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

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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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On Finding All Suboptimal Foldings of an RNA Molecule
Zuker, M. (1989) · Science · doi:10.1126/science.2468181 · Cited by 1,998
Construction of a retrovirus packaging mutant and its use to produce helper-free defective retrovirus
Mann, R., Mulligan, R. C., & Baltimore, D. (1983) · Cell · doi:10.1016/0092-8674(83)90344-6 · Cited by 1,776
Human Retroviruses and Aids - 1999
KUIKEN, C. L., & Foley, B. T. (1999) · doi:10.2172/1186019 · Cited by 952
RNA Structure Prediction
Turner, D. H., Sugimoto, N., & Freier, S. M. (1988) · Annual Review of Biophysics and Biophysical Chemistry · doi:10.1146/annurev.bb.17.060188.001123 · Cited by 647
Mutations of RNA and protein sequences involved in human immunodeficiency virus type 1 packaging result in production of noninfectious virus
Aldovini, A., & Young, R. A. (1990) · Journal of Virology · doi:10.1128/jvi.64.5.1920-1926.1990 · Cited by 548
Evidence that the packaging signal of Moloney murine leukemia virus extends into the gag region
Bender, M. A., Palmer, T. D., Gelinas, R. E., & Miller, A. D. (1987) · Journal of Virology · doi:10.1128/jvi.61.5.1639-1646.1987 · Cited by 410
Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro
Skripkin, E., Paillart, J. C., Marquet, R., Ehresmann, B., & Ehresmann, C. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.11.4945 · Cited by 401
Noninfectious human immunodeficiency virus type 1 mutants deficient in genomic RNA
Gorelick, R. J., Nigida, S. M., Bess, J. W., Arthur, L. O., Henderson, L. E., & Rein, A. R. (1990) · Journal of Virology · doi:10.1128/jvi.64.7.3207-3211.1990 · Cited by 386
[17] Predicting optimal and suboptimal secondary structure for RNA
Jaeger, J. A., Turner, D. H., & Zuker, M. (1990) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(90)83019-6 · Cited by 382
Identification of a sequence required for efficient packaging of human immunodeficiency virus type 1 RNA into virions
Lever, A. M. L., Göttlinger, H. G., Haseltine, W. A., & Sodroski, J. (1989) · Journal of Virology · doi:10.1128/jvi.63.9.4085-4087.1989 · Cited by 375

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In cell mutational interference mapping experiment (in cell MIME) identifies the 5′ polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging
Smyth, R. P., Smith, M. R., Jousset, A.-C., Despons, L., Laumond, G., Decoville, T., Cattenoz, P. B., Moog, C., Jossinet, F., Mougel, M., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky152 · Cited by 37
“For example, in one study a single G to U mutation 257GCGCUC262 lead to a roughly two fold reduction in gRNA packaging (82), whereas our in cell MIME data shows that this same mutation packages 76% of wild-type (68–86% are the 5 and 95 percent confidence intervals) (Supplementary Data Files).”
Background
Mutations within Four Distinct Gag Proteins Are Required To Restore Replication of Human Immunodeficiency Virus Type 1 after Deletion Mutagenesis within the Dimerization Initiation Site
Liang, C., Rong, L., Quan, Y., Laughrea, M., Kleiman, L., & Wainberg, M. A. (1999) · Journal of Virology · doi:10.1128/jvi.73.8.7014-7020.1999 · Cited by 32
A proposal for a new HIV-1 DLS structural model
Sakuragi, J.-I., Ode, H., Sakuragi, S., Shioda, T., & Sato, H. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks156 · Cited by 29
Human Retrovirus Genomic RNA Packaging
Hanson, H. M., Willkomm, N. A., Yang, H., & Mansky, L. M. (2022) · Viruses · doi:10.3390/v14051094 · Cited by 33
Functional and Structural Characterization of 2-Amino-4-phenylthiazole Inhibitors of the HIV-1 Nucleocapsid Protein with Antiviral Activity
Mori, M., Nucci, A., Lang, M. C. D., Humbert, N., Boudier, C., Debaene, F., Cianférani, S., Catala, M., Schult-Dietrich, P., Dietrich, U., et al. (2014) · ACS Chemical Biology · doi:10.1021/cb500316h · Cited by 30
In Vitro Identification and Characterization of an Early Complex Linking HIV-1 Genomic RNA Recognition and Pr55Gag Multimerization
Roldán, A., Russell, R. S., Marchand, B., Götte, M., Liang, C., & Wainberg, M. A. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m405632200 · Cited by 31
Identification of Small Molecule Inhibitors of the HIV-1 Nucleocapsid–Stem-Loop 3 RNA Complex
Warui, D. M., & Baranger, A. M. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm2007694 · Cited by 30
Exploiting Genetic Interference for Antiviral Therapy
Tanner, E. J., Kirkegaard, K., & Weinberger, L. S. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005986 · Cited by 30
High Affinity Nucleocapsid Protein Binding to the μΨ RNA Packaging Signal of Rous Sarcoma Virus
Zhou, J., McAllen, J. K., Tailor, Y., & Summers, M. F. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.04.046 · Cited by 30
Base Pairing Probabilities in a Complete HIV-1 RNA
Huynen, M. A., Perelson, A. S., Vieira, W. A., & Stadler, P. F. (1996) · Journal of Computational Biology · doi:10.1089/cmb.1996.3.253 · Cited by 30
“It gives rise to a secondary structure with four hairpin loops that is equal to the structure proposed in Clever et al (1995).”
HIV RNA packaging and lentivirus-based vectors
Lever, A. M. L. (2000) · Advances in pharmacology · doi:10.1016/s1054-3589(00)48002-6 · Cited by 31
Site-Specific Characterization of HIV-1 Nucleocapsid Protein Binding to Oligonucleotides with Two Binding Sites
Avilov, S., Godet, J., Piémont, E., & Mély, Y. (2009) · Biochemistry · doi:10.1021/bi8022366 · Cited by 29
“For instance, selection of viral genomic RNA for packaging into virions is mediated by binding of the NC domain within Gag to the ψ encapsidation sequence within the untranslated region of the HIV-1 genome (2).”
BackgroundMethodInfluential
Structure of SL4 RNA from the HIV-1 Packaging Signal,
Kerwood, D. J., Cavaluzzi, M. J., & Borer, P. N. (2001) · Biochemistry · doi:10.1021/bi0111909 · Cited by 29
A HIV-1 Minimal Gag Protein Is Superior to Nucleocapsid at in Vitro tRNA3Lys Annealing and Exhibits Multimerization-induced Inhibition of Reverse Transcription
Roldan, A., Warren, O. U., Russell, R. S., Liang, C., & Wainberg, M. A. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m501310200 · Cited by 29
Stable Protein–RNA Interaction Involves the Terminal Domains of Bluetongue Virus mRNA, but Not the Terminally Conserved Sequences
Theron, J., & Nel, L. H. (1997) · Virology · doi:10.1006/viro.1996.8389 · Cited by 29
Deletion Mutagenesis within the Dimerization Initiation Site of Human Immunodeficiency Virus Type 1 Results in Delayed Processing of the p2 Peptide from Precursor Proteins
Liang, C., Rong, L., Cherry, E., Kleiman, L., Laughrea, M., & Wainberg, M. (1999) · Journal of Virology · doi:10.1128/jvi.73.7.6147-6151.1999 · Cited by 32
A Structured RNA Motif Is Involved in Correct Placement of the tRNA 3 Lys Primer onto the Human Immunodeficiency Virus Genome
Beerens, N., Klaver, B., & Berkhout, B. (2000) · Journal of Virology · doi:10.1128/jvi.74.5.2227-2238.2000 · Cited by 29
Influence of gag and RRE Sequences on HIV-1 RNA Packaging Signal Structure and Function
Kharytonchyk, S., Brown, J. D., Stilger, K. L., Yasin, S., Iyer, A. S., Collins, J. T., Summers, M. F., & Telesnitsky, A. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.05.029 · Cited by 28
Lentiviral Gene Therapy Vectors: Challenges and Future Directions
Tomás, H. A., Ana, F., Paula, M., & Coroadinha, A. S. (2013) · InTech eBooks · doi:10.5772/52534 · Cited by 29
“The localization and sequence of packaging signal was identified as the main responsible for the packaging of viral RNA [15] suggesting that modified RNAs with Ψ could also be packaged into virions.”
Background
Identification of Specific Small Molecule Ligands for Stem Loop 3 Ribonucleic Acid of the Packaging Signal Ψ of Human Immunodeficiency Virus-1
Warui, D. M., & Baranger, A. M. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm900599v · Cited by 28
Footprinting, circular dichroism and UV melting studies on neomycin B binding to the packaging region of human immunodeficiency virus type-1 RNA
McPike, M. P. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf402 · Cited by 28
Sequences in the 5′ and 3′ R Elements of Human Immunodeficiency Virus Type 1 Critical for Efficient Reverse Transcription
Ohi, Y., & Clever, J. L. (2000) · Journal of Virology · doi:10.1128/jvi.74.18.8324-8334.2000 · Cited by 28
Self-citation
Beyond Plasma Membrane Targeting: Role of the MA domain of Gag in Retroviral Genome Encapsidation
Parent, L. J., & Gudleski-O'Regan, N. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.04.072 · Cited by 30
An Extended RNA Binding Site for the Yeast Branch Point-binding Protein and the Role of Its Zinc Knuckle Domains in RNA Binding*
Garrey, S. M., Voelker, R., & Berglund, J. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m603137200 · Cited by 28
Nonreciprocal Pseudotyping: Murine Leukemia Virus Proteins Cannot Efficiently Package Spleen Necrosis Virus-Based Vector RNA
Certo, J. L., Shook, B. F., Yin, P., Snider, J., & Hu, W.-S. (1998) · Journal of Virology · doi:10.1128/jvi.72.7.5408-5413.1998 · Cited by 32
“The Gag polyprotein has been shown to interact with the packaging signal in viral RNA and to select the RNA for packaging (4, 9, 10, 25, 26, 29, 30, 37, 43, 51).”
Background
Use of virtual screening for discovering antiretroviral compounds interacting with the HIV-1 nucleocapsid protein
Mori, M., Schult-Dietrich, P., Szafarowicz, B., Humbert, N., Debaene, F., Cianférani, S., Dietrich, U., Mély, Y., & Botta, M. (2012) · Virus Research · doi:10.1016/j.virusres.2012.05.011 · Cited by 26
Structural polymorphism of the HIV-1 leader region explored by computational methods
Kasprzak, W. K. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki1015 · Cited by 27
An Evolved RNA Recognition Motif That Suppresses HIV-1 Tat/TAR-Dependent Transcription
Crawford, D. W., Blakeley, B. D., Chen, P., Sherpa, C., Grice, S. F. J. L., Laird‐Offringa, I. A., & McNaughton, B. R. (2016) · ACS Chemical Biology · doi:10.1021/acschembio.6b00145 · Cited by 26
“(54, 55) These multiple cis-acting elements bind different ligands and support long-range inter- and intramolecular interaction(s) that facilitate genome transcription, translation, RNA dimerization/packaging and splicing.”
Background
Multiple biological roles associated with the Rous sarcoma virus 5' untranslated RNA U5-IR stem and loop
Miller, J. T., Ge, Z., Morris, S., Das, K., & Leis, J. P. (1997) · Journal of Virology · doi:10.1128/jvi.71.10.7648-7656.1997 · Cited by 25
A Tryptophan-Rich Hexapeptide Inhibits Nucleic Acid Destabilization Chaperoned by the HIV-1 Nucleocapsid Protein
Raja, C., Ferner, J., Dietrich, U., Avilov, S., Ficheux, D., Darlix, J., de ROCQUIGNY, H., Schwalbe, H., & Mély, Y. (2006) · Biochemistry · doi:10.1021/bi052560m · Cited by 25
Viral Membrane Fusion Proteins and RNA Sorting Mechanisms for the Molecular Delivery by Exosomes
Zubarev, I. V., Vladimirtsev, D., Vorontsova, M. V., Blatov, I., Shevchenko, K. G., Zvereva, S. D., Lunev, E. A., Файзулоев, Е. Б., & Barlev, N. (2021) · Cells · doi:10.3390/cells10113043 · Cited by 24
“The packaging signal (the psi region) folds into four stem-loop structures (SL1, SL2, SL3, SL4) [186,187].”
Background
Conformational Pathway for the Kissing Complex→Extended Dimer Transition of the SL1 Stem-Loop from Genomic HIV-1 RNA as Monitored by Targeted Molecular Dynamics Techniques
Aci‐Sèche, S., Mazier, S., & Genest, D. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.06.009 · Cited by 24
Synonymous site conservation in the HIV-1 genome
Mayrose, I., Stern, A., Burdelova, E. O., Sabo, Y., Laham-Karam, N., Zamostiano, R., Bacharach, E., & Pupko, T. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-164 · Cited by 25
“A third known functional element that was detected as a significantly conserved stretch is SL4 [32,33], which serves as part of the RNA packaging signal and is located in gag (Stretch 15 in Table 2).”
Background
Role of the nucleocapsid region in HIV-1 Gag assembly as investigated by quantitative fluorescence-based microscopy
de ROCQUIGNY, H., Meshri, S. E. E., Richert, L., Didier, P., Darlix, J., & Mély, Y. (2014) · Virus Research · doi:10.1016/j.virusres.2014.06.009 · Cited by 28
The HIV-1 major splice donor D1 is activated by splicing enhancer elements within the leader region and the p17-inhibitory sequence
Asang, C., Erkelenz, S., & Schaal, H. (2012) · Virology · doi:10.1016/j.virol.2012.06.004 · Cited by 23
“…the RNA stem loop structure, which can be adopted by the HIV-1 major 50 ss (Harrison and Lever, 1992; Baudin et al., 1993; Sakaguchi et al., 1993; Clever et al., 1995; Amarasinghe et al., 2000), impairs the accessibility of D1 for U1 snRNA binding (Abbink and Berkhout, 2008;Zychlinski et al.,…”
Background
Plasma Membrane Anchoring and Gag:Gag Multimerization on Viral RNA Are Critical Properties of HIV-1 Gag Required To Mediate Efficient Genome Packaging
Duchon, A. A., Santos, S., Chen, J., Brown, M., Nikolaitchik, O. A., Tai, S., Chao, J. A., Freed, E. O., Pathak, V. K., & Hu, W.-S. (2021) · mBio · doi:10.1128/mbio.03254-21 · Cited by 23
“contained discrete, high-affinity NC binding sites that would allow selection of HIV-1 RNA (12).”
BackgroundInfluential

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: green
www.ncbi.nlm.nih.gov
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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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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