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Paturi S, Deshmukh MV. NMR resonance assignments of 18.5 kDa complex of Arabidopsis thaliana DRB7.2:DRB4 interaction domains. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:173-178. [PMID: 37256435 DOI: 10.1007/s12104-023-10137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/24/2023] [Indexed: 06/01/2023]
Abstract
In higher eukaryotes, the dsRNA binding proteins (dsRBPs) assist the corresponding Dicer in the cleavage of dsRNA precursors to effect post-transcriptional gene regulation through RNA interference. In contrast, the DRB7.2:DRB4 complex in Arabidopsis thaliana acts as a potent inhibitor of Dicer-like 3 (DCL3) processing by sequestering endogenous inverted-repeat dsRNA precursors. DRB7.2 possesses a single dsRNA Binding Domain (dsRBD) flanked by unstructured N- and C-terminal regions. Whereas, DRB4 has two concatenated N-terminal dsRBDs and a long unstructured C-terminus harboring a small domain of unidentified function, D3. Here, we present near-complete backbone and partial side chain assignments of the interaction domains, DRB7.2M (i.e., DRB7.2 (71-162)) and DRB4D3 (i.e., DRB4 (294-355)) as a complex. Our findings establish the groundwork for future structural, dynamic, and functional research on DRB7.2 and DRB4, and provide clues for the endo-IR pathway in plants.
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Affiliation(s)
- Sneha Paturi
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Mandar V Deshmukh
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India.
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2
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Abstract
With the increasing understanding of fundamentals of gene silencing pathways in plants, various tools and techniques for downregulating the expression of a target gene have been developed across multiple plant species. This chapter provides an insight into the molecular mechanisms of gene silencing and highlights the advancements in various gene silencing approaches. The prominent aspects of different gene silencing methods, their advantages and disadvantages have been discussed. A succinct discussion on the newly emerged microRNA-based technologies like microRNA-induced gene silencing (MIGS) and microRNA-mediated virus-induced gene silencing (MIR-VIGS) are also presented. We have also discussed the gene-editing system like CRISPR-Cas. The prominent bottlenecks in gene silencing methods are the off-target effects and lack of universal applicability. However, the tremendous growth in understanding of this field reflects the potentials for improvements in the currently available approaches and the development of new widely applicable methods for easy, fast, and efficient functional characterization of plant genes.
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Affiliation(s)
- Prachi Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Kirankumar S Mysore
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, USA
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3
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Incarbone M, Clavel M, Monsion B, Kuhn L, Scheer H, Vantard É, Poignavent V, Dunoyer P, Genschik P, Ritzenthaler C. Immunocapture of dsRNA-bound proteins provides insight into Tobacco rattle virus replication complexes and reveals Arabidopsis DRB2 to be a wide-spectrum antiviral effector. THE PLANT CELL 2021; 33:3402-3420. [PMID: 34436604 PMCID: PMC8566308 DOI: 10.1093/plcell/koab214] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 08/17/2021] [Indexed: 05/02/2023]
Abstract
Plant RNA viruses form organized membrane-bound replication complexes to replicate their genomes. This process requires virus- and host-encoded proteins and leads to the production of double-stranded RNA (dsRNA) replication intermediates. Here, we describe the use of Arabidopsis thaliana expressing GFP-tagged dsRNA-binding protein (B2:GFP) to pull down dsRNA and associated proteins in planta upon infection with Tobacco rattle virus (TRV). Mass spectrometry analysis of the dsRNA-B2:GFP-bound proteins from infected plants revealed the presence of viral proteins and numerous host proteins. Among a selection of nine host candidate proteins, eight showed relocalization upon infection, and seven of these colocalized with B2-labeled TRV replication complexes. Infection of A. thaliana T-DNA mutant lines for eight such factors revealed that genetic knockout of dsRNA-BINDING PROTEIN 2 (DRB2) leads to increased TRV accumulation and DRB2 overexpression caused a decrease in the accumulation of four different plant RNA viruses, indicating that DRB2 has a potent and wide-ranging antiviral activity. We propose B2:GFP-mediated pull down of dsRNA to be a versatile method to explore virus replication complex proteomes and to discover key host virus replication factors. Given the universality of dsRNA, development of this tool holds great potential to investigate RNA viruses in other host organisms.
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Affiliation(s)
- Marco Incarbone
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
- Author for correspondence: (M.I.), (C.R.)
| | - Marion Clavel
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Baptiste Monsion
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Scheer
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Émilie Vantard
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Vianney Poignavent
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Patrice Dunoyer
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Christophe Ritzenthaler
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
- Author for correspondence: (M.I.), (C.R.)
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4
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Paturi S, Deshmukh MV. A Glimpse of "Dicer Biology" Through the Structural and Functional Perspective. Front Mol Biosci 2021; 8:643657. [PMID: 34026825 PMCID: PMC8138440 DOI: 10.3389/fmolb.2021.643657] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/07/2021] [Indexed: 01/05/2023] Open
Abstract
The RNA interference pathway (RNAi) is executed by two core enzymes, Dicer and Argonaute, for accomplishing a tailored transcriptional and post-transcriptional gene regulation. Dicer, an RNase III enzyme, initiates the RNAi pathway, plays a pivotal role in fighting infection against pathogens, and acts as a housekeeping enzyme for cellular homeostasis. Here, we review structure-based functional insights of Dicer and its domains present in a diverse group of organisms. Although Dicer and its domains are evolutionarily conserved from microsporidian parasites to humans, recent cryo-electron microscopy structures of Homo sapiens Dicer and Drosophila melanogaster Dicer-2 suggest characteristic variations in the mechanism of the dsRNA substrate recognition. Interestingly, the necessity for more than one functionally distinct Dicer paralogs in insects and plants compared with a single Dicer in other eukaryotic life forms implies Dicer’s role in the interplay of RNAi and other defense mechanisms. Based on the structural and mechanistic information obtained during the last decade, we aim to highlight the significance of key Dicer domains that are crucial to Dicer specific recognition and precise cleavage of dsRNA substrates. Further, the role of Dicer in the formation of Argonaute-based RNA-induced silencing complex (RISC) assembly formation, Dicer’s ability to regulate a complex protein interaction network, and its role in other cellular processes, as well as its therapeutic potentials, are emphasized.
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Affiliation(s)
- Sneha Paturi
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India
| | - Mandar V Deshmukh
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India
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5
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Scheer H, de Almeida C, Ferrier E, Simonnot Q, Poirier L, Pflieger D, Sement FM, Koechler S, Piermaria C, Krawczyk P, Mroczek S, Chicher J, Kuhn L, Dziembowski A, Hammann P, Zuber H, Gagliardi D. The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis. Nat Commun 2021; 12:1298. [PMID: 33637717 PMCID: PMC7910438 DOI: 10.1038/s41467-021-21382-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based on in vitro and in planta data, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3' terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb Arabidopsis growth and development.
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Affiliation(s)
- Hélène Scheer
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Caroline de Almeida
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Emilie Ferrier
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Quentin Simonnot
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Laure Poirier
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - François M Sement
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Sandrine Koechler
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Christina Piermaria
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Paweł Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Johana Chicher
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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6
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Zhang W, Zhu Z, Du P, Zhang C, Yan H, Wang W, Li W. NtRBP45, a nuclear RNA-binding protein of Nicotiana tabacum, facilitates post-transcriptional gene silencing. PLANT DIRECT 2020; 4:e00294. [PMID: 33615112 PMCID: PMC7880056 DOI: 10.1002/pld3.294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
The tobacco RBP45 is a nuclear RNA binding protein (RBP). In this study, we identified that the gene expression of NtRBP45 was significantly up-regulated upon the Tobacco mosaic virus infection and the central region of the protein accounted for its nuclear localization. In particular, using a green fluorescent protein-based transient suppression assay, we uncovered that the transiently overexpressed NtRBP45 was able to enhance local post-transcriptional gene silencing (PTGS), facilitate siRNA accumulation, and compromise the RNA silencing suppression mediated by Tomato aspermy virus 2b protein. Deletion mutagenesis showed that both the N- and C-terminal regions of NtRBP45 were necessary for enhancing PTGS. The data overall indicated a novel RNA silencing factor that might participate in antiviral defense.
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Affiliation(s)
- Wangbin Zhang
- College of Plant ScienceTarim UniversityAlarPR China
- Southern Xinjiang Key Laboratory of IPMTarim UniversityAlarPR China
| | - Zongcai Zhu
- College of Plant ScienceTarim UniversityAlarPR China
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingPR China
| | - Peixiu Du
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingPR China
| | - Chao Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingPR China
| | - Hailin Yan
- College of Plant ScienceTarim UniversityAlarPR China
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingPR China
| | - Wenguo Wang
- Key Laboratory of Development and Application of Rural Renewable EnergyMinistry of Agriculture and Rural AffairsChengduPR China
| | - Weimin Li
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingPR China
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7
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Incarbone M, Scheer H, Hily JM, Kuhn L, Erhardt M, Dunoyer P, Altenbach D, Ritzenthaler C. Characterization of a DCL2-Insensitive Tomato Bushy Stunt Virus Isolate Infecting Arabidopsis thaliana. Viruses 2020; 12:E1121. [PMID: 33023227 PMCID: PMC7650723 DOI: 10.3390/v12101121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 12/17/2022] Open
Abstract
Tomato bushy stunt virus (TBSV), the type member of the genus Tombusvirus in the family Tombusviridae is one of the best studied plant viruses. The TBSV natural and experimental host range covers a wide spectrum of plants including agricultural crops, ornamentals, vegetables and Nicotiana benthamiana. However, Arabidopsis thaliana, the well-established model organism in plant biology, genetics and plant-microbe interactions is absent from the list of known TBSV host plant species. Most of our recent knowledge of the virus life cycle has emanated from studies in Saccharomyces cerevisiae, a surrogate host for TBSV that lacks crucial plant antiviral mechanisms such as RNA interference (RNAi). Here, we identified and characterized a TBSV isolate able to infect Arabidopsis with high efficiency. We demonstrated by confocal and 3D electron microscopy that in Arabidopsis TBSV-BS3Ng replicates in association with clustered peroxisomes in which numerous spherules are induced. A dsRNA-centered immunoprecipitation analysis allowed the identification of TBSV-associated host components including DRB2 and DRB4, which perfectly localized to replication sites, and NFD2 that accumulated in larger viral factories in which peroxisomes cluster. By challenging knock-out mutants for key RNAi factors, we showed that TBSV-BS3Ng undergoes a non-canonical RNAi defensive reaction. In fact, unlike other RNA viruses described, no 22nt TBSV-derived small RNA are detected in the absence of DCL4, indicating that this virus is DCL2-insensitive. The new Arabidopsis-TBSV-BS3Ng pathosystem should provide a valuable new model for dissecting plant-virus interactions in complement to Saccharomyces cerevisiae.
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Affiliation(s)
- Marco Incarbone
- Institut de Biologie de Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (H.S.); (M.E.); (P.D.)
| | - Hélene Scheer
- Institut de Biologie de Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (H.S.); (M.E.); (P.D.)
| | - Jean-Michel Hily
- IFV, Le Grau-Du-Roi, Université de Strasbourg, INRAE, SVQV UNR-A 1131, 68000 Colmar, France;
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, 67000 Strasbourg, France;
| | - Mathieu Erhardt
- Institut de Biologie de Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (H.S.); (M.E.); (P.D.)
| | - Patrice Dunoyer
- Institut de Biologie de Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (H.S.); (M.E.); (P.D.)
| | - Denise Altenbach
- Bioreba AG, Christoph Merian Ring 7, CH-4153 Reinach, Switzerland;
| | - Christophe Ritzenthaler
- Institut de Biologie de Moléculaire des Plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France; (H.S.); (M.E.); (P.D.)
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8
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Potuschak T, Palatnik J, Schommer C, Sierro N, Ivanov NV, Kwon Y, Genschik P, Davière J, Otten L. Inhibition of Arabidopsis thaliana CIN-like TCP transcription factors by Agrobacterium T-DNA-encoded 6B proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1303-1317. [PMID: 31659801 PMCID: PMC7187390 DOI: 10.1111/tpj.14591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/03/2019] [Indexed: 05/26/2023]
Abstract
Agrobacterium T-DNA-encoded 6B proteins cause remarkable growth effects in plants. Nicotiana otophora carries two cellular T-DNAs with three slightly divergent 6b genes (TE-1-6b-L, TE-1-6b-R and TE-2-6b) originating from a natural transformation event. In Arabidopsis thaliana, expression of 2×35S:TE-2-6b, but not 2×35S:TE-1-6b-L or 2×35S:TE-1-6b-R, led to plants with crinkly leaves, which strongly resembled mutants of the miR319a/TCP module. This module is composed of MIR319A and five CIN-like TCP (TEOSINTHE BRANCHED1, CYCLOIDEA and PROLIFERATING CELL NUCLEAR ANTIGEN BINDING FACTOR) genes (TCP2, TCP3, TCP4, TCP10 and TCP24) targeted by miR319a. The CIN-like TCP genes encode transcription factors and are required for cell division arrest at leaf margins during development. MIR319A overexpression causes excessive growth and crinkly leaves. TE-2-6b plants did not show increased miR319a levels, but the mRNA levels of the TCP4 target gene LOX2 were decreased, as in jaw-D plants. Co-expression of green fluorescent protein (GFP)-tagged TCPs with native or red fluorescent protein (RFP)-tagged TE-6B proteins led to an increase in TCP protein levels and formation of numerous cytoplasmic dots containing 6B and TCP proteins. Yeast double-hybrid experiments confirmed 6B/TCP binding and showed that TE-1-6B-L and TE-1-6B-R bind a smaller set of TCP proteins than TE-2-6B. A single nucleotide mutation in TE-1-6B-R enlarged its TCP-binding repertoire to that of TE-2-6B and caused a crinkly phenotype in Arabidopsis. Deletion analysis showed that TE-2-6B targets the TCP4 DNA-binding domain and directly interferes with transcriptional activation. Taken together, these results provide detailed insights into the mechanism of action of the N. otophora TE-encoded 6b genes.
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Affiliation(s)
- Thomas Potuschak
- Institut de Biologie Moléculaire des Plantes (IBMP)Rue du Général Zimmer 1267084StrasbourgFrance
| | - Javier Palatnik
- IBR‐CONICETPredio CCTOcampo y Esmeralda s/n2000RosarioArgentina
| | - Carla Schommer
- IBR‐CONICETPredio CCTOcampo y Esmeralda s/n2000RosarioArgentina
| | - Nicolas Sierro
- PMI R&DPhilip Morris Products S. A.Quai Jeanrenaud 52000NeuchâtelSwitzerland
| | - Nikolai V. Ivanov
- PMI R&DPhilip Morris Products S. A.Quai Jeanrenaud 52000NeuchâtelSwitzerland
| | - Yerim Kwon
- Institut de Biologie Moléculaire des Plantes (IBMP)Rue du Général Zimmer 1267084StrasbourgFrance
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes (IBMP)Rue du Général Zimmer 1267084StrasbourgFrance
| | - Jean‐Michel Davière
- Institut de Biologie Moléculaire des Plantes (IBMP)Rue du Général Zimmer 1267084StrasbourgFrance
| | - Léon Otten
- Institut de Biologie Moléculaire des Plantes (IBMP)Rue du Général Zimmer 1267084StrasbourgFrance
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9
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Kakiyama S, Tabara M, Nishibori Y, Moriyama H, Fukuhara T. Long DCL4-substrate dsRNAs efficiently induce RNA interference in plant cells. Sci Rep 2019; 9:6920. [PMID: 31061468 PMCID: PMC6502814 DOI: 10.1038/s41598-019-43443-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 02/26/2019] [Indexed: 12/29/2022] Open
Abstract
RNA interference (RNAi) is induced by the direct transfer of double-stranded RNAs (dsRNAs) into protoplasts prepared from Arabidopsis thaliana seedlings. In this protoplast RNAi system, we compared the efficacies of various-sized dsRNAs (between 21 and 139 nucleotides [nt]) for inducing RNAi and assessed the dsRNA-cleaving activities of Dicer-like 3 (DCL3) and 4 (DCL4). After the direct transfer of dsRNAs into protoplasts, cleaved RNA products of 21 nt were detected from long 130- or 500-nt dsRNAs by DCL4 but not from 37-nt dsRNAs. These results indicate that DCL4 preferentially cleaves long dsRNAs in protoplasts, consistent with our previous biochemical data regarding the substrate specificity of DCL4. Direct transfer of long dsRNAs of approximately 130 nt into protoplasts induces RNAi much more effectively (by approximately 60- to 400-fold) than direct transfer of short 37-nt dsRNAs. Although transfer of 21-nt dsRNAs into protoplasts induced RNAi without DCL4 activity, the induction of RNAi was less effective (by approximately 0.01-fold) compared with long dsRNAs. These results indicate that cleavage of long dsRNAs exceeding 100 nt by DCL4 into 21-nt dsRNAs is essential for efficient induction of RNAi in plant cells.
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Affiliation(s)
- Sayaka Kakiyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Midori Tabara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Yuki Nishibori
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Hiromitsu Moriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan. .,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
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10
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Monsion B, Incarbone M, Hleibieh K, Poignavent V, Ghannam A, Dunoyer P, Daeffler L, Tilsner J, Ritzenthaler C. Efficient Detection of Long dsRNA in Vitro and in Vivo Using the dsRNA Binding Domain from FHV B2 Protein. FRONTIERS IN PLANT SCIENCE 2018; 9:70. [PMID: 29449856 PMCID: PMC5799278 DOI: 10.3389/fpls.2018.00070] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/12/2018] [Indexed: 05/17/2023]
Abstract
Double-stranded RNA (dsRNA) plays essential functions in many biological processes, including the activation of innate immune responses and RNA interference. dsRNA also represents the genetic entity of some viruses and is a hallmark of infections by positive-sense single-stranded RNA viruses. Methods for detecting dsRNA rely essentially on immunological approaches and their use is often limited to in vitro applications, although recent developments have allowed the visualization of dsRNA in vivo. Here, we report the sensitive and rapid detection of long dsRNA both in vitro and in vivo using the dsRNA binding domain of the B2 protein from Flock house virus. In vitro, we adapted the system for the detection of dsRNA either enzymatically by northwestern blotting or by direct fluorescence labeling on fixed samples. In vivo, we produced stable transgenic Nicotiana benthamiana lines allowing the visualization of dsRNA by fluorescence microscopy. Using these techniques, we were able to discriminate healthy and positive-sense single-stranded RNA virus-infected material in plants and insect cells. In N. benthamiana, our system proved to be very potent for the spatio-temporal visualization of replicative RNA intermediates of a broad range of positive-sense RNA viruses, including high- vs. low-copy number viruses.
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Affiliation(s)
- Baptiste Monsion
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Marco Incarbone
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Kamal Hleibieh
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Vianney Poignavent
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Ahmed Ghannam
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Patrice Dunoyer
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
| | - Laurent Daeffler
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Jens Tilsner
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Christophe Ritzenthaler
- Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, Strasbourg, France
- *Correspondence: Christophe Ritzenthaler
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Chiliveri SC, Aute R, Rai U, Deshmukh MV. DRB4 dsRBD1 drives dsRNA recognition in Arabidopsis thaliana tasi/siRNA pathway. Nucleic Acids Res 2017; 45:8551-8563. [PMID: 28575480 PMCID: PMC5737894 DOI: 10.1093/nar/gkx481] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 05/17/2017] [Indexed: 12/22/2022] Open
Abstract
In Arabidopsis thaliana, endogenous trans-acting and exogenous siRNA pathways are initiated by the interaction of DRB4 with trigger dsRNA. Further, DCL4:DRB4 complex cleaves the dsRNA into 21 bp siRNA. Understanding molecular determinants and mechanistic details of dsRNA recognition by DRB4 is vital for inducing long-term RNAi-mediated gene regulation in plants. Here, we present solution structures of individual and concatenated DRB4 dsRBDs and demonstrate modes of dsRNA binding by employing NMR, ITC and site-specific mutagenesis. While both dsRBDs adopt the canonical α−β−β−β−α fold, key structural differences and ms-μs dynamics located at the RNA binding region were observed for dsRBD1. These features favor dsRBD1 to orient itself and make stronger tripartite contact with dsRNA, a feature missing in dsRBD2. Additionally, the inter-domain orientation induced by the linker restricts the mobility of dsRBD2, resulting in the steric hindrance of α1 helix in dsRBD2, and leads in further reduction of its dsRNA binding activity. Our study deciphers functional roles of DRB4 domains by showing that dsRBD1 drives the tasiRNA/siRNA pathway. Furthermore, we identify a potential role of the C-terminal region of DRB4 in protein:protein interaction as it possesses six PxxP motifs, binds to Zn2+ and contains a small structural domain.
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Affiliation(s)
| | - Ramdas Aute
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Upasana Rai
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Mandar V Deshmukh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
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Montavon T, Kwon Y, Zimmermann A, Michel F, Dunoyer P. New DRB complexes for new DRB functions in plants. RNA Biol 2017; 14:1637-1641. [PMID: 28665774 DOI: 10.1080/15476286.2017.1343787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Double-stranded RNA binding (DRB) proteins are generally considered as promoting cofactors of Dicer or Dicer-like (DCL) proteins that ensure efficient and precise production of small RNAs, the sequence-specificity guide of RNA silencing processes in both plants and animals. However, the characterization of a new clade of DRB proteins in Arabidopsis has recently challenged this view by showing that DRBs can also act as potent inhibitors of DCL processing. This is achieved through sequestration of a specific class of small RNA precursors, the endogenous inverted-repeat (endoIR) dsRNAs, thereby selectively preventing production of their associated small RNAs, the endoIR-siRNAs. Here, we concisely summarize the main findings obtained from the characterization of these new DRB proteins and discuss how the existence of such complexes can support a potential, yet still elusive, biological function of plant endoIR-siRNAs.
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Affiliation(s)
- Thomas Montavon
- a Université de Strasbourg, CNRS, IBMP UPR , Strasbourg , France
| | - Yerim Kwon
- a Université de Strasbourg, CNRS, IBMP UPR , Strasbourg , France
| | - Aude Zimmermann
- a Université de Strasbourg, CNRS, IBMP UPR , Strasbourg , France
| | - Fabrice Michel
- a Université de Strasbourg, CNRS, IBMP UPR , Strasbourg , France
| | - Patrice Dunoyer
- a Université de Strasbourg, CNRS, IBMP UPR , Strasbourg , France
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Tschopp MA, Iki T, Brosnan CA, Jullien PE, Pumplin N. A complex of Arabidopsis DRB proteins can impair dsRNA processing. RNA (NEW YORK, N.Y.) 2017; 23:782-797. [PMID: 28232389 PMCID: PMC5393186 DOI: 10.1261/rna.059519.116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/13/2017] [Indexed: 05/17/2023]
Abstract
Small RNAs play an important role in regulating gene expression through transcriptional and post-transcriptional gene silencing. Biogenesis of small RNAs from longer double-stranded (ds) RNA requires the activity of dicer-like ribonucleases (DCLs), which in plants are aided by dsRNA binding proteins (DRBs). To gain insight into this pathway in the model plant Arabidopsis, we searched for interactors of DRB4 by immunoprecipitation followed by mass spectrometry-based fingerprinting and discovered DRB7.1. This interaction, verified by reciprocal coimmunoprecipitation and bimolecular fluorescence complementation, colocalizes with markers of cytoplasmic siRNA bodies and nuclear dicing bodies. In vitro experiments using tobacco BY-2 cell lysate (BYL) revealed that the complex of DRB7.1/DRB4 impairs cleavage of diverse dsRNA substrates into 24-nucleotide (nt) small interfering (si) RNAs, an action performed by DCL3. DRB7.1 also negates the action of DRB4 in enhancing accumulation of 21-nt siRNAs produced by DCL4. Overexpression of DRB7.1 in Arabidopsis altered accumulation of siRNAs in a manner reminiscent of drb4 mutant plants, suggesting that DRB7.1 can antagonize the function of DRB4 in siRNA accumulation in vivo as well as in vitro. Specifically, enhanced accumulation of siRNAs from an endogenous inverted repeat correlated with enhanced DNA methylation, suggesting a biological impact for DRB7.1 in regulating epigenetic marks. We further demonstrate that RNase three-like (RTL) proteins RTL1 and RTL2 cleave dsRNA when expressed in BYL, and that this activity is impaired by DRB7.1/DRB4. Investigating the DRB7.1-DRB4 interaction thus revealed that a complex of DRB proteins can antagonize, rather than promote, RNase III activity and production of siRNAs in plants.
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Affiliation(s)
| | - Taichiro Iki
- Department of Biology, ETH Zürich, 8092 Zürich, Switzerland
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | | | - Pauline E Jullien
- Department of Biology, ETH Zürich, 8092 Zürich, Switzerland
- IRD, 34394 Montpellier, France
| | - Nathan Pumplin
- Department of Biology, ETH Zürich, 8092 Zürich, Switzerland
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