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Yuan Z, Pan J, Chen C, Tang Y, Zhang H, Guo J, Yang X, Chen L, Li C, Zhao K, Wang Q, Yang B, Sun C, Deng X, Wang P. DRB2 Modulates Leaf Rolling by Regulating Accumulation of MicroRNAs Related to Leaf Development in Rice. Int J Mol Sci 2022; 23:ijms231911147. [PMID: 36232465 PMCID: PMC9570175 DOI: 10.3390/ijms231911147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/28/2022] Open
Abstract
As an important agronomic trait in rice (Oryza sativa), moderate leaf rolling helps to maintain the erectness of leaves and minimize shadowing between leaves, leading to improved photosynthetic efficiency and grain yield. However, the molecular mechanisms underlying rice leaf rolling still need to be elucidated. Here, we isolated a rice mutant, rl89, showing adaxially rolled leaf phenotype due to decreased number and size of bulliform cells. We confirmed that the rl89 phenotypes were caused by a single nucleotide substitution in OsDRB2 (LOC_Os10g33970) gene encoding DOUBLE-STRANDED RNA-BINDING2. This gene was constitutively expressed, and its encoded protein was localized to both nucleus and cytoplasm. Yeast two-hybrid assay showed that OsDRB2 could interact with DICER-LIKE1 (DCL1) and OsDRB1-2 respectively. qRT-PCR analysis of 29 related genes suggested that defects of the OsDRB2-miR166-OsHBs pathway could play an important role in formation of the rolled leaf phenotype of rl89, in which OsDRB2 mutation reduced miR166 accumulation, resulting in elevated expressions of the class III homeodomain-leucine zipper genes (such as OsHB1, 3 and 5) involved in leaf polarity and/or morphology development. Moreover, OsDRB2 mutation also reduced accumulation of miR160, miR319, miR390, and miR396, which could cause the abnormal leaf development in rl89 by regulating expressions of their target genes related to leaf development.
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Affiliation(s)
- Zhaodi Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jihong Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Congping Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yulin Tang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongshan Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jia Guo
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaorong Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Longfei Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunyan Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Ke Zhao
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Qian Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Bin Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (X.D.); (P.W.)
| | - Pingrong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (X.D.); (P.W.)
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Wang S, Lv X, Zhang J, Chen D, Chen S, Fan G, Ma C, Wang Y. Roles of E3 Ubiquitin Ligases in Plant Responses to Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23042308. [PMID: 35216424 PMCID: PMC8878164 DOI: 10.3390/ijms23042308] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 01/09/2023] Open
Abstract
Plants are frequently exposed to a variety of abiotic stresses, such as those caused by salt, drought, cold, and heat. All of these stressors can induce changes in the proteoforms, which make up the proteome of an organism. Of the many different proteoforms, protein ubiquitination has attracted a lot of attention because it is widely involved in the process of protein degradation; thus regulates many plants molecular processes, such as hormone signal transduction, to resist external stresses. Ubiquitin ligases are crucial in substrate recognition during this ubiquitin modification process. In this review, the molecular mechanisms of plant responses to abiotic stresses from the perspective of ubiquitin ligases have been described. This information is critical for a better understanding of plant molecular responses to abiotic stresses.
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Affiliation(s)
- Shuang Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (S.W.); (J.Z.)
| | - Xiaoyan Lv
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China;
| | - Jialin Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (S.W.); (J.Z.)
| | - Daniel Chen
- Judy Genshaft Honors College and College of Arts and Sciences, University of South Florida, Tampa, FL 33620, USA;
| | - Sixue Chen
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institude, University of Florida, Gainesville, FL 32610, USA;
| | - Guoquan Fan
- Industrial Crops Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Chunquan Ma
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (S.W.); (J.Z.)
- Correspondence: (C.M.); (Y.W.)
| | - Yuguang Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (S.W.); (J.Z.)
- Correspondence: (C.M.); (Y.W.)
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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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Sun D, Li Y, Ma Z, Yan X, Li N, Shang B, Hu X, Cui K, Koiwa H, Zhang X. The epigenetic factor FVE orchestrates cytoplasmic SGS3-DRB4-DCL4 activities to promote transgene silencing in Arabidopsis. SCIENCE ADVANCES 2021; 7:7/32/eabf3898. [PMID: 34348894 PMCID: PMC8336953 DOI: 10.1126/sciadv.abf3898] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/15/2021] [Indexed: 05/27/2023]
Abstract
Posttranscriptional gene silencing (PTGS) is a regulatory mechanism to suppress undesired transcripts. Here, we identified Flowering locus VE (FVE), a well-known epigenetic component, as a new player in cytoplasmic PTGS. Loss-of-function fve mutations substantially reduced the accumulation of transgene-derived small interfering RNAs (siRNAs). FVE interacts with suppressor of gene silencing 3 (SGS3), a master component in PTGS. FVE promotes SGS3 homodimerization that is essential for its function. FVE can bind to single-stranded RNA and double-stranded RNA (dsRNA) with moderate affinities, while its truncated form FVE-8 has a significantly increased binding affinity to dsRNA. These affinities affect the association and channeling of SGS3-RNA to downstream dsRNA binding protein 4 (DRB4)/Dicer-like protein 2/4 (DCL2/4) complexes. Hence, FVE, but not FVE-8, biochemically enhances the DRB4/DCL2/4 activity in vitro. We surmise that FVE promotes production of transgene-derived siRNAs through concertedly tuning SGS3-DRB4/DCL2/4 functions. Thus, this study revealed a noncanonical role of FVE in PTGS.
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Affiliation(s)
- Di Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Niankui Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Baoshuan Shang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Xiaomei Hu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Kai Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming 650224, China
| | - Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
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5
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Lim GH, Zhu S, Zhang K, Hoey T, Deragon JM, Kachroo A, Kachroo P. The analogous and opposing roles of double-stranded RNA-binding proteins in bacterial resistance. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1627-1638. [PMID: 30843586 DOI: 10.1093/jxb/erz019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
The Arabidopsis plasma membrane-localized resistance protein RPM1 is degraded upon the induction of the hypersensitive response (HR) triggered in response to its own activation or that of other unrelated resistance (R) proteins. We investigated the role of RPM1 turnover in RPM1-mediated resistance and showed that degradation of RPM1 is not associated with HR or resistance mediated by this R protein. Likewise, the runaway cell death phenotype in the lsd1 mutant was not associated with RPM1 degradation and did not alter RPM1-derived resistance. RPM1 stability and RPM1-mediated resistance were dependent on the double-stranded RNA binding (DRB) proteins 1 and 4. Interestingly, the function of DRB1 in RPM1-mediated resistance was not associated with its role in pre-miRNA processing. The DRB3 and DRB5 proteins negatively regulated RPM1-mediated resistance and a mutation in these completely or partially restored resistance in the drb1, drb2, and drb4 mutant backgrounds. Conversely, plants overexpressing DRB5 showed attenuated RPM1-mediated resistance. A similar role for DRBs in basal and R-mediated resistance suggests that these proteins play a general role in bacterial resistance.
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Affiliation(s)
- Gah-Hyun Lim
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - Shifeng Zhu
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - Kai Zhang
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Timothy Hoey
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - Jean-Marc Deragon
- Université de Perpignan Via Domitia, CNRS UMR, Perpignan Cedex, France
| | - Aardra Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - Pradeep Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
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6
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RNA Interference: A Natural Immune System of Plants to Counteract Biotic Stressors. Cells 2019; 8:cells8010038. [PMID: 30634662 PMCID: PMC6356646 DOI: 10.3390/cells8010038] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/01/2019] [Accepted: 01/07/2019] [Indexed: 02/06/2023] Open
Abstract
During plant-pathogen interactions, plants have to defend the living transposable elements from pathogens. In response to such elements, plants activate a variety of defense mechanisms to counteract the aggressiveness of biotic stressors. RNA interference (RNAi) is a key biological process in plants to inhibit gene expression both transcriptionally and post-transcriptionally, using three different groups of proteins to resist the virulence of pathogens. However, pathogens trigger an anti-silencing mechanism through the expression of suppressors to block host RNAi. The disruption of the silencing mechanism is a virulence strategy of pathogens to promote infection in the invaded hosts. In this review, we summarize the RNA silencing pathway, anti-silencing suppressors, and counter-defenses of plants to viral, fungal, and bacterial pathogens.
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7
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Lim GH, Hoey T, Zhu S, Clavel M, Yu K, Navarre D, Kachroo A, Deragon JM, Kachroo P. COP1, a negative regulator of photomorphogenesis, positively regulates plant disease resistance via double-stranded RNA binding proteins. PLoS Pathog 2018; 14:e1006894. [PMID: 29513740 PMCID: PMC5871017 DOI: 10.1371/journal.ppat.1006894] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/27/2018] [Accepted: 01/22/2018] [Indexed: 11/18/2022] Open
Abstract
The E3 ubiquitin ligase COP1 (Constitutive Photomorphogenesis 1) is a well known component of the light-mediated plant development that acts as a repressor of photomorphogenesis. Here we show that COP1 positively regulates defense against turnip crinkle virus (TCV) and avrRPM1 bacteria by contributing to stability of resistance (R) protein HRT and RPM1, respectively. HRT and RPM1 levels and thereby pathogen resistance is significantly reduced in the cop1 mutant background. Notably, the levels of at least two double-stranded RNA binding (DRB) proteins DRB1 and DRB4 are reduced in the cop1 mutant background suggesting that COP1 affects HRT stability via its effect on the DRB proteins. Indeed, a mutation in either drb1 or drb4 resulted in degradation of HRT. In contrast to COP1, a multi-subunit E3 ligase encoded by anaphase-promoting complex (APC) 10 negatively regulates DRB4 and TCV resistance but had no effect on DRB1 levels. We propose that COP1-mediated positive regulation of HRT is dependent on a balance between COP1 and negative regulators that target DRB1 and DRB4.
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Affiliation(s)
- Gah-Hyun Lim
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - Timothy Hoey
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - Shifeng Zhu
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - Marion Clavel
- Université de Perpignan Via Domitia, CNRS UMR5096 LGDP, Perpignan, France
| | - Keshun Yu
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - Duroy Navarre
- U.S. Department of Agriculture–Agricultural Research Service, Washington State University, Prosser, WA, United States of America
| | - Aardra Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - Jean-Marc Deragon
- Université de Perpignan Via Domitia, CNRS UMR5096 LGDP, Perpignan, France
| | - Pradeep Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
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8
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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9
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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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10
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Sawano H, Matsuzaki T, Usui T, Tabara M, Fukudome A, Kanaya A, Tanoue D, Hiraguri A, Horiguchi G, Ohtani M, Demura T, Kozaki T, Ishii K, Moriyama H, Fukuhara T. Double-stranded RNA-binding protein DRB3 negatively regulates anthocyanin biosynthesis by modulating PAP1 expression in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2017; 130:45-55. [PMID: 27995376 DOI: 10.1007/s10265-016-0886-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
The model plant Arabidopsis thaliana has five double-stranded RNA-binding proteins (DRB1-DRB5), two of which, DRB1 and DRB4, are well characterized. In contrast, the functions of DRB2, DRB3 and DRB5 have yet to be elucidated. In this study, we tried to uncover their functions using drb mutants and DRB-over-expressed lines. In over-expressed lines of all five DRB genes, the over-expression of DRB2 or DRB3 (DRB2ox or DRB3ox) conferred a downward-curled leaf phenotype, but the expression profiles of ten small RNAs were similar to that of the wild-type (WT) plant. Phenotypes were examined in response to abiotic stresses. Both DRB2ox and DRB3ox plants exhibited salt-tolerance. When these plants were exposed to cold stress, drb2 and drb3 over-accumulated anthocyanin but DRB2ox and DRB3ox did not. Therefore, the over-expression of DRB2 or DRB3 had pleiotropic effects on host plants. Microarray and deep-sequencing analyses indicated that several genes encoding key enzymes for anthocyanin biosynthesis, including chalcone synthase (CHS), dihydroflavonol reductase (DFR) and anthocyanidin synthase (ANS), were down-regulated in DRB3ox plants. When DRB3ox was crossed with the pap1-D line, which is an activation-tagged transgenic line that over-expresses the key transcription factor PAP1 (Production of anthocyanin pigmentation1) for anthocyanin biosynthesis, over-expression of DRB3 suppressed the expression of PAP1, CHS, DFR and ANS genes. DRB3 negatively regulates anthocyanin biosynthesis by modulating the level of PAP1 transcript. Since two different small RNAs regulate PAP1 gene expression, a possible function of DRB3 for small RNA biogenesis is discussed.
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Affiliation(s)
- Hikaru Sawano
- Departments of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Takuma Matsuzaki
- Departments of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Tomoyuki Usui
- Departments of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Midori Tabara
- Departments of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Akihito Fukudome
- Departments of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
- Molecular and Environmental Plant Sciences, Department of Horticultural Sciences, Vegetable and Fruit Development Center, Texas A&M University, College Station, TX, 77843, USA
| | - Akihiro Kanaya
- Departments of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Daichi Tanoue
- Departments of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Akihiro Hiraguri
- Department of Clinical Plant Science, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo, 184-8584, Japan
| | - Gorou Horiguchi
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima, Tokyo, Japan
| | - Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Toshinori Kozaki
- Departments of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
- Innovation Advancement Organization, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Kazuo Ishii
- Departments of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Hiromitsu Moriyama
- Departments of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Toshiyuki Fukuhara
- Departments 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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11
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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 MOLECULAR BIOLOGY 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] [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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12
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Reis RS, Hart-Smith G, Eamens AL, Wilkins MR, Waterhouse PM. MicroRNA Regulatory Mechanisms Play Different Roles in Arabidopsis. J Proteome Res 2015; 14:4743-51. [DOI: 10.1021/acs.jproteome.5b00616] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rodrigo S. Reis
- School
of Biological Sciences, University of Sydney, Macleay Building A12, Sydney, NSW 2006, Australia
- Faculty
of Agriculture and Environment, University of Sydney, Eveleigh, NSW 2015, Australia
| | - Gene Hart-Smith
- Systems
Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Andrew L. Eamens
- School
of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Marc R. Wilkins
- Systems
Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Peter M. Waterhouse
- School
of Biological Sciences, University of Sydney, Macleay Building A12, Sydney, NSW 2006, Australia
- Centre
for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia
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