title: Alternative reading frame selection mediated by a tRNA-like domain of an internal ribosome entry site.
abstract: The dicistrovirus intergenic region internal ribosome entry site (IRES) utilizes a unique mechanism, involving P-site tRNA mimicry, to directly assemble 80S ribosomes and initiate translation at a specific non-AUG codon in the ribosomal A site. A subgroup of dicistrovirus genomes contains an additional stem-loop 5'-adjacent to the IRES and a short open reading frame (ORFx) that overlaps the viral structural polyprotein ORF (ORF2) in the +1 reading frame. Using mass spectrometry and extensive mutagenesis, we show that, besides directing ORF2 translation, the Israeli acute paralysis dicistrovirus IRES also directs ORFx translation. The latter is mediated by a UG base pair adjacent to the P-site tRNA-mimicking domain. An ORFx peptide was detected in virus-infected honey bees by multiple reaction monitoring mass spectrometry. Finally, the 5' stem-loop increases IRES activity and may couple translation of the two major ORFs of the virus. This study reveals a novel viral strategy in which a tRNA-like IRES directs precise, initiator Met-tRNA-independent translation of two overlapping ORFs.
authors.affiliation: Department of Biochemistry and Molecular Biology and  Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada.
authors.forename: Qian
authors.initials: Q
authors.lastname: Ren
authors.forename: Qing S
authors.initials: QS
authors.lastname: Wang
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Firth
authors.forename: Mandy M Y
authors.initials: MM
authors.lastname: Chan
authors.forename: Joost W
authors.initials: JW
authors.lastname: Gouw
authors.forename: M Marta
authors.initials: MM
authors.lastname: Guarna
authors.forename: Leonard J
authors.initials: LJ
authors.lastname: Foster
authors.forename: John F
authors.initials: JF
authors.lastname: Atkins
authors.forename: Eric
authors.initials: E
authors.lastname: Jan
mesh_terms: D000818:Animals; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D001516:Bees / Q000821:virology; D018076:DNA, Complementary / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D056629:Dicistroviridae / Q000235:genetics; D015852:Eukaryotic Initiation Factor-2 / Q000378:metabolism; D039562:Eukaryotic Initiation Factor-4F / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010442:Peptide Chain Initiation, Translational / Q000235:genetics; D011679:Pupa / Q000821:virology; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics*; D016364:Reading Frames / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics*; D012641:Selection, Genetic
chemical_list: D018076:DNA, Complementary; D021901:DNA, Intergenic; D015852:Eukaryotic Initiation Factor-2; D039562:Eukaryotic Initiation Factor-4F; D012343:RNA, Transfer