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Zenge C, Ordureau A. Ubiquitin system mutations in neurological diseases. Trends Biochem Sci 2024:S0968-0004(24)00154-3. [PMID: 38972780 DOI: 10.1016/j.tibs.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/31/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024]
Abstract
Neuronal ubiquitin balance impacts the fate of countless cellular proteins, and its disruption is associated with various neurological disorders. The ubiquitin system is critical for proper neuronal cell state transitions and the clearance of misfolded or aggregated proteins that threaten cellular integrity. This article reviews the state of and recent advancements in our understanding of the disruptions to components of the ubiquitin system, in particular E3 ligases and deubiquitylases, in neurodevelopmental and neurodegenerative diseases. Specific focus is on enzymes with recent progress in their characterization, including identifying enzyme-substrate pairs, the use of stem cell and animal models, and the development of therapeutics for ubiquitin-related diseases.
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Affiliation(s)
- Colin Zenge
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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2
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Gao H, Chen Z, Zhao L, Ji C, Xing F. Cellular functions, molecular signalings and therapeutic applications: Translational potential of deubiquitylating enzyme USP9X as a drug target in cancer treatment. Biochim Biophys Acta Rev Cancer 2024; 1879:189099. [PMID: 38582329 DOI: 10.1016/j.bbcan.2024.189099] [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: 08/29/2023] [Revised: 11/13/2023] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
Protein ubiquitination, one of the most significant post-translational modifications, plays an important role in controlling the proteins activity in diverse cellular processes. The reversible process of protein ubiquitination, known as deubiquitination, has emerged as a critical mechanism for maintaining cellular homeostasis. The deubiquitinases (DUBs), which participate in deubiquitination process are increasingly recognized as potential candidates for drug discovery. Among these DUBs, ubiquitin-specific protease 9× (USP9X), a highly conserved member of the USP family, exhibits versatile functions in various cellular processes, including the regulation of cell cycle, protein endocytosis, apoptosis, cell polarity, immunological microenvironment, and stem cell characteristics. The dysregulation and abnormal activities of USP9X are influenced by intricate cellular signaling pathway crosstalk and upstream non-coding RNAs. The complex expression patterns and controversial clinical significance of USP9X in cancers suggest its potential as a prognostic biomarker. Furthermore, USP9X inhibitors has shown promising antitumor activity and holds the potential to overcome therapeutic resistance in preclinical models. However, a comprehensive summary of the role and molecular functions of USP9X in cancer progression is currently lacking. In this review, we provide a comprehensive delineation of USP9X participation in numerous critical cellular processes, complicated signaling pathways within the tumor microenvironment, and its potential translational applications to combat therapeutic resistance. By systematically summarizing the updated molecular mechanisms of USP9X in cancer biology, this review aims to contribute to the advancement of cancer therapeutics and provide essential insights for specialists and clinicians in the development of improved cancer treatment strategies.
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Affiliation(s)
- Hongli Gao
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Zhiguang Chen
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Liang Zhao
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Ce Ji
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China.
| | - Fei Xing
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang 110004, China.
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3
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Hinterndorfer K, Laporte MH, Mikus F, Tafur L, Bourgoint C, Prouteau M, Dey G, Loewith R, Guichard P, Hamel V. Ultrastructure expansion microscopy reveals the cellular architecture of budding and fission yeast. J Cell Sci 2022; 135:286062. [PMID: 36524422 PMCID: PMC10112979 DOI: 10.1242/jcs.260240] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
ABSTRACT
The budding and fission yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have served as invaluable model organisms to study conserved fundamental cellular processes. Although super-resolution microscopy has in recent years paved the way to a better understanding of the spatial organization of molecules in cells, its wide use in yeasts has remained limited due to the specific know-how and instrumentation required, contrasted with the relative ease of endogenous tagging and live-cell fluorescence microscopy. To facilitate super-resolution microscopy in yeasts, we have extended the ultrastructure expansion microscopy (U-ExM) method to both S. cerevisiae and S. pombe, enabling a 4-fold isotropic expansion. We demonstrate that U-ExM allows imaging of the microtubule cytoskeleton and its associated spindle pole body, notably unveiling the Sfi1p–Cdc31p spatial organization on the appendage bridge structure. In S. pombe, we validate the method by monitoring the homeostatic regulation of nuclear pore complex number through the cell cycle. Combined with NHS-ester pan-labelling, which provides a global cellular context, U-ExM reveals the subcellular organization of these two yeast models and provides a powerful new method to augment the already extensive yeast toolbox.
This article has an associated First Person interview with Kerstin Hinterndorfer and Felix Mikus, two of the joint first authors of the paper.
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Affiliation(s)
- Kerstin Hinterndorfer
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Marine H. Laporte
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Felix Mikus
- European Molecular Biology Laboratory 2 Cell Biology and Biophysics , , Heidelberg , Germany
| | - Lucas Tafur
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Clélia Bourgoint
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Manoel Prouteau
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Gautam Dey
- European Molecular Biology Laboratory 2 Cell Biology and Biophysics , , Heidelberg , Germany
| | - Robbie Loewith
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Paul Guichard
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
| | - Virginie Hamel
- University of Geneva 1 Department of Molecular and Cellular Biology , , Geneva , Switzerland
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Elu N, Osinalde N, Ramirez J, Presa N, Rodriguez JA, Prieto G, Mayor U. Identification of substrates for human deubiquitinating enzymes (DUBs): An up-to-date review and a case study for neurodevelopmental disorders. Semin Cell Dev Biol 2022; 132:120-131. [PMID: 35042675 DOI: 10.1016/j.semcdb.2022.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 12/15/2022]
Abstract
Similar to the reversal of kinase-mediated protein phosphorylation by phosphatases, deubiquitinating enzymes (DUBs) oppose the action of E3 ubiquitin ligases and reverse the ubiquitination of proteins. A total of 99 human DUBs, classified in 7 families, allow in this way for a precise control of cellular function and homeostasis. Ubiquitination regulates a myriad of cellular processes, and is altered in many pathological conditions. Thus, ubiquitination-regulating enzymes are increasingly regarded as potential candidates for therapeutic intervention. In this context, given the predicted easier pharmacological control of DUBs relative to E3 ligases, a significant effort is now being directed to better understand the processes and substrates regulated by each DUB. Classical studies have identified specific DUB substrate candidates by traditional molecular biology techniques in a case-by-case manner. Lately, single experiments can identify thousands of ubiquitinated proteins at a specific cellular context and narrow down which of those are regulated by a given DUB, thanks to the development of new strategies to isolate and enrich ubiquitinated material and to improvements in mass spectrometry detection capabilities. Here we present an overview of both types of studies, discussing the criteria that, in our view, need to be fulfilled for a protein to be considered as a high-confidence substrate of a given DUB. Applying these criteria, we have manually reviewed the relevant literature currently available in a systematic manner, and identified 650 high-confidence substrates of human DUBs. We make this information easily accessible to the research community through an updated version of the DUBase website (https://ehubio.ehu.eus/dubase/). Finally, in order to illustrate how this information can contribute to a better understanding of the physiopathological role of DUBs, we place a special emphasis on a subset of these enzymes that have been associated with neurodevelopmental disorders.
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Affiliation(s)
- Nagore Elu
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, UPV/EHU, Vitoria-Gasteiz 01006, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Natalia Presa
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Gorka Prieto
- Department of Communications Engineering, University of the Basque Country (UPV/EHU), Bilbao 48013, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain; Ikerbasque, Basque Foundation for Science, Bilbao 48013, Spain.
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5
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Laporte MH, Bouhlel IB, Bertiaux E, Morrison CG, Giroud A, Borgers S, Azimzadeh J, Bornens M, Guichard P, Paoletti A, Hamel V. Human SFI1 and Centrin form a complex critical for centriole architecture and ciliogenesis. EMBO J 2022; 41:e112107. [PMID: 36125182 DOI: 10.15252/embj.2022112107] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2022] Open
Abstract
Over the course of evolution, the centrosome function has been conserved in most eukaryotes, but its core architecture has evolved differently in some clades, with the presence of centrioles in humans and a spindle pole body (SPB) in yeast. Similarly, the composition of these two core elements has diverged, with the exception of Centrin and SFI1, which form a complex in yeast to initiate SPB duplication. However, it remains unclear whether this complex exists at centrioles and whether its function has been conserved. Here, using expansion microscopy, we demonstrate that human SFI1 is a centriolar protein that associates with a pool of Centrin at the distal end of the centriole. We also find that both proteins are recruited early during procentriole assembly and that depletion of SFI1 results in the loss of the distal pool of Centrin, without altering centriole duplication. Instead, we show that SFI1/Centrin complex is essential for centriolar architecture, CEP164 distribution, and CP110 removal during ciliogenesis. Together, our work reveals a conserved SFI1/Centrin module displaying divergent functions between mammals and yeast.
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Affiliation(s)
- Marine H Laporte
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Imène B Bouhlel
- Institut Curie, UMR 144, CNRS, PSL University, Paris, France
| | - Eloïse Bertiaux
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Ciaran G Morrison
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.,Centre for Chromosome Biology, School of Biological and Chemical Sciences, National University of Ireland Galway, Galway, Ireland
| | - Alexia Giroud
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Susanne Borgers
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | | | - Michel Bornens
- Institut Curie, UMR 144, CNRS, PSL University, Paris, France
| | - Paul Guichard
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Anne Paoletti
- Institut Curie, UMR 144, CNRS, PSL University, Paris, France
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
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6
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Conformational Plasticity of Centrin 1 from Toxoplasma gondii in Binding to the Centrosomal Protein SFI1. Biomolecules 2022; 12:biom12081115. [PMID: 36009009 PMCID: PMC9406199 DOI: 10.3390/biom12081115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 12/01/2022] Open
Abstract
Centrins are calcium (Ca2+)-binding proteins that are involved in many cellular functions including centrosome regulation. A known cellular target of centrins is SFI1, a large centrosomal protein containing multiple repeats that represent centrin-binding motifs. Recently, a protein homologous to yeast and mammalian SFI1, denominated TgSFI1, which shares SFI1-repeat organization, was shown to colocalize at centrosomes with centrin 1 from Toxoplasma gondii (TgCEN1). However, the molecular details of the interaction between TgCEN1 and TgSFI1 remain largely unknown. Herein, combining different biophysical methods, including isothermal titration calorimetry, nuclear magnetic resonance, circular dichroism, and fluorescence spectroscopy, we determined the binding properties of TgCEN1 and its individual N- and C-terminal domains to synthetic peptides derived from distinct repeats of TgSFI1. Overall, our data indicate that the repeats in TgSFI1 constitute binding sites for TgCEN1, but the binding modes of TgCEN1 to the repeats differ appreciably in terms of binding affinity, Ca2+ sensitivity, and lobe-specific interaction. These results suggest that TgCEN1 displays remarkable conformational plasticity, allowing for the distinct repeats in TgSFI1 to possess precise modes of TgCEN1 binding and regulation during Ca2+ sensing, which appears to be crucial for the dynamic association of TgCEN1 with TgSFI1 in the centrosome architecture.
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7
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Tkach JM, Philip R, Sharma A, Strecker J, Durocher D, Pelletier L. Global cellular response to chemical perturbation of PLK4 activity and abnormal centrosome number. eLife 2022; 11:73944. [PMID: 35758262 PMCID: PMC9236612 DOI: 10.7554/elife.73944] [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: 09/16/2021] [Accepted: 06/04/2022] [Indexed: 11/13/2022] Open
Abstract
Centrosomes act as the main microtubule organizing center (MTOC) in metazoans. Centrosome number is tightly regulated by limiting centriole duplication to a single round per cell cycle. This control is achieved by multiple mechanisms, including the regulation of the protein kinase PLK4, the most upstream facilitator of centriole duplication. Altered centrosome numbers in mouse and human cells cause p53-dependent growth arrest through poorly defined mechanisms. Recent work has shown that the E3 ligase TRIM37 is required for cell cycle arrest in acentrosomal cells. To gain additional insights into this process, we undertook a series of genome-wide CRISPR/Cas9 screens to identify factors important for growth arrest triggered by treatment with centrinone B, a selective PLK4 inhibitor. We found that TRIM37 is a key mediator of growth arrest after partial or full PLK4 inhibition. Interestingly, PLK4 cellular mobility decreased in a dose-dependent manner after centrinone B treatment. In contrast to recent work, we found that growth arrest after PLK4 inhibition correlated better with PLK4 activity than with mitotic length or centrosome number. These data provide insights into the global response to changes in centrosome number and PLK4 activity and extend the role for TRIM37 in regulating the abundance, localization, and function of centrosome proteins.
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Affiliation(s)
- Johnny M Tkach
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Reuben Philip
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Amit Sharma
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Jonathan Strecker
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
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8
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Jiang H, Wang C, Hou Z, Wang Y, Qiao J, Li H. Case report: NUT carcinoma with MXI1::NUTM1 fusion characterized by abdominopelvic lesions and ovarian masses in a middle-aged female. Front Oncol 2022; 12:1091877. [PMID: 36741693 PMCID: PMC9890191 DOI: 10.3389/fonc.2022.1091877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/08/2022] [Indexed: 01/13/2023] Open
Abstract
Background Nuclear protein of the testis (NUT) carcinoma is a rare subset of poorly differentiated, highly aggressive malignancy defined by NUTM1 gene rearrangements. Only three NUT cases of probable ovarian origin have been reported. Case presentation We report a case of NUT carcinoma in a 53-year-old female who presented with extensive abdominopelvic lesions and bilateral ovarian masses suggestive of advanced ovarian cancer. This patient was admitted to our hospital due to abdominal pain and distension for over two months. Imaging examinations suggested a possible malignancy of bilateral adnexal origin. This patient first underwent diagnostic laparoscopy. After receiving neoadjuvant chemotherapy, she underwent cytoreductive surgery. Surgical pathology showed infiltration of monotonous round tumor cells with no apparent differentiation characteristics. Immunohistochemistry (IHC) revealed nuclear expression of the NUT protein. And MXI1::NUTM1 fusion was identified by next-generation sequencing (NGS). Herein, we introduce an unusual NUT carcinoma and describe the clinical, imaging, and pathological features. In addition, we briefly reviewed the published literature and discussed the possibility of primary gynecological NUT carcinoma. Conclusions Identifying a NUT carcinoma arising from the abdominopelvic cavity is essential, and we underscore the need for NUT testing in undifferentiated malignant neoplasms that appear in this clinical setting. Although it is unclear from which origin this tumor arose, proper classification is essential for treatment planning.
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Affiliation(s)
- Huahua Jiang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Chao Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Zheng Hou
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yuxiang Wang
- Department of Pathology, School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, China
| | - Jie Qiao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Huajun Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
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9
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Lai MC, Chen YP, Li DA, Yu JS, Hung HY, Tarn WY. DDX3 interacts with USP9X and participates in deubiquitination of the anti-apoptotic protein MCL1. FEBS J 2021; 289:1043-1061. [PMID: 34606682 DOI: 10.1111/febs.16219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 08/26/2021] [Accepted: 10/01/2021] [Indexed: 01/19/2023]
Abstract
Here, we describe a novel interaction between the RNA helicase DDX3 and the deubiquitinase ubiquitin-specific peptidase 9 X-linked (USP9X) in human cells. Domain mapping studies reveal that the C-terminal region of DDX3 interacted with the N terminus of USP9X. USP9X was predominantly localized in the cytoplasm where the interaction between DDX3 and USP9X occurred. USP9X was not visibly enriched in cytoplasmic stress granules (SGs) under oxidative stress conditions, whereas overexpression of GFP-DDX3 induced SG formation and recruited USP9X to SGs in HeLa cells. Luciferase reporter assays showed that depletion of USP9X had no significant effect on DDX3-mediated translation. Given that DDX3 is not ubiquitinated upon ubiquitin overexpression, it is unlikely that DDX3 serves as a substrate of USP9X. Importantly, we found that ubiquitinated MCL1 was accumulated upon depletion of USP9X and/or DDX3 in MG132-treated cells, suggesting that USP9X and DDX3 play a role in regulating MCL1 protein stability and anti-apoptotic function. This study indicates that DDX3 exerts anti-apoptotic effects probably by coordinating with USP9X in promoting MCL1 deubiquitination.
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Affiliation(s)
- Ming-Chih Lai
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Department of Colorectal Surgery, New Taipei Municipal Tucheng Hospital, Taiwan
| | - Yi-Pin Chen
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Ding-An Li
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-Yuan Hung
- Department of Colorectal Surgery, New Taipei Municipal Tucheng Hospital, Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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10
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Nickson CM, Fabbrizi MR, Carter RJ, Hughes JR, Kacperek A, Hill MA, Parsons JL. USP9X Is Required to Maintain Cell Survival in Response to High-LET Radiation. Front Oncol 2021; 11:671431. [PMID: 34277417 PMCID: PMC8281306 DOI: 10.3389/fonc.2021.671431] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/15/2021] [Indexed: 12/26/2022] Open
Abstract
Ionizing radiation (IR) principally acts through induction of DNA damage that promotes cell death, although the biological effects of IR are more broad ranging. In fact, the impact of IR of higher-linear energy transfer (LET) on cell biology is generally not well understood. Critically, therefore, the cellular enzymes and mechanisms responsible for enhancing cell survival following high-LET IR are unclear. To this effect, we have recently performed siRNA screening to identify deubiquitylating enzymes that control cell survival specifically in response to high-LET α-particles and protons, in comparison to low-LET X-rays and protons. From this screening, we have now thoroughly validated that depletion of the ubiquitin-specific protease 9X (USP9X) in HeLa and oropharyngeal squamous cell carcinoma (UMSCC74A) cells using small interfering RNA (siRNA), leads to significantly decreased survival of cells after high-LET radiation. We consequently investigated the mechanism through which this occurs, and demonstrate that an absence of USP9X has no impact on DNA damage repair post-irradiation nor on apoptosis, autophagy, or senescence. We discovered that USP9X is required to stabilize key proteins (CEP55 and CEP131) involved in centrosome and cilia formation and plays an important role in controlling pericentrin-rich foci, particularly in response to high-LET protons. This was also confirmed directly by demonstrating that depletion of CEP55/CEP131 led to both enhanced radiosensitivity of cells to high-LET protons and amplification of pericentrin-rich foci. Our evidence supports the importance of USP9X in maintaining centrosome function and biogenesis and which is crucial particularly in the cellular response to high-LET radiation.
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Affiliation(s)
- Catherine M. Nickson
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Maria Rita Fabbrizi
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Rachel J. Carter
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Jonathan R. Hughes
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Andrzej Kacperek
- Clatterbridge Cancer Centre NHS Foundation Trust, Bebington, United Kingdom
| | - Mark A. Hill
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Gray Laboratories, Oxford, United Kingdom
| | - Jason L. Parsons
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
- Clatterbridge Cancer Centre NHS Foundation Trust, Bebington, United Kingdom
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11
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Liao Y, Shao Z, Liu Y, Xia X, Deng Y, Yu C, Sun W, Kong W, He X, Liu F, Guo Z, Chen G, Tang D, Gan H, Liu J, Huang H. USP1-dependent RPS16 protein stability drives growth and metastasis of human hepatocellular carcinoma cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:201. [PMID: 34154657 PMCID: PMC8215741 DOI: 10.1186/s13046-021-02008-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/07/2021] [Indexed: 02/08/2023]
Abstract
Background Hepatocellular carcinoma (HCC) remains a medical challenge due to its high proliferation and metastasis. Although deubiquitinating enzymes (DUBs) play a key role in regulating protein degradation, their pathological roles in HCC have not been fully elucidated. Methods By using biomass spectrometry, co-immunoprecipitation, western blotting and immunofluorescence assays, we identify ribosomal protein S16 (RPS16) as a key substrate of ubiquitin-specific peptidase 1 (USP1). The role of USP1-RPS16 axis in the progression of HCC was evaluated in cell cultures, in xenograft mouse models, and in clinical observations. Results We show that USP1 interacts with RPS16. The depletion of USP1 increases the level of K48-linked ubiquitinated-RPS16, leading to proteasome-dependent RPS16 degradation. In contrast, overexpression of USP1-WT instead of USP1-C90A (DUB inactivation mutant) reduces the level of K48-linked ubiquitinated RPS16, thereby stabilizing RPS16. Consequently, USP1 depletion mimics RPS16 deficiency with respect to the inhibition of growth and metastasis, whereas transfection-enforced re-expression of RPS16 restores oncogenic-like activity in USP1-deficient HCC cells. Importantly, the high expression of USP1 and RPS16 in liver tissue is a prognostic factor for poor survival of HCC patients. Conclusions These findings reveal a previously unrecognized role for the activation of USP1-RPS16 pathway in driving HCC, which may be further developed as a novel strategy for cancer treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02008-3.
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Affiliation(s)
- Yuning Liao
- Institute of Digestive Disease of Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, 511500, Qingyuan, Guangdong, China.,Affiliated Cancer Hospital & institute of Guangzhou Medical University,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, Guangdong, China
| | - Zhenlong Shao
- Affiliated Cancer Hospital & institute of Guangzhou Medical University,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, Guangdong, China
| | - Yuan Liu
- Affiliated Cancer Hospital & institute of Guangzhou Medical University,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, Guangdong, China
| | - Xiaohong Xia
- Affiliated Cancer Hospital & institute of Guangzhou Medical University,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, Guangdong, China
| | - Yuanfei Deng
- Department of Pathology, First People's Hospital of Foshan, 528000, Foshan, Guangdong, China
| | - Cuifu Yu
- Affiliated Cancer Hospital & institute of Guangzhou Medical University,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, Guangdong, China
| | - Wenshuang Sun
- Affiliated Cancer Hospital & institute of Guangzhou Medical University,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, Guangdong, China
| | - Weiyao Kong
- Affiliated Cancer Hospital & institute of Guangzhou Medical University,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, Guangdong, China
| | - Xiaoyue He
- Affiliated Cancer Hospital & institute of Guangzhou Medical University,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, Guangdong, China
| | - Fang Liu
- Department of Pathology, First People's Hospital of Foshan, 528000, Foshan, Guangdong, China
| | - Zhiqiang Guo
- Institute of Digestive Disease of Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, 511500, Qingyuan, Guangdong, China
| | - Guoxing Chen
- Institute of Digestive Disease of Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, 511500, Qingyuan, Guangdong, China
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, 75390, Dallas, Texas, USA
| | - Huoye Gan
- Institute of Digestive Disease of Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, 511500, Qingyuan, Guangdong, China.
| | - Jinbao Liu
- Institute of Digestive Disease of Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, 511500, Qingyuan, Guangdong, China. .,Affiliated Cancer Hospital & institute of Guangzhou Medical University,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, Guangdong, China.
| | - Hongbiao Huang
- Institute of Digestive Disease of Guangzhou Medical University, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, 511500, Qingyuan, Guangdong, China. .,Affiliated Cancer Hospital & institute of Guangzhou Medical University,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, Guangdong, China.
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12
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Rüthnick D, Vitale J, Neuner A, Schiebel E. The N-terminus of Sfi1 and yeast centrin Cdc31 provide the assembly site for a new spindle pole body. J Cell Biol 2021; 220:211743. [PMID: 33523111 PMCID: PMC7852455 DOI: 10.1083/jcb.202004196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/20/2020] [Accepted: 12/18/2020] [Indexed: 12/31/2022] Open
Abstract
The spindle pole body (SPB) provides microtubule-organizing functions in yeast and duplicates exactly once per cell cycle. The first step in SPB duplication is the half-bridge to bridge conversion via the antiparallel dimerization of the centrin (Cdc31)-binding protein Sfi1 in anaphase. The bridge, which is anchored to the old SPB on the proximal end, exposes free Sfi1 N-termini (N-Sfi1) at its distal end. These free N-Sfi1 promote in G1 the assembly of the daughter SPB (dSPB) in a yet unclear manner. This study shows that N-Sfi1 including the first three Cdc31 binding sites interacts with the SPB components Spc29 and Spc42, triggering the assembly of the dSPB. Cdc31 binding to N-Sfi1 promotes Spc29 recruitment and is essential for satellite formation. Furthermore, phosphorylation of N-Sfi1 has an inhibitory effect and delays dSPB biogenesis until G1. Taking these data together, we provide an understanding of the initial steps in SPB assembly and describe a new function of Cdc31 in the recruitment of dSPB components.
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Affiliation(s)
- Diana Rüthnick
- Center for Molecular Biology, University of Heidelberg, German Cancer Research Center-Center for Molecular Biology Alliance, Heidelberg, Germany
| | - Jlenia Vitale
- Center for Molecular Biology, University of Heidelberg, German Cancer Research Center-Center for Molecular Biology Alliance, Heidelberg, Germany
| | - Annett Neuner
- Center for Molecular Biology, University of Heidelberg, German Cancer Research Center-Center for Molecular Biology Alliance, Heidelberg, Germany
| | - Elmar Schiebel
- Center for Molecular Biology, University of Heidelberg, German Cancer Research Center-Center for Molecular Biology Alliance, Heidelberg, Germany
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13
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Basar MA, Beck DB, Werner A. Deubiquitylases in developmental ubiquitin signaling and congenital diseases. Cell Death Differ 2021; 28:538-556. [PMID: 33335288 PMCID: PMC7862630 DOI: 10.1038/s41418-020-00697-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Metazoan development from a one-cell zygote to a fully formed organism requires complex cellular differentiation and communication pathways. To coordinate these processes, embryos frequently encode signaling information with the small protein modifier ubiquitin, which is typically attached to lysine residues within substrates. During ubiquitin signaling, a three-step enzymatic cascade modifies specific substrates with topologically unique ubiquitin modifications, which mediate changes in the substrate's stability, activity, localization, or interacting proteins. Ubiquitin signaling is critically regulated by deubiquitylases (DUBs), a class of ~100 human enzymes that oppose the conjugation of ubiquitin. DUBs control many essential cellular functions and various aspects of human physiology and development. Recent genetic studies have identified mutations in several DUBs that cause developmental disorders. Here we review principles controlling DUB activity and substrate recruitment that allow these enzymes to regulate ubiquitin signaling during development. We summarize key mechanisms of how DUBs control embryonic and postnatal differentiation processes, highlight developmental disorders that are caused by mutations in particular DUB members, and describe our current understanding of how these mutations disrupt development. Finally, we discuss how emerging tools from human disease genetics will enable the identification and study of novel congenital disease-causing DUBs.
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Affiliation(s)
- Mohammed A Basar
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David B Beck
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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14
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Yamamoto S, Kitagawa D. Emerging insights into symmetry breaking in centriole duplication: updated view on centriole duplication theory. Curr Opin Struct Biol 2020; 66:8-14. [PMID: 32956908 DOI: 10.1016/j.sbi.2020.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 11/15/2022]
Abstract
Centriole duplication occurs once per cell cycle. Since only a single daughter centriole is assembled adjacent to each mother centriole, symmetry around the mother centriole must be broken in the process of centriole duplication. Recent studies have established that Plk4, a master kinase for centriole duplication, can self-assemble into condensates, and have suggested that this Plk4 self-assembly is the key to symmetry breaking. Here, we present the current hypotheses for how Plk4 could break symmetry around the mother centriole via autonomous regulation. After this initial symmetry-breaking process, the ring-to-dot conversion of Plk4 around the mother centriole completes the selection of the site for procentriole formation. We also discuss how this dynamic transition contributes to the strict regulation of centriole duplication.
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Affiliation(s)
- Shohei Yamamoto
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Daiju Kitagawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.
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15
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Heydeck W, Bayless BA, Stemm-Wolf AJ, O'Toole ET, Fabritius AS, Ozzello C, Nguyen M, Winey M. Tetrahymena Poc5 is a transient basal body component that is important for basal body maturation. J Cell Sci 2020; 133:jcs.240838. [PMID: 32350068 DOI: 10.1242/jcs.240838] [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: 10/20/2019] [Accepted: 04/06/2020] [Indexed: 01/26/2023] Open
Abstract
Basal bodies (BBs) are microtubule-based organelles that act as a template for and stabilize cilia at the cell surface. Centrins ubiquitously associate with BBs and function in BB assembly, maturation and stability. Human POC5 (hPOC5) is a highly conserved centrin-binding protein that binds centrins through Sfi1p-like repeats and is required for building full-length, mature centrioles. Here, we use the BB-rich cytoskeleton of Tetrahymena thermophila to characterize Poc5 BB functions. Tetrahymena Poc5 (TtPoc5) uniquely incorporates into assembling BBs and is then removed from mature BBs prior to ciliogenesis. Complete genomic knockout of TtPOC5 leads to a significantly increased production of BBs, yet a markedly reduced ciliary density, both of which are rescued by reintroduction of TtPoc5. A second Tetrahymena POC5-like gene, SFR1, is similarly implicated in modulating BB production. When TtPOC5 and SFR1 are co-deleted, cell viability is compromised and BB overproduction is exacerbated. Overproduced BBs display defective transition zone formation and a diminished capacity for ciliogenesis. This study uncovers a requirement for Poc5 in building mature BBs, providing a possible functional link between hPOC5 mutations and impaired cilia.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Westley Heydeck
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Brian A Bayless
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Alexander J Stemm-Wolf
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Eileen T O'Toole
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Amy S Fabritius
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Courtney Ozzello
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Marina Nguyen
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Mark Winey
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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