A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing

Nature. 2014 Nov 27;515(7528):591-5. doi: 10.1038/nature13709. Epub 2014 Sep 7.

Abstract

To prime reverse transcription, retroviruses require annealing of a transfer RNA molecule to the U5 primer binding site (U5-PBS) region of the viral genome. The residues essential for primer annealing are initially locked in intramolecular interactions; hence, annealing requires the chaperone activity of the retroviral nucleocapsid (NC) protein to facilitate structural rearrangements. Here we show that, unlike classical chaperones, the Moloney murine leukaemia virus NC uses a unique mechanism for remodelling: it specifically targets multiple structured regions in both the U5-PBS and tRNA(Pro) primer that otherwise sequester residues necessary for annealing. This high-specificity and high-affinity binding by NC consequently liberates these sequestered residues--which are exactly complementary--for intermolecular interactions. Furthermore, NC utilizes a step-wise, entropy-driven mechanism to trigger both residue-specific destabilization and residue-specific release. Our structures of NC bound to U5-PBS and tRNA(Pro) reveal the structure-based mechanism for retroviral primer annealing and provide insights as to how ATP-independent chaperones can target specific RNAs amidst the cellular milieu of non-target RNAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Genome, Viral / genetics
  • Humans
  • Models, Molecular*
  • Moloney murine leukemia virus* / chemistry
  • Moloney murine leukemia virus* / genetics
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleocapsid Proteins* / chemistry
  • Nucleocapsid Proteins* / metabolism
  • Protein Binding
  • Protein Structure, Tertiary
  • RNA, Transfer* / chemistry
  • RNA, Transfer* / metabolism
  • RNA, Viral / chemistry*
  • RNA, Viral / metabolism*
  • Reverse Transcription / genetics
  • Reverse Transcription / physiology*

Substances

  • Nucleocapsid Proteins
  • RNA, Viral
  • RNA, Transfer

Associated data

  • PDB/2MQT
  • PDB/2MQV
  • PDB/2MS0
  • PDB/2MS1