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Angelova MT, Dimitrova DG, Da Silva B, Marchand V, Jacquier C, Achour C, Brazane M, Goyenvalle C, Bourguignon-Igel V, Shehzada S, Khouider S, Lence T, Guerineau V, Roignant JY, Antoniewski C, Teysset L, Bregeon D, Motorin Y, Schaefer MR, Carré C. tRNA 2'-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila. Nucleic Acids Res 2020; 48:2050-2072. [PMID: 31943105 PMCID: PMC7038984 DOI: 10.1093/nar/gkaa002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 12/14/2022] Open
Abstract
2′-O-Methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNAPhe, tRNATrp and tRNALeu, while CG5220 methylates position C32 in the same tRNAs and also targets additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as lifespan reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalyzing Nm at specific tRNAs and small RNA-induced gene silencing pathways.
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Affiliation(s)
- Margarita T Angelova
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Dilyana G Dimitrova
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Bruno Da Silva
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Virginie Marchand
- Next-Generation Sequencing Core Facility, UMS2008 IBSLor CNRS-Université de Lorraine-INSERM, BioPôle, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Caroline Jacquier
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Cyrinne Achour
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Mira Brazane
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Catherine Goyenvalle
- Eucaryiotic Translation, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biological Adaptation and Ageing, Institut de Biologie Paris Seine, 9 Quai Saint bernard, 75005 Paris, France
| | - Valérie Bourguignon-Igel
- Next-Generation Sequencing Core Facility, UMS2008 IBSLor CNRS-Université de Lorraine-INSERM, BioPôle, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France.,Ingénierie Moléculaire et Physiopathologie Articulaire, UMR7365, CNRS - Université de Lorraine, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Salman Shehzada
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Souraya Khouider
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Tina Lence
- Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany
| | - Vincent Guerineau
- Institut de Chimie de Substances Naturelles, Centre de Recherche de Gif CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Jean-Yves Roignant
- Institute of Molecular Biology, Ackermannweg 4, 55128, Mainz, Germany.,Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Christophe Antoniewski
- ARTbio Bioinformatics Analysis Facility, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Laure Teysset
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
| | - Damien Bregeon
- Eucaryiotic Translation, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biological Adaptation and Ageing, Institut de Biologie Paris Seine, 9 Quai Saint bernard, 75005 Paris, France
| | - Yuri Motorin
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR7365, CNRS - Université de Lorraine, 9 avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France
| | - Matthias R Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Clément Carré
- Transgenerational Epigenetics & small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, 9 Quai Saint Bernard, 75005 Paris, France
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Huang Y, Ren HT, Zou Q, Wang YQ, Zhang JL, Yu XL. Computational identification and characterization of miRNAs and their target genes from five cyprinidae fishes. Saudi J Biol Sci 2015; 24:1126-1135. [PMID: 28855803 PMCID: PMC5562384 DOI: 10.1016/j.sjbs.2015.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 05/02/2015] [Accepted: 05/06/2015] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are a kind of small single-strand RNA molecules with lengths of 18–25 nt, which do not encode any proteins. They play an essential role in gene expression regulation by binding to their target genes, leading to translational repression or transcript degradation. In this study, 23 miRNAs were predicted from five cyprinidae fishes by using a bioinformatics-based gene search based on blasting ESTs and GSS in NCBI, of which 21 miRNA genes have not been previously reported. To prove their validity, five of the computationally predicted miRNAs were verified by RTPCR, their transcripts were successfully detected, and, 46 potential target genes for these miRNAs were predicted, most target genes encode transcription factors, they are involved in signal transduction, metabolism and development processes.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Hong-Tao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin, China
| | - Yu-Qin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Ji-Liang Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xue-Li Yu
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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Besnard-Guérin C, Jacquier C, Pidoux J, Deddouche S, Antoniewsk C. The cricket paralysis virus suppressor inhibits microRNA silencing mediated by the Drosophila Argonaute-2 protein. PLoS One 2015; 10:e0120205. [PMID: 25793377 PMCID: PMC4368812 DOI: 10.1371/journal.pone.0120205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/20/2015] [Indexed: 11/25/2022] Open
Abstract
Small RNAs are potent regulators of gene expression. They also act in defense pathways against invading nucleic acids such as transposable elements or viruses. To counteract these defenses, viruses have evolved viral suppressors of RNA silencing (VSRs). Plant viruses encoded VSRs interfere with siRNAs or miRNAs by targeting common mediators of these two pathways. In contrast, VSRs identified in insect viruses to date only interfere with the siRNA pathway whose effector Argonaute protein is Argonaute-2 (Ago-2). Although a majority of Drosophila miRNAs exerts their silencing activity through their loading into the Argonaute-1 protein, recent studies highlighted that a fraction of miRNAs can be loaded into Ago-2, thus acting as siRNAs. In light of these recent findings, we re-examined the role of insect VSRs on Ago-2-mediated miRNA silencing in Drosophila melanogaster. Using specific reporter systems in cultured Schneider-2 cells and transgenic flies, we showed here that the Cricket Paralysis virus VSR CrPV1-A but not the Flock House virus B2 VSR abolishes silencing by miRNAs loaded into the Ago-2 protein. Thus, our results provide the first evidence that insect VSR have the potential to directly interfere with the miRNA silencing pathway.
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Affiliation(s)
- Corinne Besnard-Guérin
- Drosophila Genetics and Epigenetics, Institut de Biologie Paris Seine, CNRS UMR7622 & Université Pierre et Marie Curie, 9 quai Saint-Bernard, F75005, Paris, France
| | - Caroline Jacquier
- Drosophila Genetics and Epigenetics, Institut de Biologie Paris Seine, CNRS UMR7622 & Université Pierre et Marie Curie, 9 quai Saint-Bernard, F75005, Paris, France
| | - Josette Pidoux
- Drosophila Genetics and Epigenetics, Institut de Biologie Paris Seine, CNRS UMR7622 & Université Pierre et Marie Curie, 9 quai Saint-Bernard, F75005, Paris, France
| | - Safia Deddouche
- Drosophila Genetics and Epigenetics, Institut de Biologie Paris Seine, CNRS UMR7622 & Université Pierre et Marie Curie, 9 quai Saint-Bernard, F75005, Paris, France
| | - Christophe Antoniewsk
- Drosophila Genetics and Epigenetics, Institut de Biologie Paris Seine, CNRS UMR7622 & Université Pierre et Marie Curie, 9 quai Saint-Bernard, F75005, Paris, France
- * E-mail:
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