may reflect a more effective future therapeutic strategy for pancreatic cancer patients. © 2018 The Authors. IUBMB Life published by Wiley Periodicals,Inc. on behalf of International Union of Biochemistry and Molecular Biology, 71(1):57-65, 2019.
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Affiliation(s)
- Yihui Ma
- Department of PathologyZhengzhou University1st Affiliated Hospital, ZhengzhouChina
| | - Jingjing Xu
- Department of PathologyZhengzhou University1st Affiliated Hospital, ZhengzhouChina
| | - Pei Huang
- Department of PathologyZhengzhou University1st Affiliated Hospital, ZhengzhouChina
| | - Xue Bai
- Department of PathologyZhengzhou University1st Affiliated Hospital, ZhengzhouChina
| | - Hanqing Gao
- Department of PathologyZhengzhou University1st Affiliated Hospital, ZhengzhouChina
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15
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UBE2E1 Is Preferentially Expressed in the Cytoplasm of Slow-Twitch Fibers and Protects Skeletal Muscles from Exacerbated Atrophy upon Dexamethasone Treatment. Cells 2018; 7:cells7110214. [PMID: 30453501 PMCID: PMC6262581 DOI: 10.3390/cells7110214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 12/27/2022] Open
Abstract
Skeletal muscle mass is reduced during many diseases or physiological situations (disuse, aging), which results in decreased strength and increased mortality. Muscle mass is mainly controlled by the ubiquitin-proteasome system (UPS), involving hundreds of ubiquitinating enzymes (E2s and E3s) that target their dedicated substrates for subsequent degradation. We recently demonstrated that MuRF1, an E3 ubiquitin ligase known to bind to sarcomeric proteins (telethonin, α-actin, myosins) during catabolic situations, interacts with 5 different E2 enzymes and that these E2-MuRF1 couples are able to target telethonin, a small sarcomeric protein, for degradation. Amongst the E2s interacting with MuRF1, E2E1 was peculiar as the presence of the substrate was necessary for optimal MuRF1-E2E1 interaction. In this work, we focused on the putative role of E2E1 during skeletal muscle atrophy. We found that E2E1 expression was restricted to type I and type IIA muscle fibers and was not detectable in type IIB fibers. This strongly suggests that E2E1 targets are fiber-specific and may be strongly linked to the contractile and metabolic properties of the skeletal muscle. However, E2E1 knockdown was not sufficient for preserving the protein content in C2C12 myotubes subjected to a catabolic state (dexamethasone treatment), suggesting that E2E1 is not involved in the development of muscle atrophy. By contrast, E2E1 knockdown aggravated the atrophying process in both catabolic C2C12 myotubes and the Tibialis anterior muscle of mice, suggesting that E2E1 has a protective effect on muscle mass.
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16
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Daou S, Barbour H, Ahmed O, Masclef L, Baril C, Sen Nkwe N, Tchelougou D, Uriarte M, Bonneil E, Ceccarelli D, Mashtalir N, Tanji M, Masson JY, Thibault P, Sicheri F, Yang H, Carbone M, Therrien M, Affar EB. Monoubiquitination of ASXLs controls the deubiquitinase activity of the tumor suppressor BAP1. Nat Commun 2018; 9:4385. [PMID: 30349006 PMCID: PMC6197237 DOI: 10.1038/s41467-018-06854-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 09/19/2018] [Indexed: 12/21/2022] Open
Abstract
The tumor suppressor and deubiquitinase (DUB) BAP1 and its Drosophila ortholog Calypso assemble DUB complexes with the transcription regulators Additional sex combs-like (ASXL1, ASXL2, ASXL3) and Asx respectively. ASXLs and Asx use their DEUBiquitinase ADaptor (DEUBAD) domain to stimulate BAP1/Calypso DUB activity. Here we report that monoubiquitination of the DEUBAD is a general feature of ASXLs and Asx. BAP1 promotes DEUBAD monoubiquitination resulting in an increased stability of ASXL2, which in turn stimulates BAP1 DUB activity. ASXL2 monoubiquitination is directly catalyzed by UBE2E family of Ubiquitin-conjugating enzymes and regulates mammalian cell proliferation. Remarkably, Calypso also regulates Asx monoubiquitination and transgenic flies expressing monoubiquitination-defective Asx mutant exhibit developmental defects. Finally, the protein levels of ASXL2, BAP1 and UBE2E enzymes are highly correlated in mesothelioma tumors suggesting the importance of this signaling axis for tumor suppression. We propose that monoubiquitination orchestrates a molecular symbiosis relationship between ASXLs and BAP1.
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Affiliation(s)
- Salima Daou
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Haithem Barbour
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Oumaima Ahmed
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Louis Masclef
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Caroline Baril
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Nadine Sen Nkwe
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Daméhan Tchelougou
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Maxime Uriarte
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, Laboratory of Proteomics and Bioanalytical Mass Spectrometry, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Derek Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Nazar Mashtalir
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Mika Tanji
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Jean-Yves Masson
- CHU de Quebec Research Center (Oncology Axis), Laval University Cancer Research Center, 9 McMahon, Quebec, PQ, G1R 2J6, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Laboratory of Proteomics and Bioanalytical Mass Spectrometry, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Haining Yang
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Michele Carbone
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, University of Montréal, Montréal, QC, H3T 1J4, Canada. .,Département de pathologie et biologie cellulaire, University of Montréal, Montréal, QC, H3C 3J7, Canada.
| | - El Bachir Affar
- Maisonneuve-Rosemont Hospital Research Center and Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada.
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17
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Pasupala N, Morrow ME, Que LT, Malynn BA, Ma A, Wolberger C. OTUB1 non-catalytically stabilizes the E2 ubiquitin-conjugating enzyme UBE2E1 by preventing its autoubiquitination. J Biol Chem 2018; 293:18285-18295. [PMID: 30282802 PMCID: PMC6254341 DOI: 10.1074/jbc.ra118.004677] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/04/2018] [Indexed: 01/08/2023] Open
Abstract
OTUB1 is a deubiquitinating enzyme that cleaves Lys-48–linked polyubiquitin chains and also regulates ubiquitin signaling through a unique, noncatalytic mechanism. OTUB1 binds to a subset of E2 ubiquitin-conjugating enzymes and inhibits their activity by trapping the E2∼ubiquitin thioester and preventing ubiquitin transfer. The same set of E2s stimulate the deubiquitinating activity of OTUB1 when the E2 is not charged with ubiquitin. Previous studies have shown that, in cells, OTUB1 binds to E2-conjugating enzymes of the UBE2D (UBCH5) and UBE2E families, as well as to UBE2N (UBC13). Cellular roles have been identified for the interaction of OTUB1 with UBE2N and members of the UBE2D family, but not for interactions with UBE2E E2 enzymes. We report here a novel role for OTUB1–E2 interactions in modulating E2 protein ubiquitination. We observe that Otub1−/− knockout mice exhibit late-stage embryonic lethality. We find that OTUB1 depletion dramatically destabilizes the E2-conjugating enzyme UBE2E1 (UBCH6) in both mouse and human OTUB1 knockout cell lines. Of note, this effect is independent of the catalytic activity of OTUB1, but depends on its ability to bind to UBE2E1. We show that OTUB1 suppresses UBE2E1 autoubiquitination in vitro and in cells, thereby preventing UBE2E1 from being targeted to the proteasome for degradation. Taken together, we provide evidence that OTUB1 rescues UBE2E1 from degradation in vivo.
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Affiliation(s)
- Nagesh Pasupala
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185 and
| | - Marie E Morrow
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185 and
| | - Lauren T Que
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185 and
| | - Barbara A Malynn
- the Department of Medicine, University of California San Francisco, San Francisco, California 94117
| | - Averil Ma
- the Department of Medicine, University of California San Francisco, San Francisco, California 94117
| | - Cynthia Wolberger
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185 and.
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18
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Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses in Brassica rapa. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5206758. [PMID: 30225257 PMCID: PMC6129857 DOI: 10.1155/2018/5206758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/25/2018] [Indexed: 01/01/2023]
Abstract
To understand ubiquitination mechanism, E2s (ubiquitin conjugating enzymes) have crucial part as they play a major role in regulating many biological processes in plants. Meanwhile, Brassica rapa is an important leafy vegetable crop and therefore its characterization along with the expression pattern of E2s under various stresses is imperative. In this study, a total of 83 genes were identified in B. rapa and were classified into four different classes based on domain information. Here, we analyzed phylogenetic relationships, collinear correlation, gene duplication, interacting network, and expression patterns of E2 genes in B. rapa. Furthermore, RT-PCR analysis for 8 multiple abiotic and hormone treatments (namely, ABA, GA, JA, BR, PEG, NaCl, and heat and cold stress) illustrated striking expression pattern under one or more treatments, speculating that these might be stress-responsive genes. The cis-elements and interaction network analyses implicate valuable clues of important function of E2 genes in development and multiple stress responses in B. rapa. This study will further facilitate functional analysis of E2s for improving stress resistance mechanism in B. rapa.
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19
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Jue D, Sang X, Liu L, Shu B, Wang Y, Xie J, Liu C, Shi S. The Ubiquitin-Conjugating Enzyme Gene Family in Longan (Dimocarpus longan Lour.): Genome-Wide Identification and Gene Expression during Flower Induction and Abiotic Stress Responses. Molecules 2018; 23:molecules23030662. [PMID: 29543725 PMCID: PMC6017367 DOI: 10.3390/molecules23030662] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 11/16/2022] Open
Abstract
Ubiquitin-conjugating enzymes (E2s or UBC enzymes) play vital roles in plant development and combat various biotic and abiotic stresses. Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical region of Southeast Asia and Australia; however the characteristics of the UBC gene family in longan remain unknown. In this study, 40 D. longan UBC genes (DlUBCs), which were classified into 15 groups, were identified in the longan genome. An RNA-seq based analysis showed that DlUBCs showed distinct expression in nine longan tissues. Genome-wide RNA-seq and qRT-PCR based gene expression analysis revealed that 11 DlUBCs were up- or down-regualted in the cultivar “Sijimi” (SJ), suggesting that these genes may be important for flower induction. Finally, qRT-PCR analysis showed that the mRNA levels of 13 DlUBCs under SA (salicylic acid) treatment, seven under methyl jasmonate (MeJA) treatment, 27 under heat treatment, and 16 under cold treatment were up- or down-regulated, respectively. These results indicated that the DlUBCs may play important roles in responses to abiotic stresses. Taken together, our results provide a comprehensive insight into the organization, phylogeny, and expression patterns of the longan UBC genes, and therefore contribute to the greater understanding of their biological roles in longan.
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Affiliation(s)
- Dengwei Jue
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China.
| | - Xuelian Sang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China.
| | - Liqin Liu
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China.
| | - Bo Shu
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China.
| | - Yicheng Wang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China.
| | - Jianghui Xie
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China.
| | - Chengming Liu
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
| | - Shengyou Shi
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China.
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20
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Sharma B, Bhatt TK. Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato. Sci Rep 2017; 7:8613. [PMID: 28819320 PMCID: PMC5561181 DOI: 10.1038/s41598-017-09121-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/14/2017] [Indexed: 11/27/2022] Open
Abstract
The ubiquitin-proteasomal degradation mechanism has gained the attention over the past decade. The E2 ubiquitin conjugating enzymes are the crucial part of ubiquitination mechanism and they are believed to hold imperative association for plant development. It accepts ubiquitin from the E1 enzyme and interacts with the E3 ligase to transfer ubiquitin or directly transfers ubiquitin to the substrate. The functional aspects of E2 ubiquitin enzymes in plant systems are unclear. Tomato is being used as a model plant and rarely explored to study E2 ubiquitin enzyme. We have utilized in-silico methods to analyze E2 enzymes in Solanum lycopersicum and 59 genes were identified with UBC family domains. The physio-chemical properties, chromosomal localization, structural organization, gene duplication, promoter analysis, gene ontology and conserved motifs were investigated along with phylogenetic analysis of tomato E2 genes exploring evolutionary relations. The gene expression analysis of RNA sequencing data revealed expression profile of tomato E2 genes in seedling, root, leaf, seed, fruit, and flower tissues. Our study aid in the understanding of distribution, expansion, evolutionary relation and probable participation in plant biological processes of tomato E2 enzymes that will facilitate strong base for future research on ubiquitin-mediated regulations in tomato and other plant systems.
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Affiliation(s)
- Bhaskar Sharma
- Department of Biotechnology, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India
| | - Tarun Kumar Bhatt
- Department of Biotechnology, Central University of Rajasthan, Bandarsindri, Ajmer, 305817, India.
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21
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Mechanism and disease association of E2-conjugating enzymes: lessons from UBE2T and UBE2L3. Biochem J 2017; 473:3401-3419. [PMID: 27729585 PMCID: PMC5095918 DOI: 10.1042/bcj20160028] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/09/2016] [Indexed: 02/07/2023]
Abstract
Ubiquitin signalling is a fundamental eukaryotic regulatory system, controlling diverse cellular functions. A cascade of E1, E2, and E3 enzymes is required for assembly of distinct signals, whereas an array of deubiquitinases and ubiquitin-binding modules edit, remove, and translate the signals. In the centre of this cascade sits the E2-conjugating enzyme, relaying activated ubiquitin from the E1 activating enzyme to the substrate, usually via an E3 ubiquitin ligase. Many disease states are associated with dysfunction of ubiquitin signalling, with the E3s being a particular focus. However, recent evidence demonstrates that mutations or impairment of the E2s can lead to severe disease states, including chromosome instability syndromes, cancer predisposition, and immunological disorders. Given their relevance to diseases, E2s may represent an important class of therapeutic targets. In the present study, we review the current understanding of the mechanism of this important family of enzymes, and the role of selected E2s in disease.
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22
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Jue D, Sang X, Shu B, Liu L, Wang Y, Jia Z, Zou Y, Shi S. Characterization and expression analysis of genes encoding ubiquitin conjugating domain-containing enzymes in Carica papaya. PLoS One 2017; 12:e0171357. [PMID: 28231288 PMCID: PMC5322903 DOI: 10.1371/journal.pone.0171357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/18/2017] [Indexed: 11/25/2022] Open
Abstract
Background Ripening affects the quality and nutritional contents of fleshy fruits and is a crucial process of fruit development. Although several studies have suggested that ubiquitin-conjugating enzyme (E2s or UBC enzymes) are involved in the regulation of fruit ripening, little is known about the function of E2s in papaya (Carica papaya). Methodology/Principal findings In the present study, we searched the papaya genome and identified 34 putative UBC genes, which were clustered into 17 phylogenetic subgroups. We also analyzed the nucleotide sequences of the papaya UBC (CpUBC) genes and found that both exon-intron junctions and sequence motifs were highly conserved among the phylogenetic subgroups. Using real-time PCR analysis, we also found that all the CpUBC genes were expressed in roots, stems, leaves, male and female flowers, and mature fruit, although the expression of some of the genes was increased or decreased in one or several specific organs. We also found that the expression of 13 and two CpUBC genes were incresesd or decreased during one and two ripening stages, respectively. Expression analyses indicates possible E2s playing a more significant role in fruit ripening for further studies. Conclusions To the best of our knowledge, this is the first reported genome-wide analysis of the papaya UBC gene family, and the results will facilitate further investigation of the roles of UBC genes in fruit ripening and will aide in the functional validation of UBC genes in papaya.
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Affiliation(s)
- Dengwei Jue
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Xuelian Sang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Bo Shu
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Liqin Liu
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Yicheng Wang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Zhiwei Jia
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Yu Zou
- Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Shengyou Shi
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
- * E-mail:
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23
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Wright JD, Mace PD, Day CL. Noncovalent Ubiquitin Interactions Regulate the Catalytic Activity of Ubiquitin Writers. Trends Biochem Sci 2016; 41:924-937. [PMID: 27614784 DOI: 10.1016/j.tibs.2016.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 11/27/2022]
Abstract
Covalent modification of substrate proteins with ubiquitin is the end result of an intricate network of protein-protein interactions. The inherent ability of the E1, E2, and E3 proteins of the ubiquitylation cascade (the ubiquitin writers) to interact with ubiquitin facilitates this process. Importantly, contact between ubiquitin and the E2/E3 writers is required for catalysis and the assembly of chains of a given linkage. However, ubiquitin is also an activator of ubiquitin-writing enzymes, with many recent studies highlighting the ability of ubiquitin to regulate activity and substrate modification. Here, we review the interactions between ubiquitin-writing enzymes and regulatory ubiquitin molecules that promote activity, and highlight the potential of these interactions to promote processive ubiquitin transfer.
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Affiliation(s)
- Joshua D Wright
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand; The Francis Crick Institute, London NW1 1AT, UK
| | - Peter D Mace
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand.
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24
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Gong M, Wang H, Chen M, Bao D, Zhu Q, Tan Q. A newly discovered ubiquitin-conjugating enzyme E2 correlated with the cryogenic autolysis of Volvariella volvacea. Gene 2016; 583:58-63. [DOI: 10.1016/j.gene.2016.02.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 01/31/2016] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
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25
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Dong C, Hu H, Jue D, Zhao Q, Chen H, Xie J, Jia L. The banana E2 gene family: Genomic identification, characterization, expression profiling analysis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 245:11-24. [PMID: 26940488 DOI: 10.1016/j.plantsci.2016.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/23/2015] [Accepted: 01/13/2016] [Indexed: 05/06/2023]
Abstract
The E2 is at the center of a cascade of Ub1 transfers, and it links activation of the Ub1 by E1 to its eventual E3-catalyzed attachment to substrate. Although the genome-wide analysis of this family has been performed in some species, little is known about analysis of E2 genes in banana. In this study, 74 E2 genes of banana were identified and phylogenetically clustered into thirteen subgroups. The predicted banana E2 genes were distributed across all 11 chromosomes at different densities. Additionally, the E2 domain, gene structure and motif compositions were analyzed. The expression of all of the banana E2 genes was analyzed in the root, stem, leaf, flower organs, five stages of fruit development and under abiotic stresses. All of the banana E2 genes, with the exception of few genes in each group, were expressed in at least one of the organs and fruit developments, which indicated that the E2 genes might involve in various aspects of the physiological and developmental processes of the banana. Quantitative RT-PCR (qRT-PCR) analysis identified that 45 E2s under drought and 33 E2s under salt were induced. To the best of our knowledge, this report describes the first genome-wide analysis of the banana E2 gene family, and the results should provide valuable information for understanding the classification, cloning and putative functions of this family.
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Affiliation(s)
- Chen Dong
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Huigang Hu
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Dengwei Jue
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Qiufang Zhao
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Hongliang Chen
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Jianghui Xie
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China
| | - Liqiang Jia
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China; South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China.
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26
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Abstract
Ubiquitin-conjugating enzymes (E2s) are the central players in the trio of enzymes responsible for the attachment of ubiquitin (Ub) to cellular proteins. Humans have ∼40 E2s that are involved in the transfer of Ub or Ub-like (Ubl) proteins (e.g., SUMO and NEDD8). Although the majority of E2s are only twice the size of Ub, this remarkable family of enzymes performs a variety of functional roles. In this review, we summarize common functional and structural features that define unifying themes among E2s and highlight emerging concepts in the mechanism and regulation of E2s.
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27
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Jue D, Sang X, Lu S, Dong C, Zhao Q, Chen H, Jia L. Genome-Wide Identification, Phylogenetic and Expression Analyses of the Ubiquitin-Conjugating Enzyme Gene Family in Maize. PLoS One 2015; 10:e0143488. [PMID: 26606743 PMCID: PMC4659669 DOI: 10.1371/journal.pone.0143488] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 11/05/2015] [Indexed: 02/07/2023] Open
Abstract
Background Ubiquitination is a post-translation modification where ubiquitin is attached to a substrate. Ubiquitin-conjugating enzymes (E2s) play a major role in the ubiquitin transfer pathway, as well as a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (Zea mays). Methodology/Principal Findings In the present study, a total of 75 putative ZmUBC genes have been identified and located in the maize genome. Phylogenetic analysis revealed that ZmUBC proteins could be divided into 15 subfamilies, which include 13 ubiquitin-conjugating enzymes (ZmE2s) and two independent ubiquitin-conjugating enzyme variant (UEV) groups. The predicted ZmUBC genes were distributed across 10 chromosomes at different densities. In addition, analysis of exon-intron junctions and sequence motifs in each candidate gene has revealed high levels of conservation within and between phylogenetic groups. Tissue expression analysis indicated that most ZmUBC genes were expressed in at least one of the tissues, indicating that these are involved in various physiological and developmental processes in maize. Moreover, expression profile analyses of ZmUBC genes under different stress treatments (4°C, 20% PEG6000, and 200 mM NaCl) and various expression patterns indicated that these may play crucial roles in the response of plants to stress. Conclusions Genome-wide identification, chromosome organization, gene structure, evolutionary and expression analyses of ZmUBC genes have facilitated in the characterization of this gene family, as well as determined its potential involvement in growth, development, and stress responses. This study provides valuable information for better understanding the classification and putative functions of the UBC-encoding genes of maize.
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Affiliation(s)
- Dengwei Jue
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Xuelian Sang
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Shengqiao Lu
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530227, China
| | - Chen Dong
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Qiufang Zhao
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Hongliang Chen
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Liqiang Jia
- Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
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28
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RING E3-Catalyzed E2 Self-Ubiquitination Attenuates the Activity of Ube2E Ubiquitin-Conjugating Enzymes. J Mol Biol 2015; 427:2290-304. [PMID: 25960396 DOI: 10.1016/j.jmb.2015.04.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/13/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
Abstract
Ubiquitination of a target protein is accomplished through sequential actions of the E1, E2s, and the E3s. E2s dictate the modification topology while E3 ligases confer substrate specificity and recruit the cognate E2. Human genome codes for ~35 different E2 proteins; all of which contain the characteristic ubiquitin-conjugating UBC core domain sufficient for catalysis. Many of these E2 enzymes also have N- or C-terminal extensions; roles of which are not very well understood. We show that the N-terminal extension of Ube2E1 undergoes intramolecular auto-ubiquitination. This self-ubiquitination activity is enhanced in the presence of interacting RING E3 ligases and results in a progressive attenuation of the E2 activity toward substrate/E3 modification. We also find that the N-terminal ubiquitination sites are conserved in all the three Ube2Es and replacing them with arginine renders all three full-length Ube2Es equally active as their core UBC domains. Based on these results, we propose that E3-catalyzed self-ubiquitination acts as a key regulatory mechanism that controls the activity of Ube2E class of ubiquitin E2s.
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29
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E Z, Zhang Y, Li T, Wang L, Zhao H. Characterization of the Ubiquitin-Conjugating Enzyme Gene Family in Rice and Evaluation of Expression Profiles under Abiotic Stresses and Hormone Treatments. PLoS One 2015; 10:e0122621. [PMID: 25902049 PMCID: PMC4406754 DOI: 10.1371/journal.pone.0122621] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 02/23/2015] [Indexed: 11/18/2022] Open
Abstract
Ubiquitin-conjugating enzyme E2s (UBCs), which catalyze the transfer of ubiquitin to substrate or E3 ligases, are key enzymes in ubiquitination modifications of target proteins. However, little is known about the knowledge of UBC gene family in rice. In this study, a total of 39 UBC encoding genes, which all contained an UBC domain with a cysteine active site, were identified in the rice genome. These were classified into fifteen distinct subfamilies based upon their sequence similarity and phylogenetic relationships. A subset of 19 OsUBC genes exhibited chromosomal duplication; 4 and 15 OsUBC genes were tandemly and segmentally duplicated, respectively. Comprehensive analyses were performed to investigate the expression profiles of OsUBC genes in various stages of vegetative and reproductive development using data from EST, Microarrays, MPSS, and real-time PCR. Many OsUBC genes exhibited abundant and tissue-specific expression patterns. Moreover, 14 OsUBCs were found to be differentially expressed under treatments with drought, or salt stresses. The expression analysis after treatments with IAA, 6-BA, GA and ABA indicated that almost all OsUBC genes were responsive to at least two of the four hormones. Several genes were significantly down-regulated under all of the hormone treatments, and most of the genes reduced by 6-BA were also reduced by GA. This study will facilitate further studies of the OsUBC gene family and provide useful clues for functional validation of OsUBCs in rice.
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Affiliation(s)
- Zhiguo E
- China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Yuping Zhang
- China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Tingting Li
- China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Lei Wang
- China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Heming Zhao
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
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30
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Clague MJ, Heride C, Urbé S. The demographics of the ubiquitin system. Trends Cell Biol 2015; 25:417-26. [PMID: 25906909 DOI: 10.1016/j.tcb.2015.03.002] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 12/17/2022]
Abstract
The ubiquitin system is a major coordinator of cellular physiology through regulation of both protein degradation and signalling pathways. A key building block of a systems-level understanding has been generated by global proteomic studies, which provide copy number estimates for each component. The aggregate of ubiquitin, conjugating enzymes (E1, E2, and E3s), and deubiquitylases (DUBs) represents ∼1.3% of total cellular protein. Complementary approaches have generated quantitative measurements of various ubiquitin pools and further subdivision into different ubiquitin chain topologies. Systematic studies aimed at associating specific enzymes (E2s and DUBs) with the dynamics of these different pools have also made significant progress. Here, we delineate the emerging picture of the most significant determinants of the cellular ubiquitin economy.
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Affiliation(s)
- Michael J Clague
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK.
| | - Claire Heride
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK
| | - Sylvie Urbé
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK
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31
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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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32
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Nguyen L, Plafker KS, Starnes A, Cook M, Klevit RE, Plafker SM. The ubiquitin-conjugating enzyme, UbcM2, is restricted to monoubiquitylation by a two-fold mechanism that involves backside residues of E2 and Lys48 of ubiquitin. Biochemistry 2014; 53:4004-14. [PMID: 24901938 PMCID: PMC4072368 DOI: 10.1021/bi500072v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Proteins
can be modified on lysines (K) with a single ubiquitin
(Ub) or with polymers of Ub (polyUb). These different configurations
and their respective topologies are primary factors for determining
whether substrates are targeted to the proteasome for degradation
or directed to nonproteolytic outcomes. We report here on the intrinsic
ubiquitylation properties
of UbcM2 (UBE2E3/UbcH9), a conserved Ub-conjugating enzyme linked
to cell proliferation, development, and the cellular antioxidant defense
system. Using a fully recombinant ubiquitylation assay,
we show that UbcM2 is severely limited in its ability to synthesize
polyUb chains with wild-type Ub. Restriction to monoubiquitylation
is governed by multiple residues on the backside of the enzyme, far
removed from its active site, and by lysine 48 of Ub. UbcM2 with mutated
backside residues can synthesize K63-linked polyUb chains and to a
lesser extent K6- and K48-linked chains. Additionally, we identified
a single residue on the backside of the enzyme that promotes monoubiquitylation.
Together, these findings reveal that a combination of noncatalytic
residues within the Ubc catalytic core domain of UbcM2 as well as
a lysine(s) within Ub can relegate a Ub-conjugating enzyme to monoubiquitylate
its cognate targets despite having the latent capacity to construct
polyUb chains. The two-fold mechanism for restricting activity to
monoubiquitylation provides
added insurance that UbcM2 will not build polyUb chains on its substrates,
even under conditions of high local Ub concentrations.
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Affiliation(s)
- Linda Nguyen
- Free Radical Biology and Aging Program, Oklahoma Medical Research Foundation , Oklahoma City, Oklahoma 73104, United States
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33
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Uversky VN. The UBE2E proteins as conjugating dispersers: extending function with extended extensions. J Mol Biol 2013; 425:4067-70. [PMID: 23871835 DOI: 10.1016/j.jmb.2013.07.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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