title: The frameshift stimulatory signal of human immunodeficiency virus type 1 group O is a pseudoknot.
abstract: Human immunodeficiency virus type 1 (HIV-1) requires a programmed -1 ribosomal frameshift to produce Gag-Pol, the precursor of its enzymatic activities. This frameshift occurs at a slippery sequence on the viral messenger RNA and is stimulated by a specific structure, downstream of the shift site. While in group M, the most abundant HIV-1 group, the frameshift stimulatory signal is an extended bulged stem-loop, we show here, using a combination of mutagenesis and probing studies, that it is a pseudoknot in group O. The mutagenesis and probing studies coupled to an in silico analysis show that group O pseudoknot is a hairpin-type pseudoknot with two coaxially stacked stems of eight base-pairs (stem 1 and stem 2), connected by single-stranded loops of 2nt (loop 1) and 20nt (loop 2). Mutations impairing formation of stem 1 or stem 2 of the pseudoknot reduce frameshift efficiency, whereas compensatory changes that allow re-formation of these stems restore the frameshift efficiency to near wild-type level. The difference between the frameshift stimulatory signal of group O and group M supports the hypothesis that these groups originate from a different monkey to human transmission.
authors.affiliation: Département de Biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, Qué., Canada H3T 1J4.
authors.forename: Martin
authors.initials: M
authors.lastname: Baril
authors.forename: Dominic
authors.initials: D
authors.lastname: Dulude
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Steinberg
authors.forename: Léa
authors.initials: L
authors.lastname: Brakier-Gingras
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D003198:Computer Simulation; D018965:Frameshifting, Ribosomal / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics*; D038621:Regulatory Sequences, Ribonucleic Acid / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral; D038621:Regulatory Sequences, Ribonucleic Acid