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

The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.

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

Open access

Clever, J, Sassetti, C, Parslow, T G·1995·Journal of Virology

DOI 10.1128/jvi.69.4.2101-2109.1995PMC PMC188876

Open this paper in CoChat — free account

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.

Integrity signals

Registry

Crossref · 10.1128/jvi.69.4.2101-2109.1995

Cites

54 of 54 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

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

Show all 54 references

Sorted by citations

HIV-1 Gag proteins: diverse functions in the virus life cycle
Freed, E. O. (1998) · Virology · doi:10.1006/viro.1998.9398 · Cited by 717
“In HIV-1, this domain has been predicted to fold into four stem-loops (SL1–SL4) with SL3 being particularly well conserved among virus isolates (Clever et al., 1995).”
Background
Structure of the HIV-1 Nucleocapsid Protein Bound to the SL3 Ψ-RNA Recognition Element
De Guzman, R. N., Wu, Z. R., Stalling, C. C., Pappalardo, L., Borer, P. N., & Summers, M. F. (1998) · Science · doi:10.1126/science.279.5349.384 · Cited by 659
Structural biology of HIV 1 1Edited by P. E. Wright
Turner, B. G., & Summers, M. F. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2354 · Cited by 470
“The HIV-1 -site contains four stemloops (SL1-SL4) that are important for ef®cient encapsidation (Clever et al., 1995; Clever & Parslow, 1997; Harrison & Lever, 1992; Hayashi et al., 1992, 1993; McBride & Panganiban, 1996; Sakaguchi et al., 1993).”
Background
High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States
Wilkinson, K. A., Gorelick, R. J., Vasa, S. M., Guex, N., Rein, A. R., Mathews, D. H., Giddings, M. C., & Weeks, K. M. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060096 · Cited by 428
Nucleic Acid Chaperone Activity of HIV‐1 Nucleocapsid Protein: Critical Role in Reverse Transcription and Molecular Mechanism
Levin, J. G., Guo, J., Rouzina, I. F., & Musier‐Forsyth, K. (2005) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(05)80006-6 · Cited by 367
NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition.
Amarasinghe, G., Guzman, R. D. D., Turner, R. B., Chancellor, K. J., Wu, Z.-R., & Summers, M. F. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3979 · Cited by 337
How retroviruses select their genomes
D'Souza, V., & Summers, M. F. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1210 · Cited by 339
eIF4E is a central node of an RNA regulon that governs cellular proliferation
Čuljković, B., Topisirović, I., Skrabanek, L. A., Ruiz‐Gutierrez, M., & Borden, K. L. B. (2006) · The Journal of Cell Biology · doi:10.1083/jcb.200607020 · Cited by 294
“…of 30 μl of 2× SDS sample buffer and heating 10 min at 95°C. Samples were loaded on 10 or 12% SDS polyacrylamide gels and separated at 50 V for 16 h at RT. RNase mapping Analyses were performed as described previously (Clever et al., 1995) and according to the manufacturer’s instructions (Ambion).”
Method
RNA Packaging
Berkowitz, R. D., Fisher, J., & Goff, S. P. (1996) · Current topics in microbiology and immunology · doi:10.1007/978-3-642-80145-7_6 · Cited by 282
Mutant human immunodeficiency virus type 1 genomes with defects in RNA dimerization or encapsidation
Clever, J., & Parslow, T. (1997) · Journal of Virology · doi:10.1128/jvi.71.5.3407-3414.1997 · Cited by 287
Self-citation
Imaging the interaction of HIV-1 genomes and Gag during assembly of individual viral particles
Jouvenet, N., Simon, S. M., & Bieniasz, P. D. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907364106 · Cited by 270
The human immunodeficiency virus type 1 encapsidation site is a multipartite RNA element composed of functional hairpin structures
McBride, M., & Panganiban, A. (1996) · Journal of Virology · doi:10.1128/jvi.70.5.2963-2973.1996 · Cited by 277
Structural Determinants and Mechanism of HIV-1 Genome Packaging
Lu, K., Heng, X., & Summers, M. F. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.04.029 · Cited by 290
NMR Detection of Structures in the HIV-1 5′-Leader RNA That Regulate Genome Packaging
Lu, K., Heng, X., Garyu, L., Monti, S., Garcia, E. L., Kharytonchyk, S., Dorjsuren, B., Kulandaivel, G., Jones, S., Hiremath, A., et al. (2011) · Science · doi:10.1126/science.1210460 · Cited by 270
Global changes in the RNA binding specificity of HIV-1 Gag regulate virion genesis
Kutluay, S. B., Zang, T., Blanco-Melo, D., Powell, C., Jannain, D., Errando, M., & Bieniasz, P. D. (2014) · Cell · doi:10.1016/j.cell.2014.09.057 · Cited by 257
“This element is highly structured (Clever et al., 1995; Harrison and Lever, 1992; McBride and Panganiban, 1996) and may exist in two conformations that favor translation versus dimerization and packaging (Lu et al., 2011a).”
Structure and Function of the Human Immunodeficiency Virus Leader RNA
Berkhout, B. (1996) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(08)60359-1 · Cited by 231
Analysis of the Initiating Events in HIV-1 Particle Assembly and Genome Packaging
Kutluay, S. B., & Bieniasz, P. D. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1001200 · Cited by 203
Role of the DIS hairpin in replication of human immunodeficiency virus type 1
Berkhout, B., & van Wamel, J. L. (1996) · Journal of Virology · doi:10.1128/jvi.70.10.6723-6732.1996 · Cited by 219
A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon
Abbink, T. E. M., & Berkhout, B. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m210291200 · Cited by 203
Retroviral nucleocapsid domains mediate the specific recognition of genomic viral RNAs by chimeric Gag polyproteins during RNA packaging in vivo
Berkowitz, R., Ohagen, A., Höglund, S., & Goff, S. (1995) · Journal of Virology · doi:10.1128/jvi.69.10.6445-6456.1995 · Cited by 215
The Leader of Human Immunodeficiency Virus Type 1 Genomic RNA Harbors an Internal Ribosome Entry Segment That Is Active during the G 2 /M Phase of the Cell Cycle
Brasey, A., López‐Lastra, M., Ohlmann, T., Beerens, N., Berkhout, B., Darlix, J., & Sonenberg, N. (2003) · Journal of Virology · doi:10.1128/jvi.77.7.3939-3949.2003 · Cited by 213
“leukemia virus-based retroviral vector MLV-Plap-HIV-1(1-336)-neo, the HIV-1”
BackgroundMethodInfluential
A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis
Paillart, J., Berthoux, L., Ottmann, M., Darlix, J., Marquet, R., Ehresmann, B., & Ehresmann, C. (1996) · Journal of Virology · doi:10.1128/jvi.70.12.8348-8354.1996 · Cited by 194
NCp7 Activates HIV-1Lai RNA Dimerization by Converting a Transient Loop-Loop Complex into a Stable Dimer
Muriaux, D. M., de ROCQUIGNY, H., Roques, B. P., & Paoletti, J. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.52.33686 · Cited by 191
Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA
Clever, J. L., Wong, M. L., & Parslow, T. G. (1996) · Journal of Virology · doi:10.1128/jvi.70.9.5902-5908.1996 · Cited by 202
Self-citation
Human immunodeficiency virus type 1 assembly, release, and maturation
Adamson, C. S., & Freed, E. O. (2007) · Advances in Pharmacology · doi:10.1016/s1054-3589(07)55010-6 · Cited by 179
Sequence-Specific Binding of Human Immunodeficiency Virus Type 1 Nucleocapsid Protein to Short Oligonucleotides
Fisher, R., Rein, A., Fivash, M., Urbaneja, M., Casas-Finet, J., Medaglia, M. V., & Henderson, L. (1998) · Journal of Virology · doi:10.1128/jvi.72.3.1902-1909.1998 · Cited by 175
The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges
Ennifar, E., Yusupov, M., Walter, P., Marquet, R., Ehresmann, B., Ehresmann, C., & Dumas, P. (1999) · Structure · doi:10.1016/s0969-2126(00)80033-7 · Cited by 163
Mutations in the kissing-loop hairpin of human immunodeficiency virus type 1 reduce viral infectivity as well as genomic RNA packaging and dimerization
Laughrea, M., Jetté, L. P., Mak, J., Kleiman, L., Liang, C., & Wainberg, M. A. (1997) · Journal of Virology · doi:10.1128/jvi.71.5.3397-3406.1997 · Cited by 162
Flexible Nature and Specific Functions of the HIV-1 Nucleocapsid Protein
Darlix, J., Godet, J., Iványi-Nagy, R., Fossé, P., Mauffret, O., & Mély, Y. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.03.037 · Cited by 158
Structure of the dimer a initiation complex of HIV-1 genomic RNA
Mujeeb, A., Clever, J. L., Billeci, T. M., James, T. L., & Parslow, T. G. (1998) · Nature Structural Biology · doi:10.1038/nsb0698-432 · Cited by 159
Self-citation
A Kissing Complex Together with a Stable Dimer Is Involved in the HIV-1Lai RNA Dimerization Process in Vitro
Muriaux, D. M., Fossé, P., & Paoletti, J. (1996) · Biochemistry · doi:10.1021/bi952822s · Cited by 152
Structure of the complex between the HIV-1 nucleocapsid protein NCp7 and the single-stranded pentanucleotide d(ACGCC)
Morellet, N., Déméné, H., Teilleux, V., Huynh‐Dinh, T., de ROCQUIGNY, H., Fournié‐Zaluski, M., & Roques, B. P. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2098 · Cited by 152
Efficient encapsidation of human immunodeficiency virus type 1 vectors and further characterization of cis elements required for encapsidation
McBride, M. S., Schwartz, M. D., & Panganiban, A. (1997) · Journal of Virology · doi:10.1128/jvi.71.6.4544-4554.1997 · Cited by 161
Nucleic Acid Sequence Discrimination by the HIV-1 Nucleocapsid Protein NCp7: A Fluorescence Study
Vuilleumier, C., Bombarda, E., Morellet, N., Gérard, D., Roques, B. P., & Mély, Y. (1999) · Biochemistry · doi:10.1021/bi991145p · Cited by 139
Human immunodeficiency virus type 1 nucleocapsid protein reduces reverse transcriptase pausing at a secondary structure near the murine leukemia virus polypurine tract
Wu, W. J., Henderson, L. E., Copeland, T. D., Gorelick, R. J., Bosche, W. J., Rein, A., & Levin, J. G. (1996) · Journal of Virology · doi:10.1128/jvi.70.10.7132-7142.1996 · Cited by 138
Role of the N-Terminal Zinc Finger of Human Immunodeficiency Virus Type 1 Nucleocapsid Protein in Virus Structure and Replication
Tanchou, V., Décimo, D., Péchoux, C., Lener, D., Rogemond, V., Berthoux, L., Ottmann, M., & Darlix, J. (1998) · Journal of Virology · doi:10.1128/jvi.72.5.4442-4447.1998 · Cited by 136
Dynamical behavior of the HIV-1 nucleocapsid protein
Lee, B. M., Guzman, R. N. D., Turner, B. G., Tjandra, N., & Summers, M. F. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1766 · Cited by 134
Dimerization of retroviral genomic RNAs: structural and functional implications
Paillart, J., Marquet, R., Skripkin, Е., Ehresmann, C., & Ehresmann, B. (1996) · Biochimie · doi:10.1016/s0300-9084(96)80010-1 · Cited by 131
Position dependence of functional hairpins important for human immunodeficiency virus type 1 RNA encapsidation in vivo
McBride, M. S., & Panganiban, A. T. (1997) · Journal of Virology · doi:10.1128/jvi.71.3.2050-2058.1997 · Cited by 131
Life of psi: How full-length HIV-1 RNAs become packaged genomes in the viral particles
Kuzembayeva, M., Dilley, K. A., Sardo, L., & Hu, W.-S. (2014) · Virology · doi:10.1016/j.virol.2014.01.019 · Cited by 141
“Following extensive biochemical probing, mutagenesis, structural, phylogenetic and in silico analysis of this leader region, elements important for packaging became better defined (Baudin et al., 1993; Clever et al., 1995a; Harrison and Lever, 1992).”
RNA Interactions in the 5′ Region of the HIV-1 Genome
Damgaard, C. K., Andersen, E. S., Knudsen, B., Gorodkin, J., & Kjems, J. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.12.010 · Cited by 130
RNA Structure and packaging signals in the 5′ leader region of the human immunodeficiency virus Type 1 genome
Clever, J. L., Miranda, & Parslow, T. G. (2002) · Journal of Virology · doi:10.1128/jvi.76.23.12381-12387.2002 · Cited by 127
“Most cellular and spliced viral RNAs, moreover, tend to be excluded from virions.”
BackgroundMethodInfluentialSelf-citation
Is HIV-1 RNA dimerization a prerequisite for packaging? Yes, no, probably?
Russell, R. S., Liang, C., & Wainberg, M. A. (2004) · Retrovirology · doi:10.1186/1742-4690-1-23 · Cited by 132
“[73] and Berkhout and van Wamel [136]) U G U G C C C G C - G”
Background
Human Immunodeficiency Virus Type 1 Vif Protein Is an Integral Component of an mRNP Complex of Viral RNA and Could Be Involved in the Viral RNA Folding and Packaging Process
Zhang, H., Pomerantz, R., Dornadula, G., & Sun, Y. (2000) · Journal of Virology · doi:10.1128/jvi.74.18.8252-8261.2000 · Cited by 127
HIV‐1 Gag–RNA Interaction Occurs at a Perinuclear/Centrosomal Site; Analysis by Confocal Microscopy and FRET
Poole, E. L., Strappe, P., Mok, H. P., Hicks, R., & Lever, A. M. L. (2005) · Traffic · doi:10.1111/j.1600-0854.2005.00312.x · Cited by 123
“Regions from FITC stained images were analysed from the cytoplasm (1,2,5,6), and the membrane (3,4,7,8), of cells transfected with either HVP (1–4) or HVPDP1 (5–8) that had been bleached (2,4,6,8), or not bleached (1,3,5,7).”
Background
Nonreciprocal Packaging of Human Immunodeficiency Virus Type 1 and Type 2 RNA: a Possible Role for the p2 Domain of Gag in RNA Encapsidation
Kaye, J. F., & Lever, A. (1998) · Journal of Virology · doi:10.1128/jvi.72.7.5877-5885.1998 · Cited by 129
A heteropolymer model study for the mechanism of protein folding
Fukugita, M., Lancaster, D., & Mitchard, M. G. (1997) · Biopolymers · doi:10.1002/(sici)1097-0282(199703)41:3 · Cited by 5
Dimeric RNA Recognition Regulates HIV-1 Genome Packaging
Nikolaitchik, O. A., Dilley, K. A., Fu, W., Gorelick, R. J., Tai, S.-H. S., Soheilian, F., Ptak, R. G., Nagashima, K., Pathak, V. K., & Hu, W.-S. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003249 · Cited by 106
Identification of a Minimal Region of the HIV-1 5′-Leader Required for RNA Dimerization, NC Binding, and Packaging
Heng, X., Kharytonchyk, S., Garcia, E. L., Lu, K., Divakaruni, S. S., LaCotti, C., Edme, K., Telesnitsky, A., & Summers, M. F. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.01.033 · Cited by 115
HIV-1 Nucleocapsid Protein as a Nucleic Acid Chaperone: Spectroscopic Study of its Helix-destabilizing Properties, Structural Binding Specificity, and Annealing Activity
Urbaneja, M. A., Wu, M. H., Casas‐Finet, J. R., & Karpel, R. L. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00043-8 · Cited by 105
Zinc Binding to the HIV-1 Nucleocapsid Protein: A Thermodynamic Investigation by Fluorescence Spectroscopy
Mély, Y., de ROCQUIGNY, H., Morellet, N., Roques, B. P., & Gérard, D. (1996) · Biochemistry · doi:10.1021/bi952587d · Cited by 104
In vitro selection of RNAs that bind to the human immunodeficiency virus type-1 gag polyprotein
Lochrie, M. A. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.14.2902 · Cited by 103
Identification of a major restriction in HIV-1 intersubtype recombination
Chin, M. P. S., Rhodes, T. D., Chen, J., Fu, W., & Hu, W.-S. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0502522102 · Cited by 104
HIV-1 RNA packaging
Lever, A. M. L. (2007) · Advances in Pharmacology · doi:10.1016/s1054-3589(07)55001-5 · Cited by 103
Dimer Initiation Signal of Human Immunodeficiency Virus Type 1: Its Role in Partner Selection during RNA Copackaging and Its Effects on Recombination
Moore, M. D., Fu, W., Nikolaitchik, O. A., Chen, J., Ptak, R. G., & Hu, W.-S. (2007) · Journal of Virology · doi:10.1128/jvi.02589-06 · Cited by 101
“The 5 untranslated region of the HIV-1 genomic RNA has been predicted to form a number of highly ordered secondary structures (3, 6), one of which, the stem-loop 1 (SL1), plays important roles in efficient RNA encapsidation and dimerization (6, 27).”
Background
NMR structure of stem-loop SL2 of the HIV-1 Ψ RNA packaging signal reveals a novel A-U-A base-triple platform 1 1Edited by I. Tinoco
Amarasinghe, G. K., Guzman, R. N. D., Turner, R. B., & Summers, M. F. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3710 · Cited by 100
Identification of potential conserved RNA secondary structure throughout influenza A coding regions
Moss, W. N., Priore, S. F., & Turner, D. H. (2011) · RNA · doi:10.1261/rna.2619511 · Cited by 102
“…in the 39 untranslated region (UTR) of many plant viruses (Weiner and Maizels 1987; Dreher 2009), the frameshifting signals that allow some viruses to encode overlapping open reading frames (ORFs) (Jacks et al. 1988; Dam et al. 1990), viral packaging signals (Clever et al. 1995), and many more.”
Background
Mapping the RNA binding sites for human immunodeficiency virus type-1 gag and NC proteins within the complete HIV-1 and -2 untranslated leader regions.
Damgaard, C., Dyhr-Mikkelsen, H., & Kjems, J. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.16.3667 · Cited by 107
Identification of a Human Immunodeficiency Virus Type 2 (HIV-2) Encapsidation Determinant and Transduction of Nondividing Human Cells by HIV-2-Based Lentivirus Vectors
Poeschla, E. M., Gilbert, J., Li, X., Huang, S., Ho, A. D., & Wong‐Staal, F. (1998) · Journal of Virology · doi:10.1128/jvi.72.8.6527-6536.1998 · Cited by 100
Human Immunodeficiency Virus Types 1 and 2 Differ in the Predominant Mechanism Used for Selection of Genomic RNA for Encapsidation
Kaye, J. F., & Lever, A. (1999) · Journal of Virology · doi:10.1128/jvi.73.4.3023-3031.1999 · Cited by 111
Effects of nucleocapsid mutations on human immunodeficiency virus assembly and RNA encapsidation
Zhang, Y., & Barklis, E. (1997) · Journal of Virology · doi:10.1128/jvi.71.9.6765-6776.1997 · Cited by 93
The Major Human Immunodeficiency Virus Type 2 (HIV-2) Packaging Signal Is Present on All HIV-2 RNA Species: Cotranslational RNA Encapsidation and Limitation of Gag Protein Confer Specificity
Griffin, S., Allen, J. F., & Lever, A. (2001) · Journal of Virology · doi:10.1128/jvi.75.24.12058-12069.2001 · Cited by 106
“However, other RNA structures situated both upstream and downstream of the splice donor have roles in encapsidation, notably, the dimerization initiation site stem-loop, or stem-loop 1 (5, 6, 8, 25, 26, 32, 44).”
Background
Impact of the terminal bulges of HIV-1 cTAR DNA on its stability and the destabilizing activity of the nucleocapsid protein NCp7.
Beltz, H., Azoulay, J., Bernacchi, S., Clamme, J., Ficheux, D., Roques, B., Darlix, J., & Mély, Y. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00244-4 · Cited by 90
Properties, Functions, and Drug Targeting of the Multifunctional Nucleocapsid Protein of the Human Immunodeficiency Virus
Darlix, J., Garrido, J. L. V., Morellet, N., Mély, Y., & de ROCQUIGNY, H. (2007) · Advances in pharmacology · doi:10.1016/s1054-3589(07)55009-x · Cited by 97
Selection and stabilization of the RNA aptamers against the human immunodeficiency virus type-1 nucleocapsid protein.
Kim, S. J., Kim, M. Y., Lee, J. H., You, J.-C., & Jeong, S. (2002) · Biochemical and Biophysical Research Communications - BBRC · doi:10.1006/bbrc.2002.6521 · Cited by 90
Proteolytic Processing of the P2/Nucleocapsid Cleavage Site Is Critical for Human Immunodeficiency Virus Type 1 RNA Dimer Maturation
Shehu-Xhilaga, M., Kraeusslich, H.-G., Pettit, S. C., Swanstrom, R. I., Jy, L., Marshall, J. A., Crowe, S. M., & Mak, J. (2001) · Journal of Virology · doi:10.1128/jvi.75.19.9156-9164.2001 · Cited by 87
Direct Mass Spectrometric Determination of the Stoichiometry and Binding Affinity of the Complexes between Nucleocapsid Protein and RNA Stem−Loop Hairpins of the HIV-1 Ψ-Recognition Element
Hagan, N., & Fabris, D. (2003) · Biochemistry · doi:10.1021/bi0348922 · Cited by 88
Affinities of Packaging Domain Loops in HIV-1 RNA for the Nucleocapsid Protein
Shubsda, M. F., Paoletti, A. C., Hudson, B. S., & Borer, P. N. (2002) · Biochemistry · doi:10.1021/bi016045+ · Cited by 87
Stem-loop SL4 of the HIV-1 psi RNA packaging signal exhibits weak affinity for the nucleocapsid protein. structural studies and implications for genome recognition.
Amarasinghe, G., Zhou, J., Miskimon, M., Chancellor, K. J., McDonald, J. A., Matthews, A. G., Miller, R. R., Rouse, M. D., & Summers, M. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.5182 · Cited by 88
“The absence of these signals is consistent with previous secondary structure predictions and accessibility mapping experiments, which demonstrated that G1, G2, and G10 are exposed.(7,10,11) Thus, the NMR data indicate that the stem of SL4 is conformationally labile, and this is consistent with the previous ®ndings.”
BackgroundMethodResultInfluential
In Vitro Evidence That the Untranslated Leader of the HIV-1 Genome Is an RNA Checkpoint That Regulates Multiple Functions through Conformational Changes
Berkhout, B., Ooms, M., Beerens, N., Huthoff, H. T., Southern, E. M., & Verhoef, K. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m200950200 · Cited by 87
Helical structure determined by NMR of the HIV‐1 (345–392)Gag sequence, surrounding p2: Implications for particle assembly and RNA packaging
Morellet, N., Druillennec, S., Lenoir, C., Bouaziz, S., & Roques, B. P. (2005) · Protein Science · doi:10.1110/ps.041087605 · Cited by 86
“It has already been demonstrated that NCp7 binds the SL3 stem loop of the HIV-1 packaging domain with a high affinity (Clever et al. 1995; De Guzman et al. 1998).”
Background
Retroviral RNA Dimerization: From Structure to Functions
Dubois, N., Marquet, R., Paillart, J., & Bernacchi, S. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00527 · Cited by 88
“…signal, Psi, which is composed of four stem-loops (SL1–SL4) (Figure 6A) (Lever et al., 1989; Aldovini and Young, 1990; Clavel and Orenstein, 1990; Clever et al., 1995; Mailler et al., 2016), although SL4, encompassing gag initiation codon, seems to be poorly stable and would be most likely in…”
Background
A high affinity binding site for the HIV-1 nucleocapsid protein.
Berglund, J., Charpentier, B., & Rosbash, M. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.5.1042 · Cited by 81
Properties and growth mechanism of the ordered aggregation of a model RNA by the HIV-1 nucleocapsid protein: an electron microscopy investigation.
Cam, É. L., Coulaud, D., Delain, E., Petitjean, P., Roques, B., Gérard, D., Stoylova, E., Vuilleumier, C., Stoylov, S. P., & Mély, Y. (1998) · Biopolymers · doi:10.1002/(sici)1097-0282(199803)45:3 · Cited by 83
An Intact TAR Element and Cytoplasmic Localization Are Necessary for Efficient Packaging of Human Immunodeficiency Virus Type 1 Genomic RNA
Helga-Maria, C., Hammarskjöld, M., & Rekosh, D. M. (1999) · Journal of Virology · doi:10.1128/jvi.73.5.4127-4135.1999 · Cited by 83
On the Selective Packaging of Genomic RNA by HIV-1
Comas‐García, M., Davis, S. R., & Rein, A. R. (2016) · Viruses · doi:10.3390/v8090246 · Cited by 85
“Most in vitro studies have focused on testing the hypothesis that Ψ is a high‐affinity binding site for Gag; hence, they have concentrated on measuring the affinity of Gag, as well as NC, to RNAs (≤600 bases) that are small compared to the length of the HIV‐1 gRNA [32–34].”
Background
The major HIV-1 packaging signal is an extended bulged stem loop whose structure is altered on interaction with the gag polyprotein
Zeffman, A., Hassard, S., Varani, G., & Lever, A. M. L. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3611 · Cited by 80
Genetic Dissociation of the Encapsidation and Reverse Transcription Functions in the 5′ R Region of Human Immunodeficiency Virus Type 1
Clever, J. L., Eckstein, D. A., & Parslow, T. G. (1999) · Journal of Virology · doi:10.1128/jvi.73.1.101-109.1999 · Cited by 72
Self-citation
Structure of the intact stem and bulge of HIV-1 Psi-RNA stem-loop SL1.
Lawrence, D. C., Stover, C., Noznitsky, J., Wu, Z.-R., & Summers, M. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01305-0 · Cited by 75
Sensing peptide–oligonucleotide interactions by a two-color fluorescence label: application to the HIV-1 nucleocapsid protein
Shvadchak, V., Klymchenko, A., de Rocquigny, H., & Mély, Y. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn1083 · Cited by 68
Infectious Molecular Clones with the Nonhomologous Dimer Initiation Sequences Found in Different Subtypes of Human Immunodeficiency Virus Type 1 Can Recombine and Initiate a Spreading Infection In Vitro
Louis, D. C. S., Gotte, D., Sanders‐Buell, E., Ritchey, D. W., Salminen, M. O., Carr, J. K., & McCutchan, F. E. (1998) · Journal of Virology · doi:10.1128/jvi.72.5.3991-3998.1998 · Cited by 70
Sequences Downstream of the 5′ Splice Donor Site Are Required for both Packaging and Dimerization of Human Immunodeficiency Virus Type 1 RNA
Russell, R. S., Hu, J., Bériault, V., Mouland, A. J., Kleiman, L., Wainberg, M. A., & Liang, C. (2002) · Journal of Virology · doi:10.1128/jvi.77.1.84-96.2003 · Cited by 70
“assay experiments were done based on previously described protocols (7, 8).”
BackgroundMethod
Location of cis-acting signals important for RNA encapsidation in the leader sequence of human immunodeficiency virus type 2
McCann, E., & Lever, A. (1997) · Journal of Virology · doi:10.1128/jvi.71.5.4133-4137.1997 · Cited by 75
Possible Role of Dimerization in Human Immunodeficiency Virus Type 1 Genome RNA Packaging
Sakuragi, J.-I., Ueda, S., Iwamoto, A., & Shioda, T. (2003) · Journal of Virology · doi:10.1128/jvi.77.7.4060-4069.2003 · Cited by 69
“In the 5 untranslated region of HIV-1 RNA, the RNA is predicted to form seven stem-loop structures (TAR, R/U5, U5/L, SL1, SL2, SL3, and SL4) (7, 34).”
Background
Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome
Gherghe, C., Lombo, T., Leonard, C. W., Datta, S. A. K., Bess, J. W., Gorelick, R. J., Rein, A., & Weeks, K. M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006897107 · Cited by 69
“Although theΨ region of this vector is partially derived from murine sarcoma virus (14), it is nearly identical to MuLVover the 5′ 1,040 nt and differs fromMuLVat two positions within MiDAS.”
BackgroundMethod
Three-dimensional folding of an RNA hairpin required for packaging HIV-1.
Pappalardo, L., Kerwood, D., Pelczer, I., & Borer, P. N. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2046 · Cited by 53
Use of HIV as a gene transfer vector.
Pluta, K. D., & Kacprzak, M. M. (2009) · Acta Biochimica Polonica · doi:10.18388/abp.2009_2490 · Cited by 76
“6) (Clever et al., 1995).”
Identification of a high affinity nucleocapsid protein binding element within the moloney murine leukemia virus Ψ-RNA packaging signal: implications for genome recognition
D’Souza, V. M., Melamed, J., Habib, D., Pullen, K. E., Wallace, K., & Summers, M. F. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5139 · Cited by 66
Stem-loop structure in the 5′ region of potato virus X genome required for plus-strand RNA accumulation
Miller, E. D., Plante, C. A., Kim, K., Brown, J. W., & Hemenway, C. L. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2174 · Cited by 66
“For the retrovirus HIV-1, the encapsidation signal ( ) consists of four SL structures, SL1-SL4 (Clever et al., 1995).”
Background
Duplication of the Primary Encapsidation and Dimer Linkage Region of Human Immunodeficiency Virus Type 1 RNA Results in the Appearance of Monomeric RNA in Virions
Sakuragi, J.-I., Shioda, T., & Panganiban, A. T. (2001) · Journal of Virology · doi:10.1128/jvi.75.6.2557-2565.2001 · Cited by 66
Efficient gene transfer by a human immunodeficiency virus type 1 (HIV-1)-derived vector utilizing a stable HIV packaging cell line.
Corbeau, P., Kraus, G., & Wong-staal, F. (1996) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.93.24.14070 · Cited by 70
Fluorescent Amino Acid Undergoing Excited State Intramolecular Proton Transfer for Site-Specific Probing and Imaging of Peptide Interactions
Sholokh, M., Zamotaiev, O. M., Das, R., Postupalenko, V. Y., Richert, L., Dujardin, D., Zaporozhets, O. A., Pivovarenko, V. G., Klymchenko, A. S., & Mély, Y. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp508748e · Cited by 65
Contributions of Viral Splice Sites and cis -Regulatory Elements to Lentivirus Vector Function
Cui, Y. R., Iwakuma, T., & Chang, L.-J. (1999) · Journal of Virology · doi:10.1128/jvi.73.7.6171-6176.1999 · Cited by 65
Multiple, Switchable Protein:RNA Interactions Regulate Human Immunodeficiency Virus Type 1 Assembly
Bieniasz, P. D., & Telesnitsky, A. (2018) · Annual Review of Virology · doi:10.1146/annurev-virology-092917-043448 · Cited by 66
A critical role for the TAR element in promoting efficient human immunodeficiency virus type 1 reverse transcription
Harrich, D., Ulich, C., & Gaynor, R. B. (1996) · Journal of Virology · doi:10.1128/jvi.70.6.4017-4027.1996 · Cited by 64
Functional analysis of the 5′ untranslated region of potexvirus RNA reveals a role in viral replication and cell-to-cell movement
Lough, T. J., Lee, R. H., Emerson, S. J., Forster, R. L. S., & Lucas, W. J. (2006) · Virology · doi:10.1016/j.virol.2006.03.043 · Cited by 63
Cooperative and Specific Binding of Vif to the 5′ Region of HIV-1 Genomic RNA
Henriet, S., Richer, D., Bernacchi, S., Decroly, É., Vigne, R., Ehresmann, B., Ehresmann, C., Paillart, J., & Marquet, R. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.09.025 · Cited by 63
DashengandRIRE2. A Nonautonomous Long Terminal Repeat Element and Its Putative Autonomous Partner in the Rice Genome
Jiang, N., Jordan, I. K., & Wessler, S. R. (2002) · PLANT PHYSIOLOGY · doi:10.1104/pp.015412 · Cited by 61
HIV-1 Pr55Gagbinds genomic and spliced RNAs with different affinity and stoichiometry
Bernacchi, S., Abd El-Wahab, E. W., Dubois, N., Hijnen, M., Smyth, R. P., Mak, J., Marquet, R., & Paillart, J.-C. (2017) · RNA Biology · doi:10.1080/15476286.2016.1256533 · Cited by 61
Initiation of HIV Reverse Transcription
Isel, C., Ehresmann, C., & Marquet, R. (2010) · Viruses · doi:10.3390/v2010213 · Cited by 59
“interactions [36-40]; 2) the tRNA3/LysRS complex is maintained together via an interaction between the anticodon of tRNA3 and the N-terminal anticodon binding domain of the synthetase [4].”
Background

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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks