Distinct and evolutionary conserved structural features of the human nuclear exosome complex.

Piotr Gerlach,Elena Conti,Jan M Schuller,Fabien Bonneau,Peter Reichelt,Jérôme Basquin,Sebastian Falk

doi:10.7554/elife.38686

Abstract

The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to date have focused on the yeast system. Here, we reconstituted and studied the properties of a recombinant 14-subunit human nuclear exosome complex. In biochemical assays, the human exosome embeds a longer RNA channel than its yeast counterpart. The 3.8 Å resolution cryo-EM structure of the core complex bound to a single-stranded RNA reveals that the RNA channel path is formed by two distinct features of the hDIS3 exoribonuclease: an open conformation and a domain organization more similar to bacterial RNase II than to yeast Rrp44. The cryo-EM structure of the holo-complex shows how obligate nuclear cofactors position the hMTR4 helicase at the entrance of the core complex, suggesting a striking structural conservation from lower to higher eukaryotes.

Highlights

The eukaryotic RNA exosome is a conserved and versatile ribonuclease complex involved in many RNA quality-control and turnover pathways in both nuclear and cytoplasmic compartments
It became apparent that the yeast exosome has a human counterpart in the so-called PM-Scl complex, which had been identified as the target of autoantibodies in patients suffering from polymyositis-scleroderma overlap syndrome (PM-Scl) (Allmang et al, 1999b)
Since the structure of the yeast exosome core has been discussed in several publications (Falk et al, 2017; Kowalinski et al, 2016; Liu et al, 2006; Makino et al, 2013; Wasmuth et al, 2014), we will refer to human exosome components (EXOSC) of the 9-subunit barrel with the corresponding names from S. cerevisiae, namely hCSL4 = EXOSC1, hRRP4 = EXOSC2, hRRP40 = EXOSC3, hRRP41 = EXOSC4, hRRP46 = EXOSC5, hMTR3 = EXOSC6, hRRP42 = EXOSC7, hRRP43 = EXOSC8 and hRRP45 = EXOSC9

Summary

Introduction

The eukaryotic RNA exosome is a conserved and versatile ribonuclease complex involved in many RNA quality-control and turnover pathways in both nuclear and cytoplasmic compartments. Besides eliminating defective and superfluous transcripts, the exosome has processing functions in the maturation of nuclear RNA precursors, such as ribosomal RNAs (rRNAs) and small nucleolar RNAs (snoRNAs) (reviewed in Chlebowski et al, 2013; Zinder and Lima, 2017). The exosome was originally discovered in S. cerevisiae as a complex of ribosomal RNA processing (Rrp) factors (Mitchell et al, 1997). While the yeast exosome has been extensively studied in the past two decades, mechanistic studies on the human complex have generally lagged behind

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Conclusion