A ribosome-binding, 3' translational enhancer has a T-shaped structure and engages in a long-distance RNA-RNA interaction

J Virol. 2012 Sep;86(18):9828-42. doi: 10.1128/JVI.00677-12. Epub 2012 Jul 3.

Abstract

Many plant RNA viruses contain elements in their 3' untranslated regions (3' UTRs) that enhance translation. The PTE (Panicum mosaic virus-like translational enhancer) of Pea enation mosaic virus (PEMV) binds to eukaryotic initiation factor 4E (eIF4E), but how this affects translation from the 5' end is unknown. We have discovered a three-way branched element just upstream of the PEMV PTE that engages in a long-distance kissing-loop interaction with a coding sequence hairpin that is critical for the translation of a reporter construct and the accumulation of the viral genome in vivo. Loss of the long-distance interaction was more detrimental than elimination of the adjacent PTE, indicating that the RNA-RNA interaction supports additional translation functions besides relocating the PTE to the 5' end. The branched element is predicted by molecular modeling and molecular dynamics to form a T-shaped structure (TSS) similar to the ribosome-binding TSS of Turnip crinkle virus (TCV). The PEMV element binds to plant 80S ribosomes with a K(d) (dissociation constant) of 0.52 μM and to 60S subunits with a K(d) of 0.30 μM. Unlike the TCV TSS, the PEMV element also binds 40S subunits (K(d), 0.36 μM). Mutations in the element that suppressed translation reduced either ribosome binding or the RNA-RNA interaction, suggesting that ribosome binding is important for function. This novel, multifunctional element is designated a kl-TSS (kissing-loop T-shaped structure) to distinguish it from the TCV TSS. The kl-TSS has sequence and structural features conserved with the upper portion of most PTE-type elements, which, with the exception of the PEMV PTE, can engage in similar long-distance RNA-RNA interactions.

Publication types

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

MeSH terms

  • 3' Untranslated Regions
  • 5' Untranslated Regions
  • Base Sequence
  • Binding Sites / genetics
  • Carmovirus / genetics
  • Carmovirus / metabolism
  • Enhancer Elements, Genetic*
  • Genome, Viral
  • Models, Molecular
  • Molecular Sequence Data
  • Mosaic Viruses / genetics*
  • Mosaic Viruses / metabolism*
  • Nucleic Acid Conformation
  • Protein Biosynthesis
  • RNA, Viral / chemistry
  • RNA, Viral / genetics*
  • RNA, Viral / metabolism*
  • Ribosomes / genetics
  • Ribosomes / metabolism

Substances

  • 3' Untranslated Regions
  • 5' Untranslated Regions
  • RNA, Viral