The Halastavi árva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism

Cell Rep. 2020 Dec 8;33(10):108476. doi: 10.1016/j.celrep.2020.108476.


Dicistrovirus intergenic region internal ribosomal entry sites (IGR IRESs) do not require initiator tRNA, an AUG codon, or initiation factors and jumpstart translation from the middle of the elongation cycle via formation of IRES/80S complexes resembling the pre-translocation state. eEF2 then translocates the [codon-anticodon]-mimicking pseudoknot I (PKI) from ribosomal A sites to P sites, bringing the first sense codon into the decoding center. Halastavi árva virus (HalV) contains an IGR that is related to previously described IGR IRESs but lacks domain 2, which enables these IRESs to bind to individual 40S ribosomal subunits. By using in vitro reconstitution and cryoelectron microscopy (cryo-EM), we now report that the HalV IGR IRES functions by the simplest initiation mechanism that involves binding to 80S ribosomes such that PKI is placed in the P site, so that the A site contains the first codon that is directly accessible for decoding without prior eEF2-mediated translocation of PKI.

Keywords: Cricket paralysis virus; Halastavi árva virus; IRES; SERBP1; SERPINE1 mRNA binding protein 1; dicistrovirus; intergenic region; internal ribosomal entry site; pseudoknot; ribosome.

Publication types

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

MeSH terms

  • Anticodon
  • Codon / metabolism
  • Cryoelectron Microscopy / methods
  • DNA, Intergenic / metabolism
  • Internal Ribosome Entry Sites / genetics*
  • Internal Ribosome Entry Sites / physiology
  • Peptide Chain Initiation, Translational / genetics*
  • Peptide Chain Initiation, Translational / physiology
  • Peptide Elongation Factor 2 / metabolism
  • Peptide Initiation Factors / genetics
  • Positive-Strand RNA Viruses / genetics*
  • Positive-Strand RNA Viruses / metabolism
  • Protein Biosynthesis / genetics
  • RNA, Messenger / metabolism
  • RNA, Viral / genetics
  • Ribosomes / metabolism
  • Virus Replication / genetics
  • Virus Replication / physiology
  • Viruses / metabolism


  • Anticodon
  • Codon
  • DNA, Intergenic
  • Internal Ribosome Entry Sites
  • Peptide Elongation Factor 2
  • Peptide Initiation Factors
  • RNA, Messenger
  • RNA, Viral