The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana.

Heike Lange,Dominique Gagliardi,François M Sement,Sébastien Aubourg,Lauriane Kuhn,Véronique Brunaud,Caroline Bérard,Sandrine Balzergue,Philippe Hammann,Johana Chicher,Nathalie Bouteiller,Hélène Zuber,Marie-Laure Martin-Magniette,Hervé Vaucheret

doi:10.1371/journal.pgen.1004564

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.

Highlights

Efficient processing and degradation of RNA is a key process for the post-transcriptional control of gene expression
We have previously shown that AtMTR4 is a predominantly nucleolar protein required for the efficient degradation of misprocessed 5.8S rRNA precursors and specific fragments of the 59 external transcribed spacer (59 ETS), a byproduct released during processing of three rRNAs from their common precursor transcript [13]
The requirement for AtMTR4 in efficient rRNA production is reflected by the phenotype of mtr4 mutants, which show a characteristic combination of developmental growth defects observed in ribosomal protein mutants and in other Arabidopsis mutants lacking putative ribosome biogenesis factors such as nucleolin [14,15,16,17,18,19]

Summary

Introduction

Efficient processing and degradation of RNA is a key process for the post-transcriptional control of gene expression. Cytoplasmic and nuclear exosomes are activated by the RNA helicases SKI2 and MTR4, respectively [6,7,8]. In both yeast and human MTR4 is an essential protein required for all functions of the nuclear exosome [9,10]. The requirement for AtMTR4 in efficient rRNA production is reflected by the phenotype of mtr mutants, which show a characteristic combination of developmental growth defects observed in ribosomal protein mutants and in other Arabidopsis mutants lacking putative ribosome biogenesis factors such as nucleolin [14,15,16,17,18,19]

Methods

Results

Discussion

Conclusion