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Nielsen CPS, Arribas-Hernández L, Han L, Reichel M, Woessmann J, Daucke R, Bressendorff S, López-Márquez D, Andersen SU, Pumplin N, Schoof EM, Brodersen P. Evidence for an RNAi-independent role of Arabidopsis DICER-LIKE2 in growth inhibition and basal antiviral resistance. THE PLANT CELL 2024; 36:2289-2309. [PMID: 38466226 PMCID: PMC11132882 DOI: 10.1093/plcell/koae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 12/13/2023] [Accepted: 01/28/2024] [Indexed: 03/12/2024]
Abstract
Flowering plant genomes encode four or five DICER-LIKE (DCL) enzymes that produce small interfering RNAs (siRNAs) and microRNAs, which function in RNA interference (RNAi). Different RNAi pathways in plants effect transposon silencing, antiviral defense, and endogenous gene regulation. DCL2 acts genetically redundantly with DCL4 to confer basal antiviral defense. However, DCL2 may also counteract DCL4 since knockout of DCL4 causes growth defects that are suppressed by DCL2 inactivation. Current models maintain that RNAi via DCL2-dependent siRNAs is the biochemical basis of both effects. Here, we report that DCL2-mediated antiviral resistance and growth defects cannot be explained by the silencing effects of DCL2-dependent siRNAs. Both functions are defective in genetic backgrounds that maintain high levels of DCL2-dependent siRNAs, either with specific point mutations in DCL2 or with reduced DCL2 dosage because of heterozygosity for dcl2 knockout alleles. Intriguingly, all DCL2 functions require its catalytic activity, and the penetrance of DCL2-dependent growth phenotypes in dcl4 mutants correlates with DCL2 protein levels but not with levels of major DCL2-dependent siRNAs. We discuss this requirement and correlation with catalytic activity but not with resulting siRNAs, in light of other findings that reveal a DCL2 function in innate immunity activation triggered by cytoplasmic double-stranded RNA.
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Affiliation(s)
- Carsten Poul Skou Nielsen
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Laura Arribas-Hernández
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Lijuan Han
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Marlene Reichel
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jakob Woessmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Bygningstorvet, DK-2800 Lyngby, Denmark
| | - Rune Daucke
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Bygningstorvet, DK-2800 Lyngby, Denmark
| | - Simon Bressendorff
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Diego López-Márquez
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Nathan Pumplin
- Swiss Federal Institute of Technology, Institute of Molecular Plant Biology, Universitätsstrasse 2, CH-8092 Zürich, Switzerland
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Bygningstorvet, DK-2800 Lyngby, Denmark
| | - Peter Brodersen
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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2
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Bélanger S, Kramer MC, Payne HA, Hui AY, Slotkin RK, Meyers BC, Staub JM. Plastid dsRNA transgenes trigger phased small RNA-based gene silencing of nuclear-encoded genes. THE PLANT CELL 2023; 35:3398-3412. [PMID: 37309669 PMCID: PMC10473229 DOI: 10.1093/plcell/koad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/16/2023] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
Plastid transformation technology has been widely used to express traits of potential commercial importance, though the technology has been limited to traits that function while sequestered in the organelle. Prior research indicates that plastid contents can escape from the organelle, suggesting a possible mechanism for engineering plastid transgenes to function in other cellular locations. To test this hypothesis, we created tobacco (Nicotiana tabacum cv. Petit Havana) plastid transformants that express a fragment of the nuclear-encoded Phytoene desaturase (PDS) gene capable of catalyzing post-transcriptional gene silencing if RNA escapes into the cytoplasm. We found multiple lines of direct evidence that plastid-encoded PDS transgenes affect nuclear PDS gene silencing: knockdown of the nuclear-encoded PDS mRNA and/or its apparent translational inhibition, biogenesis of 21-nucleotide (nt) phased small interfering RNAs (phasiRNAs), and pigment-deficient plants. Furthermore, plastid-expressed dsRNA with no cognate nuclear-encoded pairing partner also produced abundant 21-nt phasiRNAs in the cytoplasm, demonstrating that a nuclear-encoded template is not required for siRNA biogenesis. Our results indicate that RNA escape from plastids to the cytoplasm occurs generally, with functional consequences that include entry into the gene silencing pathway. Furthermore, we uncover a method to produce plastid-encoded traits with functions outside of the organelle and open additional fields of study in plastid development, compartmentalization, and small RNA biogenesis.
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Affiliation(s)
- Sébastien Bélanger
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - Marianne C Kramer
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - Hayden A Payne
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - Alice Y Hui
- Plastomics Inc, 1100 Corporate Square Drive, St. Louis, MO 63132, USA
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Jeffrey M Staub
- Plastomics Inc, 1100 Corporate Square Drive, St. Louis, MO 63132, USA
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Clavel M, Lechner E, Incarbone M, Vincent T, Cognat V, Smirnova E, Lecorbeiller M, Brault V, Ziegler-Graff V, Genschik P. Atypical molecular features of RNA silencing against the phloem-restricted polerovirus TuYV. Nucleic Acids Res 2021; 49:11274-11293. [PMID: 34614168 PMCID: PMC8565345 DOI: 10.1093/nar/gkab802] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/25/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022] Open
Abstract
In plants and some animal lineages, RNA silencing is an efficient and adaptable defense mechanism against viruses. To counter it, viruses encode suppressor proteins that interfere with RNA silencing. Phloem-restricted viruses are spreading at an alarming rate and cause substantial reduction of crop yield, but how they interact with their hosts at the molecular level is still insufficiently understood. Here, we investigate the antiviral response against phloem-restricted turnip yellows virus (TuYV) in the model plant Arabidopsis thaliana. Using a combination of genetics, deep sequencing, and mechanical vasculature enrichment, we show that the main axis of silencing active against TuYV involves 22-nt vsiRNA production by DCL2, and their preferential loading into AGO1. Moreover, we identify vascular secondary siRNA produced from plant transcripts and initiated by DCL2-processed AGO1-loaded vsiRNA. Unexpectedly, and despite the viral encoded VSR P0 previously shown to mediate degradation of AGO proteins, vascular AGO1 undergoes specific post-translational stabilization during TuYV infection. Collectively, our work uncovers the complexity of antiviral RNA silencing against phloem-restricted TuYV and prompts a re-assessment of the role of its suppressor of silencing P0 during genuine infection.
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Affiliation(s)
- Marion Clavel
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Esther Lechner
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Marco Incarbone
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Timothée Vincent
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Valerie Cognat
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Ekaterina Smirnova
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Maxime Lecorbeiller
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | | | - Véronique Ziegler-Graff
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Pascal Genschik
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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Ferrafiat L, Pflieger D, Singh J, Thieme M, Böhrer M, Himber C, Gerbaud A, Bucher E, Pikaard CS, Blevins T. The NRPD1 N-terminus contains a Pol IV-specific motif that is critical for genome surveillance in Arabidopsis. Nucleic Acids Res 2019; 47:9037-9052. [PMID: 31372633 PMCID: PMC6753494 DOI: 10.1093/nar/gkz618] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 07/03/2019] [Accepted: 07/11/2019] [Indexed: 12/29/2022] Open
Abstract
RNA-guided surveillance systems constrain the activity of transposable elements (TEs) in host genomes. In plants, RNA polymerase IV (Pol IV) transcribes TEs into primary transcripts from which RDR2 synthesizes double-stranded RNA precursors for small interfering RNAs (siRNAs) that guide TE methylation and silencing. How the core subunits of Pol IV, homologs of RNA polymerase II subunits, diverged to support siRNA biogenesis in a TE-rich, repressive chromatin context is not well understood. Here we studied the N-terminus of Pol IV’s largest subunit, NRPD1. Arabidopsis lines harboring missense mutations in this N-terminus produce wild-type (WT) levels of NRPD1, which co-purifies with other Pol IV subunits and RDR2. Our in vitro transcription and genomic analyses reveal that the NRPD1 N-terminus is critical for robust Pol IV-dependent transcription, siRNA production and DNA methylation. However, residual RNA-directed DNA methylation observed in one mutant genotype indicates that Pol IV can operate uncoupled from the high siRNA levels typically observed in WT plants. This mutation disrupts a motif uniquely conserved in Pol IV, crippling the enzyme's ability to inhibit retrotransposon mobilization. We propose that the NRPD1 N-terminus motif evolved to regulate Pol IV function in genome surveillance.
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Affiliation(s)
- Laura Ferrafiat
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - David Pflieger
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Jasleen Singh
- Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA.,Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Michael Thieme
- Botanisches Institut, Universität Basel, CH-4056 Basel, Switzerland
| | - Marcel Böhrer
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Christophe Himber
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Aude Gerbaud
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Etienne Bucher
- Botanisches Institut, Universität Basel, CH-4056 Basel, Switzerland
| | - Craig S Pikaard
- Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA.,Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Todd Blevins
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France
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Katsarou K, Mitta E, Bardani E, Oulas A, Dadami E, Kalantidis K. DCL-suppressed Nicotiana benthamiana plants: valuable tools in research and biotechnology. MOLECULAR PLANT PATHOLOGY 2019; 20:432-446. [PMID: 30343523 PMCID: PMC6637889 DOI: 10.1111/mpp.12761] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
RNA silencing is a universal mechanism involved in development, epigenetic modifications and responses to biotic and abiotic stresses. The major components of this mechanism are Dicer-like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) proteins. Understanding the role of each component is of great scientific and agronomic importance. Plants, including Nicotiana benthamiana, an important plant model, usually possess four DCL proteins, each of which has a specific role, namely being responsible for the production of an exclusive small RNA population. Here, we used RNA interference (RNAi) technology to target DCL proteins and produced single and combinatorial mutants for DCL. We analysed the phenotype for each DCL knockdown plant, together with the small RNA profile, by next-generation sequencing (NGS). We also investigated transgene expression, as well as viral infections, and were able to show that DCL suppression results in distinct developmental defects, changes in small RNA populations, increases in transgene expression and, finally, higher susceptibility in certain RNA viruses. Therefore, these plants are excellent tools for the following: (i) to study the role of DCL enzymes; (ii) to overexpress proteins of interest; and (iii) to understand the complex relationship between the plant silencing mechanism and biotic or abiotic stresses.
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Affiliation(s)
- Konstantina Katsarou
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
| | - Eleni Mitta
- Department of BiologyUniversity of CreteHeraklionGreece
| | | | - Anastasis Oulas
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
- Present address:
Bioinformatics Group, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Elena Dadami
- Department of BiologyUniversity of CreteHeraklionGreece
- Present address:
RLP AgroScience, AlPlantaNeustadtGermany
| | - Kriton Kalantidis
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
- Department of BiologyUniversity of CreteHeraklionGreece
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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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