Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA

Viruses. 2017 Apr 26;9(5):93. doi: 10.3390/v9050093.

Abstract

The genomic RNA of the retrotransposon Ty1 is packaged as a dimer into virus-like particles. The 5' terminus of Ty1 RNA harbors cis-acting sequences required for translation initiation, packaging and initiation of reverse transcription (TIPIRT). To identify RNA motifs involved in dimerization and packaging, a structural model of the TIPIRT domain in vitro was developed from single-nucleotide resolution RNA structural data. In general agreement with previous models, the first 326 nucleotides of Ty1 RNA form a pseudoknot with a 7-bp stem (S1), a 1-nucleotide interhelical loop and an 8-bp stem (S2) that delineate two long, structured loops. Nucleotide substitutions that disrupt either pseudoknot stem greatly reduced helper-Ty1-mediated retrotransposition of a mini-Ty1, but only mutations in S2 destabilized mini-Ty1 RNA in cis and helper-Ty1 RNA in trans. Nested in different loops of the pseudoknot are two hairpins with complementary 7-nucleotide motifs at their apices. Nucleotide substitutions in either motif also reduced retrotransposition and destabilized mini- and helper-Ty1 RNA. Compensatory mutations that restore base-pairing in the S2 stem or between the hairpins rescued retrotransposition and RNA stability in cis and trans. These data inform a model whereby a Ty1 RNA kissing complex with two intermolecular kissing-loop interactions initiates dimerization and packaging.

Keywords: RNA kissing complex; RNA packaging; RNA secondary structure; SHAPE analysis; Saccharomyces cerevisiae; Ty1; kissing loop; long terminal repeat-retrotransposon; pseudoknot.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Dimerization
  • Nucleic Acid Conformation
  • Nucleotide Motifs
  • Peptide Chain Initiation, Translational
  • RNA / chemistry*
  • RNA / metabolism*
  • RNA, Viral / genetics
  • Retroelements*
  • Retroviridae / genetics
  • Reverse Transcription
  • Saccharomyces cerevisiae / genetics*
  • Transcription, Genetic

Substances

  • RNA, Viral
  • Retroelements
  • RNA