tRNA-mRNA mimicry drives translation initiation from a viral IRES

Nat Struct Mol Biol. 2008 Jan;15(1):57-64. doi: 10.1038/nsmb1351. Epub 2007 Dec 23.

Abstract

Internal ribosome entry site (IRES) RNAs initiate protein synthesis in eukaryotic cells by a noncanonical cap-independent mechanism. IRESes are critical for many pathogenic viruses, but efforts to understand their function are complicated by the diversity of IRES sequences as well as by limited high-resolution structural information. The intergenic region (IGR) IRESes of the Dicistroviridae viruses are powerful model systems to begin to understand IRES function. Here we present the crystal structure of a Dicistroviridae IGR IRES domain that interacts with the ribosome's decoding groove. We find that this RNA domain precisely mimics the transfer RNA anticodon-messenger RNA codon interaction, and its modeled orientation on the ribosome helps explain translocation without peptide bond formation. When combined with a previous structure, this work completes the first high-resolution description of an IRES RNA and provides insight into how RNAs can manipulate complex biological machines.

Publication types

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

MeSH terms

  • Anticodon / genetics
  • Binding Sites
  • Hepacivirus / genetics
  • Models, Genetic
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protein Biosynthesis*
  • RNA, Messenger / chemistry*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Transfer / chemistry*
  • RNA, Transfer / genetics
  • RNA, Transfer / metabolism
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • RNA, Viral / metabolism
  • Ribosomes / genetics
  • Ribosomes / physiology*

Substances

  • Anticodon
  • RNA, Messenger
  • RNA, Viral
  • RNA, Transfer

Associated data

  • PDB/3B31