lifesciences
Innopsys

The RNA Helicase 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.

Credits:

Lange H1, Zuber H1, Sement FM1, Chicher J2, Kuhn L2, Hammann P2, Brunaud V3, Bérard C4, Bouteiller N5, Balzergue S3, Aubourg S3, Martin-Magniette ML6, Vaucheret H5, Gagliardi D1.

  • 1. Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France.
  • 2. Platforme Protéomique Strasbourg-Esplanade, Centre National de la Recherche Scientifique, FRC 1589, Université de Strasbourg, Strasbourg, France.
  • 3. Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165, Université d'Evry Val d'Essonne, Saclay Plant Sciences, ERL CNRS 8196, Evry, France.
  • 4. UMR AgroParisTech-INRA MIA 518, Paris, France.
  • 5. Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France.
  • 6. 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.

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