title: SHAPE analysis of the 5' end of the Mason-Pfizer monkey virus (MPMV) genomic RNA reveals structural elements required for genome dimerization.
abstract: Earlier genetic and structural prediction analyses revealed that the packaging determinants of Mason Pfizer monkey virus (MPMV) include two discontinuous core regions at the 5' end of its genomic RNA. RNA secondary structure predictions suggested that these packaging determinants fold into several stem-loops (SLs). To experimentally validate this structural model, we employed selective 2' hydroxyl acylation analyzed by primer extension (SHAPE), which examines the flexibility of the RNA backbone at each nucleotide position. Our SHAPE data validated several predicted structural motifs, including U5/Gag long-range interactions (LRIs), a stretch of single-stranded purine (ssPurine)-rich region, and a distinctive G-C-rich palindromic (pal) SL. Minimum free-energy structure predictions, phylogenetic, and in silico modeling analyses of different MPMV strains revealed that the U5 and gag sequences involved in the LRIs differ minimally within strains and maintain a very high degree of complementarity. Since the pal SL forms a helix loop containing a canonical "GC" dyad, it may act as a RNA dimerization initiation site (DIS), enabling the virus to package two copies of its genome. Analyses of wild-type and pal mutant RNAs revealed that disruption of pal sequence strongly affected RNA dimerization. However, when in vitro transcribed trans-complementary pal mutants were incubated together showed RNA dimerization was restored authenticating that the pal loop (5'-CGGCCG-3') functions as DIS.
authors.forename: Suriya J
authors.initials: SJ
authors.lastname: Aktar
authors.forename: Ayesha
authors.initials: A
authors.lastname: Jabeen
authors.forename: Lizna M
authors.initials: LM
authors.lastname: Ali
authors.forename: Valérie
authors.initials: V
authors.lastname: Vivet-Boudou
authors.forename: Roland
authors.initials: R
authors.lastname: Marquet
authors.forename: Tahir A
authors.initials: TA
authors.lastname: Rizvi
mesh_terms: D000215:Acylation; D001483:Base Sequence; D017124:Conserved Sequence; D017931:DNA Primers / Q000737:chemistry; D019281:Dimerization; D016679:Genome, Viral; D055029:Inverted Repeat Sequences; D016093:Mason-Pfizer monkey virus / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D022821:RNA Splice Sites; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics; D019065:Virus Assembly
chemical_list: D017931:DNA Primers; D022821:RNA Splice Sites; D012367:RNA, Viral
keywords: Mason Pfizer monkey virus (MPMV); RNA dimerization; RNA packaging signal; dimerization initiation site (DIS); long-range interaction (LRI)