A DEAD-box protein acts through RNA to promote HIV-1 Rev-RRE assembly

Nucleic Acids Res. 2017 May 5;45(8):4632-4641. doi: 10.1093/nar/gkx206.


The HIV-1 Rev protein activates nuclear export of unspliced and partially spliced viral RNA transcripts, which encode the viral genome and the genes encoding viral structural proteins, by binding to and oligomerizing on the Rev Response Element (RRE). The human DEAD-box protein 1 (DDX1) enhances the RNA export activity of Rev through an unknown mechanism. Using a single-molecule assembly assay and various DDX1 mutants, we show that DDX1 acts through the RRE RNA to specifically accelerate the nucleation step of the Rev-RRE assembly process. Single-molecule Förster resonance energy transfer (smFRET) experiments using donor-labeled Rev and acceptor-labeled DDX1 show that both proteins can associate with a single RRE molecule. However, simultaneous interaction is only observed in a subset of binding events and does not explain the extent to which DDX1 promotes the nucleation step of Rev-RRE assembly. Together, these results are consistent with a model wherein DDX1 acts as an RNA chaperone, remodeling the RRE into a conformation that is pre-organized to bind the first Rev monomer, thereby promoting the overall Rev-RRE assembly process.

Publication types

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

MeSH terms

  • Binding Sites
  • Biological Transport
  • Carbocyanines / chemistry
  • DEAD-box RNA Helicases / genetics*
  • DEAD-box RNA Helicases / metabolism
  • Fluorescence Resonance Energy Transfer
  • Fluorescent Dyes / chemistry
  • Gene Expression
  • Genes, env*
  • HIV-1 / genetics*
  • HIV-1 / growth & development
  • HIV-1 / metabolism
  • Host-Pathogen Interactions
  • Humans
  • Nucleic Acid Conformation
  • Protein Binding
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • RNA, Viral / chemistry
  • RNA, Viral / genetics*
  • RNA, Viral / metabolism
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Rhodamines / chemistry
  • Single Molecule Imaging
  • Staining and Labeling
  • Sulfonic Acids / chemistry
  • Virus Assembly / genetics*


  • Alexa Fluor 555
  • Alexa Fluor 647
  • Carbocyanines
  • Fluorescent Dyes
  • RNA, Messenger
  • RNA, Viral
  • Recombinant Fusion Proteins
  • Rhodamines
  • Sulfonic Acids
  • DDX1 protein, human
  • DEAD-box RNA Helicases