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Scarpitti MR, Warrick JE, Yoder EL, Kearse MG. A noncanonical RNA-binding domain of the fragile X protein, FMRP, elicits translational repression independent of mRNA G-quadruplexes. J Biol Chem 2022; 298:102660. [PMID: 36328245 PMCID: PMC9712993 DOI: 10.1016/j.jbc.2022.102660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2022] Open
Abstract
Loss of functional fragile X mental retardation protein (FMRP) causes fragile X syndrome, the leading form of inherited intellectual disability and the most common monogenic cause of autism spectrum disorders. FMRP is an RNA-binding protein that controls neuronal mRNA localization and translation. FMRP is thought to inhibit translation elongation after being recruited to target transcripts via binding RNA G-quadruplexes (G4s) within the coding sequence. Here, we directly test this model and report that FMRP inhibits translation independent of mRNA G4s. Furthermore, we found that the RGG box motif together with its natural C-terminal domain forms a noncanonical RNA-binding domain (ncRBD) that is essential for translational repression. The ncRBD elicits broad RNA-binding ability and binds to multiple reporter mRNAs and all four homopolymeric RNAs. Serial deletion analysis of the ncRBD identified that the regions required for mRNA binding and translational repression overlap but are not identical. Consistent with FMRP stalling elongating ribosomes and causing the accumulation of slowed 80S ribosomes, transcripts bound by FMRP via the ncRBD cosediment with heavier polysomes and were present in puromycin-resistant ribosome complexes. Together, this work identifies a ncRBD and translational repression domain that shifts our understanding of how FMRP inhibits translation independent of mRNA G4s.
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Affiliation(s)
- MaKenzie R Scarpitti
- The Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Julia E Warrick
- The Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Evelyn L Yoder
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Michael G Kearse
- The Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.
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2
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Yang J, Hall JE, Jose PA, Chen K, Zeng C. Comprehensive insights in GRK4 and hypertension: From mechanisms to potential therapeutics. Pharmacol Ther 2022; 239:108194. [DOI: 10.1016/j.pharmthera.2022.108194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/30/2022] [Accepted: 04/21/2022] [Indexed: 11/24/2022]
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3
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Kieffer F, Hilal F, Gay AS, Debayle D, Pronot M, Poupon G, Lacagne I, Bardoni B, Martin S, Gwizdek C. Combining affinity purification and mass spectrometry to define the network of the nuclear proteins interacting with the N-terminal region of FMRP. Front Mol Biosci 2022; 9:954087. [PMID: 36237573 PMCID: PMC9553004 DOI: 10.3389/fmolb.2022.954087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Fragile X-Syndrome (FXS) represents the most common inherited form of intellectual disability and the leading monogenic cause of Autism Spectrum Disorders. In most cases, this disease results from the absence of expression of the protein FMRP encoded by the FMR1 gene (Fragile X messenger ribonucleoprotein 1). FMRP is mainly defined as a cytoplasmic RNA-binding protein regulating the local translation of thousands of target mRNAs. Interestingly, FMRP is also able to shuttle between the nucleus and the cytoplasm. However, to date, its roles in the nucleus of mammalian neurons are just emerging. To broaden our insight into the contribution of nuclear FMRP in mammalian neuronal physiology, we identified here a nuclear interactome of the protein by combining subcellular fractionation of rat forebrains with pull‐ down affinity purification and mass spectrometry analysis. By this approach, we listed 55 candidate nuclear partners. This interactome includes known nuclear FMRP-binding proteins as Adar or Rbm14 as well as several novel candidates, notably Ddx41, Poldip3, or Hnrnpa3 that we further validated by target‐specific approaches. Through our approach, we identified factors involved in different steps of mRNA biogenesis, as transcription, splicing, editing or nuclear export, revealing a potential central regulatory function of FMRP in the biogenesis of its target mRNAs. Therefore, our work considerably enlarges the nuclear proteins interaction network of FMRP in mammalian neurons and lays the basis for exciting future mechanistic studies deepening the roles of nuclear FMRP in neuronal physiology and the etiology of the FXS.
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Affiliation(s)
- Félicie Kieffer
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Fahd Hilal
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Anne-Sophie Gay
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Delphine Debayle
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Marie Pronot
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Gwénola Poupon
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Iliona Lacagne
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Barbara Bardoni
- Université Côte d'Azur, Institut National de la Santé Et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Stéphane Martin
- Université Côte d'Azur, Institut National de la Santé Et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Carole Gwizdek
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
- *Correspondence: Carole Gwizdek,
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4
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Chen Y, Guo L, Han M, Zhang S, Chen Y, Zou J, Bai S, Cheng G, Zeng Y. Cerebellum Neuropathology and Motor Skill Deficits in Fragile X Syndrome. Int J Dev Neurosci 2022; 82:557-568. [DOI: 10.1002/jdn.10217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Yu‐shan Chen
- Brain Science and Advanced Technology Institute, School of Medicine Wuhan University of Science and Technology Wuhan China
| | - Liu Guo
- Brain Science and Advanced Technology Institute, School of Medicine Wuhan University of Science and Technology Wuhan China
| | - Man Han
- Brain Science and Advanced Technology Institute, School of Medicine Wuhan University of Science and Technology Wuhan China
| | - Si‐ming Zhang
- Brain Science and Advanced Technology Institute, School of Medicine Wuhan University of Science and Technology Wuhan China
| | - Yi‐qi Chen
- Brain Science and Advanced Technology Institute, School of Medicine Wuhan University of Science and Technology Wuhan China
| | - Jia Zou
- Brain Science and Advanced Technology Institute, School of Medicine Wuhan University of Science and Technology Wuhan China
| | - Shu‐yuan Bai
- Brain Science and Advanced Technology Institute, School of Medicine Wuhan University of Science and Technology Wuhan China
| | - Gui‐rong Cheng
- Brain Science and Advanced Technology Institute, School of Medicine Wuhan University of Science and Technology Wuhan China
| | - Yan Zeng
- Brain Science and Advanced Technology Institute, School of Medicine Wuhan University of Science and Technology Wuhan China
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5
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D’Incal C, Broos J, Torfs T, Kooy RF, Vanden Berghe W. Towards Kinase Inhibitor Therapies for Fragile X Syndrome: Tweaking Twists in the Autism Spectrum Kinase Signaling Network. Cells 2022; 11:cells11081325. [PMID: 35456004 PMCID: PMC9029738 DOI: 10.3390/cells11081325] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 12/12/2022] Open
Abstract
Absence of the Fragile X Mental Retardation Protein (FMRP) causes autism spectrum disorders and intellectual disability, commonly referred to as the Fragile X syndrome. FMRP is a negative regulator of protein translation and is essential for neuronal development and synapse formation. FMRP is a target for several post-translational modifications (PTMs) such as phosphorylation and methylation, which tightly regulate its cellular functions. Studies have indicated the involvement of FMRP in a multitude of cellular pathways, and an absence of FMRP was shown to affect several neurotransmitter receptors, for example, the GABA receptor and intracellular signaling molecules such as Akt, ERK, mTOR, and GSK3. Interestingly, many of these molecules function as protein kinases or phosphatases and thus are potentially amendable by pharmacological treatment. Several treatments acting on these kinase-phosphatase systems have been shown to be successful in preclinical models; however, they have failed to convincingly show any improvements in clinical trials. In this review, we highlight the different protein kinase and phosphatase studies that have been performed in the Fragile X syndrome. In our opinion, some of the paradoxical study conclusions are potentially due to the lack of insight into integrative kinase signaling networks in the disease. Quantitative proteome analyses have been performed in several models for the FXS to determine global molecular processes in FXS. However, only one phosphoproteomics study has been carried out in Fmr1 knock-out mouse embryonic fibroblasts, and it showed dysfunctional protein kinase and phosphatase signaling hubs in the brain. This suggests that the further use of phosphoproteomics approaches in Fragile X syndrome holds promise for identifying novel targets for kinase inhibitor therapies.
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Affiliation(s)
- Claudio D’Incal
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium; (C.D.); (J.B.); (T.T.)
- Department of Medical Genetics, University of Antwerp, 2000 Antwerp, Belgium;
| | - Jitse Broos
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium; (C.D.); (J.B.); (T.T.)
| | - Thierry Torfs
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium; (C.D.); (J.B.); (T.T.)
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, 2000 Antwerp, Belgium;
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium; (C.D.); (J.B.); (T.T.)
- Correspondence: ; Tel.: +0032-(0)-32-652-657
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6
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Bleuzé L, Triaca V, Borreca A. FMRP-Driven Neuropathology in Autistic Spectrum Disorder and Alzheimer's disease: A Losing Game. Front Mol Biosci 2021; 8:699613. [PMID: 34760921 PMCID: PMC8573832 DOI: 10.3389/fmolb.2021.699613] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/24/2021] [Indexed: 12/28/2022] Open
Abstract
Fragile X mental retardation protein (FMRP) is an RNA binding protein (RBP) whose absence is essentially associated to Fragile X Syndrome (FXS). As an RNA Binding Protein (RBP), FMRP is able to bind and recognize different RNA structures and the control of specific mRNAs is important for neuronal synaptic plasticity. Perturbations of this pathway have been associated with the autistic spectrum. One of the FMRP partners is the APP mRNA, the main protagonist of Alzheimer’s disease (AD), thereby regulating its protein level and metabolism. Therefore FMRP is associated to two neurodevelopmental and age-related degenerative conditions, respectively FXS and AD. Although these pathologies are characterized by different features, they have been reported to share a number of common molecular and cellular players. The aim of this review is to describe the double-edged sword of FMRP in autism and AD, possibly allowing the elucidation of key shared underlying mechanisms and neuronal circuits. As an RBP, FMRP is able to regulate APP expression promoting the production of amyloid β fragments. Indeed, FXS patients show an increase of amyloid β load, typical of other neurological disorders, such as AD, Down syndrome, Parkinson’s Disease, etc. Beyond APP dysmetabolism, the two neurodegenerative conditions share molecular targets, brain circuits and related cognitive deficits. In this review, we will point out the potential common neuropathological pattern which needs to be addressed and we will hopefully contribute to clarifying the complex phenotype of these two neurorological disorders, in order to pave the way for a novel, common disease-modifying therapy.
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Affiliation(s)
- Louis Bleuzé
- University de Rennes 1, Rennes, France.,Humanitas Clinical and Research Center-IRCCS, Rozzano (Mi), Italy
| | - Viviana Triaca
- Institute of Biochemistry and Cell Biology, National Research Council (CNR-IBBC), International Campus A. Buzzati Traverso, Monterotondo, Italy
| | - Antonella Borreca
- Humanitas Clinical and Research Center-IRCCS, Rozzano (Mi), Italy.,Institute of Neuroscience-National Research Council (CNR-IN), Milan, Italy
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7
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Gilmer O, Quignon E, Jousset AC, Paillart JC, Marquet R, Vivet-Boudou V. Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond. Viruses 2021; 13:1894. [PMID: 34696322 PMCID: PMC8537439 DOI: 10.3390/v13101894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques.
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Affiliation(s)
| | | | | | | | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67000 Strasbourg, France; (O.G.); (E.Q.); (A.-C.J.); (J.-C.P.)
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR9002, F-67000 Strasbourg, France; (O.G.); (E.Q.); (A.-C.J.); (J.-C.P.)
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8
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Abstract
GABAB receptors are implicated in numerous central nervous system-based behaviours and mechanisms, including cognitive processing in preclinical animal models. Homeostatic changes in the expression and function of these receptors across brain structures have been found to affect cognitive processing. Numerous preclinical studies have focused on the role of GABAB receptors in learning, memory and cognition per se with some interesting, although sometimes contradictory, findings. The majority of the existing clinical literature focuses on alterations in GABAB receptor function in conditions and disorders whose main symptomatology includes deficits in cognitive processing. The aim of this chapter is to delineate the role of GABAB receptors in cognitive processes in health and disease of animal models and human clinical populations. More specifically, this review aims to present literature on the role of GABAB receptors in animal models with cognitive deficits, especially those of learning and memory. Further, it aims to capture the progress and advances of research studies on the effects of GABAB receptor compounds in neurodevelopmental and neurodegenerative conditions with cognitive dysfunctions. The neurodevelopmental conditions covered include autism spectrum disorders, fragile X syndrome and Down's syndrome and the neurodegenerative conditions discussed are Alzheimer's disease, epilepsy and autoimmune anti-GABAB encephalitis. Although some findings are contradictory, results indicate a possible therapeutic role of GABAB receptor compounds for the treatment of cognitive dysfunction and learning/memory impairments for some of these conditions, especially in neurodegeneration. Moreover, future research efforts should aim to develop selective GABAB receptor compounds with minimal, if any, side effects.
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9
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Wirecki TK, Merdas K, Bernat A, Boniecki MJ, Bujnicki JM, Stefaniak F. RNAProbe: a web server for normalization and analysis of RNA structure probing data. Nucleic Acids Res 2020; 48:W292-W299. [PMID: 32504492 PMCID: PMC7319577 DOI: 10.1093/nar/gkaa396] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/02/2020] [Accepted: 06/05/2020] [Indexed: 02/03/2023] Open
Abstract
RNA molecules play key roles in all living cells. Knowledge of the structural characteristics of RNA molecules allows for a better understanding of the mechanisms of their action. RNA chemical probing allows us to study the susceptibility of nucleotides to chemical modification, and the information obtained can be used to guide secondary structure prediction. These experimental results can be analyzed using various computational tools, which, however, requires additional, tedious steps (e.g., further normalization of the reactivities and visualization of the results), for which there are no fully automated methods. Here, we introduce RNAProbe, a web server that facilitates normalization, analysis, and visualization of the low-pass SHAPE, DMS and CMCT probing results with the modification sites detected by capillary electrophoresis. RNAProbe automatically analyzes chemical probing output data and turns tedious manual work into a one-minute assignment. RNAProbe performs normalization based on a well-established protocol, utilizes recognized secondary structure prediction methods, and generates high-quality images with structure representations and reactivity heatmaps. It summarizes the results in the form of a spreadsheet, which can be used for comparative analyses between experiments. Results of predictions with normalized reactivities are also collected in text files, providing interoperability with bioinformatics workflows. RNAProbe is available at https://rnaprobe.genesilico.pl.
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Affiliation(s)
- Tomasz K Wirecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Katarzyna Merdas
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Agata Bernat
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Michał J Boniecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.,Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland
| | - Filip Stefaniak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
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10
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Prieto M, Folci A, Martin S. Post-translational modifications of the Fragile X Mental Retardation Protein in neuronal function and dysfunction. Mol Psychiatry 2020; 25:1688-1703. [PMID: 31822816 DOI: 10.1038/s41380-019-0629-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/17/2022]
Abstract
The Fragile X Mental Retardation Protein (FMRP) is an RNA-binding protein essential to the regulation of local translation at synapses. In the mammalian brain, synapses are constantly formed and eliminated throughout development to achieve functional neuronal networks. At the molecular level, thousands of proteins cooperate to accomplish efficient neuronal communication. Therefore, synaptic protein levels and their functional interactions need to be tightly regulated. FMRP generally acts as a translational repressor of its mRNA targets. FMRP is the target of several post-translational modifications (PTMs) that dynamically regulate its function. Here we provide an overview of the PTMs controlling the FMRP function and discuss how their spatiotemporal interplay contributes to the physiological regulation of FMRP. Importantly, FMRP loss-of-function leads to Fragile X syndrome (FXS), a rare genetic developmental condition causing a range of neurological alterations including intellectual disability (ID), learning and memory impairments, autistic-like features and seizures. Here, we also explore the possibility that recently reported missense mutations in the FMR1 gene disrupt the PTM homoeostasis of FMRP, thus participating in the aetiology of FXS. This suggests that the pharmacological targeting of PTMs may be a promising strategy to develop innovative therapies for patients carrying such missense mutations.
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Affiliation(s)
- Marta Prieto
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France
| | | | - Stéphane Martin
- Université Côte d'Azur, INSERM, CNRS, IPMC, Valbonne, France.
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11
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Suardi GAM, Haddad LA. FMRP ribonucleoprotein complexes and RNA homeostasis. ADVANCES IN GENETICS 2020; 105:95-136. [PMID: 32560791 DOI: 10.1016/bs.adgen.2020.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Fragile Mental Retardation 1 gene (FMR1), at Xq27.3, encodes the fragile mental retardation protein (FMRP), and displays in its 5'-untranslated region a series of polymorphic CGG triplet repeats that may undergo dynamic mutation. Fragile X syndrome (FXS) is the leading cause of inherited intellectual disability among men, and is most frequently due to FMR1 full mutation and consequent transcription repression. FMR1 premutations may associate with at least two other clinical conditions, named fragile X-associated primary ovarian insufficiency (FXPOI) and tremor and ataxia syndrome (FXTAS). While FXPOI and FXTAS appear to be mediated by FMR1 mRNA accumulation, relative reduction of FMRP, and triplet repeat translation, FXS is due to the lack of the RNA-binding protein FMRP. Besides its function as mRNA translation repressor in neuronal and stem/progenitor cells, RNA editing roles have been assigned to FMRP. In this review, we provide a brief description of FMR1 transcribed microsatellite and associated clinical disorders, and discuss FMRP molecular roles in ribonucleoprotein complex assembly and trafficking, as well as aspects of RNA homeostasis affected in FXS cells.
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Affiliation(s)
- Gabriela Aparecida Marcondes Suardi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luciana Amaral Haddad
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
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12
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Cataloguing and Selection of mRNAs Localized to Dendrites in Neurons and Regulated by RNA-Binding Proteins in RNA Granules. Biomolecules 2020; 10:biom10020167. [PMID: 31978946 PMCID: PMC7072219 DOI: 10.3390/biom10020167] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
Spatiotemporal translational regulation plays a key role in determining cell fate and function. Specifically, in neurons, local translation in dendrites is essential for synaptic plasticity and long-term memory formation. To achieve local translation, RNA-binding proteins in RNA granules regulate target mRNA stability, localization, and translation. To date, mRNAs localized to dendrites have been identified by comprehensive analyses. In addition, mRNAs associated with and regulated by RNA-binding proteins have been identified using various methods in many studies. However, the results obtained from these numerous studies have not been compiled together. In this review, we have catalogued mRNAs that are localized to dendrites and are associated with and regulated by the RNA-binding proteins fragile X mental retardation protein (FMRP), RNA granule protein 105 (RNG105, also known as Caprin1), Ras-GAP SH3 domain binding protein (G3BP), cytoplasmic polyadenylation element binding protein 1 (CPEB1), and staufen double-stranded RNA binding proteins 1 and 2 (Stau1 and Stau2) in RNA granules. This review provides comprehensive information on dendritic mRNAs, the neuronal functions of mRNA-encoded proteins, the association of dendritic mRNAs with RNA-binding proteins in RNA granules, and the effects of RNA-binding proteins on mRNA regulation. These findings provide insights into the mechanistic basis of protein-synthesis-dependent synaptic plasticity and memory formation and contribute to future efforts to understand the physiological implications of local regulation of dendritic mRNAs in neurons.
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13
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Maurin T, Lebrigand K, Castagnola S, Paquet A, Jarjat M, Popa A, Grossi M, Rage F, Bardoni B. HITS-CLIP in various brain areas reveals new targets and new modalities of RNA binding by fragile X mental retardation protein. Nucleic Acids Res 2019; 46:6344-6355. [PMID: 29668986 PMCID: PMC6158598 DOI: 10.1093/nar/gky267] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 03/29/2018] [Indexed: 01/19/2023] Open
Abstract
Fragile X syndrome (FXS), the most common form of inherited intellectual disability, is due to the functional deficiency of the fragile X mental retardation protein (FMRP), an RNA-binding protein involved in translational regulation of many messenger RNAs, playing key roles in synaptic morphology and plasticity. To date, no effective treatment for FXS is available. We searched for FMRP targets by HITS-CLIP during early development of multiple mouse brain regions (hippocampus, cortex and cerebellum) at a time of brain development when FMRP is most highly expressed and synaptogenesis reaches a peak. We identified the largest dataset of mRNA targets of FMRP available in brain and we defined their cellular origin. We confirmed the G-quadruplex containing structure as an enriched motif in FMRP RNA targets. In addition to four less represented motifs, our study points out that, in the brain, CTGKA is the prominent motif bound by FMRP, which recognizes it when not engaged in Watson–Crick pairing. All of these motifs negatively modulated the expression level of a reporter protein. While the repertoire of FMRP RNA targets in cerebellum is quite divergent, the ones of cortex and hippocampus are vastly overlapping. In these two brain regions, the Phosphodiesterase 2a (Pde2a) mRNA is a prominent target of FMRP, which modulates its translation and intracellular transport. This enzyme regulates the homeostasis of cAMP and cGMP and represents a novel and attractive therapeutic target to treat FXS.
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Affiliation(s)
- Thomas Maurin
- Université Côte d'Azur, CNRS, IPMC, 06560 Valbonne, France.,CNRS LIA « Neogenex », 06560 Valbonne, France
| | | | - Sara Castagnola
- Université Côte d'Azur, CNRS, IPMC, 06560 Valbonne, France.,CNRS LIA « Neogenex », 06560 Valbonne, France
| | - Agnès Paquet
- Université Côte d'Azur, CNRS, IPMC, 06560 Valbonne, France
| | - Marielle Jarjat
- Université Côte d'Azur, CNRS, IPMC, 06560 Valbonne, France.,CNRS LIA « Neogenex », 06560 Valbonne, France
| | - Alexandra Popa
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
| | - Mauro Grossi
- Université Côte d'Azur, CNRS, IPMC, 06560 Valbonne, France.,CNRS LIA « Neogenex », 06560 Valbonne, France
| | - Florence Rage
- CNRS, Institut de Génétique Moléculaire, 34293 Montpellier, France
| | - Barbara Bardoni
- CNRS LIA « Neogenex », 06560 Valbonne, France.,Université Côte d'Azur, INSERM, CNRS, IPMC, 06560 Valbonne, France
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14
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Maurin T, Bardoni B. Fragile X Mental Retardation Protein: To Be or Not to Be a Translational Enhancer. Front Mol Biosci 2018; 5:113. [PMID: 30619879 PMCID: PMC6297276 DOI: 10.3389/fmolb.2018.00113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/26/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Thomas Maurin
- Université Côte d'Azur, CNRS UMR7275, Institute of Molecular and Cellular Pharmacology, Valbonne, France.,CNRS LIA "Neogenex", Valbonne, France
| | - Barbara Bardoni
- CNRS LIA "Neogenex", Valbonne, France.,Université Côte d'Azur, INSERM, CNRS UMR7275, Institute of Molecular and Cellular Pharmacology, Valbonne, France
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15
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Gallagher C, Ramos A. Joining the dots - protein-RNA interactions mediating local mRNA translation in neurons. FEBS Lett 2018; 592:2932-2947. [PMID: 29856909 DOI: 10.1002/1873-3468.13121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/24/2018] [Accepted: 05/30/2018] [Indexed: 01/26/2023]
Abstract
Establishing and maintaining the complex network of connections required for neuronal communication requires the transport and in situ translation of large groups of mRNAs to create local proteomes. In this Review, we discuss the regulation of local mRNA translation in neurons and the RNA-binding proteins that recognise RNA zipcode elements and connect the mRNAs to the cellular transport networks, as well as regulate their translation control. However, mRNA recognition by the regulatory proteins is mediated by the combinatorial action of multiple RNA-binding domains. This increases the specificity and affinity of the interaction, while allowing the protein to recognise a diverse set of targets and mediate a range of mechanisms for translational regulation. The structural and molecular understanding of the interactions can be used together with novel microscopy and transcriptome-wide data to build a mechanistic framework for the regulation of local mRNA translation.
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Affiliation(s)
- Christopher Gallagher
- Institute of Structural and Molecular Biology, University College London, UK.,The Francis Crick Institute, London, UK
| | - Andres Ramos
- Institute of Structural and Molecular Biology, University College London, UK
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16
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Castagnola S, Bardoni B, Maurin T. The Search for an Effective Therapy to Treat Fragile X Syndrome: Dream or Reality? Front Synaptic Neurosci 2017; 9:15. [PMID: 29163124 PMCID: PMC5681520 DOI: 10.3389/fnsyn.2017.00015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/16/2017] [Indexed: 12/22/2022] Open
Abstract
Fragile X Syndrome (FXS) is the most common form of intellectual disability and a primary cause of autism. It originates from the lack of the Fragile X Mental Retardation Protein (FMRP), which is an RNA-binding protein encoded by the Fragile X Mental Retardation Gene 1 (FMR1) gene. Multiple roles have been attributed to this protein, ranging from RNA transport (from the nucleus to the cytoplasm, but also along neurites) to translational control of mRNAs. Over the last 20 years many studies have found a large number of FMRP mRNA targets, but it is still not clear which are those playing a critical role in the etiology of FXS. So far, no therapy for FXS has been found, making the quest for novel targets of considerable importance. Several pharmacological approaches have been attempted, but, despite some promising preclinical results, no strategy gave successful outcomes, due either to the induction of major side effects or to the lack of improvement of the phenotypes. However, these studies suggested that, in order to measure the effectiveness of a specific treatment, trials should be redesigned and new endpoints defined in FXS patients. Nevertheless, the search for new therapeutic targets for FXS is very active. In this context, the advances in animal modeling, coupled with better understanding of neurobiology and physiopathology of FXS, are of crucial importance in developing new selected treatments. Here, we discuss the pathways that were recently linked to the physiopathology of FXS (mGluR, GABAR, insulin, Insulin-like Growth Factor 1 (IGF-1), MPP-9, serotonin, oxytocin and endocannabinoid signaling) and that suggest new approaches to find an effective therapy for this disorder. Our goal with this review article is to summarize some recent relevant findings on FXS treatment strategies in order to have a clearer view of the different pathways analyzed to date emphasizing those shared with other synaptic disorders.
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Affiliation(s)
- Sara Castagnola
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Barbara Bardoni
- Université Côte d'Azur, INSERM, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Thomas Maurin
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
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17
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Steury MD, McCabe LR, Parameswaran N. G Protein-Coupled Receptor Kinases in the Inflammatory Response and Signaling. Adv Immunol 2017; 136:227-277. [PMID: 28950947 DOI: 10.1016/bs.ai.2017.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
G protein-coupled receptor kinases (GRKs) are serine/threonine kinases that regulate a large and diverse class of G protein-coupled receptors (GPCRs). Through GRK phosphorylation and β-arrestin recruitment, GPCRs are desensitized and their signal terminated. Recent work on these kinases has expanded their role from canonical GPCR regulation to include noncanonical regulation of non-GPCR and nonreceptor substrates through phosphorylation as well as via scaffolding functions. Owing to these and other regulatory roles, GRKs have been shown to play a critical role in the outcome of a variety of physiological and pathophysiological processes including chemotaxis, signaling, migration, inflammatory gene expression, etc. This diverse set of functions for these proteins makes them popular targets for therapeutics. Role for these kinases in inflammation and inflammatory disease is an evolving area of research currently pursued in many laboratories. In this review, we describe the current state of knowledge on various GRKs pertaining to their role in inflammation and inflammatory diseases.
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Affiliation(s)
| | - Laura R McCabe
- Michigan State University, East Lansing, MI, United States
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18
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Abekhoukh S, Sahin HB, Grossi M, Zongaro S, Maurin T, Madrigal I, Kazue-Sugioka D, Raas-Rothschild A, Doulazmi M, Carrera P, Stachon A, Scherer S, Drula Do Nascimento MR, Trembleau A, Arroyo I, Szatmari P, Smith IM, Milà M, Smith AC, Giangrande A, Caillé I, Bardoni B. New insights into the regulatory function of CYFIP1 in the context of WAVE- and FMRP-containing complexes. Dis Model Mech 2017; 10:463-474. [PMID: 28183735 PMCID: PMC5399562 DOI: 10.1242/dmm.025809] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 02/02/2017] [Indexed: 12/19/2022] Open
Abstract
Cytoplasmic FMRP interacting protein 1 (CYFIP1) is a candidate gene for intellectual disability (ID), autism, schizophrenia and epilepsy. It is a member of a family of proteins that is highly conserved during evolution, sharing high homology with its Drosophila homolog, dCYFIP. CYFIP1 interacts with the Fragile X mental retardation protein (FMRP, encoded by the FMR1 gene), whose absence causes Fragile X syndrome, and with the translation initiation factor eIF4E. It is a member of the WAVE regulatory complex (WRC), thus representing a link between translational regulation and the actin cytoskeleton. Here, we present data showing a correlation between mRNA levels of CYFIP1 and other members of the WRC. This suggests a tight regulation of the levels of the WRC members, not only by post-translational mechanisms, as previously hypothesized. Moreover, we studied the impact of loss of function of both CYFIP1 and FMRP on neuronal growth and differentiation in two animal models - fly and mouse. We show that these two proteins antagonize each other's function not only during neuromuscular junction growth in the fly but also during new neuronal differentiation in the olfactory bulb of adult mice. Mechanistically, FMRP and CYFIP1 modulate mTor signaling in an antagonistic manner, likely via independent pathways, supporting the results obtained in mouse as well as in fly at the morphological level. Collectively, our results illustrate a new model to explain the cellular roles of FMRP and CYFIP1 and the molecular significance of their interaction.
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Affiliation(s)
- Sabiha Abekhoukh
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne, France.,CNRS Associated International Laboratory (LIA) 'Neogenex', 06560 Valbonne, France
| | - H Bahar Sahin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,CNRS, UMR7104, 67400 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Mauro Grossi
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne, France.,CNRS Associated International Laboratory (LIA) 'Neogenex', 06560 Valbonne, France
| | - Samantha Zongaro
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne, France.,CNRS Associated International Laboratory (LIA) 'Neogenex', 06560 Valbonne, France
| | - Thomas Maurin
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne, France.,CNRS Associated International Laboratory (LIA) 'Neogenex', 06560 Valbonne, France
| | - Irene Madrigal
- Biochemistry and Molecular Genetics Department, Hospital Clinic, 08036 Barcelona, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain.,IDIBAPS, Barcelona, Spain
| | - Daniele Kazue-Sugioka
- Université Côte d'Azur, Nice, France.,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne, France.,CNRS Associated International Laboratory (LIA) 'Neogenex', 06560 Valbonne, France.,Instituto de Pesquisa Pelé Pequeno Principe, Curitiba 80250-060, Brazil
| | - Annick Raas-Rothschild
- Institute of Rare Diseases, Institute of Medical Genetics, The Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Mohamed Doulazmi
- Sorbonne Universités, Université Pierre et Marie Curie, Univ Paris 06, CNRS UMR8256, IBPS, Neuroscience Paris Seine, France
| | - Pilar Carrera
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,CNRS, UMR7104, 67400 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Andrea Stachon
- Instituto de Pesquisa Pelé Pequeno Principe, Curitiba 80250-060, Brazil
| | - Steven Scherer
- Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | | | - Alain Trembleau
- Sorbonne Universités, Université Pierre et Marie Curie, Univ Paris 06, CNRS UMR8256, IBPS, Neuroscience Paris Seine, France
| | - Ignacio Arroyo
- Center for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - Peter Szatmari
- Centre for Addiction and Mental Health, Hospital for Sick Children, Department of Psychiatry, University of Toronto, Canada, M5G 1X8
| | - Isabel M Smith
- Departments of Pediatrics and Psychology & Neuroscience, Dalhousie University and IWK Health Centre, Halifax, Canada, B3K 6R8
| | - Montserrat Milà
- Biochemistry and Molecular Genetics Department, Hospital Clinic, 08036 Barcelona, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain.,IDIBAPS, Barcelona, Spain
| | - Adam C Smith
- Instituto de Pesquisa Pelé Pequeno Principe, Curitiba 80250-060, Brazil.,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto and Program in Laboratory Medicine, University Health Network, Toronto, Canada
| | - Angela Giangrande
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,CNRS, UMR7104, 67400 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67400 Illkirch, France.,Université de Strasbourg, 67404 Illkirch, France
| | - Isabelle Caillé
- Sorbonne Universités, Université Pierre et Marie Curie, Univ Paris 06, CNRS UMR8256, IBPS, Neuroscience Paris Seine, France.,Sorbonne Paris Cité, Université Paris Diderot-Paris 7, 75013 Paris, France
| | - Barbara Bardoni
- Université Côte d'Azur, Nice, France .,CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, 06560 Valbonne, France.,CNRS Associated International Laboratory (LIA) 'Neogenex', 06560 Valbonne, France
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19
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Anderson BR, Chopra P, Suhl JA, Warren ST, Bassell GJ. Identification of consensus binding sites clarifies FMRP binding determinants. Nucleic Acids Res 2016; 44:6649-59. [PMID: 27378784 PMCID: PMC5001617 DOI: 10.1093/nar/gkw593] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/17/2016] [Indexed: 12/30/2022] Open
Abstract
Fragile X mental retardation protein (FMRP) is a multifunctional RNA-binding protein with crucial roles in neuronal development and function. Efforts aimed at elucidating how FMRP target mRNAs are selected have produced divergent sets of target mRNA and putative FMRP-bound motifs, and a clear understanding of FMRP's binding determinants has been lacking. To clarify FMRP's binding to its target mRNAs, we produced a shared dataset of FMRP consensus binding sequences (FCBS), which were reproducibly identified in two published FMRP CLIP sequencing datasets. This comparative dataset revealed that of the various sequence and structural motifs that have been proposed to specify FMRP binding, the short sequence motifs TGGA and GAC were corroborated, and a novel TAY motif was identified. In addition, the distribution of the FCBS set demonstrates that FMRP preferentially binds to the coding region of its targets but also revealed binding along 3' UTRs in a subset of target mRNAs. Beyond probing these putative motifs, the FCBS dataset of reproducibly identified FMRP binding sites is a valuable tool for investigating FMRP targets and function.
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Affiliation(s)
- Bart R Anderson
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joshua A Suhl
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
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