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Kaushik A, Parashar S, Ambasta RK, Kumar P. Ubiquitin E3 ligases assisted technologies in protein degradation: Sharing pathways in neurodegenerative disorders and cancer. Ageing Res Rev 2024; 96:102279. [PMID: 38521359 DOI: 10.1016/j.arr.2024.102279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
E3 ligases, essential components of the ubiquitin-proteasome-mediated protein degradation system, play a critical role in cellular regulation. By covalently attaching ubiquitin (Ub) molecules to target proteins, these ligases mark them for degradation, influencing various bioprocesses. With over 600 E3 ligases identified, there is a growing realization of their potential as therapeutic candidates for addressing proteinopathies in cancer and neurodegenerative disorders (NDDs). Recent research has highlighted the need to delve deeper into the intricate roles of E3 ligases as nexus points in the pathogenesis of both cancer and NDDs. Their dysregulation is emerging as a common thread linking these seemingly disparate diseases, necessitating a comprehensive understanding of their molecular intricacies. Herein, we have discussed (i) the fundamental mechanisms through which different types of E3 ligases actively participate in selective protein degradation in cancer and NDDs, followed by an examination of common E3 ligases playing pivotal roles in both situations, emphasising common players. Moving to, (ii) the functional domains and motifs of E3 ligases involved in ubiquitination, we have explored their interactions with specific substrates in NDDs and cancer. Additionally, (iii) we have explored techniques like PROTAC, molecular glues, and other state-of-the-art methods for hijacking neurotoxic and oncoproteins. Lastly, (iv) we have provided insights into ongoing clinical trials, offering a glimpse into the evolving landscape of E3-based therapeutics for cancer and NDDs. Unravelling the intricate network of E3 ligase-mediated regulation holds the key to unlocking targeted therapies that address the specific molecular signatures of individual patients, heralding a new era in personalized medicines.
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Affiliation(s)
- Aastha Kaushik
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Somya Parashar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University-Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India.
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Yang B, Pei J, Lu C, Wang Y, Shen M, Qin X, Huang Y, Yang X, Zhao X, Ma S, Song Z, Liang Y, Wang H, Wang J. RNF144A promotes antiviral responses by modulating STING ubiquitination. EMBO Rep 2023; 24:e57528. [PMID: 37955227 PMCID: PMC10702816 DOI: 10.15252/embr.202357528] [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: 05/24/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023] Open
Abstract
Stimulator of interferon (IFN) genes (STING, also named MITA, ERIS, MPYS, or TMEM173) plays an essential role in DNA virus- or cytosolic DNA-triggered innate immune responses. Here, we demonstrate that the RING-in-between RING (RBR) E3 ubiquitin ligase family member RING-finger protein (RNF) 144A interacts with STING and promotes its K6-linked ubiquitination at K236, thereby enhancing STING translocation from the ER to the Golgi and downstream signaling pathways. The K236R mutant of STING displays reduced activity in promoting innate immune signal transduction. Overexpression of RNF144A upregulates HSV-1- or cytosolic DNA-induced immune responses, while knockdown of RNF144A expression has the opposite effect. In addition, Rnf144a-deficient cells exhibit impaired DNA virus- or cytosolic DNA-triggered signaling, and RNF144A protects mice from DNA virus infection. In contrast, RNF144A does not affect RNA virus- or cytosolic RNA-triggered innate immune responses. Taken together, our findings identify a new positive regulator of DNA virus- or cytosolic DNA-triggered signaling pathways and a critical ubiquitination site important for fully functional STING during antiviral responses.
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Affiliation(s)
- Bo Yang
- Xinxiang Key Laboratory of Inflammation and ImmunologyXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
| | - Jinyong Pei
- Xinxiang Key Laboratory of Inflammation and ImmunologyXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
| | - Chen Lu
- Xinxiang Key Laboratory of Inflammation and ImmunologyXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
| | - Yi Wang
- Xinxiang Key Laboratory of Inflammation and ImmunologyXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
| | - Mengyang Shen
- Xinxiang Key Laboratory of Inflammation and ImmunologyXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
| | - Xiao Qin
- Xinxiang Key Laboratory of Inflammation and ImmunologyXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
| | - Yulu Huang
- Xinxiang Key Laboratory of Inflammation and ImmunologyXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
| | - Xi Yang
- Xinxiang Key Laboratory of Inflammation and ImmunologyXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
| | - Xin Zhao
- Department of Laboratory MedicineThe Third Affiliated Hospital of Xinxiang Medical UniversityXinxiangChina
| | - Shujun Ma
- Xinxiang Key Laboratory of Inflammation and ImmunologyXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
| | - Zhishan Song
- Xinxiang Key Laboratory of Inflammation and ImmunologyXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
| | - Yinming Liang
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
- Ping Yuan LaboratoryXinxiangChina
| | - Hui Wang
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
| | - Jie Wang
- Xinxiang Key Laboratory of Inflammation and ImmunologyXinxiang Medical UniversityXinxiangChina
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangChina
- Henan Key Laboratory of Immunology and Targeted DrugXinxiang Medical UniversityXinxiangChina
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Hayashida R, Kikuchi R, Imai K, Kojima W, Yamada T, Iijima M, Sesaki H, Tanaka K, Matsuda N, Yamano K. Elucidation of ubiquitin-conjugating enzymes that interact with RBR-type ubiquitin ligases using a liquid-liquid phase separation-based method. J Biol Chem 2022; 299:102822. [PMID: 36563856 PMCID: PMC9860496 DOI: 10.1016/j.jbc.2022.102822] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
RING-between RING (RBR)-type ubiquitin (Ub) ligases (E3s) such as Parkin receive Ub from Ub-conjugating enzymes (E2s) in response to ligase activation. However, the specific E2s that transfer Ub to each RBR-type ligase are largely unknown because of insufficient methods for monitoring their interaction. To address this problem, we have developed a method that detects intracellular interactions between E2s and activated Parkin. Fluorescent homotetramer Azami-Green fused with E2 and oligomeric Ash (Assembly helper) fused with Parkin form a liquid-liquid phase separation (LLPS) in cells only when E2 and Parkin interact. Using this method, we identified multiple E2s interacting with activated Parkin on damaged mitochondria during mitophagy. Combined with in vitro ubiquitination assays and bioinformatics, these findings revealed an underlying consensus sequence for E2 interactions with activated Parkin. Application of this method to other RBR-type E3s including HOIP, HHARI, and TRIAD1 revealed that HOIP forms an LLPS with its substrate NEMO in response to a proinflammatory cytokine and that HHARI and TRIAD1 form a cytosolic LLPS independent of Ub-like protein NEDD8. Since an E2-E3 interaction is a prerequisite for RBR-type E3 activation and subsequent substrate ubiquitination, the method we have established here can be an in-cell tool to elucidate the potentially novel mechanisms involved in RBR-type E3s.
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Affiliation(s)
- Ryota Hayashida
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Reika Kikuchi
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Waka Kojima
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tatsuya Yamada
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Miho Iijima
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Keiji Tanaka
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Koji Yamano
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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Ding H, Wang Y, Cui Y, Chen Z, Li Y, Yang J, Yang Y, Chen T, Xia D, Li C, Xu C, Ding C, Zhao J. Comprehensive analysis of the expression and prognosis for RBR E3 ubiquitin ligases in lung adenocarcinoma. Thorac Cancer 2022; 13:2459-2472. [PMID: 35820682 PMCID: PMC9436683 DOI: 10.1111/1759-7714.14577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/25/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the most common subtype of non‐small cell lung cancer and has a poor prognosis. RBR E3 ubiquitin ligases are a special class of E3 ubiquitin ligases which contain three zinc‐bing domains that catalyze ubiquitin to substrate proteins. The RBR family of E3 ubiquitin ligases has been reported in various human malignancies, but the roles of RBR E3 ubiquitin ligases in LUAD remain unclear. Methods By using TCGA and Kaplan–Meier plotter databases, we examined the expression and prognostic value of RBR E3 ubiquitin ligases. cBioPortal was used to analyze genetic mutations. The STRING database was used to build a protein interactive network. GO, KEGG, and GSEA were performed to investigate the potential biological functions of RBR E3 ubiquitin ligases. Results The expression of ARIH2, RNF144B, RNF216, and RNF217 was significantly related to the clinicopathological parameters and prognosis in LUAD patients. GSEA enrichment result showed ARIH2, RNF144B, RNF216, and RNF217 were all associated with NADH dehydrogenase complex assembly. GO functional enrichment analysis revealed that four RBR E3 ubiquitin ligases and their interactors were most correlated with ubiquitin‐protein transferase activity. KEGG pathway analysis indicated they were associated with cytosolic DNA‐sensing pathway, RIG‐I‐like receptor signaling pathway and NF‐kappa B signaling pathway. Conclusions Our comprehensive bioinformatic analysis revealed that ARIH2, RNF144B, RNF216, and RNF217 may be new prognostic biomarkers and these findings will help to better understand the distinct roles of RBR E3 ubiquitin ligases in LUAD.
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Affiliation(s)
- Hao Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuxin Wang
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, Suzhou, China
| | - Yuan Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhike Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yu Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yang Yang
- Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, School of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Tengfei Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Dian Xia
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Xuzhou Medical University, Xuzhou, China
| | - Chang Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chun Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Cheng Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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Ho SR, Lee YC, Ittmann MM, Lin FT, Chan KS, Lin WC. RNF144A deficiency promotes PD-L1 protein stabilization and carcinogen-induced bladder tumorigenesis. Cancer Lett 2021; 520:344-360. [PMID: 34400221 DOI: 10.1016/j.canlet.2021.08.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/21/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022]
Abstract
RNF144A is a DNA damage-induced E3 ubiquitin ligase that targets proteins involved in genome instability for degradation, e.g., DNA-PKcs and BMI1. RNF144A is frequently mutated or epigenetically silenced in cancer, providing the rationale to evaluate RNF144A loss of function in tumorigenesis. Here we report that RNF144A-deficient mice are more prone to the development of bladder tumors upon carcinogen exposure. In addition to DNA-PKcs and BMI1, we identify the immune checkpoint protein PD-L1 as a novel degradation target of RNF144A, since these proteins are expressed at higher levels in Rnf144a KO tumors. RNF144A interacts with PD-L1 in the plasma membrane and intracellular vesicles and promotes poly-ubiquitination and degradation of PD-L1. Therefore, Rnf144a KO stabilizes PD-L1 and leads to a reduction of tumor-infiltrating CD8+ T cell populations in the BBN-induced bladder tumors. The bladder tumors developed in WT and Rnf144a KO mice primarily express CK5 and CK14, markers of basal cancer subtype, as expected in BBN-induced bladder tumors. Intriguingly, the Rnf144a KO tumors also express GATA3, a marker for the luminal subtype, suggesting that RNF144A loss of function promotes features of cellular differentiation. Such differentiation features in Rnf144a KO tumors likely result from a decrease of EGFR expression, consistent with the reported role of RNF144A in maintaining EGFR expression. In summary, for the first time our study demonstrates the in vivo tumor suppressor activity of RNF144A upon carcinogenic insult. Loss of RNF144A promotes the expression of DNA-PKcs, BMI1 and PD-L1, likely contributing to the carcinogen-induced bladder tumorigenesis.
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Affiliation(s)
- Shiuh-Rong Ho
- Section of Hematology/Oncology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yu-Cheng Lee
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Michael M Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine, Michael E. DeBakey Department of Veterans Affairs Medical Center, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fang-Tsyr Lin
- Section of Hematology/Oncology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Keith Syson Chan
- Department of Pathology and Laboratory Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Weei-Chin Lin
- Section of Hematology/Oncology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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Chain reactions: molecular mechanisms of RBR ubiquitin ligases. Biochem Soc Trans 2021; 48:1737-1750. [PMID: 32677670 PMCID: PMC7458406 DOI: 10.1042/bst20200237] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Ubiquitination is a fundamental post-translational modification that regulates almost all aspects of cellular signalling and is ultimately catalysed by the action of E3 ubiquitin ligases. The RING-between-RING (RBR) family of E3 ligases encompasses 14 distinct human enzymes that are defined by a unique domain organisation and catalytic mechanism. Detailed characterisation of several RBR ligase family members in the last decade has revealed common structural and mechanistic features. At the same time these studies have highlighted critical differences with respect to autoinhibition, activation and catalysis. Importantly, the majority of RBR E3 ligases remain poorly studied, and thus the extent of diversity within the family remains unknown. In this mini-review we outline the current understanding of the RBR E3 mechanism, structure and regulation with a particular focus on recent findings and developments that will shape the field in coming years.
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RNF217 regulates iron homeostasis through its E3 ubiquitin ligase activity by modulating ferroportin degradation. Blood 2021; 138:689-705. [PMID: 33895792 PMCID: PMC8394904 DOI: 10.1182/blood.2020008986] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/24/2021] [Indexed: 12/14/2022] Open
Abstract
RNF217 functions as a novel E3 ubiquitin ligase, mediating the degradation of the iron exporter FPN and regulating iron homeostasis. Rnf217 expression is upregulated by Tet1-mediated demethylation; loss of Tet1 stabilizes FPN and impairs the response to iron overload.
Ferroportin (FPN), the body’s sole iron exporter, is essential for maintaining systemic iron homeostasis. In response to either increased iron or inflammation, hepatocyte-secreted hepcidin binds to FPN, inducing its internalization and subsequent degradation. However, the E3 ubiquitin ligase that underlies FPN degradation has not been identified. Here, we report the identification and characterization of a novel mechanism involving the RNF217-mediated degradation of FPN. A combination of 2 different E3 screens revealed that the Rnf217 gene is a target of Tet1, mediating the ubiquitination and subsequent degradation of FPN. Interestingly, loss of Tet1 expression causes an accumulation of FPN and an impaired response to iron overload, manifested by increased iron accumulation in the liver together with decreased iron in the spleen and duodenum. Moreover, we found that the degradation and ubiquitination of FPN could be attenuated by mutating RNF217. Finally, using 2 conditional knockout mouse lines, we found that knocking out Rnf217 in macrophages increases splenic iron export by stabilizing FPN, whereas knocking out Rnf217 in intestinal cells appears to increase iron absorption. These findings suggest that the Tet1-RNF217-FPN axis regulates iron homeostasis, revealing new therapeutic targets for FPN-related diseases.
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Zhang CJ, Xiang L, Chen XJ, Wang XY, Wu KC, Zhang BW, Chen DF, Jin GH, Zhang H, Chen YC, Liu WQ, Li ML, Ma Y, Jin ZB. Ablation of Mature miR-183 Leads to Retinal Dysfunction in Mice. Invest Ophthalmol Vis Sci 2020; 61:12. [PMID: 32176259 PMCID: PMC7401733 DOI: 10.1167/iovs.61.3.12] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Purpose The microRNA cluster miR-183C, which includes miR-183 and two other genes, is critical for multiple sensory systems. In mouse retina, removal of this cluster results in photoreceptor defects in polarization, phototransduction, and outer segment elongation. However, the individual roles of the three components of this cluster are not clearly known. We studied the separate role of mouse miR-183 in in vivo. Methods miR-183 knockout mice were generated using the CRISPR/Cas9 genome-editing system. Electroretinography were carried out to investigate the changes of retinal structures and function. miR-183 was overexpressed by subretinal adeno-associated virus (AAV) injection in vivo. Rnf217, a target of miR-183 was overexpressed by cell transfection of the photoreceptor-derived cell line 661W in vitro. RNA sequencing and quantitative real-time polymerase chain reaction (qRT-PCR) were performed to compare the gene expression changes in AAV-injected mice and transfected cells. Results The miR-183 knockout mice showed progressively attenuated electroretinogram responses. Over- or under-expression of Rnf217, a direct target of miR-183, misregulated expression of cilia-related BBSome genes. Rnf217 overexpression also led to compromised electroretinography responses in WT mice, indicating that it may contribute to functional abnormalities in miR-183 knockout mice. Conclusions miR-183 is essential for mouse retinal function mediated directly and indirectly through Rnf217 and cilia-related genes. Our findings provide valuable insights into the explanation and analysis of the regulatory role of the individual miR-183 in miR-183C.
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Miyamoto K, Migita K, Saito K. Solution structure of the zinc finger domain of human RNF144A ubiquitin ligase. Protein Sci 2020; 29:1836-1842. [PMID: 32557973 DOI: 10.1002/pro.3903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/12/2020] [Accepted: 06/13/2020] [Indexed: 12/14/2022]
Abstract
RNF144A is involved in protein ubiquitination and functions as an ubiquitin-protein ligase (E3) via its RING finger domain (RNF144A RING). RNF144A is associated with degradation of heat-shock protein family A member 2 (HSPA2), which leads to the suppression of breast cancer cell proliferation. In this study, the solution structure of RNF144A RING was determined using nuclear magnetic resonance. Moreover, using a metallochromic indicator, we spectrophotometrically determined the stoichiometry of zinc ions and elucidated that RNF144A RING binds two zinc atoms. This structural analysis provided the position and range of the active site of RNF144A RING at the atomic level, which contributes to the creation of artificial RING fingers having the specific ubiquitin-conjugating enzyme (E2)-binding capability.
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Affiliation(s)
- Kazuhide Miyamoto
- Department of Pharmaceutical Health Care, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo, Japan
| | - Kaori Migita
- Department of Pharmaceutical Health Care, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo, Japan
| | - Kazuki Saito
- Department of Pharmaceutical Health Care, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo, Japan
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Wang P, Dai X, Jiang W, Li Y, Wei W. RBR E3 ubiquitin ligases in tumorigenesis. Semin Cancer Biol 2020; 67:131-144. [PMID: 32442483 DOI: 10.1016/j.semcancer.2020.05.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/28/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023]
Abstract
RING-in-between-RING (RBR) E3 ligases are one class of E3 ligases that is characterized by the unique RING-HECT hybrid mechanism to function with E2s to transfer ubiquitin to target proteins for degradation. Emerging evidence has demonstrated that RBR E3 ligases play essential roles in neurodegenerative diseases, infection, inflammation and cancer. Accumulated evidence has revealed that RBR E3 ligases exert their biological functions in various types of cancers by modulating the degradation of tumor promoters or suppressors. Hence, we summarize the differential functions of RBR E3 ligases in a variety of human cancers. In general, ARIH1, RNF14, RNF31, RNF144B, RNF216, and RBCK1 exhibit primarily oncogenic roles, whereas ARIH2, PARC and PARK2 mainly have tumor suppressive functions. Moreover, the underlying mechanisms by which different RBR E3 ligases are involved in tumorigenesis and progression are also described. We discuss the further investigation is required to comprehensively understand the critical role of RBR E3 ligases in carcinogenesis. We hope our review can stimulate the researchers to deeper explore the mechanism of RBR E3 ligases-mediated carcinogenesis and to develop useful inhibitors of these oncogenic E3 ligases for cancer therapy.
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Affiliation(s)
- Peter Wang
- School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Xiaoming Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA, USA
| | - Wenxiao Jiang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Yuyun Li
- School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA, USA.
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Xing G, Jing H, Zhang L, Cao Y, Li L, Zhao K, Dong Z, Chen W, Wang H, Cao R, Xiong WC, Mei L. A mechanism in agrin signaling revealed by a prevalent Rapsyn mutation in congenital myasthenic syndrome. eLife 2019; 8:e49180. [PMID: 31549961 PMCID: PMC6779466 DOI: 10.7554/elife.49180] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Neuromuscular junction is a synapse between motoneurons and skeletal muscles, where acetylcholine receptors (AChRs) are concentrated to control muscle contraction. Studies of this synapse have contributed to our understanding of synapse assembly and pathological mechanisms of neuromuscular disorders. Nevertheless, underlying mechanisms of NMJ formation was not well understood. To this end, we took a novel approach - studying mutant genes implicated in congenital myasthenic syndrome (CMS). We showed that knock-in mice carrying N88K, a prevalent CMS mutation of Rapsyn (Rapsn), died soon after birth with profound NMJ deficits. Rapsn is an adapter protein that bridges AChRs to the cytoskeleton and possesses E3 ligase activity. In investigating how N88K impairs the NMJ, we uncovered a novel signaling pathway by which Agrin-LRP4-MuSK induces tyrosine phosphorylation of Rapsn, which is required for its self-association and E3 ligase activity. Our results also provide insight into pathological mechanisms of CMS.
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Affiliation(s)
- Guanglin Xing
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Hongyang Jing
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Lei Zhang
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Yu Cao
- Department of Neuroscience and Regenerative MedicineAugusta UniversityAugustaUnited States
| | - Lei Li
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Kai Zhao
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
- Department of Neuroscience and Regenerative MedicineAugusta UniversityAugustaUnited States
| | - Zhaoqi Dong
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Wenbing Chen
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Hongsheng Wang
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Rangjuan Cao
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Wen-Cheng Xiong
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
- Louis Stokes Cleveland Veterans Affairs Medical CenterClevelandUnited States
| | - Lin Mei
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
- Louis Stokes Cleveland Veterans Affairs Medical CenterClevelandUnited States
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12
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RNF144A functions as a tumor suppressor in breast cancer through ubiquitin ligase activity-dependent regulation of stability and oncogenic functions of HSPA2. Cell Death Differ 2019; 27:1105-1118. [PMID: 31406303 DOI: 10.1038/s41418-019-0400-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/19/2019] [Accepted: 07/22/2019] [Indexed: 01/27/2023] Open
Abstract
Deregulation of E3 ubiquitin ligases is intimately implicated in breast cancer pathogenesis and progression, but the underlying mechanisms still remain elusive. Here we report that RING finger protein 144A (RNF144A), a poorly characterized member of the RING-in-between-RING family of E3 ubiquitin ligases, functions as a tumor suppressor in breast cancer. RNF144A was downregulated in a subset of primary breast tumors and restoration of RNF144A suppressed breast cancer cell proliferation, colony formation, migration, invasion in vitro, tumor growth, and lung metastasis in vivo. In contrast, knockdown of RNF144A promoted malignant phenotypes of breast cancer cells. Quantitative proteomics and biochemical analysis revealed that RNF144A interacted with and targeted heat-shock protein family A member 2 (HSPA2), a putative oncoprotein that is frequently upregulated in human cancer and promotes tumor growth and progression, for ubiquitination and degradation. Notably, the ligase activity-defective mutants of RNF144A impaired its ability to induce ubiquitination and degradation of HSPA2, and to suppress breast cancer cell proliferation, migration, and invasion as compared with its wild-type counterpart. Moreover, RNF144A-mediated suppression of breast cancer cell proliferation, migration, and invasion was rescued by ectopic HSPA2 expression. Clinically, low RNF144A and high HSPA2 expression in breast cancer patients was correlated with aggressive clinicopathological characteristics and decreased overall and disease-free survival. Collectively, these findings reveal a previously unappreciated role for RNF144A in suppression of breast cancer growth and metastasis, and identify RNF144A as the first, to our knowledge, E3 ubiquitin ligase for HSPA2 in human cancer.
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13
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Luo L, Zhu D, Huang R, Xiong L, Mehjabin R, He L, Liao L, Li Y, Zhu Z, Wang Y. Molecular cloning and preliminary functional analysis of six RING-between-ring (RBR) genes in grass carp (Ctenopharyngodon idellus). FISH & SHELLFISH IMMUNOLOGY 2019; 87:62-72. [PMID: 30610929 DOI: 10.1016/j.fsi.2018.12.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/18/2018] [Accepted: 12/31/2018] [Indexed: 06/09/2023]
Abstract
Ubiquitination is a post-translational modification of proteins that is widely present in eukaryotic cells. There is increasing evidence that ubiquitinated proteins play crucial roles in the immune response process. In mammals, RING-between-RING (RBR) proteins play a key role in regulating immune signaling as the important E3 ubiquitin ligases during ubiquitination. However, the function of RBR in fish is still unclear. In the present study, six RBR genes (RNF19A, RNF19B, RNF144AA, RNF144AB, RNF144B and RNF217) of grass carp (Ctenopharyngodon idellus) were cloned and characterized. Similar to mammals, all six members of RBR family contained RING, in-between-ring (IBR) and transmembrane (TM) domains. These genes were constitutively expressed in all studied tissues, but the relative expression level differed. Following grass carp reovirus(GCRV) infection, the expression of six RBR genes in liver, gill, spleen and intestine significantly altered. Additionally, their expression in Ctenopharyngodon idellus kidney (CIK) cells was significantly increased after GCRV infection. And deficiency of RNF144B in CIK with small interference RNA (siRNA) up-regulated polyinosinic:polycytidylic acid poly(I:C))-induced inflammatory cytokines production, including IFN-I, TNF-α, IL-6, and transcription factor IRF3, which demonstrated that RNF144B was a negative regulator of inflammatory cytokines. Our results suggested that the RBR might play a vital role in regulating immune signaling and laid the foundation for the further mechanism research of RBR in fishes.
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Affiliation(s)
- Lifei Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Denghui Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rong Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lv Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rumana Mehjabin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Libo He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lanjie Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yongming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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14
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Ho SR, Lin WC. RNF144A sustains EGFR signaling to promote EGF-dependent cell proliferation. J Biol Chem 2018; 293:16307-16323. [PMID: 30171075 DOI: 10.1074/jbc.ra118.002887] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/01/2018] [Indexed: 11/06/2022] Open
Abstract
RNF144A is a single-pass transmembrane RBR E3 ligase that interacts with and degrades cytoplasmic DNA-PKcs, which is an epidermal growth factor receptor (EGFR)-interacting partner. Interestingly, RNF144A expression is positively correlated with EGFR mRNA and protein levels in several types of cancer. However, the relationship between RNF144A and EGFR is poorly understood. This study reports an unexpected role for RNF144A in the regulation of EGF/EGFR signaling and EGF-dependent cell proliferation. EGFR ligands, but not DNA-damaging agents, induce a DNA-PKcs-independent interaction between RNF144A and EGFR. RNF144A promotes EGFR ubiquitination, maintains EGFR protein, and prolongs EGF/EGFR signaling during EGF stimulation. Moreover, depletion of RNF144A by multiple independent approaches results in a decrease in EGFR expression and EGF/EGFR signaling. RNF144A knockout cells also fail to mount an immediate response to EGF for activation of G1/S progression genes. Consequently, depletion of RNF144A reduces EGF-dependent cell proliferation. These defects may be at least in part due to a role for RNF144A in regulating EGFR transport in the intracellular vesicles during EGF treatment.
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Affiliation(s)
- Shiuh-Rong Ho
- From the Section of Hematology/Oncology, Department of Medicine
| | - Weei-Chin Lin
- From the Section of Hematology/Oncology, Department of Medicine, .,the Department of Molecular and Cellular Biology, and.,the Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030
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15
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Mechanism of parkin activation by phosphorylation. Nat Struct Mol Biol 2018; 25:623-630. [PMID: 29967542 DOI: 10.1038/s41594-018-0088-7] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 06/12/2018] [Indexed: 12/25/2022]
Abstract
Mutations in the ubiquitin ligase parkin are responsible for a familial form of Parkinson's disease. Parkin and the PINK1 kinase regulate a quality-control system for mitochondria. PINK1 phosphorylates ubiquitin on the outer membrane of damaged mitochondria, thus leading to recruitment and activation of parkin via phosphorylation of its ubiquitin-like (Ubl) domain. Here, we describe the mechanism of parkin activation by phosphorylation. The crystal structure of phosphorylated Bactrocera dorsalis (oriental fruit fly) parkin in complex with phosphorylated ubiquitin and an E2 ubiquitin-conjugating enzyme reveals that the key activating step is movement of the Ubl domain and release of the catalytic RING2 domain. Hydrogen/deuterium exchange and NMR experiments with the various intermediates in the activation pathway confirm and extend the interpretation of the crystal structure to mammalian parkin. Our results rationalize previously unexplained Parkinson's disease mutations and the presence of internal linkers that allow large domain movements in parkin.
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16
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Walden H, Rittinger K. RBR ligase-mediated ubiquitin transfer: a tale with many twists and turns. Nat Struct Mol Biol 2018; 25:440-445. [PMID: 29735995 DOI: 10.1038/s41594-018-0063-3] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/29/2018] [Indexed: 12/28/2022]
Abstract
RBR ligases are an enigmatic class of E3 ubiquitin ligases that combine properties of RING and HECT-type E3s and undergo multilevel regulation through autoinhibition, post-translational modifications, multimerization and interaction with binding partners. Here, we summarize recent progress in RBR structures and function, which has uncovered commonalities in the mechanisms by which different family members transfer ubiquitin through a multistep process. However, these studies have also highlighted clear differences in the activity of different family members, suggesting that each RBR ligase has evolved specific properties to fit the biological process it regulates.
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Affiliation(s)
- Helen Walden
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, Scotland, UK.
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK.
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17
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RBR-type E3 ubiquitin ligase RNF144A targets PARP1 for ubiquitin-dependent degradation and regulates PARP inhibitor sensitivity in breast cancer cells. Oncotarget 2017; 8:94505-94518. [PMID: 29212245 PMCID: PMC5706891 DOI: 10.18632/oncotarget.21784] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/23/2017] [Indexed: 01/06/2023] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1), a critical DNA repair protein, is frequently upregulated in breast tumors with a key role in breast cancer progression. Consequently, PARP inhibitors have emerged as promising therapeutics for breast cancers with DNA repair deficiencies. However, relatively little is known about the regulatory mechanism of PARP1 expression and the determinants of PARP inhibitor sensitivity in breast cancer cells. Here, we report that ring finger protein 144A (RNF144A), a RING-between-RING (RBR)-type E3 ubiquitin ligase with an unexplored functional role in human cancers, interacts with PARP1 through its carboxy-terminal region containing the transmembrane domain, and targets PARP1 for ubiquitination and subsequent proteasomal degradation. Moreover, induced expression of RNF144A decreases PARP1 protein levels and renders breast cancer cells resistant to the clinical-grade PARP inhibitor olaparib. Conversely, knockdown of endogenous RNF144A increases PARP1 protein levels and enhances cellular sensitivity to olaparib. Together, these findings define RNF144A as a novel regulator of PARP1 protein abundance and a potential determinant of PARP inhibitor sensitivity in breast cancer cells, which may eventually guide the optimal use of PARP inhibitors in the clinic.
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18
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Dove KK, Klevit RE. RING-Between-RING E3 Ligases: Emerging Themes amid the Variations. J Mol Biol 2017; 429:3363-3375. [PMID: 28827147 DOI: 10.1016/j.jmb.2017.08.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 11/30/2022]
Abstract
Covalent, reversible, post-translational modification of cellular proteins with the small modifier, ubiquitin (Ub), regulates virtually every known cellular process in eukaryotes. The process is carried out by a trio of enzymes: a Ub-activating (E1) enzyme, a Ub-conjugating (E2) enzyme, and a Ub ligase (E3) enzyme. RING-in-Between-RING (RBR) E3s constitute one of three classes of E3 ligases and are defined by a RING-HECT-hybrid mechanism that utilizes a E2-binding RING domain and a second domain (called RING2) that contains an active site Cys required for the formation of an obligatory E3~Ub intermediate. Albeit a small class, RBR E3s in humans regulate diverse cellular process. This review focuses on non-Parkin members such as HOIP/HOIL-1L (the only E3s known to generate linear Ub chains), HHARI and TRIAD1, both of which have been recently demonstrated to work together with Cullin RING E3 ligases. We provide a brief historical background and highlight, summarize, and discuss recent developments in the young field of RBR E3s. Insights reviewed here include new understandings of the RBR Ub-transfer mechanism, specifically the role of RING1 and various Ub-binding sites, brief structural comparisons among members, and different modes of auto-inhibition and activation.
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Affiliation(s)
- Katja K Dove
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA, United States.
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19
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Park S, Foote PK, Krist DT, Rice SE, Statsyuk AV. UbMES and UbFluor: Novel probes for ring-between-ring (RBR) E3 ubiquitin ligase PARKIN. J Biol Chem 2017; 292:16539-16553. [PMID: 28710279 DOI: 10.1074/jbc.m116.773200] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 07/03/2017] [Indexed: 12/30/2022] Open
Abstract
Ring-between-ring (RBR) E3 ligases have been implicated in autoimmune disorders and neurodegenerative diseases. The functions of many RBR E3s are poorly defined, and their regulation is complex, involving post-translational modifications and allosteric regulation with other protein partners. The functional complexity of RBRs, coupled with the complexity of the native ubiquitination reaction that requires ATP and E1 and E2 enzymes, makes it difficult to study these ligases for basic research and therapeutic purposes. To address this challenge, we developed novel chemical probes, ubiquitin C-terminal fluorescein thioesters UbMES and UbFluor, to qualitatively and quantitatively assess the activity of the RBR E3 ligase PARKIN in a simple experimental setup and in real time using fluorescence polarization. First, we confirmed that PARKIN does not require an E2 enzyme for substrate ubiquitination, lysine selection, and polyubiquitin chain formation. Second, we confirmed that UbFluor quantitatively detects naturally occurring activation states of PARKIN caused by Ser65 phosphorylation (pPARKIN) and phosphorylated ubiquitin (pUb). Third, we showed that both pUb and the ubiquitin-accepting substrate contribute to maximal pPARKIN ubiquitin conjugation turnover. pUb enhances the transthiolation step, whereas the substrate clears the pPARKIN∼Ub thioester intermediate. Finally, we established that UbFluor can quantify activation or inhibition of PARKIN by structural mutations. These results demonstrate the feasibility of using UbFluor for quantitative studies of the biochemistry of RBR E3s and for high-throughput screening of small-molecule activators or inhibitors of PARKIN and other RBR E3 ligases.
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Affiliation(s)
- Sungjin Park
- From the Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois 60611
| | - Peter K Foote
- the Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and
| | - David T Krist
- the Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and
| | - Sarah E Rice
- From the Department of Cell and Molecular Biology, Northwestern University, Chicago, Illinois 60611
| | - Alexander V Statsyuk
- the Chemistry of Life Processes Institute, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, and .,the Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas 77204-5037
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