title: The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana.
abstract: The RNA exosome is the major 3'-5' RNA degradation machine of eukaryotic cells and participates in processing, surveillance and turnover of both nuclear and cytoplasmic RNA. In both yeast and human, all nuclear functions of the exosome require the RNA helicase MTR4. We show that the Arabidopsis core exosome can associate with two related RNA helicases, AtMTR4 and HEN2. Reciprocal co-immunoprecipitation shows that each of the RNA helicases co-purifies with the exosome core complex and with distinct sets of specific proteins. While AtMTR4 is a predominantly nucleolar protein, HEN2 is located in the nucleoplasm and appears to be excluded from nucleoli. We have previously shown that the major role of AtMTR4 is the degradation of rRNA precursors and rRNA maturation by-products. Here, we demonstrate that HEN2 is involved in the degradation of a large number of polyadenylated nuclear exosome substrates such as snoRNA and miRNA precursors, incompletely spliced mRNAs, and spurious transcripts produced from pseudogenes and intergenic regions. Only a weak accumulation of these exosome substrate targets is observed in mtr4 mutants, suggesting that MTR4 can contribute, but plays rather a minor role for the degradation of non-ribosomal RNAs and cryptic transcripts in Arabidopsis. Consistently, transgene post-transcriptional gene silencing (PTGS) is marginally affected in mtr4 mutants, but increased in hen2 mutants, suggesting that it is mostly the nucleoplasmic exosome that degrades aberrant transgene RNAs to limit their entry in the PTGS pathway. Interestingly, HEN2 is conserved throughout green algae, mosses and land plants but absent from metazoans and other eukaryotic lineages. Our data indicate that, in contrast to human and yeast, plants have two functionally specialized RNA helicases that assist the exosome in the degradation of specific nucleolar and nucleoplasmic RNA populations, respectively.
authors.affiliation: Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France.
authors.forename: Heike
authors.initials: H
authors.lastname: Lange
authors.affiliation: Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Zuber
authors.affiliation: Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France.
authors.forename: François M
authors.initials: FM
authors.lastname: Sement
authors.affiliation: Platforme Protéomique Strasbourg-Esplanade, Centre National de la Recherche Scientifique, FRC 1589, Université de Strasbourg, Strasbourg, France.
authors.forename: Johana
authors.initials: J
authors.lastname: Chicher
authors.affiliation: Platforme Protéomique Strasbourg-Esplanade, Centre National de la Recherche Scientifique, FRC 1589, Université de Strasbourg, Strasbourg, France.
authors.forename: Lauriane
authors.initials: L
authors.lastname: Kuhn
authors.affiliation: Platforme Protéomique Strasbourg-Esplanade, Centre National de la Recherche Scientifique, FRC 1589, Université de Strasbourg, Strasbourg, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Hammann
authors.affiliation: Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165, Université d'Evry Val d'Essonne, Saclay Plant Sciences, ERL CNRS 8196, Evry, France.
authors.forename: Véronique
authors.initials: V
authors.lastname: Brunaud
authors.affiliation: UMR AgroParisTech-INRA MIA 518, Paris, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Bérard
authors.affiliation: Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Bouteiller
authors.affiliation: Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165, Université d'Evry Val d'Essonne, Saclay Plant Sciences, ERL CNRS 8196, Evry, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Balzergue
authors.affiliation: Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165, Université d'Evry Val d'Essonne, Saclay Plant Sciences, ERL CNRS 8196, Evry, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Aubourg
authors.affiliation: Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165, Université d'Evry Val d'Essonne, Saclay Plant Sciences, ERL CNRS 8196, Evry, France; UMR AgroParisTech-INRA MIA 518, Paris, France.
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Martin-Magniette
authors.affiliation: Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Vaucheret
authors.affiliation: Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Gagliardi
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism; D002467:Cell Nucleus / Q000235:genetics; D055354:Exosomes / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D020365:RNA Helicases / Q000235:genetics* / Q000378:metabolism; D020871:RNA Stability / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000235:genetics / Q000378:metabolism
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D035683:MicroRNAs; D020365:RNA Helicases; D012333:RNA, Messenger; D020537:RNA, Small Nucleolar; C076747:NHLH2 protein, human; C512513:MTREX protein, human