Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex

Cell. 2018 Jun 14;173(7):1663-1677.e21. doi: 10.1016/j.cell.2018.05.041.

Abstract

The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4.

Keywords: RNA degradation; RNA-protein complex; SF2; exoribonuclease; exosome; helicase; hydrolase; nuclear; ribonuclease; translocase.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain
  • Cryoelectron Microscopy
  • DNA / genetics
  • DNA / metabolism
  • DNA Helicases / metabolism*
  • Exoribonucleases / chemistry
  • Exoribonucleases / metabolism
  • Exosome Multienzyme Ribonuclease Complex / chemistry
  • Exosome Multienzyme Ribonuclease Complex / metabolism*
  • Humans
  • Image Processing, Computer-Assisted
  • Membrane Proteins / chemistry
  • Membrane Proteins / metabolism
  • Protein Binding
  • Protein Structure, Quaternary
  • RNA / genetics
  • RNA / metabolism*
  • RNA Helicases / chemistry
  • RNA Helicases / metabolism*
  • RNA Stability
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / metabolism
  • Schizosaccharomyces / metabolism
  • Schizosaccharomyces pombe Proteins / chemistry
  • Schizosaccharomyces pombe Proteins / metabolism
  • Substrate Specificity

Substances

  • MPP6 protein, human
  • Membrane Proteins
  • Saccharomyces cerevisiae Proteins
  • Schizosaccharomyces pombe Proteins
  • RNA
  • DNA
  • Exoribonucleases
  • Exosome Multienzyme Ribonuclease Complex
  • DIS3 protein, human
  • EXOSC10 protein, human
  • SKIV2L2 protein, human
  • DNA Helicases
  • RNA Helicases