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Rosa E Silva I, Smetana JHC, de Oliveira JF. A comprehensive review on DDX3X liquid phase condensation in health and neurodevelopmental disorders. Int J Biol Macromol 2024; 259:129330. [PMID: 38218270 DOI: 10.1016/j.ijbiomac.2024.129330] [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: 11/22/2023] [Revised: 12/22/2023] [Accepted: 01/06/2024] [Indexed: 01/15/2024]
Abstract
DEAD-box helicases are global regulators of liquid-liquid phase separation (LLPS), a process that assembles membraneless organelles inside cells. An outstanding member of the DEAD-box family is DDX3X, a multi-functional protein that plays critical roles in RNA metabolism, including RNA transcription, splicing, nucleocytoplasmic export, and translation. The diverse functions of DDX3X result from its ability to bind and remodel RNA in an ATP-dependent manner. This capacity enables the protein to act as an RNA chaperone and an RNA helicase, regulating ribonucleoprotein complex assembly. DDX3X and its orthologs from mouse, yeast (Ded1), and C. elegans (LAF-1) can undergo LLPS, driving the formation of neuronal granules, stress granules, processing bodies or P-granules. DDX3X has been related to several human conditions, including neurodevelopmental disorders, such as intellectual disability and autism spectrum disorder. Although the research into the pathogenesis of aberrant biomolecular condensation in neurodegenerative diseases is increasing rapidly, the role of LLPS in neurodevelopmental disorders is underexplored. This review summarizes current findings relevant for DDX3X phase separation in neurodevelopment and examines how disturbances in the LLPS process can be related to neurodevelopmental disorders.
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Affiliation(s)
- Ivan Rosa E Silva
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, SP, Brazil
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2
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Fan WW, Xu T, Gao J, Zhang HY, Li Y, Hu DD, Gao S, Zhang JH, Liu X, Liu D, Li PL, Wong CCL, Yao XB, Shi YY, Yang ZY, Wang XS, Ruan K. A bivalent inhibitor against TDRD3 to suppress phase separation of methylated G3BP1. Chem Commun (Camb) 2024; 60:762-765. [PMID: 38126399 DOI: 10.1039/d3cc04654k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The formation of membrane-less organelles is driven by multivalent weak interactions while mediation of such interactions by small molecules remains an unparalleled challenge. Here, we uncovered a bivalent inhibitor that blocked the recruitment of TDRD3 by the two methylated arginines of G3BP1. Relative to the monovalent inhibitor, this bivalent inhibitor demonstrated an enhanced binding affinity to TDRD3 and capability to suppress the phase separation of methylated G3BP1, TDRD3, and RNAs, and in turn inhibit the stress granule growth in cells. Our result paves a new path to mediate multivalent interactions involved in SG assembly for potential combinational chemotherapy by bivalent inhibitors.
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Affiliation(s)
- Wei-Wei Fan
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Tian Xu
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Jia Gao
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Han-Yu Zhang
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Yan Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China.
| | - Duo-Duo Hu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China.
| | - Shuaixin Gao
- Center for Precision Medicine Multi-omics Research, Peking University Health Science Center, Peking University First Hospital; School of Basic Medical Sciences, Peking University Health Science Center; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jia-Hai Zhang
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Xing Liu
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Dan Liu
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Pi-Long Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Catherine C L Wong
- Center for Precision Medicine Multi-omics Research, Peking University Health Science Center, Peking University First Hospital; School of Basic Medical Sciences, Peking University Health Science Center; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xue-Biao Yao
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Yun-Yu Shi
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Zhen-Ye Yang
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Xi-Sheng Wang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China.
| | - Ke Ruan
- The First Affiliated Hospital & School of Life Sciences, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
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3
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Saha S, Huang SYN, Yang X, Saha LK, Sun Y, Khandagale P, Jenkins LM, Pommier Y. The TDRD3-USP9X complex and MIB1 regulate TOP3B homeostasis and prevent deleterious TOP3B cleavage complexes. Nat Commun 2023; 14:7524. [PMID: 37980342 PMCID: PMC10657456 DOI: 10.1038/s41467-023-43151-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023] Open
Abstract
TOP3B is stabilized by TDRD3. Hypothesizing that TDRD3 recruits a deubiquitinase, we find that TOP3B interacts with USP9X via TDRD3. Inactivation of USP9X destabilizes TOP3B, and depletion of both TDRD3 and USP9X does not promote further TOP3B ubiquitylation. Additionally, we observe that MIB1 mediates the ubiquitylation and proteasomal degradation of TOP3B by directly interacting with TOP3B independently of TDRD3. Combined depletion of USP9X, TDRD3 and MIB1 causes no additional increase in TOP3B levels compared to MIB1 knockdown alone indicating that the TDRD3-USP9X complex works downstream of MIB1. To comprehend why cells degrade TOP3B in the absence of TDRD3, we measured TOP3Bccs. Lack of TDRD3 increases TOP3Bccs in DNA and RNA, and induced R-loops, γH2AX and growth defect. Biochemical experiments confirm that TDRD3 increases the turnover of TOP3B. Our work provides molecular insights into the mechanisms by which TDRD3 protect cells from deleterious TOP3Bccs which are otherwise removed by TRIM41.
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Affiliation(s)
- Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Liton Kumar Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yilun Sun
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Prashant Khandagale
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Lisa M Jenkins
- Collaborative Protein Technology Resource, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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Chen M, Wang Z, Li W, Chen Y, Xiao Q, Shang X, Huang X, Wei Z, Ji X, Liu Y. Crystal structure of Tudor domain of TDRD3 in complex with a small molecule antagonist. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194962. [PMID: 37499935 DOI: 10.1016/j.bbagrm.2023.194962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023]
Abstract
Tudor domain-containing protein 3 (TDRD3) is involved in regulating transcription and translation, promoting breast cancer progression, and modulating neurodevelopment and mental health, making it a promising therapeutic target for associated diseases. The Tudor domain of TDRD3 is essential for its biological functions, and targeting this domain with potent and selective chemical probes may modulate its engagement with chromatin and related functions. Here we reported a study of TDRD3 antagonist following on our earlier work on the development of the SMN antagonist, Compound 1, and demonstrated that TDRD3 can bind effectively to Compound 2, a triple-ring analog of Compound 1. Our structural analysis suggested that the triple-ring compound bound better to TDRD3 due to its smaller side chain at Y566 compared to W102 in SMN. We also revealed that adding a small hydrophobic group to the N-methyl site of Compound 1 can improve binding. These findings provide a path for identifying antagonists for single canonical Tudor domain-containing proteins such as TDRD3 and SMN.
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Affiliation(s)
- Meixia Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Zhuowen Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Weiguo Li
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Yichang Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Qin Xiao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Xinci Shang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Xiaolei Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Zhengguo Wei
- School of Biology and Basic Medical Science, Soochow University, Suzhou, Jiangsu 215021, PR China
| | - Xinyue Ji
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China.
| | - Yanli Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, Jiangsu 215123, PR China.
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Ma H, Liu M, Fu R, Feng J, Ren H, Cao J, Shi M. Phase separation in innate immune response and inflammation-related diseases. Front Immunol 2023; 14:1086192. [PMID: 36860877 PMCID: PMC9970293 DOI: 10.3389/fimmu.2023.1086192] [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: 11/02/2022] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
Inflammation induced by nonspecific pathogenic or endogenous danger signals is an essential mechanism of innate immune response. The innate immune responses are rapidly triggered by conserved germline-encoded receptors that recognize broad patterns indicative of danger, with subsequent signal amplification by modular effectors, which have been the subject of intense investigation for many years. Until recently, however, the critical role of intrinsic disorder-driven phase separation in facilitating innate immune responses went largely unappreciated. In this review, we discuss emerging evidences that many innate immune receptors, effectors, and/or interactors function as "all-or-nothing" switch-like hubs to stimulate acute and chronic inflammation. By concentrating or relegating modular signaling components to phase-separated compartments, cells construct flexible and spatiotemporal distributions of key signaling events to ensure rapid and effective immune responses to a myriad of potentially harmful stimuli.
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Affiliation(s)
- Huihui Ma
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Mingxi Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Rao Fu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jia Feng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Haoran Ren
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jingyan Cao
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ming Shi
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
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Binda O, Juillard F, Ducassou JN, Kleijwegt C, Paris G, Didillon A, Baklouti F, Corpet A, Couté Y, Côté J, Lomonte P. SMA-linked SMN mutants prevent phase separation properties and SMN interactions with FMRP family members. Life Sci Alliance 2022; 6:6/1/e202201429. [PMID: 36375840 PMCID: PMC9684302 DOI: 10.26508/lsa.202201429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
Although recent advances in gene therapy provide hope for spinal muscular atrophy (SMA) patients, the pathology remains the leading genetic cause of infant mortality. SMA is a monogenic pathology that originates from the loss of the SMN1 gene in most cases or mutations in rare cases. Interestingly, several SMN1 mutations occur within the TUDOR methylarginine reader domain of SMN. We hypothesized that in SMN1 mutant cases, SMA may emerge from aberrant protein-protein interactions between SMN and key neuronal factors. Using a BioID proteomic approach, we have identified and validated a number of SMN-interacting proteins, including fragile X mental retardation protein (FMRP) family members (FMRFM). Importantly, SMA-linked SMNTUDOR mutant forms (SMNST) failed to interact with FMRFM In agreement with the recent work, we define biochemically that SMN forms droplets in vitro and these droplets are stabilized by RNA, suggesting that SMN could be involved in the formation of membraneless organelles, such as Cajal nuclear bodies. Finally, we found that SMN and FMRP co-fractionate with polysomes, in an RNA-dependent manner, suggesting a potential role in localized translation in motor neurons.
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Affiliation(s)
- Olivier Binda
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France .,University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ottawa, Canada
| | - Franceline Juillard
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Julia Novion Ducassou
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Constance Kleijwegt
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France,Université de Montpellier, CNRS UMR 9002, Institut de Génétique Humaine, Montpellier, France
| | - Geneviève Paris
- University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ottawa, Canada
| | - Andréanne Didillon
- University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ottawa, Canada
| | - Faouzi Baklouti
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Armelle Corpet
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Jocelyn Côté
- University of Ottawa, Faculty of Medicine, Department of Cellular and Molecular Medicine, Ottawa, Canada
| | - Patrick Lomonte
- Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, LabEx DEV2CAN, Institut NeuroMyoGène-Pathophysiology and Genetics of Neuron and Muscle, Team Chromatin Dynamics, Nuclear Domains, Virus, Lyon, France
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Fonteneau G, Redding A, Hoag-Lee H, Sim ES, Heinrich S, Gaida MM, Grabocka E. Stress Granules Determine the Development of Obesity-Associated Pancreatic Cancer. Cancer Discov 2022; 12:1984-2005. [PMID: 35674408 PMCID: PMC9357213 DOI: 10.1158/2159-8290.cd-21-1672] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/25/2022] [Accepted: 06/06/2022] [Indexed: 02/07/2023]
Abstract
Obesity is a global epidemic and a major predisposing factor for cancer. Increasing evidence shows that obesity-associated stress is a key driver of cancer risk and progression. Previous work has identified the phase-separation organelles, stress granules (SG), as mutant KRAS-dependent mediators of stress adaptation. However, the dependence of tumorigenesis on these organelles is unknown. Here, we establish a causal link between SGs and pancreatic ductal adenocarcinoma (PDAC). Importantly, we uncover that dependence on SGs is drastically heightened in obesity-associated PDAC. Furthermore, we identify a previously unknown regulator and component of SGs, namely, the serine/arginine protein kinase 2 (SRPK2), as a specific determinant of SG formation in obesity-associated PDAC. We show that SRPK2-mediated SG formation in obesity-associated PDAC is driven by hyperactivation of the IGF1/PI3K/mTOR/S6K1 pathway and that S6K1 inhibition selectively attenuates SGs and impairs obesity-associated PDAC development. SIGNIFICANCE : We show that stress adaptation via the phase-separation organelles SGs mediates PDAC development. Moreover, preexisting stress conditions such as obesity are a driving force behind tumor SG dependence, and enhanced SG levels are key determinants and a chemopreventive target for obesity-associated PDAC. This article is highlighted in the In This Issue feature, p. 1825.
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Affiliation(s)
- Guillaume Fonteneau
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Alexandra Redding
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Hannah Hoag-Lee
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Edward S. Sim
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Current Address: University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Stefan Heinrich
- Department of Surgery, University Medical Center Mainz, JGU-Mainz, 55131 Mainz, Germany
| | - Matthias M. Gaida
- Institute of Pathology, University Medical Center Mainz, JGU-Mainz, 55131 Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz, JGU-Mainz, 55131 Mainz, Germany
- Joint Unit Immunopathology, Institute of Pathology, University Medical Center, JGU-Mainz and TRON, Translational Oncology at the University Medical Center, JGU-Mainz, 55131 Mainz, Germany
| | - Elda Grabocka
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
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Li W, Jiang C, Zhang E. Advances in the phase separation-organized membraneless organelles in cells: a narrative review. Transl Cancer Res 2022; 10:4929-4946. [PMID: 35116344 PMCID: PMC8797891 DOI: 10.21037/tcr-21-1111] [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: 06/28/2021] [Accepted: 10/29/2021] [Indexed: 11/26/2022]
Abstract
Membraneless organelles (MLOs) are micro-compartments that lack delimiting membranes, concentrating several macro-molecules with a high local concentration in eukaryotic cells. Recent studies have shown that MLOs have pivotal roles in multiple biological processes, including gene transcription, RNA metabolism, translation, protein modification, and signal transduction. These biological processes in cells have essential functions in many diseases, such as cancer, neurodegenerative diseases, and virus-related diseases. The liquid-liquid phase separation (LLPS) microenvironment within cells is thought to be the driving force for initiating the formation of micro-compartments with a liquid-like property, becoming an important organizing principle for MLOs to mediate organism responses. In this review, we comprehensively elucidated the formation of these MLOs and the relationship between biological functions and associated diseases. The mechanisms underlying the influence of protein concentration and valency on phase separation in cells are also discussed. MLOs undergoing the LLPS process have diverse functions, including stimulation of some adaptive and reversible responses to alter the transcriptional or translational processes, regulation of the concentrations of biomolecules in living cells, and maintenance of cell morphogenesis. Finally, we highlight that the development of this field could pave the way for developing novel therapeutic strategies for the treatment of LLPS-related diseases based on the understanding of phase separation in the coming years.
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Affiliation(s)
- Weihan Li
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
| | - Chenwei Jiang
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
| | - Erhao Zhang
- Department of Immunology, School of Medicine, Nantong University, Nantong, China.,Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, China
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9
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Deater M, Tamhankar M, Lloyd RE. TDRD3 is an antiviral restriction factor that promotes IFN signaling with G3BP1. PLoS Pathog 2022; 18:e1010249. [PMID: 35085371 PMCID: PMC8824378 DOI: 10.1371/journal.ppat.1010249] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/08/2022] [Accepted: 01/05/2022] [Indexed: 12/19/2022] Open
Abstract
Stress granules (SGs) are highly dynamic cytoplasmic foci that form in response to activation of the integrated stress response (ISR) that results in eIF2α phosphorylation and global translation shutdown. Stress granules, which are largely nucleated by G3BP1, serve as hubs for mRNA triage, but there is mounting evidence that they also perform cell signaling functions that are vital to cell survival, particularly during viral infection. We previously showed that SG formation leads to NFκB activation and JNK signaling and that this association may be due in part to G3BP1-dependent recruitment of PKR to SGs. Others have reported close associations between G3BP1 and various innate immune PRRs of the type 1 interferon signaling system, including RIG-I. We also reported SG assembly dynamics is dependent on the arginine-methylation status of G3BP1. Another protein that rapidly localizes to SGs, TDRD3, is a methyl reader protein that performs transcriptional activation and adaptor functions within the nucleus, but neither the mechanism nor its function in SGs is clear. Here, we present evidence that TDRD3 localizes to SGs partly based upon methylation potential of G3BP1. We also characterize granules that TDRD3 forms during overexpression and show that these granules can form in the absence of G3BP but also contain translation components found in canonical SGs. We also show for the first time that SGs recruit additional interferon effectors IRF3, IRF7, TBK1, and Sting, and provide evidence that TDRD3 may play a role in recruitment of these factors. We also present evidence that TDRD3 is a novel antiviral protein that is cleaved by enteroviral 2A proteinase. G3BP1 and TDRD3 knockdown in cells results in altered transcriptional regulation of numerous IFN effectors in complex modulatory patterns that are distinctive for G3BP1 and TDRD3. Overall, we describe a novel role of TDRD3 in innate immunity in which G3BP1 and TDRD3 may coordinate to play important roles in regulation of innate antiviral defenses. When cells are exposed to environmental stresses, such as oxidative stress and viral infection, it induces a cellular response leading to the formation of Stress Granules (SGs) composed of stalled translation initiation complexes (RNA-binding proteins and mRNA) and many other cellular proteins. SGs are also considered to be antiviral structures when they form during viral infection, but viruses can block SG formation to facilitate their survival, often by targeting the essential SG protein G3BP1. Here, we show that a methyl reader protein, TDRD3, localizes to SGs partly based on the methylation potential of G3BP1, and may play a role in the recruitment of innate immune factors to SGs. Further, when overexpressed, TDRD3 can also form SG-like structures independently of G3BP1. We also present evidence that TDRD3 is a novel antiviral protein. Virus replication is enhanced in the absence of both TDRD3 and G3BP1, and virus infection leads to cleavage of TDRD3 by the enterovirus proteinase 2A. Finally, we also show that depletion of TDRD3 and G3BP1 together in cells leads to restriction of transcriptional activation of numerous IFN effectors in response to dsRNA. The patterns of transcriptional activation are distinctive for G3BP1 and TDRD3. We conclude that TDRD3 may play a novel and important role in the regulation of the host antiviral response.
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Affiliation(s)
- Matthew Deater
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Manasi Tamhankar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard E. Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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10
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Asadi MR, Rahmanpour D, Moslehian MS, Sabaie H, Hassani M, Ghafouri-Fard S, Taheri M, Rezazadeh M. Stress Granules Involved in Formation, Progression and Metastasis of Cancer: A Scoping Review. Front Cell Dev Biol 2021; 9:745394. [PMID: 34604242 PMCID: PMC8485071 DOI: 10.3389/fcell.2021.745394] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/25/2021] [Indexed: 12/15/2022] Open
Abstract
The assembly of stress granules (SGs) is a well-known cellular strategy for reducing stress-related damage and promoting cell survival. SGs have become important players in human health, in addition to their fundamental role in the stress response. The critical role of SGs in cancer cells in formation, progression, and metastasis makes sense. Recent researchers have found that several SG components play a role in tumorigenesis and cancer metastasis via tumor-associated signaling pathways and other mechanisms. Gene-ontology analysis revealed the role of these protein components in the structure of SGs. Involvement in the translation process, regulation of mRNA stability, and action in both the cytoplasm and nucleus are among the main features of SG proteins. The present scoping review aimed to consider all studies on the effect of SGs on cancer formation, proliferation, and metastasis and performed based on a six-stage methodology structure and the PRISMA guideline. A systematic search of seven databases for qualified articles was conducted before July 2021. Publications were screened, and quantitative and qualitative analysis was performed on the extracted data. Go analysis was performed on seventy-one SGs protein components. Remarkably G3BP1, TIA1, TIAR, and YB1 have the largest share among the proteins considered in the studies. Altogether, this scoping review tries to demonstrate and provide a comprehensive summary of the role of SGs in the formation, progression, and metastasis of cancer by reviewing all studies.
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Affiliation(s)
- Mohammad Reza Asadi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Dara Rahmanpour
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Hani Sabaie
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Hassani
- Student Research Committee, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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11
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Cai T, Yu Z, Wang Z, Liang C, Richard S. Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. J Biol Chem 2021; 297:100821. [PMID: 34029587 PMCID: PMC8141346 DOI: 10.1016/j.jbc.2021.100821] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022] Open
Abstract
Viral proteins are known to be methylated by host protein arginine methyltransferases (PRMTs) necessary for the viral life cycle, but it remains unknown whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins are methylated. Herein, we show that PRMT1 methylates SARS-CoV-2 nucleocapsid (N) protein at residues R95 and R177 within RGG/RG motifs, preferred PRMT target sequences. We confirmed arginine methylation of N protein by immunoblotting viral proteins extracted from SARS-CoV-2 virions isolated from cell culture. Type I PRMT inhibitor (MS023) or substitution of R95 or R177 with lysine inhibited interaction of N protein with the 5'-UTR of SARS-CoV-2 genomic RNA, a property required for viral packaging. We also defined the N protein interactome in HEK293 cells, which identified PRMT1 and many of its RGG/RG substrates, including the known interacting protein G3BP1 as well as other components of stress granules (SGs), which are part of the host antiviral response. Methylation of R95 regulated the ability of N protein to suppress the formation of SGs, as R95K substitution or MS023 treatment blocked N-mediated suppression of SGs. Also, the coexpression of methylarginine reader Tudor domain-containing protein 3 quenched N protein-mediated suppression of SGs in a dose-dependent manner. Finally, pretreatment of VeroE6 cells with MS023 significantly reduced SARS-CoV-2 replication. Because type I PRMT inhibitors are already undergoing clinical trials for cancer treatment, inhibiting arginine methylation to target the later stages of the viral life cycle such as viral genome packaging and assembly of virions may represent an additional therapeutic application of these drugs.
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Affiliation(s)
- Ting Cai
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada
| | - Zhenbao Yu
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada
| | - Zhen Wang
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research and Department of Medicine, Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Chen Liang
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research and Department of Medicine, Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada.
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12
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Wang L, Yang W, Li B, Yuan S, Wang F. Response to stress in biological disorders: Implications of stress granule assembly and function. Cell Prolif 2021; 54:e13086. [PMID: 34170048 PMCID: PMC8349659 DOI: 10.1111/cpr.13086] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022] Open
Abstract
It is indispensable for cells to adapt and respond to environmental stresses, in order for organisms to survive. Stress granules (SGs) are condensed membrane‐less organelles dynamically formed in the cytoplasm of eukaryotes cells to cope with diverse intracellular or extracellular stress factors, with features of liquid‐liquid phase separation. They are composed of multiple constituents, including translationally stalled mRNAs, translation initiation factors, RNA‐binding proteins and also non‐RNA‐binding proteins. SG formation is triggered by stress stimuli, viral infection and signal transduction, while aberrant assembly of SGs may contribute to tissue degenerative diseases. Recently, a growing body of evidence has emerged on SG response mechanisms for cells facing high temperatures, oxidative stress and osmotic stress. In this review, we aim to summarize factors affecting SGs assembly, present the impact of SGs on germ cell development and other biological processes. We particularly emphasize the significance of recently reported RNA modifications in SG stress responses. In parallel, we also review all current perspectives on the roles of SGs in male germ cells, with a particular focus on the dynamics of SG assembly.
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Affiliation(s)
- Lingjuan Wang
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Weina Yang
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Bin Li
- Tianjin Medical University General Hospital, Tianjin, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shuiqiao Yuan
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
| | - Fengli Wang
- Institute Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China
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13
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Courchaine EM, Barentine AES, Straube K, Lee DR, Bewersdorf J, Neugebauer KM. DMA-tudor interaction modules control the specificity of in vivo condensates. Cell 2021; 184:3612-3625.e17. [PMID: 34115980 DOI: 10.1016/j.cell.2021.05.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/21/2020] [Accepted: 05/07/2021] [Indexed: 12/31/2022]
Abstract
Biomolecular condensation is a widespread mechanism of cellular compartmentalization. Because the "survival of motor neuron protein" (SMN) is implicated in the formation of three different membraneless organelles (MLOs), we hypothesized that SMN promotes condensation. Unexpectedly, we found that SMN's globular tudor domain was sufficient for dimerization-induced condensation in vivo, whereas its two intrinsically disordered regions (IDRs) were not. Binding to dimethylarginine (DMA) modified protein ligands was required for condensate formation by the tudor domains in SMN and at least seven other fly and human proteins. Remarkably, asymmetric versus symmetric DMA determined whether two distinct nuclear MLOs-gems and Cajal bodies-were separate or "docked" to one another. This substructure depended on the presence of either asymmetric or symmetric DMA as visualized with sub-diffraction microscopy. Thus, DMA-tudor interaction modules-combinations of tudor domains bound to their DMA ligand(s)-represent versatile yet specific regulators of MLO assembly, composition, and morphology.
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Affiliation(s)
- Edward M Courchaine
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Andrew E S Barentine
- Cell Biology, Yale University, New Haven, CT 06520, USA; Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Korinna Straube
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Joerg Bewersdorf
- Cell Biology, Yale University, New Haven, CT 06520, USA; Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Karla M Neugebauer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Cell Biology, Yale University, New Haven, CT 06520, USA.
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14
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Moreira F, Arenas M, Videira A, Pereira F. Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa. J Mol Evol 2021; 89:384-395. [PMID: 33999213 DOI: 10.1007/s00239-021-10011-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/30/2021] [Indexed: 12/14/2022]
Abstract
DNA topoisomerase III beta (TOP3B) is unique by operating on both DNA and RNA substrates to regulate gene expression and genomic stability. Mutations in human TOP3B are linked to neurodevelopmental and cognitive disorders, highlighting its relevance for human health. Despite the emerging importance of TOP3B, its precise cellular functions and evolutionary history remain poorly understood. Here, we show that TOP3B is conserved across main metazoan groups and evolved under strong purifying selection. Subdomain IV was identified as the most conserved TOP3B region, in agreement with its role in providing the structural foundation of the protein. On the contrary, subdomain II is the less conserved, possibly because it is the most structurally flexible region of all TOP3B regions. Interestingly, TOP3B residue at position 472, previously associated with schizophrenia, is highly variable across animals, suggesting a more specific role in humans and related species. Finally, we show that all TOP3B CXXC zinc finger motifs previously identified at the protein C-terminal region are retained across metazoans. We also found that the two major methylation sites known to regulate TOP3B activity are located in the most conserved region of the C-terminal arginine-glycine-glycine (RGG) box, suggesting that a similar regulatory mechanism may operate throughout animals. Overall, our results provide a better understanding of the evolution and functional roles of TOP3B.
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Affiliation(s)
- Filipa Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua Jorge de Viterbo Ferreira 228, 4450-208, Porto, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain.,Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, 36310, Vigo, Spain.,Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Arnaldo Videira
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Rua Jorge de Viterbo Ferreira 228, 4450-208, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Filipe Pereira
- IDENTIFICA Genetic Testing, Rua Simão Bolívar 259 3º Dir Tras, 4470-214, Maia, Portugal. .,Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
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15
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Hofmann S, Kedersha N, Anderson P, Ivanov P. Molecular mechanisms of stress granule assembly and disassembly. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118876. [PMID: 33007331 DOI: 10.1016/j.bbamcr.2020.118876] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 12/11/2022]
Abstract
Stress granules (SGs) are membrane-less ribonucleoprotein (RNP)-based cellular compartments that form in the cytoplasm of a cell upon exposure to various environmental stressors. SGs contain a large set of proteins, as well as mRNAs that have been stalled in translation as a result of stress-induced polysome disassembly. Despite the fact that SGs have been extensively studied for many years, their function is still not clear. They presumably help the cell to cope with the encountered stress, and facilitate the recovery process after stress removal upon which SGs disassemble. Aberrant formation of SGs and impaired SG disassembly majorly contribute to various pathological phenomena in cancer, viral infections, and neurodegeneration. The assembly of SGs is largely driven by liquid-liquid phase separation (LLPS), however, the molecular mechanisms behind that are not fully understood. Recent studies have proposed a novel mechanism for SG formation that involves the interplay of a large interaction network of mRNAs and proteins. Here, we review this novel concept of SG assembly, and discuss the current insights into SG disassembly.
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Affiliation(s)
- Sarah Hofmann
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nancy Kedersha
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paul Anderson
- Brigham and Women's Hospital, Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
| | - Pavel Ivanov
- Brigham and Women's Hospital, Harvard Medical School, Harvard Initiative for RNA Medicine, Boston, MA 02115, USA.
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16
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de la Fuente L, Arzalluz-Luque Á, Tardáguila M, Del Risco H, Martí C, Tarazona S, Salguero P, Scott R, Lerma A, Alastrue-Agudo A, Bonilla P, Newman JRB, Kosugi S, McIntyre LM, Moreno-Manzano V, Conesa A. tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing. Genome Biol 2020; 21:119. [PMID: 32423416 PMCID: PMC7236505 DOI: 10.1186/s13059-020-02028-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/23/2020] [Indexed: 12/26/2022] Open
Abstract
Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isoform-centered functional analysis. Here, we present tappAS, the first framework to enable a comprehensive Functional Iso-Transcriptomics (FIT) analysis, which is effective at revealing the functional impact of context-specific post-transcriptional regulation. tappAS uses isoform-resolved annotation of coding and non-coding functional domains, motifs, and sites, in combination with novel analysis methods to interrogate different aspects of the functional readout of transcript variants and isoform regulation. tappAS software and documentation are available at https://app.tappas.org.
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Affiliation(s)
- Lorena de la Fuente
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
- Present Address: Bioinformatics Unit, IIS Fundación Jiménez Díaz, Madrid, Spain
| | - Ángeles Arzalluz-Luque
- Department of Statistics and Operational Research, Polytechnical University of Valencia, Valencia, Spain
| | - Manuel Tardáguila
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
- Present Address: Human Genetics Department, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Héctor Del Risco
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Cristina Martí
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Sonia Tarazona
- Department of Statistics and Operational Research, Polytechnical University of Valencia, Valencia, Spain
| | - Pedro Salguero
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Raymond Scott
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Alberto Lerma
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Ana Alastrue-Agudo
- Present Address: Human Genetics Department, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Pablo Bonilla
- Present Address: Human Genetics Department, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Jeremy R B Newman
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Department of Pathology, University of Florida, Gainesville, FL, USA
| | - Shunichi Kosugi
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Wako, Japan
| | - Lauren M McIntyre
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | | | - Ana Conesa
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
- Genetics Institute, University of Florida, Gainesville, FL, USA.
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17
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Cao X, Jin X, Liu B. The involvement of stress granules in aging and aging-associated diseases. Aging Cell 2020; 19:e13136. [PMID: 32170904 PMCID: PMC7189987 DOI: 10.1111/acel.13136] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are nonmembrane assemblies formed in cells in response to stress conditions. SGs mainly contain untranslated mRNA and a variety of proteins. RNAs and scaffold proteins with intrinsically disordered regions or RNA-binding domains are essential for the assembly of SGs, and multivalent macromolecular interactions among these components are thought to be the driving forces for SG assembly. The SG assembly process includes regulation through post-translational modification and involvement of the cytoskeletal system. During aging, many intracellular bioprocesses become disrupted by factors such as cellular environmental changes, mitochondrial dysfunction, and decline in the protein quality control system. Such changes could lead to the formation of aberrant SGs, as well as alterations in their maintenance, disassembly, and clearance. These aberrant SGs might in turn promote aging and aging-associated diseases. In this paper, we first review the latest progress on the molecular mechanisms underlying SG assembly and SG functioning under stress conditions. Then, we provide a detailed discussion of the relevance of SGs to aging and aging-associated diseases.
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Affiliation(s)
- Xiuling Cao
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture School of Forestry and Biotechnology Zhejiang A&F University Hangzhou China
- Department of Chemistry and Molecular Biology University of Gothenburg Goteborg Sweden
- Center for Large‐scale Cell‐based Screening Faculty of Science University of Gothenburg Goteborg Sweden
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18
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Bai B, van der Horst S, Cordewener JHG, America TAHP, Hanson J, Bentsink L. Seed-Stored mRNAs that Are Specifically Associated to Monosomes Are Translationally Regulated during Germination. PLANT PHYSIOLOGY 2020; 182:378-392. [PMID: 31527088 PMCID: PMC6945870 DOI: 10.1104/pp.19.00644] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/01/2019] [Indexed: 05/20/2023]
Abstract
The life cycle of many organisms includes a quiescent stage, such as bacterial or fungal spores, insect larvae, or plant seeds. Common to these stages is their low water content and high survivability during harsh conditions. Upon rehydration, organisms need to reactivate metabolism and protein synthesis. Plant seeds contain many mRNAs that are transcribed during seed development. Translation of these mRNAs occurs during early seed germination, even before the requirement of transcription. Therefore, stored mRNAs are postulated to be important for germination. How these mRNAs are stored and protected during long-term storage is unknown. The aim of this study was to investigate how mRNAs are stored in dry seeds and whether they are indeed translated during seed germination. We investigated seed polysome profiles and the mRNAs and protein complexes that are associated with these ribosomes in seeds of the model organism Arabidopsis (Arabidopsis thaliana). We showed that most stored mRNAs are associated with monosomes in dry seeds; therefore, we focus on monosomes in this study. Seed ribosome complexes are associated with mRNA-binding proteins, stress granule, and P-body proteins, which suggests regulated packing of seed mRNAs. Interestingly, ∼17% of the mRNAs that are specifically associated with monosomes are translationally up-regulated during seed germination. These mRNAs are transcribed during seed maturation, suggesting a role for this developmental stage in determining the translational fate of mRNAs during early germination.
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Affiliation(s)
- Bing Bai
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Sjors van der Horst
- Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Jan H G Cordewener
- BU Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
- Centre for BioSystems Genomics, 6700 AB Wageningen, The Netherlands
- Netherlands Proteomics Centre, 3508 TB Utrecht, The Netherlands
| | - Twan A H P America
- BU Bioscience, Plant Research International, 6700 AP Wageningen, The Netherlands
- Centre for BioSystems Genomics, 6700 AB Wageningen, The Netherlands
- Netherlands Proteomics Centre, 3508 TB Utrecht, The Netherlands
| | - Johannes Hanson
- Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Leónie Bentsink
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
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19
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Roles of Topoisomerases in Heterochromatin, Aging, and Diseases. Genes (Basel) 2019; 10:genes10110884. [PMID: 31683993 PMCID: PMC6896002 DOI: 10.3390/genes10110884] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/23/2019] [Accepted: 10/26/2019] [Indexed: 12/11/2022] Open
Abstract
Heterochromatin is a transcriptionally repressive chromatin architecture that has a low abundance of genes but an enrichment of transposons. Defects in heterochromatin can cause the de-repression of genes and transposons, leading to deleterious physiological changes such as aging, cancer, and neurological disorders. While the roles of topoisomerases in many DNA-based processes have been investigated and reviewed, their roles in heterochromatin formation and function are only beginning to be understood. In this review, we discuss recent findings on how topoisomerases can promote heterochromatin organization and impact the transcription of genes and transposons. We will focus on two topoisomerases: Top2α, which catenates and decatenates double-stranded DNA, and Top3β, which can change the topology of not only DNA, but also RNA. Both enzymes are required for normal heterochromatin formation and function, as the inactivation of either protein by genetic mutations or chemical inhibitors can result in defective heterochromatin formation and the de-silencing of transposons. These defects may contribute to the shortened lifespan and neurological disorders observed in individuals carrying mutations of Top3β. We propose that topological stress may be generated in both DNA and RNA during heterochromatin formation and function, which depend on multiple topoisomerases to resolve.
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20
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Lorton BM, Shechter D. Cellular consequences of arginine methylation. Cell Mol Life Sci 2019; 76:2933-2956. [PMID: 31101937 PMCID: PMC6642692 DOI: 10.1007/s00018-019-03140-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/22/2019] [Accepted: 05/10/2019] [Indexed: 02/07/2023]
Abstract
Arginine methylation is a ubiquitous post-translational modification. Three predominant types of arginine-guanidino methylation occur in Eukarya: mono (Rme1/MMA), symmetric (Rme2s/SDMA), and asymmetric (Rme2a/ADMA). Arginine methylation frequently occurs at sites of protein-protein and protein-nucleic acid interactions, providing specificity for binding partners and stabilization of important biological interactions in diverse cellular processes. Each methylarginine isoform-catalyzed by members of the protein arginine methyltransferase family, Type I (PRMT1-4,6,8) and Type II (PRMT5,9)-has unique downstream consequences. Methylarginines are found in ordered domains, domains of low complexity, and in intrinsically disordered regions of proteins-the latter two of which are intimately connected with biological liquid-liquid phase separation. This review highlights discoveries illuminating how arginine methylation affects genome integrity, gene transcription, mRNA splicing and mRNP biology, protein translation and stability, and phase separation. As more proteins and processes are found to be regulated by arginine methylation, its importance for understanding cellular physiology will continue to grow.
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Affiliation(s)
- Benjamin M Lorton
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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21
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Fulton MD, Brown T, Zheng YG. The Biological Axis of Protein Arginine Methylation and Asymmetric Dimethylarginine. Int J Mol Sci 2019; 20:ijms20133322. [PMID: 31284549 PMCID: PMC6651691 DOI: 10.3390/ijms20133322] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/04/2019] [Accepted: 07/04/2019] [Indexed: 12/20/2022] Open
Abstract
Protein post-translational modifications (PTMs) in eukaryotic cells play important roles in the regulation of functionalities of the proteome and in the tempo-spatial control of cellular processes. Most PTMs enact their regulatory functions by affecting the biochemical properties of substrate proteins such as altering structural conformation, protein-protein interaction, and protein-nucleic acid interaction. Amid various PTMs, arginine methylation is widespread in all eukaryotic organisms, from yeasts to humans. Arginine methylation in many situations can drastically or subtly affect the interactions of substrate proteins with their partnering proteins or nucleic acids, thus impacting major cellular programs. Recently, arginine methylation has become an important regulator of the formation of membrane-less organelles inside cells, a phenomenon of liquid-liquid phase separation (LLPS), through altering π-cation interactions. Another unique feature of arginine methylation lies in its impact on cellular physiology through its downstream amino acid product, asymmetric dimethylarginine (ADMA). Accumulation of ADMA in cells and in the circulating bloodstream is connected with endothelial dysfunction and a variety of syndromes of cardiovascular diseases. Herein, we review the current knowledge and understanding of protein arginine methylation in regards to its canonical function in direct protein regulation, as well as the biological axis of protein arginine methylation and ADMA biology.
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Affiliation(s)
- Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA.
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22
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UBAP2L arginine methylation by PRMT1 modulates stress granule assembly. Cell Death Differ 2019; 27:227-241. [PMID: 31114027 PMCID: PMC7205891 DOI: 10.1038/s41418-019-0350-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/28/2019] [Accepted: 05/03/2019] [Indexed: 02/06/2023] Open
Abstract
Stress granules (SGs) are discrete assemblies of stalled messenger ribonucleoprotein complexes (mRNPs) that form when eukaryotic cells encounter environmental stress. RNA-binding proteins (RBPs) mediate their condensation by recruiting populations of mRNPs. However, the cellular and molecular mechanisms underlying the role of ubiquitin-associated protein 2-like (UBAP2L) in the regulation of SG dynamics remain elusive. Here, we show that UBAP2L is required for both SG assembly and disassembly. UBAP2L overexpression nucleated SGs under stress-null conditions. The UBAP2L Arg–Gly–Gly (RGG) motif was required for SG competence, and mediated the recruitment of SG components, including mRNPs, RBPs, and ribosomal subunits. The domain of unknown function (DUF) of UBAP2L-mediated interaction with ras GTPase-activating protein-binding protein (G3BP)1/2, and its deletion caused the cytoplasmic–nuclear transport of UBAP2L and G3BP1/2, thereby compromising SG formation. The protein arginine methyltransferase PRMT1 asymmetrically dimethylated UBAP2L by targeting the RGG motif. Increased arginine methylation blocked, whereas its decrease enhanced UBAP2L interactions with SG components, ablating and promoting SG assembly, respectively. These results provide new insights into the mechanisms by which UBAP2L regulates SG dynamics and RNA metabolism.
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23
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Guzikowski AR, Chen YS, Zid BM. Stress-induced mRNP granules: Form and function of processing bodies and stress granules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2019; 10:e1524. [PMID: 30793528 PMCID: PMC6500494 DOI: 10.1002/wrna.1524] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/18/2018] [Accepted: 12/28/2018] [Indexed: 12/12/2022]
Abstract
In response to stress, cells must quickly reprogram gene expression to adapt and survive. This is achieved in part by altering levels of mRNAs and their translation into proteins. Recently, the formation of two stress-induced messenger ribonucleoprotein (mRNP) assemblies named stress granules and processing bodies has been postulated to directly impact gene expression during stress. These assemblies sequester and concentrate specific proteins and RNAs away from the larger cytoplasm during stress, thereby providing a layer of posttranscriptional gene regulation with the potential to directly impact mRNA levels, protein translation, and cell survival. The function of these granules has generally been ascribed either by the protein components concentrated into them or, more broadly, by global changes that occur during stress. Recent proteome- and transcriptome-wide studies have provided a more complete view of stress-induced mRNP granule composition in varied cell types and stress conditions. However, direct measurements of the phenotypic and functional consequences of stress granule and processing body formation are lacking. This leaves our understanding of their roles during stress incomplete. Continued study into the function of these granules will be an important part in elucidating how cells respond to and survive stressful environmental changes. This article is categorized under: Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Export and Localization > RNA Localization.
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Affiliation(s)
- Anna R. Guzikowski
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Yang S. Chen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Brian M. Zid
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
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24
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Mio C, Bulotta S, Russo D, Damante G. Reading Cancer: Chromatin Readers as Druggable Targets for Cancer Treatment. Cancers (Basel) 2019; 11:cancers11010061. [PMID: 30634442 PMCID: PMC6356452 DOI: 10.3390/cancers11010061] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/30/2018] [Accepted: 01/03/2019] [Indexed: 02/07/2023] Open
Abstract
The epigenetic machinery deputed to control histone post-translational modifications is frequently dysregulated in cancer cells. With epigenetics being naturally reversible, it represents a good target for therapies directed to restore normal gene expression. Since the discovery of Bromodomain and Extra Terminal (BET) inhibitors, a great effort has been spent investigating the effects of chromatin readers’ inhibition, specifically the class of proteins assigned to bind acetylated and methylated residues. So far, focused studies have been produced on epigenetic regulation, dissecting a specific class of epigenetic-related proteins or investigating epigenetic therapy in a specific tumor type. In this review, recent steps toward drug discovery on the different classes of chromatin readers have been outlined, highlighting the pros and cons of current therapeutic approaches.
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Affiliation(s)
- Catia Mio
- Department of Medical Area, University of Udine, 33100 Udine, Italy.
| | - Stefania Bulotta
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
| | - Diego Russo
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
| | - Giuseppe Damante
- Department of Medical Area, University of Udine, 33100 Udine, Italy.
- Medical Genetics Institute, University Hospital of Udine, 33100 Udine, Italy.
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25
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Rotavirus Induces Formation of Remodeled Stress Granules and P Bodies and Their Sequestration in Viroplasms To Promote Progeny Virus Production. J Virol 2018; 92:JVI.01363-18. [PMID: 30258011 DOI: 10.1128/jvi.01363-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023] Open
Abstract
Rotavirus replicates in unique virus-induced cytoplasmic inclusion bodies called viroplasms (VMs), the composition and structure of which have yet to be understood. Based on the analysis of a few proteins, earlier studies reported that rotavirus infection inhibits stress granule (SG) formation and disrupts P bodies (PBs). However, the recent demonstration that rotavirus infection induces cytoplasmic relocalization and colocalization with VMs of several nuclear hnRNPs and AU-rich element-binding proteins (ARE-BPs), which are known components of SGs and PBs, suggested the possibility of rotavirus-induced remodeling of SGs and PBs, prompting us to analyze a large number of the SG and PB components to understand the status of SGs and PBs in rotavirus-infected cells. Here we demonstrate that rotavirus infection induces molecular triage by selective exclusion of a few proteins of SGs (G3BP1 and ZBP1) and PBs (DDX6, EDC4, and Pan3) and sequestration of the remodeled/atypical cellular organelles, containing the majority of their components, in the VM. The punctate SG and PB structures are seen at about 4 h postinfection (hpi), coinciding with the appearance of small VMs, many of which fuse to form mature large VMs with progression of infection. By use of small interfering RNA (siRNA)-mediated knockdown and/or ectopic overexpression, the majority of the SG and PB components, except for ADAR1, were observed to inhibit viral protein expression and virus growth. In conclusion, this study demonstrates that VMs are highly complex supramolecular structures and that rotavirus employs a novel strategy of sequestration in the VM and harnessing of the remodeled cellular RNA recycling bins to promote its growth.IMPORTANCE Rotavirus is known to replicate in specialized virus-induced cytoplasmic inclusion bodies called viroplasms (VMs), but the composition and structure of VMs are not yet understood. Here we demonstrate that rotavirus interferes with normal SG and PB assembly but promotes formation of atypical SG-PB structures by selective exclusion of a few components and employs a novel strategy of sequestration of the remodeled SG-PB granules in the VMs to promote virus growth by modulating their negative influence on virus infection. Rotavirus VMs appear to be complex supramolecular structures formed by the union of the triad of viral replication complexes and remodeled SGs and PBs, as well as other host factors, and designed to promote productive virus infection. These observations have implications for the planning of future research with the aim of understanding the structure of the VM, the mechanism of morphogenesis of the virus, and the detailed roles of host proteins in rotavirus biology.
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26
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Ubiquilin 2 modulates ALS/FTD-linked FUS-RNA complex dynamics and stress granule formation. Proc Natl Acad Sci U S A 2018; 115:E11485-E11494. [PMID: 30442662 DOI: 10.1073/pnas.1811997115] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The ubiquitin-like protein ubiquilin 2 (UBQLN2) has been genetically and pathologically linked to the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), but its normal cellular functions are not well understood. In a search for UBQLN2-interacting proteins, we found an enrichment of stress granule (SG) components, including ALS/FTD-linked heterogeneous ribonucleoprotein fused in sarcoma (FUS). Through the use of an optimized SG detection method, we observed UBQLN2 and its interactors at SGs. A low complexity, Sti1-like repeat region in UBQLN2 was sufficient for its localization to SGs. Functionally, UBQLN2 negatively regulated SG formation. UBQLN2 increased the dynamics of FUS-RNA interaction and promoted the fluidity of FUS-RNA complexes at a single-molecule level. This solubilizing effect corresponded to a dispersal of FUS liquid droplets in vitro and a suppression of FUS SG formation in cells. ALS-linked mutations in UBQLN2 reduced its association with FUS and impaired its function in regulating FUS-RNA complex dynamics and SG formation. These results reveal a previously unrecognized role for UBQLN2 in regulating the early stages of liquid-liquid phase separation by directly modulating the fluidity of protein-RNA complexes and the dynamics of SG formation.
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27
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Ditlev JA, Case LB, Rosen MK. Who's In and Who's Out-Compositional Control of Biomolecular Condensates. J Mol Biol 2018; 430:4666-4684. [PMID: 30099028 PMCID: PMC6204295 DOI: 10.1016/j.jmb.2018.08.003] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 02/06/2023]
Abstract
Biomolecular condensates are two- and three-dimensional compartments in eukaryotic cells that concentrate specific collections of molecules without an encapsulating membrane. Many condensates behave as dynamic liquids and appear to form through liquid-liquid phase separation driven by weak, multivalent interactions between macromolecules. In this review, we discuss current models and data regarding the control of condensate composition, and we describe our current understanding of the composition of representative condensates including PML nuclear bodies, P-bodies, stress granules, the nucleolus, and two-dimensional membrane localized LAT and nephrin clusters. Specific interactions, such as interactions between modular binding domains, weaker interactions between intrinsically disorder regions and nucleic acid base pairing, and nonspecific interactions, such as electrostatic interactions and hydrophobic interactions, influence condensate composition. Understanding how specific condensate composition is determined is essential to understanding condensates as biochemical entities and ultimately discerning their cellular and organismic functions.
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Affiliation(s)
- Jonathon A Ditlev
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Lindsay B Case
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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28
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Liu J, Zhang S, Liu M, Liu Y, Nshogoza G, Gao J, Ma R, Yang Y, Wu J, Zhang J, Li F, Ruan K. Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit. FEBS J 2018; 285:2091-2103. [DOI: 10.1111/febs.14469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/21/2018] [Accepted: 04/05/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Jiuyang Liu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Shuya Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Mingqing Liu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Yaqian Liu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Jia Gao
- Center of Medical Physics and Technology Hefei Institute of Physical Science Chinese Academy of Science Hefei China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Yang Yang
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
| | - Ke Ruan
- Hefei National Laboratory for Physical Sciences at the Microscale School of Life Sciences University of Science and Technology of China Hefei China
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29
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Zakrzewicz D, Didiasova M, Krüger M, Giaimo BD, Borggrefe T, Mieth M, Hocke AC, Zakrzewicz A, Schaefer L, Preissner KT, Wygrecka M. Protein arginine methyltransferase 5 mediates enolase-1 cell surface trafficking in human lung adenocarcinoma cells. Biochim Biophys Acta Mol Basis Dis 2018; 1864:1816-1827. [PMID: 29501774 DOI: 10.1016/j.bbadis.2018.02.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/12/2018] [Accepted: 02/27/2018] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Enolase-1-dependent cell surface proteolysis plays an important role in cell invasion. Although enolase-1 (Eno-1), a glycolytic enzyme, has been found on the surface of various cells, the mechanism responsible for its exteriorization remains elusive. Here, we investigated the involvement of post-translational modifications (PTMs) of Eno-1 in its lipopolysaccharide (LPS)-triggered trafficking to the cell surface. RESULTS We found that stimulation of human lung adenocarcinoma cells with LPS triggered the monomethylation of arginine 50 (R50me) within Eno-1. The Eno-1R50me was confirmed by its interaction with the tudor domain (TD) from TD-containing 3 (TDRD3) protein recognizing methylarginines. Substitution of R50 with lysine (R50K) reduced Eno-1 association with epithelial caveolar domains, thereby diminishing its exteriorization. Similar effects were observed when pharmacological inhibitors of arginine methyltransferases were applied. Protein arginine methyltransferase 5 (PRMT5) was identified to be responsible for Eno-1 methylation. Overexpression of PRMT5 and caveolin-1 enhanced levels of membrane-bound extracellular Eno-1 and, conversely, pharmacological inhibition of PRMT5 attenuated Eno-1 cell-surface localization. Importantly, Eno-1R50me was essential for cancer cell motility since the replacement of Eno-1 R50 by lysine or the suppression of PRMT 5 activity diminished Eno-1-triggered cell invasion. CONCLUSIONS LPS-triggered Eno-1R50me enhances Eno-1 cell surface levels and thus potentiates the invasive properties of cancer cells. Strategies to target Eno-1R50me may offer novel therapeutic approaches to attenuate tumor metastasis in cancer patients.
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Affiliation(s)
- Dariusz Zakrzewicz
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany.
| | - Miroslava Didiasova
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Marcus Krüger
- Center for Molecular Medicine, University of Cologne, Germany
| | - Benedetto Daniele Giaimo
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Tilman Borggrefe
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Maren Mieth
- Department of Internal Medicine, Infectious Diseases and Pulmonary Medicine, Charité-University Medicine Berlin, Chariteplatz 1, 10117 Berlin, Germany
| | - Andreas C Hocke
- Department of Internal Medicine, Infectious Diseases and Pulmonary Medicine, Charité-University Medicine Berlin, Chariteplatz 1, 10117 Berlin, Germany
| | - Anna Zakrzewicz
- Laboratory of Experimental Surgery, Department of General and Thoracic Surgery, Justus Liebig University Giessen, Feulgenstrasse 10-12, 35385 Giessen, Germany
| | - Liliana Schaefer
- Institute of Pharmacology and Toxicology, Goethe University, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Klaus T Preissner
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Malgorzata Wygrecka
- Department of Biochemistry, Faculty of Medicine, Universities of Giessen and Marburg Lung Center, Friedrichstrasse 24, 35392 Giessen, Germany; Member of the German Center for Lung Research, Giessen, Germany
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30
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Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DTW, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfister SM, Taylor MD, Chang HY, Cho YJ. Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. Oncotarget 2018; 7:28169-82. [PMID: 27058758 PMCID: PMC5053718 DOI: 10.18632/oncotarget.8612] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 03/26/2016] [Indexed: 12/14/2022] Open
Abstract
DDX3X encodes a DEAD-box family RNA helicase (DDX3) commonly mutated in medulloblastoma, a highly aggressive cerebellar tumor affecting both children and adults. Despite being implicated in several facets of RNA metabolism, the nature and scope of DDX3′s interactions with RNA remain unclear. Here, we show DDX3 collaborates extensively with the translation initiation machinery through direct binding to 5′UTRs of nearly all coding RNAs, specific sites on the 18S rRNA, and multiple components of the translation initiation complex. Impairment of translation initiation is also evident in primary medulloblastomas harboring mutations in DDX3X, further highlighting DDX3′s role in this process. Arsenite-induced stress shifts DDX3 binding from the 5′UTR into the coding region of mRNAs concomitant with a general reduction of translation, and both the shift of DDX3 on mRNA and decreased translation are blunted by expression of a catalytically-impaired, medulloblastoma-associated DDX3R534H variant. Furthermore, despite the global repression of translation induced by arsenite, translation is preserved on select genes involved in chromatin organization in DDX3R534H-expressing cells. Thus, DDX3 interacts extensively with RNA and ribosomal machinery to help remodel the translation landscape in response to stress, while cancer-related DDX3 variants adapt this response to selectively preserve translation.
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Affiliation(s)
- Sekyung Oh
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen N Floor
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - James Purzner
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Surgery, Division of Neurosurgery, University of Toronto, ON, Canada
| | - Lance Martin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brian T Do
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Simone Schubert
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Dedeepya Vaka
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Sorana Morrissy
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Surgery, Division of Neurosurgery and Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Yisu Li
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC Canada
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Risch
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hans-Jörg Warnatz
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Christopher M Adams
- The Vincent Coates Foundation Mass Spectrometry Laboratory, Stanford University, Stanford, CA, USA
| | - Ryan D Leib
- The Vincent Coates Foundation Mass Spectrometry Laboratory, Stanford University, Stanford, CA, USA
| | - Marcus Breese
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC Canada
| | - David Malkin
- Cancer Genetic Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Department of Chemistry, University of California, Berkeley, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Surgery, Division of Neurosurgery and Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada
| | - Howard Y Chang
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Yoon-Jae Cho
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA.,Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA.,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
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31
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Tsai WC, Reineke LC, Jain A, Jung SY, Lloyd RE. Histone arginine demethylase JMJD6 is linked to stress granule assembly through demethylation of the stress granule-nucleating protein G3BP1. J Biol Chem 2017; 292:18886-18896. [PMID: 28972166 DOI: 10.1074/jbc.m117.800706] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/22/2017] [Indexed: 12/19/2022] Open
Abstract
Stress granules (SG) are membrane-less organelles that are condensates of stalled translation initiation complexes and mRNAs. SG formation is a cytoprotective response to environmental stress and results from protein interactions involving regions of low amino acid complexity and poorly defined post-translational modifications of SG components. Many RNA-binding proteins are methylated, and we previously demonstrated that the potent SG-nucleating protein G3BP1 is methylated by protein arginine methyltransferase 1 and 5 (PRMT1 and PRMT5). G3BP1 methylation represses SG formation and is reversible. Here we functionally link JMJD6 (Jumonji C domain-containing protein 6) to G3BP1 demethylation. Our findings reveal that JMJD6 is a novel SG component that interacts with G3BP1 complexes, and its expression reduces G3BP1 monomethylation and asymmetric dimethylation at three Arg residues. Knockdown of JMJD6 repressed SG formation and G3BP1 demethylation, but SG formation and G3BP1 demethylation were rescued with catalytically active but not mutant JMJD6. These results suggest that JMJD6 functions directly or indirectly as an arginine demethylase of G3BP1 that promotes SG formation.
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Affiliation(s)
- Wei-Chih Tsai
- From the Departments of Molecular Virology and Microbiology
| | - Lucas C Reineke
- From the Departments of Molecular Virology and Microbiology.,Molecular Physiology and Biophysics, and
| | - Antrix Jain
- Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Sung Yun Jung
- Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Richard E Lloyd
- From the Departments of Molecular Virology and Microbiology,
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32
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Gulay SP, Bista S, Varshney A, Kirmizialtin S, Sanbonmatsu KY, Dinman JD. Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle. Nucleic Acids Res 2017; 45:4958-4971. [PMID: 28334755 PMCID: PMC5416885 DOI: 10.1093/nar/gkx112] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/06/2017] [Indexed: 11/15/2022] Open
Abstract
Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges from the large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5.8S rRNA. These analyses reveal hot spots of fluctuations that set the stage for large-scale conformational changes essential for translocation and enable the first molecular dynamics simulation of an 80S complex. Comprehensive datasets of rRNA base flexibilities provide a unique resource to the structural biology community that can be computationally mined to complement ongoing research toward the goal of understanding the dynamic ribosome.
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Affiliation(s)
- Suna P Gulay
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sujal Bista
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Amitabh Varshney
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Serdal Kirmizialtin
- Chemistry Program, New York University Abu Dhabi, Abu Dhabi, UAE.,The New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Karissa Y Sanbonmatsu
- The New Mexico Consortium, Los Alamos, NM 87544, USA.,Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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33
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Harvey R, Dezi V, Pizzinga M, Willis AE. Post-transcriptional control of gene expression following stress: the role of RNA-binding proteins. Biochem Soc Trans 2017; 45:1007-14. [PMID: 28710288 PMCID: PMC5655797 DOI: 10.1042/bst20160364] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/13/2017] [Accepted: 06/14/2017] [Indexed: 12/19/2022]
Abstract
The ability of mammalian cells to modulate global protein synthesis in response to cellular stress is essential for cell survival. While control of protein synthesis is mediated by the regulation of eukaryotic initiation and elongation factors, RNA-binding proteins (RBPs) provide a crucial additional layer to post-transcriptional regulation. RBPs bind specific RNA through conserved RNA-binding domains and ensure that the information contained within the genome and transcribed in the form of RNA is exported to the cytoplasm, chemically modified, and translated prior to folding into a functional protein. Thus, this group of proteins, through mediating translational reprogramming, spatial reorganisation, and chemical modification of RNA molecules, have a major influence on the robust cellular response to external stress and toxic injury.
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Affiliation(s)
- Robert Harvey
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, U.K
| | - Veronica Dezi
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, U.K
| | | | - Anne E Willis
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, U.K.
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34
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Ahmad M, Shen W, Li W, Xue Y, Zou S, Xu D, Wang W. Topoisomerase 3β is the major topoisomerase for mRNAs and linked to neurodevelopment and mental dysfunction. Nucleic Acids Res 2017; 45:2704-2713. [PMID: 28039324 PMCID: PMC5389537 DOI: 10.1093/nar/gkw1293] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/13/2016] [Indexed: 12/22/2022] Open
Abstract
Human cells contain five topoisomerases in the nucleus and cytoplasm, but which one is the major topoisomerase for mRNAs is unclear. To date, Top3β is the only known topoisomerase that possesses RNA topoisomerase activity, binds mRNA translation machinery and interacts with an RNA-binding protein, FMRP, to promote synapse formation; and Top3β gene deletion has been linked to schizophrenia. Here, we show that Top3β is also the most abundant mRNA-binding topoisomerase in cells. Top3β, but not other topoisomerases, contains a distinctive RNA-binding domain; and deletion of this domain diminishes the amount of Top3β that associates with mRNAs, indicating that Top3β is specifically targeted to mRNAs by its RNA binding domain. Moreover, Top3β mutants lacking either its RNA-binding domain or catalytic residue fail to promote synapse formation, suggesting that Top3β requires both its mRNA-binding and catalytic activity to facilitate neurodevelopment. Notably, Top3β proteins bearing point mutations from schizophrenia and autism individuals are defective in association with FMRP; whereas one of the mutants is also deficient in binding mRNAs, catalyzing RNA topoisomerase reaction, and promoting synapse formation. Our data suggest that Top3β is the major topoisomerase for mRNAs, and requires both RNA binding and catalytic activity to promote neurodevelopment and prevent mental dysfunction.
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Affiliation(s)
- Muzammil Ahmad
- Genome Instability and Chromatin-Remodeling Section, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Weiping Shen
- Genome Instability and Chromatin-Remodeling Section, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Wen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yutong Xue
- Genome Instability and Chromatin-Remodeling Section, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Sige Zou
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weidong Wang
- Genome Instability and Chromatin-Remodeling Section, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
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35
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Tudor Domain Containing Protein 3 Promotes Tumorigenesis and Invasive Capacity of Breast Cancer Cells. Sci Rep 2017; 7:5153. [PMID: 28698590 PMCID: PMC5506013 DOI: 10.1038/s41598-017-04955-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023] Open
Abstract
Tudor domain containing protein 3 (TDRD3) is a modular protein identified based on its ability to recognize methylated arginine motifs through its Tudor domain. We have previously shown that TDRD3 localizes to cytoplasmic stress granules, a structure shown to promote survival upon treatment with chemotherapeutic drugs in cancer cells. Here, we report TDRD3 as a novel regulator of cell proliferation and invasion in breast cancer cells. Our study also demonstrates that TDRD3 depletion inhibits tumor formation and metastasis to the lung in vivo. Furthermore, we show that TDRD3 regulates the expression of a number of key genes associated with promotion of breast cancer tumorigenesis and disease progression. Strikingly, we report that TDRD3 regulates some of these key targets at the level of translation. These findings provide the first experimental demonstration of a functional role for TDRD3 in promoting breast cancer development and progression, and identify TDRD3 as a potential new therapeutic target for breast cancer.
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36
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Ahmad M, Xu D, Wang W. Type IA topoisomerases can be "magicians" for both DNA and RNA in all domains of life. RNA Biol 2017; 14:854-864. [PMID: 28534707 DOI: 10.1080/15476286.2017.1330741] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Topoisomerases solve critical topological problems in DNA metabolism and have long been regarded as the "magicians" of the DNA world. Here we present views from 2 of our recent studies indicating that Type IA topoisomerases from all domains of life often possess dual topoisomerase activities for both DNA and RNA. In animals, one of the 2 Type IA topoisomerases, Top3β, contains an RNA-binding domain, possesses RNA topoisomerase activity, binds mRNAs, interacts with mRNA-binding proteins, and associates with active mRNA translation machinery. The RNA-binding domain is required for Top3β to bind mRNAs and promote normal neurodevelopment. Top3β forms a highly conserved complex with Tudor-domain-containing 3 (TDRD3), a protein known to interact with translation factors, histones, RNA polymerase II, single stranded DNA and RNA. Top3β requires TDRD3 for its association with the mRNA translation machinery. We suggest that Type IA topoisomerases can be "magicians" for not only DNA, but also RNA; and they may solve topological problems for both nucleic acids in all domains of life. In animals, Top3β-TDRD3 is a dual-activity topoisomerase complex that can act on DNA to stimulate transcription, and on mRNA to promote translation.
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Affiliation(s)
- Muzammil Ahmad
- a Genome Instability and Chromatin-Remodeling Section , National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Dongyi Xu
- b State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences , Peking University , Beijing , China
| | - Weidong Wang
- a Genome Instability and Chromatin-Remodeling Section , National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
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37
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Alberti S, Mateju D, Mediani L, Carra S. Granulostasis: Protein Quality Control of RNP Granules. Front Mol Neurosci 2017; 10:84. [PMID: 28396624 PMCID: PMC5367262 DOI: 10.3389/fnmol.2017.00084] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/10/2017] [Indexed: 12/14/2022] Open
Abstract
Ribonucleoprotein (RNP) granules transport, store, or degrade messenger RNAs, thereby indirectly regulating protein synthesis. Normally, RNP granules are highly dynamic compartments. However, because of aging or severe environmental stress, RNP granules, in particular stress granules (SGs), convert into solid, aggregate-like inclusions. There is increasing evidence that such RNA-protein inclusions are associated with several age-related neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS), fronto-temporal dementia (FTD) and Alzheimer's disease (AD). Thus, understanding what triggers the conversion of RNP granules into aggregates and identifying the cellular players that control RNP granules will be critical to develop treatments for these diseases. In this review article, we discuss recent insight into RNP and SG formation. More specifically, we examine the evidence for liquid-liquid phase separation (LLPS) as an organizing principle of RNP granules and the role of aggregation-prone RNA-binding proteins (RBPs) in this process. We further discuss recent findings that liquid-like SGs can sequester misfolded proteins, which promote an aberrant conversion of liquid SGs into solid aggregates. Importantly, very recent studies show that a specific protein quality control (PQC) process prevents the accumulation of misfolding-prone proteins in SGs and, by doing so, maintains the dynamic state of SGs. This quality control process has been referred to as granulostasis and it relies on the specific action of the HSPB8-BAG3-HSP70 complex. Additional players such as p97/valosin containing protein (VCP) and other molecular chaperones (e.g., HSPB1) participate, directly or indirectly, in granulostasis, and ensure the timely elimination of defective ribosomal products and other misfolded proteins from SGs. Finally, we discuss recent findings that, in the stress recovery phase, SGs are preferentially disassembled with the assistance of chaperones, and we discuss evidence for a back-up system that targets aberrant SGs to the aggresome for autophagy-mediated clearance. Altogether the findings discussed here provide evidence for an intricate network of interactions between RNP granules and various components of the PQC machinery. Molecular chaperones in particular are emerging as key players that control the composition and dynamics of RNP granules, which may be important to protect against age-related diseases.
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Affiliation(s)
- Simon Alberti
- Alberti Lab, Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Germany
| | - Daniel Mateju
- Alberti Lab, Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Germany
| | - Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, Center for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia Modena, Italy
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, Center for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia Modena, Italy
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38
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Disruption of Stress Granule Formation by the Multifunctional Cricket Paralysis Virus 1A Protein. J Virol 2017; 91:JVI.01779-16. [PMID: 28003491 DOI: 10.1128/jvi.01779-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 12/15/2016] [Indexed: 12/26/2022] Open
Abstract
Stress granules (SGs) are cytosolic ribonucleoprotein aggregates that are induced during cellular stress. Several viruses modulate SG formation, suggesting that SGs have an impact on virus infection. However, the mechanisms and impact of modulating SG assembly in infected cells are not completely understood. In this study, we identify the dicistrovirus cricket paralysis virus 1A (CrPV-1A) protein that functions to inhibit SG assembly during infection. Moreover, besides inhibiting RNA interference, CrPV-1A also inhibits host transcription, which indirectly modulates SG assembly. Thus, CrPV-1A is a multifunctional protein. We identify a key R146A residue that is responsible for these effects, and mutant CrPV(R146A) virus infection is attenuated in Drosophila melanogaster S2 cells and adult fruit flies and results in increased SG formation. Treatment of CrPV(R146A)-infected cells with actinomycin D, which represses transcription, restores SG assembly suppression and viral yield. In summary, CrPV-1A modulates several cellular processes to generate a cellular environment that promotes viral translation and replication.IMPORTANCE RNA viruses encode a limited set of viral proteins to modulate an array of cellular processes in order to facilitate viral replication and inhibit antiviral defenses. In this study, we identified a viral protein, called CrPV-1A, within the dicistrovirus cricket paralysis virus that can inhibit host transcription, modulate viral translation, and block a cellular process called stress granule assembly. We also identified a specific amino acid within CrPV-1A that is important for these cellular processes and that mutant viruses containing mutations of CrPV-1A attenuate virus infection. We also demonstrate that the CrPV-1A protein can also modulate cellular processes in human cells, suggesting that the mode of action of CrPV-1A is conserved. We propose that CrPV-1A is a multifunctional, versatile protein that creates a cellular environment in virus-infected cells that permits productive virus infection.
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39
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Narayanan N, Wang Z, Li L, Yang Y. Arginine methylation of USP9X promotes its interaction with TDRD3 and its anti-apoptotic activities in breast cancer cells. Cell Discov 2017; 3:16048. [PMID: 28101374 PMCID: PMC5206711 DOI: 10.1038/celldisc.2016.48] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/20/2016] [Indexed: 12/23/2022] Open
Abstract
The Tudor domain-containing proteins are characterized by their specific interactions with methylated protein motifs, including methyl-arginines and methyl-lysines. The Tudor domain-containing protein 3 (TDRD3) is one of the major methyl-arginine effector molecules that recognizes methylated arginine residues on histones and the C-terminal domain of RNA polymerase II, and activates transcription. However, majority of the cellular TDRD3 localizes to the cytoplasm and its functions there are still elusive. Here, we have identified ubiquitin-specific protease 9 X-linked (USP9X) as a TDRD3-interacting protein by GST (glutathione S-transferase) pull-down and co-immunoprecipitation. Detailed characterization suggests that the interaction between TDRD3 and USP9X is mediated through the Tudor domain of TDRD3 and the arginine methylation of USP9X. This interaction plays a critical role in TDRD3 protein stability, as knockdown of USP9X expression leads to increased TDRD3 ubiquitination. We also found that USP9X co-localizes with TDRD3 in cytoplasmic stress granules and this localization is diminished in Tdrd3-null mouse embryonic fibroblast cells, suggesting that TDRD3 is essential for USP9X stress granule localization. Furthermore, we found that one of the USP9X de-ubiquitination targets, myeloid cell leukemia protein 1, is regulated by TDRD3, indicating that TDRD3 potentially regulates USP9X de-ubiquitinase activity. Finally, we show that knockdown of TDRD3 expression sensitizes breast cancer cells to chemotherapeutic drug-induced apoptosis, likely due to its regulation of USP9X. This study provides a novel candidate strategy for targeting apoptosis pathways in cancer therapy.
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Affiliation(s)
- Nithya Narayanan
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center , Duarte, CA, USA
| | - Zhihao Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center , Duarte, CA, USA
| | - Ling Li
- Division of Hematopoietic Stem Cell and Leukemia Research, Department of Hematology and HCT, Beckman Research Institute, City of Hope Cancer Center , Duarte, CA, USA
| | - Yanzhong Yang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center , Duarte, CA, USA
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40
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Su C, Gao X, Yang W, Zhao Y, Fu X, Cui X, Zhang C, Xin L, Ren Y, Li L, Shui W, Yang X, Wei M, Yang J. Phosphorylation of Tudor-SN, a novel substrate of JNK, is involved in the efficient recruitment of Tudor-SN into stress granules. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:562-571. [PMID: 28011284 DOI: 10.1016/j.bbamcr.2016.12.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/12/2016] [Accepted: 12/18/2016] [Indexed: 12/24/2022]
Abstract
Posttranslational modifications of certain stress granule (SG) proteins are closely related to the assembly of SGs, a type of cytoplasmic foci structure. Our previous studies revealed that the Tudor staphylococcal nuclease (Tudor-SN) protein participates in the formation of SGs. However, the functional significance of potential Tudor-SN modifications during stress has not been reported. In this study, we demonstrated that the Tudor-SN protein was phosphorylated at threonine 103 (T103) upon stimulation with arsenite. In addition, c-Jun N-terminal kinase (JNK) was found to be responsible for Tudor-SN phosphorylation at the T103 site. We further illustrated that either a T103A mutation or the suppression of phosphorylation of T103 by the JNK inhibitor SP600125 inhibited the efficient recruitment of Tudor-SN into SGs. In addition, the T103A mutation could affect the physical binding of Tudor-SN with the G3BP (Ras-GAP SH3 domain-binding protein) protein but not with the HuR (Hu antigen R) protein and AGTR1-3'UTR (3'-untranslated region of angiotensin II receptor, type 1) mRNA cargo. These data suggested that JNK-enhanced Tudor-SN phosphorylation promotes the interaction between Tudor-SN and G3BP and facilitates the efficient recruitment of Tudor-SN into SGs under conditions of sodium arsenite-induced oxidative stress. This finding provides novel insights into the physiological function of Tudor-SN modification.
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Affiliation(s)
- Chao Su
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Xingjie Gao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Wendong Yang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Yali Zhao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Xue Fu
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Xiaoteng Cui
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Chunyan Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Lingbiao Xin
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Yuanyuan Ren
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China
| | - Lixin Li
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Wenqing Shui
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Xi Yang
- Department of Immunology, University of Manitoba, 471 Apotex Centre, 750 McDermot Avenue, Winnipeg R3E 0T5, Canada
| | - Minxin Wei
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin 300070, China.
| | - Jie Yang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Laboratory of Molecular Immunology, Research Center of Basic Medical Science, Tianjin Medical University, Tianjin 300070, China; Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin 300070, China; Key Laboratory of Educational Ministry of China, Tianjin Medical University, Tianjin 300070, China.
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41
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Tsai WC, Gayatri S, Reineke LC, Sbardella G, Bedford MT, Lloyd RE. Arginine Demethylation of G3BP1 Promotes Stress Granule Assembly. J Biol Chem 2016; 291:22671-22685. [PMID: 27601476 DOI: 10.1074/jbc.m116.739573] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/15/2016] [Indexed: 12/22/2022] Open
Abstract
Stress granules (SGs) are cytoplasmic condensates of stalled messenger ribonucleoprotein complexes (mRNPs) that form when eukaryotic cells encounter environmental stress. RNA-binding proteins are enriched for arginine methylation and facilitate SG assembly through interactions involving regions of low amino acid complexity. How methylation of specific RNA-binding proteins regulates RNA granule assembly has not been characterized. Here, we examined the potent SG-nucleating protein Ras-GAP SH3-binding protein 1 (G3BP1), and found that G3BP1 is differentially methylated on specific arginine residues by protein arginine methyltransferase (PRMT) 1 and PRMT5 in its RGG domain. Several genetic and biochemical interventions that increased methylation repressed SG assembly, whereas interventions that decreased methylation promoted SG assembly. Arsenite stress quickly and reversibly decreased asymmetric arginine methylation on G3BP1. These data indicate that arginine methylation in the RGG domain prevents large SG assembly and rapid demethylation is a novel signal that regulates SG formation.
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Affiliation(s)
- Wei-Chih Tsai
- From the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Sitaram Gayatri
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Science Park, Smithville, Texas 78957, and
| | - Lucas C Reineke
- From the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Gianluca Sbardella
- Epigenetic Med Chem Lab, Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Science Park, Smithville, Texas 78957, and
| | - Richard E Lloyd
- From the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030,
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DNA and RNA topoisomerase activities of Top3β are promoted by mediator protein Tudor domain-containing protein 3. Proc Natl Acad Sci U S A 2016; 113:E5544-51. [PMID: 27582462 DOI: 10.1073/pnas.1605517113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Topoisomerase 3β (Top3β) can associate with the mediator protein Tudor domain-containing protein 3 (TDRD3) to participate in two gene expression processes of transcription and translation. Despite the apparent importance of TDRD3 in binding with Top3β and directing it to cellular compartments critical for gene expression, the biochemical mechanism of how TDRD3 can affect the functions of Top3β is not known. We report here sensitive biochemical assays for the activities of Top3β on DNA and RNA substrates in resolving topological entanglements and for the analysis of TDRD3 functions. TDRD3 stimulates the relaxation activity of Top3β on hypernegatively supercoiled DNA and changes the reaction from a distributive to a processive mode. Both supercoil retention assays and binding measurement by fluorescence anisotropy reveal a heretofore unknown preference for binding single-stranded nucleic acids over duplex. Whereas TDRD3 has a structure-specific binding preference, it does not discriminate between DNA and RNA. This unique property for binding with nucleic acids can have an important function in serving as a hub to form nucleoprotein complexes on DNA and RNA. To gain insight into the roles of Top3β on RNA metabolism, we designed an assay by annealing two single-stranded RNA circles with complementary sequences. Top3β is capable of converting two such single-stranded RNA circles into a double-stranded RNA circle, and this strand-annealing activity is enhanced by TDRD3. These results demonstrate that TDRD3 can enhance the biochemical activities of Top3β on both DNA and RNA substrates, in addition to its function of targeting Top3β to critical sites in subcellular compartments.
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Francisco-Velilla R, Fernandez-Chamorro J, Ramajo J, Martinez-Salas E. The RNA-binding protein Gemin5 binds directly to the ribosome and regulates global translation. Nucleic Acids Res 2016; 44:8335-51. [PMID: 27507887 PMCID: PMC5041490 DOI: 10.1093/nar/gkw702] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/31/2016] [Indexed: 12/21/2022] Open
Abstract
RNA-binding proteins (RBPs) play crucial roles in all organisms. The protein Gemin5 harbors two functional domains. The N-terminal domain binds to snRNAs targeting them for snRNPs assembly, while the C-terminal domain binds to IRES elements through a non-canonical RNA-binding site. Here we report a comprehensive view of the Gemin5 interactome; most partners copurified with the N-terminal domain via RNA bridges. Notably, Gemin5 sediments with the subcellular ribosome fraction, and His-Gemin5 binds to ribosome particles via its N-terminal domain. The interaction with the ribosome was lost in F381A and Y474A Gemin5 mutants, but not in W14A and Y15A. Moreover, the ribosomal proteins L3 and L4 bind directly with Gemin5, and conversely, Gemin5 mutants impairing the binding to the ribosome are defective in the interaction with L3 and L4. The overall polysome profile was affected by Gemin5 depletion or overexpression, concomitant to an increase or a decrease, respectively, of global protein synthesis. Gemin5, and G5-Nter as well, were detected on the polysome fractions. These results reveal the ribosome-binding capacity of the N-ter moiety, enabling Gemin5 to control global protein synthesis. Our study uncovers a crosstalk between this protein and the ribosome, and provides support for the view that Gemin5 may control translation elongation.
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Affiliation(s)
| | | | - Jorge Ramajo
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, 28049-Madrid, Spain
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44
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Poblete-Durán N, Prades-Pérez Y, Vera-Otarola J, Soto-Rifo R, Valiente-Echeverría F. Who Regulates Whom? An Overview of RNA Granules and Viral Infections. Viruses 2016; 8:v8070180. [PMID: 27367717 PMCID: PMC4974515 DOI: 10.3390/v8070180] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/10/2016] [Accepted: 06/21/2016] [Indexed: 12/22/2022] Open
Abstract
After viral infection, host cells respond by mounting an anti-viral stress response in order to create a hostile atmosphere for viral replication, leading to the shut-off of mRNA translation (protein synthesis) and the assembly of RNA granules. Two of these RNA granules have been well characterized in yeast and mammalian cells, stress granules (SGs), which are translationally silent sites of RNA triage and processing bodies (PBs), which are involved in mRNA degradation. This review discusses the role of these RNA granules in the evasion of anti-viral stress responses through virus-induced remodeling of cellular ribonucleoproteins (RNPs).
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Affiliation(s)
- Natalia Poblete-Durán
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Yara Prades-Pérez
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago 8330024, Chile.
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
| | - Fernando Valiente-Echeverría
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Independencia 1027, Santiago, 8389100, Chile.
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45
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Protter DSW, Parker R. Principles and Properties of Stress Granules. Trends Cell Biol 2016; 26:668-679. [PMID: 27289443 DOI: 10.1016/j.tcb.2016.05.004] [Citation(s) in RCA: 1006] [Impact Index Per Article: 125.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 12/27/2022]
Abstract
Stress granules are assemblies of untranslating messenger ribonucleoproteins (mRNPs) that form from mRNAs stalled in translation initiation. Stress granules form through interactions between mRNA-binding proteins that link together populations of mRNPs. Interactions promoting stress granule formation include conventional protein-protein interactions as well as interactions involving intrinsically disordered regions (IDRs) of proteins. Assembly and disassembly of stress granules are modulated by various post-translational modifications as well as numerous ATP-dependent RNP or protein remodeling complexes, illustrating that stress granules represent an active liquid wherein energy input maintains their dynamic state. Stress granule formation modulates the stress response, viral infection, and signaling pathways. Persistent or aberrant stress granule formation contributes to neurodegenerative disease and some cancers.
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Affiliation(s)
- David S W Protter
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA.
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46
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Ahmad M, Xue Y, Lee SK, Martindale JL, Shen W, Li W, Zou S, Ciaramella M, Debat H, Nadal M, Leng F, Zhang H, Wang Q, Siaw GEL, Niu H, Pommier Y, Gorospe M, Hsieh TS, Tse-Dinh YC, Xu D, Wang W. RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals. Nucleic Acids Res 2016; 44:6335-49. [PMID: 27257063 PMCID: PMC4994864 DOI: 10.1093/nar/gkw508] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022] Open
Abstract
DNA Topoisomerases are essential to resolve topological problems during DNA metabolism in all species. However, the prevalence and function of RNA topoisomerases remain uncertain. Here, we show that RNA topoisomerase activity is prevalent in Type IA topoisomerases from bacteria, archaea, and eukarya. Moreover, this activity always requires the conserved Type IA core domains and the same catalytic residue used in DNA topoisomerase reaction; however, it does not absolutely require the non-conserved carboxyl-terminal domain (CTD), which is necessary for relaxation reactions of supercoiled DNA. The RNA topoisomerase activity of human Top3β differs from that of Escherichia coli topoisomerase I in that the former but not the latter requires the CTD, indicating that topoisomerases have developed distinct mechanisms during evolution to catalyze RNA topoisomerase reactions. Notably, Top3β proteins from several animals associate with polyribosomes, which are units of mRNA translation, whereas the Top3 homologs from E. coli and yeast lack the association. The Top3β-polyribosome association requires TDRD3, which directly interacts with Top3β and is present in animals but not bacteria or yeast. We propose that RNA topoisomerases arose in the early RNA world, and that they are retained through all domains of DNA-based life, where they mediate mRNA translation as part of polyribosomes in animals.
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Affiliation(s)
- Muzammil Ahmad
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Yutong Xue
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Seung Kyu Lee
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- RNA Regulation Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Weiping Shen
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Wen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, PeKing University, Beijing 1000871, China
| | - Sige Zou
- Translational Gerontology Branch, National Institute on Aging, National Institute of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Maria Ciaramella
- Institute of Biosciences and Bioresources, National Research Council of Italy, Naples 80131, Italy
| | - Hélène Debat
- Institut Jacques Monod, CNRS-Université Paris Diderot-UMR7592, 15 rue Hélène Brion, 75205 Paris Cedex, France
| | - Marc Nadal
- Institut Jacques Monod, CNRS-Université Paris Diderot-UMR7592, 15 rue Hélène Brion, 75205 Paris Cedex, France
| | - Fenfei Leng
- Department of Chemistry & Biochemistry, Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Hongliang Zhang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Quan Wang
- Molecular and Cellular Biochemistry Department, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Grace Ee-Lu Siaw
- Institute of Cellular Organistic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hengyao Niu
- Molecular and Cellular Biochemistry Department, Indiana University, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Myriam Gorospe
- RNA Regulation Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Tao-Shih Hsieh
- Institute of Cellular Organistic Biology, Academia Sinica, Taipei 11529, Taiwan Department of Biochemistry, Duke University Medical Center, Durham, NC 73532, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry & Biochemistry, Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, PeKing University, Beijing 1000871, China
| | - Weidong Wang
- Genome Instability and Chromatin Remodeling Section, Lab of Genetics, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
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Valentin-Vega YA, Wang YD, Parker M, Patmore DM, Kanagaraj A, Moore J, Rusch M, Finkelstein D, Ellison DW, Gilbertson RJ, Zhang J, Kim HJ, Taylor JP. Cancer-associated DDX3X mutations drive stress granule assembly and impair global translation. Sci Rep 2016; 6:25996. [PMID: 27180681 PMCID: PMC4867597 DOI: 10.1038/srep25996] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/21/2016] [Indexed: 12/26/2022] Open
Abstract
DDX3X is a DEAD-box RNA helicase that has been implicated in multiple aspects of RNA metabolism including translation initiation and the assembly of stress granules (SGs). Recent genomic studies have reported recurrent DDX3X mutations in numerous tumors including medulloblastoma (MB), but the physiological impact of these mutations is poorly understood. Here we show that a consistent feature of MB-associated mutations is SG hyper-assembly and concomitant translation impairment. We used CLIP-seq to obtain a comprehensive assessment of DDX3X binding targets and ribosome profiling for high-resolution assessment of global translation. Surprisingly, mutant DDX3X expression caused broad inhibition of translation that impacted DDX3X targeted and non-targeted mRNAs alike. Assessment of translation efficiency with single-cell resolution revealed that SG hyper-assembly correlated precisely with impaired global translation. SG hyper-assembly and translation impairment driven by mutant DDX3X were rescued by a genetic approach that limited SG assembly and by deletion of the N-terminal low complexity domain within DDX3X. Thus, in addition to a primary defect at the level of translation initiation caused by DDX3X mutation, SG assembly itself contributes to global translation inhibition. This work provides mechanistic insights into the consequences of cancer-related DDX3X mutations, suggesting that globally reduced translation may provide a context-dependent survival advantage that must be considered as a possible contributor to tumorigenesis.
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Affiliation(s)
- Yasmine A. Valentin-Vega
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yong-Dong Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Deanna M. Patmore
- Department of Oncology, Cambridge Cancer Centre, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Anderson Kanagaraj
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jennifer Moore
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David W. Ellison
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Richard J. Gilbertson
- Department of Oncology, Cambridge Cancer Centre, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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48
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Ravel-Chapuis A, Klein Gunnewiek A, Bélanger G, Crawford Parks TE, Côté J, Jasmin BJ. Staufen1 impairs stress granule formation in skeletal muscle cells from myotonic dystrophy type 1 patients. Mol Biol Cell 2016; 27:1728-39. [PMID: 27030674 PMCID: PMC4884064 DOI: 10.1091/mbc.e15-06-0356] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 03/25/2016] [Indexed: 11/11/2022] Open
Abstract
Myotonic dystrophy (DM1) is caused by an expansion of CUG repeats (CUG(exp)) in the DMPK mRNA 3'UTR. CUG(exp)-containing mRNAs become toxic to cells by misregulating RNA-binding proteins. Here we investigated the consequence of this RNA toxicity on the cellular stress response. We report that cell stress efficiently triggers formation of stress granules (SGs) in proliferating, quiescent, and differentiated muscle cells, as shown by the appearance of distinct cytoplasmic TIA-1- and DDX3-containing foci. We show that Staufen1 is also dynamically recruited into these granules. Moreover, we discovered that DM1 myoblasts fail to properly form SGs in response to arsenite. This blockage was not observed in DM1 fibroblasts, demonstrating a cell type-specific defect. DM1 myoblasts display increased expression and sequestration of toxic CUG(exp) mRNAs compared with fibroblasts. Of importance, down-regulation of Staufen1 in DM1 myoblasts rescues SG formation. Together our data show that Staufen1 participates in the inhibition of SG formation in DM1 myoblasts. These results reveal that DM1 muscle cells fail to properly respond to stress, thereby likely contributing to the complex pathogenesis of DM1.
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Affiliation(s)
- Aymeric Ravel-Chapuis
- Department of Cellular and Molecular Medicine and Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Amanda Klein Gunnewiek
- Department of Cellular and Molecular Medicine and Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Guy Bélanger
- Department of Cellular and Molecular Medicine and Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Tara E Crawford Parks
- Department of Cellular and Molecular Medicine and Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jocelyn Côté
- Department of Cellular and Molecular Medicine and Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Bernard J Jasmin
- Department of Cellular and Molecular Medicine and Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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DDX3 Interacts with Influenza A Virus NS1 and NP Proteins and Exerts Antiviral Function through Regulation of Stress Granule Formation. J Virol 2016; 90:3661-75. [PMID: 26792746 DOI: 10.1128/jvi.03010-15] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/14/2016] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED DDX3 belongs to the DEAD box RNA helicase family and is a multifunctional protein affecting the life cycle of a variety of viruses. However, its role in influenza virus infection is unknown. In this study, we explored the potential role of DDX3 in influenza virus life cycle and discovered that DDX3 is an antiviral protein. Since many host proteins affect virus life cycle by interacting with certain components of the viral machinery, we first verified whether DDX3 has any viral interaction partners. Immunoprecipitation studies revealed NS1 and NP as direct interaction partners of DDX3. Stress granules (SGs) are known to be antiviral and do form in influenza virus-infected cells expressing defective NS1 protein. Additionally, a recent study showed that DDX3 is an important SG-nucleating factor. We thus explored whether DDX3 plays a role in influenza virus infection through regulation of SGs. Our results showed that SGs were formed in infected cells upon infection with a mutant influenza virus lacking functional NS1 (del NS1) protein, and DDX3 colocalized with NP in SGs. We further determined that the DDX3 helicase domain did not interact with NS1 and NP; however, it was essential for DDX3 localization in virus-induced SGs. Knockdown of DDX3 resulted in impaired SG formation and led to increased virus titers. Taken together, our results identified DDX3 as an antiviral protein with a role in virus-induced SG formation. IMPORTANCE DDX3 is a multifunctional RNA helicase and has been reported to be involved in regulating various virus life cycles. However, its function during influenza A virus infection remains unknown. In this study, we demonstrated that DDX3 is capable of interacting with influenza virus NS1 and NP proteins; DDX3 and NP colocalize in the del NS1 virus-induced SGs. Furthermore, knockdown of DDX3 impaired SG formation and led to a decreased virus titer. Thus, we provided evidence that DDX3 is an antiviral protein during influenza virus infection and its antiviral activity is through regulation of SG formation. Our findings provide knowledge about the function of DDX3 in the influenza virus life cycle and information for future work on manipulating the SG pathway and its components to fight influenza virus infection.
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50
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Aulas A, Vande Velde C. Alterations in stress granule dynamics driven by TDP-43 and FUS: a link to pathological inclusions in ALS? Front Cell Neurosci 2015; 9:423. [PMID: 26557057 PMCID: PMC4615823 DOI: 10.3389/fncel.2015.00423] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/06/2015] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are RNA-containing cytoplasmic foci formed in response to stress exposure. Since their discovery in 1999, over 120 proteins have been described to be localized to these structures (in 154 publications). Most of these components are RNA binding proteins (RBPs) or are involved in RNA metabolism and translation. SGs have been linked to several pathologies including inflammatory diseases, cancer, viral infection, and neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). In ALS and FTD, the majority of cases have no known etiology and exposure to external stress is frequently proposed as a contributor to either disease initiation or the rate of disease progression. Of note, both ALS and FTD are characterized by pathological inclusions, where some well-known SG markers localize with the ALS related proteins TDP-43 and FUS. We propose that TDP-43 and FUS serve as an interface between genetic susceptibility and environmental stress exposure in disease pathogenesis. Here, we will discuss the role of TDP-43 and FUS in SG dynamics and how disease-linked mutations affect this process.
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Affiliation(s)
- Anaïs Aulas
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal Montréal, QC, Canada ; Department of Biochemistry, Université de Montréal Montréal, QC, Canada
| | - Christine Vande Velde
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal Montréal, QC, Canada ; Department of Neurosciences, Université de Montréal Montréal, QC, Canada
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