UPF1-like helicase grip on nucleic acids dictates processivity

Nat Commun. 2018 Sep 14;9(1):3752. doi: 10.1038/s41467-018-06313-y.

Abstract

Helicases are molecular engines which translocate along nucleic acids (NA) to unwind double-strands or remodel NA-protein complexes. While they have an essential role in genome structure and expression, the rules dictating their processivity remain elusive. Here, we developed single-molecule methods to investigate helicase binding lifetime on DNA. We found that UPF1, a highly processive helicase central to nonsense-mediated mRNA decay (NMD), tightly holds onto NA, allowing long lasting action. Conversely, the structurally similar IGHMBP2 helicase has a short residence time. UPF1 mutants with variable grip on DNA show that grip tightness dictates helicase residence time and processivity. In addition, we discovered via functional studies that a decrease in UPF1 grip impairs NMD efficiency in vivo. Finally, we propose a three-state model with bound, sliding and unbound molecular clips, that can accurately predict the modulation of helicase processivity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / metabolism*
  • DNA-Binding Proteins / metabolism*
  • Humans
  • Nonsense Mediated mRNA Decay*
  • Nucleic Acids / metabolism*
  • RNA Helicases / metabolism*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Time Factors
  • Trans-Activators / metabolism*
  • Transcription Factors / metabolism*

Substances

  • DNA-Binding Proteins
  • IGHMBP2 protein, human
  • Nucleic Acids
  • Saccharomyces cerevisiae Proteins
  • Trans-Activators
  • Transcription Factors
  • DNA
  • NAM7 protein, S cerevisiae
  • RNA Helicases
  • UPF1 protein, human