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Zheng L, Zhang C, Wu J, Li Y. Detecting the Interaction of Double-stranded RNA Binding Protein, Viral Protein and Primary miRNA Transcript by Co-immunoprecipitation in planta. Bio Protoc 2018; 8:e2840. [PMID: 34286045 DOI: 10.21769/bioprotoc.2840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/17/2018] [Accepted: 04/23/2018] [Indexed: 11/02/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in plant growth, development, and response to infection by microbes. Double-stranded RNA binding protein 1 (DRB1) facilitates the processing of primary miRNA transcripts into mature miRNAs. Recently, we found that NS3 protein encoded by rice stripe virus (RSV) associates with DRB1 and promotes miRNA biogenesis during RSV infection ( Zheng et al., 2017 ). RNA co-immunoprecipitation (RIP) method was applied to identity association patterns among DRB1, NS3, and miRNA transcript.
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Affiliation(s)
- Lijia Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Vector-borne Virus Research Center, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Vector-borne Virus Research Center, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianguo Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Vector-borne Virus Research Center, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi Li
- The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
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Clavel M, Pélissier T, Montavon T, Tschopp MA, Pouch-Pélissier MN, Descombin J, Jean V, Dunoyer P, Bousquet-Antonelli C, Deragon JM. Evolutionary history of double-stranded RNA binding proteins in plants: identification of new cofactors involved in easiRNA biogenesis. Plant Mol Biol 2016; 91:131-47. [PMID: 26858002 DOI: 10.1007/s11103-016-0448-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 02/03/2016] [Indexed: 05/27/2023]
Abstract
In this work, we retrace the evolutionary history of plant double-stranded RNA binding proteins (DRBs), a group of non-catalytic factors containing one or more double-stranded RNA binding motif (dsRBM) that play important roles in small RNA biogenesis and functions. Using a phylogenetic approach, we show that multiple dsRBM DRBs are systematically composed of two different types of dsRBMs evolving under different constraints and likely fulfilling complementary functions. In vascular plants, four distinct clades of multiple dsRBM DRBs are always present with the exception of Brassicaceae species, that do not possess member of the newly identified clade we named DRB6. We also identified a second new and highly conserved DRB family (we named DRB7) whose members possess a single dsRBM that shows concerted evolution with the most C-terminal dsRBM domain of the Dicer-like 4 (DCL4) proteins. Using a BiFC approach, we observed that Arabidopsis thaliana DRB7.2 (AtDRB7.2) can directly interact with AtDRB4 but not with AtDCL4 and we provide evidence that both AtDRB7.2 and AtDRB4 participate in the epigenetically activated siRNAs pathway.
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Affiliation(s)
- Marion Clavel
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Thierry Pélissier
- UMR 6293 CNRS - INSERM U1103 - GreD, Clermont Université, 24 avenue des Landais, B.P. 80026, 63171, Aubière Cedex, France
| | - Thomas Montavon
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Marie-Aude Tschopp
- Department of Biology LFW D17/D18, ETH Zürich, Universitätsstrasse 2, 8092, Zurich, Switzerland
| | - Marie-Noëlle Pouch-Pélissier
- UMR 6293 CNRS - INSERM U1103 - GreD, Clermont Université, 24 avenue des Landais, B.P. 80026, 63171, Aubière Cedex, France
| | - Julie Descombin
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Viviane Jean
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Patrice Dunoyer
- Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357, Université de Strasbourg, Strasbourg Cedex, France
| | - Cécile Bousquet-Antonelli
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- CNRS UMR5096 LGDP, Perpignan Cedex, France
| | - Jean-Marc Deragon
- UMR5096 LGDP, Université de Perpignan Via Domitia, 58 Avenue Paul Alduy, 66860, Perpignan Cedex, France.
- CNRS UMR5096 LGDP, Perpignan Cedex, France.
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