SHAPE analysis of the 5′ end of the Mason-Pfizer monkey virus (MPMV) genomic RNA reveals structural elements required for genome dimerization

Suriya J. Aktar, Ayesha Jabeen, Lizna M. Ali, Valérie Vivet-Boudou, Roland Marquet, Tahir A. Rizvi

Research output: Contribution to journalArticlepeer-review

16 Citations (Scopus)

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 longrange 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 transcomplementary pal mutants were incubated together showed RNA dimerization was restored authenticating that the pal loop (5′ -CGGCCG-3′ ) functions as DIS.

Original languageEnglish
Pages (from-to)1648-1658
Number of pages11
JournalRNA
Volume19
Issue number12
DOIs
Publication statusPublished - Dec 2013

Keywords

  • Dimerization initiation site (DIS)
  • Long-range interaction (LRI)
  • Mason Pfizer monkey virus (MPMV)
  • RNA dimerization
  • RNA packaging signal

ASJC Scopus subject areas

  • Molecular Biology

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