title: Internal translation initiation from HIV-1 transcripts is conferred by a common RNA structure.
abstract: Alternative splicing of the human immunodeficiency virus 1 (HIV-1) RNA transcripts produces mRNAs encoding nine different viral proteins. The leader of each contains a common non-coding exon at the 5' end. Previous studies showed that the leaders from the common exon-containing transcripts gag, nef, vif, vpr and vpu can direct protein synthesis through internal ribosome entry sites (IRESs) with varying efficiencies. Here we explored whether the common exon acts as an IRES element in the context of all the 5' leaders or if each harbors a distinct IRES. We also explored the relationship between the IRESs and initiation codon selection. We find that the common exon adopts a similar conformation in every leader we explored and that the sequence and structure is required for IRES activity. We also find that each leader uses a scanning mechanism for start codon identification. Together, our data point to a model in which the common exon on HIV-1 transcripts acts as the ribosome landing pad, recruiting preinitiation complexes upstream of the initiation codon, followed by scanning to each transcript's initiator AUG.
authors.affiliation: Department of Biochemistry and Molecular Genetics and University of Colorado Denver School of Medicine, Aurora, CO USA.
authors.forename: Terra-Dawn M
authors.initials: TD
authors.lastname: Plank
authors.affiliation: Department of Pharmacology, University of Colorado Denver, School of Medicine, Aurora, CO USA.
authors.forename: James T
authors.initials: JT
authors.lastname: Whitehurst
authors.affiliation: Department of Biochemistry, McGill University, Montreal, Quebec, QC Canada.
authors.forename: Regina
authors.initials: R
authors.lastname: Cencic
authors.affiliation: Department of Biochemistry, McGill University, Montreal, Quebec, QC Canada; The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, QC Canada.
authors.forename: Jerry
authors.initials: J
authors.lastname: Pelletier
authors.affiliation: Department of Biochemistry and Molecular Genetics and University of Colorado Denver School of Medicine, Aurora, CO USA; Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, CO USA.
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Kieft
keywords: HIV-1; IRES; common exon; translation initiation; viral RNA