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Cited by 307HIV Research and TreatmentRNA and protein synthesis mechanismsRNA Research and Splicing

RNA secondary structure and binding sites for gag gene products in the 5’ packaging signal of human immunodeficiency virus type 1

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Clever, J, Sassetti, C, Parslow, T G·1995·Journal of Virology
DOI 10.1128/jvi.69.4.2101-2109.1995PMC PMC188876
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Abstract

The selective encapsidation of retroviral RNA requires sequences in the Gag protein, as well as a cis-acting RNA packaging signal (psi site) near the 5' end of the genomic transcript. Gag protein of human immunodeficiency virus type 1 (HIV-1) has recently been found to bind specifically to the HIV-1 psi element in vitro. Here we report studies aimed at mapping features within the genetically defined psi locus that are required for binding of HIV-1 Gag or of its processed nucleocapsid derivative. The full-length HIV-1 Gag (p55) and nucleocapsid (p15) sequences were expressed as glutathione S-transferase (GST) fusion proteins in Escherichia coli. In a gel shift assay containing excess competitor tRNA, affinity-purified GST-p15 and GST-p55 proteins bound to a 206-nucleotide psi RNA element spanning the major splice donor and gag start codons but did not bind to antisense psi transcripts. Quantitative filter-binding assays revealed that both GST-p55 and GST-p15 bound to this RNA sequence with identical affinities (apparent Kd congruent to 5 x 10(-8) M), indicating that all major determinants of psi binding affinity reside within the nucleocapsid portion of Gag. Chemical and RNase accessibility mapping, coupled with computerized sequence analysis, suggested a model for psi RNA structure comprising four independent stem-loops. Filter-binding studies revealed that RNAs corresponding to three of these hypothetical stem-loops can each function as a independent Gag binding site and that each is bound with approximately fourfold-lower apparent affinity than the full-length psi locus. Interaction of Gag with these regions is likely to play a major role in directing HIV-1 RNA encapsidation in vivo.

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Crossref · 10.1128/jvi.69.4.2101-2109.1995

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  • Structured motifs in RNA packaging elements often include stem-loops, bulges, and unpaired purine-rich sequences that serve as high-affinity Gag binding sites.

    “These structured motifs often include stem-loops, bulges, and unpaired purine-rich sequences that serve as high-affinity Gag binding sites”

    From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Clever et al. 1995

  • RNA packaging elements form complex secondary and tertiary structures across diverse retroviruses, including HIV-1, MMTV, MPMV, and FIV.

    “Structure–function studies across diverse retroviruses, including HIV-1, MMTV, MPMV, and FIV, have consistently demonstrated that RNA packaging elements form complex secondary and tertiary structures.”

    From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Clever et al. 1995

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Authors
Clever, J., Sassetti, C., & Parslow, T. G.
Affiliations
University of California, San Francisco (US)
ORCID
Sassetti, C
Venue
Journal of Virology
Publisher
American Society for Microbiology
Published
1995-04
Volume
69
Issue
4
Pages
2101-2109
ISSN
  • 0022-538X (ISSN-L)
  • 1098-5514
DOI
10.1128/jvi.69.4.2101-2109.1995
PMC
PMC188876
OpenAlex
W2122273986
Cited by
307
References
54
Citations by year
2026: 1 · 2025: 1 · 2024: 2 · 2023: 3 · 2022: 6 · 2021: 9 · 2020: 4 · 2018: 7 · 2017: 9 · 2016: 7 · 2015: 4 · 2014: 10 · 2013: 12 · 2012: 13
FWCI
6.52
Type
journal article
Language
en
Open access
Licence
journals.asm.org/non-commercial-tdm-license (tdm)
Locations
  • Journal of Virology (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health (5r01ai029313-06, 5r01gm037036-03)
  • National Institute of General Medical Sciences (GM37036)
  • National Institute of Allergy and Infectious Diseases (AI-07395, AI29313, T32AI007395)
Topics
  • Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords
HIV-1, RNA secondary structure, Gag protein, RNA-protein interactions, RNA encapsidation, stem-loop structure, binding affinity, retroviral RNA
MeSH terms
Base Sequence, Molecular Sequence Data, Nucleic Acid Conformation, Protein Binding, RNA, Viral, HIV-1, Gene Products, gag, DNA Primers

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