Abstract
The RNA exosome provides eukaryotic cells with an essential 3′–5′ exoribonucleolytic activity, which processes or eliminates many classes of RNAs. Its nine-subunit core (Exo9) is structurally related to prokaryotic phosphorolytic exoribonucleases. Yet, yeast and animal Exo9s have lost the primordial phosphorolytic capacity and rely instead on associated hydrolytic ribonucleases for catalytic activity. Here, we demonstrate that Arabidopsis Exo9 has retained a distributive phosphorolytic activity, which contributes to rRNA maturation processes, the hallmark of exosome function. High-density mapping of 3′ extremities of rRNA maturation intermediates reveals the intricate interplay between three exoribonucleolytic activities coordinated by the plant exosome. Interestingly, the analysis of RRP41 protein diversity across eukaryotes suggests that Exo9’s intrinsic activity operates throughout the green lineage, and possibly in some earlier-branching non-plant eukaryotes. Our results reveal a remarkable evolutionary variation of this essential RNA degradation machine in eukaryotes.
Highlights
The RNA exosome provides eukaryotic cells with an essential 3′–5′ exoribonucleolytic activity, which processes or eliminates many classes of RNAs
Some amino acids required for phosphorolytic activity were noticed to be present in RRP41 from Arabidopsis and rice[8]
To test for the conservation in Arabidopsis of all the amino acids required for phosphorolytic activity, we compared RRP41 sequences from Arabidopsis thaliana, Sulfolobus solfataricus, Archaeoglobus fulgidus, Pyrococcus abyssi and Methanothermobacter thermautotrophicus
Summary
The RNA exosome provides eukaryotic cells with an essential 3′–5′ exoribonucleolytic activity, which processes or eliminates many classes of RNAs. The role of RRP6L3 is entirely unknown and its functional relationship with the exosome remains elusive It is unknown whether plant Exo[9] has retained an intrinsic ribonucleolytic activity similar to its structurally related complexes in prokaryotes or whether plant Exo[9] is inactive as its yeast and animal counterparts. We demonstrate that the purified Arabidopsis exosome core complex is endowed with a phosphorolytic activity conferred by the RRP41 subunit In vivo, this intrinsic phosphorolytic activity of Exo[9] cooperates with the hydrolytic exoribonucleolytic activities of RRP6L2 and RRP44 for the elimination of rRNA maturation by-products and the processing/degradation of 5.8S rRNA precursors, two prototypical functions of the RNA exosome in eukaryotes. Several Amoebozoa, the human pathogen Naegleria fowleri or Capsaspora owczarzaki, a singlecelled eukaryote, which is a close unicellular relative of metazoans, possess a potentially active RRP41, raising the interesting possibility that an active Exo[9] might exist in non-plant eukaryotes
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