The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase

EMBO J. 2014 Dec 1;33(23):2829-46. doi: 10.15252/embj.201488757. Epub 2014 Oct 15.


The exosome is a conserved multi-subunit ribonuclease complex that functions in 3' end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10-subunit core complex of the exosome (Exo-10) physically and functionally interacts with the Rrp6 exoribonuclease and its associated cofactor Rrp47, the helicase Mtr4 and Mpp6. Here, we show that binding of Mtr4 to Exo-10 in vitro is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N-terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N-terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C-terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6-Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome.

Keywords: RNA degradation; X‐ray crystallography; nuclear exosome; yeast genetics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Blotting, Western
  • Calorimetry
  • Chromatography, Gel
  • Crystallization
  • DEAD-box RNA Helicases / chemistry
  • DEAD-box RNA Helicases / metabolism*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism*
  • Electrophoresis, Polyacrylamide Gel
  • Escherichia coli
  • Exosome Multienzyme Ribonuclease Complex / chemistry
  • Exosome Multienzyme Ribonuclease Complex / metabolism*
  • Fluorescence Polarization
  • Models, Molecular*
  • Multiprotein Complexes / chemistry
  • Multiprotein Complexes / metabolism*
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / metabolism*
  • Oligonucleotide Probes
  • Protein Conformation
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism*
  • Rosaniline Dyes
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / metabolism*


  • DNA-Binding Proteins
  • LRP1 protein, S cerevisiae
  • Multiprotein Complexes
  • Nuclear Proteins
  • Oligonucleotide Probes
  • RNA-Binding Proteins
  • Rosaniline Dyes
  • Saccharomyces cerevisiae Proteins
  • Coomassie blue
  • Exosome Multienzyme Ribonuclease Complex
  • RRP6 protein, S cerevisiae
  • MTR4 protein, S cerevisiae
  • DEAD-box RNA Helicases