Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging

Anjana Krishnan, Lizna M. Ali, Suresha G. Prabhu, Vineeta N. Pillai, Akhil Chameettachal, Valérie Vivet-Boudou, Serena Bernacchi, Farah Mustafa, Roland Marquet, Tahir Aziz Rizvi

Research output: Contribution to journalArticlepeer-review


The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous regions within the 5' end of the gRNA that assumes a higher order structure harboring several structural motifs. To better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ sequences using genetic, biochemical, and structure-function relationship approaches. Our mutational analysis revealed that the unpaired U85CUG88 stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput selective 2' hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences, with substitutions in the U85CUG88 stretch, revealed that these mutations had limited structural impact and maintained nucleotides 80-92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our data suggest that the single-stranded U85CUG88 sequence is important during FIV RNA packaging. Filter-binding assays performed using purified FIV Pr50Gag on WT and mutant U85CUG88 ψ RNAs led to reduced levels of Pr50Gag binding to mutant U85CUG88 ψ RNAs, indicating that the U85CUG88 stretch is crucial for ψ RNA-Pr50Gag interactions. Delineating sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of FIV-based vectors for human gene therapy.

Original languageEnglish
Pages (from-to)68-88
Number of pages21
Issue number1
Publication statusPublished - Dec 18 2023


  • feline immunodeficiency virus
  • filter-binding assays
  • Gag/RNA interactions
  • hSHAPE
  • retroviruses
  • RNA packaging signal (ψ)
  • RNA secondary structure

ASJC Scopus subject areas

  • Molecular Biology


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