title: Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses.
abstract: Small RNAs play essential regulatory roles in genome stability, development, and responses to biotic and abiotic stresses in most eukaryotes. In plants, the RNaseIII enzyme DICER-LIKE1 (DCL1) produces miRNAs, whereas DCL2, DCL3, and DCL4 produce various size classes of siRNAs. Plants also encode RNASE THREE-LIKE (RTL) enzymes that lack DCL-specific domains and whose function is largely unknown. We found that virus infection induces RTL1 expression, suggesting that this enzyme could play a role in plant-virus interaction. To first investigate the biochemical activity of RTL1 independent of virus infection, small RNAs were sequenced from transgenic plants constitutively expressing RTL1. These plants lacked almost all DCL2-, DCL3-, and DCL4-dependent small RNAs, indicating that RTL1 is a general suppressor of plant siRNA pathways. In vivo and in vitro assays revealed that RTL1 prevents siRNA production by cleaving dsRNA prior to DCL2-, DCL3-, and DCL4-processing. The substrate of RTL1 cleavage is likely long-perfect (or near-perfect) dsRNA, consistent with the RTL1-insensitivity of miRNAs, which derive from DCL1-processing of short-imperfect dsRNA. Virus infection induces RTL1 mRNA accumulation, but viral proteins that suppress RNA silencing inhibit RTL1 activity, suggesting that RTL1 has evolved as an inducible antiviral defense that could target dsRNA intermediates of viral replication, but that a broad range of viruses counteract RTL1 using the same protein toolbox used to inhibit antiviral RNA silencing. Together, these results reveal yet another level of complexity in the evolutionary battle between viruses and plant defenses.
authors.affiliation: Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, Versailles, France.|Université Paris-Sud, Université Paris-Saclay, Orsay, France.
authors.forename: Nahid
authors.initials: N
authors.lastname: Shamandi
authors.affiliation: URGI, INRA, Versailles, France.
authors.forename: Matthias
authors.initials: M
authors.lastname: Zytnicki
authors.affiliation: CNRS, UMR 5096, LGDP, Perpignan, France.|Université Perpignan Via Domitia, UMR 5096, LGDP, Perpignan, France.
authors.forename: Cyril
authors.initials: C
authors.lastname: Charbonnel
authors.affiliation: Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Emilie
authors.initials: E
authors.lastname: Elvira-Matelot
authors.affiliation: Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Aurore
authors.initials: A
authors.lastname: Bochnakian
authors.affiliation: CNRS, UMR 5096, LGDP, Perpignan, France.|Université Perpignan Via Domitia, UMR 5096, LGDP, Perpignan, France.
authors.forename: Pascale
authors.initials: P
authors.lastname: Comella
authors.affiliation: Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Allison C
authors.initials: AC
authors.lastname: Mallory
authors.affiliation: Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Gersende
authors.initials: G
authors.lastname: Lepère
authors.affiliation: CNRS, UMR 5096, LGDP, Perpignan, France.|Université Perpignan Via Domitia, UMR 5096, LGDP, Perpignan, France.
authors.forename: Julio
authors.initials: J
authors.lastname: Sáez-Vásquez
authors.affiliation: Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, Versailles, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Vaucheret
mesh_terms: D019943:Amino Acid Substitution; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics / Q000378:metabolism / Q000821:virology*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D019184:Carmovirus / Q000502:physiology; D019295:Computational Biology / Q000379:methods; D017799:Cucumovirus / Q000502:physiology; D018506:Gene Expression Regulation, Plant; D054884:Host-Pathogen Interactions; D007527:Isoenzymes / Q000235:genetics / Q000378:metabolism; D016297:Mutagenesis, Site-Directed; D050505:Mutant Proteins / Q000235:genetics / Q000378:metabolism; D030821:Plants, Genetically Modified / Q000201:enzymology / Q000235:genetics / Q000378:metabolism / Q000821:virology; D017354:Point Mutation; D012328:RNA Viruses / Q000502:physiology*; D012333:RNA, Messenger / Q000378:metabolism; D018749:RNA, Plant / Q000037:antagonists & inhibitors* / Q000378:metabolism; D034741:RNA, Small Interfering / Q000037:antagonists & inhibitors* / Q000378:metabolism; D011993:Recombinant Fusion Proteins / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D017898:Tobamovirus / Q000502:physiology; D017806:Tymovirus / Q000502:physiology
chemical_list: D029681:Arabidopsis Proteins; D007527:Isoenzymes; D050505:Mutant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant; D034741:RNA, Small Interfering; C000607386:RTL1 protein, Arabidopsis; D011993:Recombinant Fusion Proteins; D012097:Repressor Proteins