1
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Ye L, Gribling-Burrer AS, Bohn P, Kibe A, Börtlein C, Ambi UB, Ahmad S, Olguin-Nava M, Smith M, Caliskan N, von Kleist M, Smyth RP. Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging. Nat Struct Mol Biol 2022; 29:306-319. [PMID: 35347312 PMCID: PMC9010304 DOI: 10.1038/s41594-022-00746-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 02/14/2022] [Indexed: 11/09/2022]
Abstract
RNA dimerization is the noncovalent association of two human immunodeficiency virus-1 (HIV-1) genomes. It is a conserved step in the HIV-1 life cycle and assumed to be a prerequisite for binding to the viral structural protein Pr55Gag during genome packaging. Here, we developed functional analysis of RNA structure-sequencing (FARS-seq) to comprehensively identify sequences and structures within the HIV-1 5' untranslated region (UTR) that regulate this critical step. Using FARS-seq, we found nucleotides important for dimerization throughout the HIV-1 5' UTR and identified distinct structural conformations in monomeric and dimeric RNA. In the dimeric RNA, key functional domains, such as stem-loop 1 (SL1), polyadenylation signal (polyA) and primer binding site (PBS), folded into independent structural motifs. In the monomeric RNA, SL1 was reconfigured into long- and short-range base pairings with polyA and PBS, respectively. We show that these interactions disrupt genome packaging, and additionally show that the PBS-SL1 interaction unexpectedly couples the PBS with dimerization and Pr55Gag binding. Altogether, our data provide insights into late stages of HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging.
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Affiliation(s)
- Liqing Ye
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Anne-Sophie Gribling-Burrer
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Patrick Bohn
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Anuja Kibe
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Charlene Börtlein
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Uddhav B. Ambi
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Shazeb Ahmad
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Marco Olguin-Nava
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Maureen Smith
- grid.13652.330000 0001 0940 3744P5 Systems Medicine of Infectious Disease, Robert Koch-Institute, Berlin, Germany
| | - Neva Caliskan
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany ,grid.8379.50000 0001 1958 8658Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Max von Kleist
- grid.13652.330000 0001 0940 3744P5 Systems Medicine of Infectious Disease, Robert Koch-Institute, Berlin, Germany
| | - Redmond P. Smyth
- grid.498164.6Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany ,grid.8379.50000 0001 1958 8658Faculty of Medicine, University of Würzburg, Würzburg, Germany
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2
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Bieniasz P, Telesnitsky A. Multiple, Switchable Protein:RNA Interactions Regulate Human Immunodeficiency Virus Type 1 Assembly. Annu Rev Virol 2018; 5:165-183. [PMID: 30048218 DOI: 10.1146/annurev-virology-092917-043448] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) particle assembly requires several protein:RNA interactions that vary widely in their character, from specific recognition of highly conserved and structured viral RNA elements to less specific interactions with variable RNA sequences. Genetic, biochemical, biophysical, and structural studies have illuminated how virion morphogenesis is accompanied by dramatic changes in the interactions among the protein and RNA virion components. The 5' leader RNA element drives RNA recognition by Gag upon initiation of HIV-1 assembly and can assume variable conformations that influence translation, dimerization, and Gag recognition. As Gag multimerizes on the plasma membrane, forming immature particles, its RNA binding specificity transiently changes, enabling recognition of the A-rich composition of the viral genome. Initiation of assembly may also be regulated by occlusion of the membrane binding surface of Gag by tRNA. Finally, recent work has suggested that RNA interactions with viral enzymes may activate and ensure the accuracy of virion maturation.
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Affiliation(s)
- Paul Bieniasz
- Laboratory of Retrovirology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA;
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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3
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Kharytonchyk S, Brown JD, Stilger K, Yasin S, Iyer AS, Collins J, Summers MF, Telesnitsky A. Influence of gag and RRE Sequences on HIV-1 RNA Packaging Signal Structure and Function. J Mol Biol 2018; 430:2066-2079. [PMID: 29787767 PMCID: PMC6082134 DOI: 10.1016/j.jmb.2018.05.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/22/2022]
Abstract
The packaging signal (Ψ) and Rev-responsive element (RRE) enable unspliced HIV-1 RNAs' export from the nucleus and packaging into virions. For some retroviruses, engrafting Ψ onto a heterologous RNA is sufficient to direct encapsidation. In contrast, HIV-1 RNA packaging requires 5' leader Ψ elements plus poorly defined additional features. We previously defined minimal 5' leader sequences competitive with intact Ψ for HIV-1 packaging, and here examined the potential roles of additional downstream elements. The findings confirmed that together, HIV-1 5' leader Ψ sequences plus a nuclear export element are sufficient to specify packaging. However, RNAs trafficked using a heterologous export element did not compete well with RNAs using HIV-1's RRE. Furthermore, some RNA additions to well-packaged minimal vectors rendered them packaging-defective. These defects were rescued by extending gag sequences in their native context. To understand these packaging defects' causes, in vitro dimerization properties of RNAs containing minimal packaging elements were compared to RNAs with sequence extensions that were or were not compatible with packaging. In vitro dimerization was found to correlate with packaging phenotypes, suggesting that HIV-1 evolved to prevent 5' leader residues' base pairing with downstream residues and misfolding of the packaging signal. Our findings explain why gag sequences have been implicated in packaging and show that RRE's packaging contributions appear more specific than nuclear export alone. Paired with recent work showing that sequences upstream of Ψ can dictate RNA folds, the current work explains how genetic context of minimal packaging elements contributes to HIV-1 RNA fate determination.
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Affiliation(s)
- Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5620, United States
| | - Joshua D Brown
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Krista Stilger
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5620, United States
| | - Saif Yasin
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Aishwarya S Iyer
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - John Collins
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5620, United States
| | - Michael F Summers
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5620, United States.
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4
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Smyth RP, Smith MR, Jousset AC, Despons L, Laumond G, Decoville T, Cattenoz P, Moog C, Jossinet F, Mougel M, Paillart JC, von Kleist M, Marquet R. 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. Nucleic Acids Res 2018; 46:e57. [PMID: 29514260 PMCID: PMC5961354 DOI: 10.1093/nar/gky152] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/02/2018] [Accepted: 03/01/2018] [Indexed: 12/28/2022] Open
Abstract
Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5' region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5' PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production.
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Affiliation(s)
- Redmond P Smyth
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Maureen R Smith
- Freie Universität Berlin, Department of Mathematics and Computer Science, Arnimallee 6, 14195 Berlin, Germany
| | - Anne-Caroline Jousset
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Laurence Despons
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Géraldine Laumond
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Thomas Decoville
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Pierre Cattenoz
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Christiane Moog
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Fabrice Jossinet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Marylène Mougel
- IRIM CNRS UMR9004, Université de Montpellier, Montpellier, France
| | - Jean-Christophe Paillart
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Max von Kleist
- Freie Universität Berlin, Department of Mathematics and Computer Science, Arnimallee 6, 14195 Berlin, Germany
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
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5
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Keane SC, Summers MF. NMR Studies of the Structure and Function of the HIV-1 5'-Leader. Viruses 2016; 8:v8120338. [PMID: 28009832 PMCID: PMC5192399 DOI: 10.3390/v8120338] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 12/25/2022] Open
Abstract
The 5′-leader of the human immunodeficiency virus type 1 (HIV-1) genome plays several critical roles during viral replication, including differentially establishing mRNA versus genomic RNA (gRNA) fates. As observed for proteins, the function of the RNA is tightly regulated by its structure, and a common paradigm has been that genome function is temporally modulated by structural changes in the 5′-leader. Over the past 30 years, combinations of nucleotide reactivity mapping experiments with biochemistry, mutagenesis, and phylogenetic studies have provided clues regarding the secondary structures of stretches of residues within the leader that adopt functionally discrete domains. More recently, nuclear magnetic resonance (NMR) spectroscopy approaches have been developed that enable direct detection of intra- and inter-molecular interactions within the intact leader, providing detailed insights into the structural determinants and mechanisms that regulate HIV-1 genome packaging and function.
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Affiliation(s)
- Sarah C Keane
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
| | - Michael F Summers
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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6
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Bernacchi S, Abd El-Wahab EW, Dubois N, Hijnen M, Smyth RP, Mak J, Marquet R, Paillart JC. HIV-1 Pr55 Gag binds genomic and spliced RNAs with different affinity and stoichiometry. RNA Biol 2016; 14:90-103. [PMID: 27841704 DOI: 10.1080/15476286.2016.1256533] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The HIV-1 Pr55Gag precursor specifically selects genomic RNA (gRNA) from a large variety of cellular and spliced viral RNAs (svRNAs), however the molecular mechanisms of this selective recognition remains poorly understood. To gain better understanding of this process, we analyzed the interactions between Pr55Gag and a large panel of viral RNA (vRNA) fragments encompassing the main packaging signal (Psi) and its flanking regions by fluorescence spectroscopy. We showed that the gRNA harbors a high affinity binding site which is absent from svRNA species, suggesting that this site might be crucial for selecting the HIV-1 genome. Our stoichiometry analysis of protein/RNA complexes revealed that few copies of Pr55Gag specifically associate with the 5' region of the gRNA. Besides, we found that gRNA dimerization significantly impacts Pr55Gag binding, and we confirmed that the internal loop of stem-loop 1 (SL1) in Psi is crucial for specific interaction with Pr55Gag. Our analysis of gRNA fragments of different length supports the existence of a long-range tertiary interaction involving sequences upstream and downstream of the Psi region. This long-range interaction might promote optimal exposure of SL1 for efficient Pr55Gag recognition. Altogether, our results shed light on the molecular mechanisms allowing the specific selection of gRNA by Pr55Gag among a variety of svRNAs, all harboring SL1 in their first common exon.
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Affiliation(s)
- Serena Bernacchi
- a Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN , Strasbourg , France
| | - Ekram W Abd El-Wahab
- a Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN , Strasbourg , France
| | - Noé Dubois
- a Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN , Strasbourg , France
| | - Marcel Hijnen
- b Centre for Virology, Burnet Institute , Melbourne , Victoria , Australia.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria , Australia
| | - Redmond P Smyth
- a Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN , Strasbourg , France
| | - Johnson Mak
- b Centre for Virology, Burnet Institute , Melbourne , Victoria , Australia.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria , Australia.,d School of Medicine, Faculty of Health, Deakin University , Geelong , Victoria , Australia.,e Commonwealth Scientific and Industrial Research Organization, Livestock Industries, Australian Animal Health Laboratory , Geelong , Victoria , Australia
| | - Roland Marquet
- a Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN , Strasbourg , France
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7
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NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome. Proc Natl Acad Sci U S A 2016; 113:13033-13038. [PMID: 27791166 DOI: 10.1073/pnas.1614785113] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5'-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a 2H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5'-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5' (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a 2H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones.
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8
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The Life-Cycle of the HIV-1 Gag-RNA Complex. Viruses 2016; 8:v8090248. [PMID: 27626439 PMCID: PMC5035962 DOI: 10.3390/v8090248] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/16/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) replication is a highly regulated process requiring the recruitment of viral and cellular components to the plasma membrane for assembly into infectious particles. This review highlights the recent process of understanding the selection of the genomic RNA (gRNA) by the viral Pr55Gag precursor polyprotein, and the processes leading to its incorporation into viral particles.
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9
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Sükösd Z, Andersen ES, Seemann SE, Jensen MK, Hansen M, Gorodkin J, Kjems J. Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain. Nucleic Acids Res 2015; 43:10168-79. [PMID: 26476446 PMCID: PMC4666355 DOI: 10.1093/nar/gkv1039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/30/2015] [Indexed: 11/30/2022] Open
Abstract
A distance constrained secondary structural model of the ≈10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential roles in replication and evolution for the virus.
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Affiliation(s)
- Zsuzsanna Sükösd
- BiRC, Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Ebbe S Andersen
- iNANO, Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Stefan E Seemann
- RTH, Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark
| | - Mads Krogh Jensen
- BiRC, Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Mathias Hansen
- BiRC, Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jan Gorodkin
- RTH, Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark
| | - Jørgen Kjems
- iNANO, Interdisciplinary Nanoscience Center, Aarhus University, DK-8000 Aarhus C, Denmark
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10
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Specific recognition of the HIV-1 genomic RNA by the Gag precursor. Nat Commun 2014; 5:4304. [PMID: 24986025 DOI: 10.1038/ncomms5304] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 06/05/2014] [Indexed: 11/08/2022] Open
Abstract
During assembly of HIV-1 particles in infected cells, the viral Pr55(Gag) protein (or Gag precursor) must select the viral genomic RNA (gRNA) from a variety of cellular and viral spliced RNAs. However, there is no consensus on how Pr55(Gag) achieves this selection. Here, by using RNA binding and footprinting assays, we demonstrate that the primary Pr55(Gag) binding site on the gRNA consists of the internal loop and the lower part of stem-loop 1 (SL1), the upper part of which initiates gRNA dimerization. A double regulation ensures specific binding of Pr55(Gag) to the gRNA despite the fact that SL1 is also present in spliced viral RNAs. The region upstream of SL1, which is present in all HIV-1 RNAs, prevents binding to SL1, but this negative effect is counteracted by sequences downstream of SL4, which are unique to the gRNA.
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11
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Das AT, Vrolijk MM, Harwig A, Berkhout B. Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging. Retrovirology 2012; 9:59. [PMID: 22828074 PMCID: PMC3432602 DOI: 10.1186/1742-4690-9-59] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 07/04/2012] [Indexed: 01/29/2023] Open
Abstract
Background The TAR hairpin is present at both the 5′ and 3′ end of the HIV-1 RNA genome. The 5′ element binds the viral Tat protein and is essential for Tat-mediated activation of transcription. We recently observed that complete TAR deletion is allowed in the context of an HIV-1 variant that does not depend on this Tat-TAR axis for transcription. Mutations that open the 5′ stem-loop structure did however affect the leader RNA conformation and resulted in a severe replication defect. In this study, we set out to analyze which step of the HIV-1 replication cycle is affected by this conformational change of the leader RNA. Results We demonstrate that opening the 5′ TAR structure through a deletion in either side of the stem region caused aberrant dimerization and reduced packaging of the unspliced viral RNA genome. In contrast, truncation of the TAR hairpin through deletions in both sides of the stem did not affect RNA dimer formation and packaging. Conclusions These results demonstrate that, although the TAR hairpin is not essential for RNA dimerization and packaging, mutations in TAR can significantly affect these processes through misfolding of the relevant RNA signals.
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Affiliation(s)
- Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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12
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Sakuragi JI, Ode H, Sakuragi S, Shioda T, Sato H. A proposal for a new HIV-1 DLS structural model. Nucleic Acids Res 2012; 40:5012-22. [PMID: 22328732 PMCID: PMC3367192 DOI: 10.1093/nar/gks156] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The dimer initiation site/dimer linkage sequence (DIS/DLS) region of the human immunodeficiency virus type 1 (HIV-1) RNA genome is suggested to play essential roles at various stages of the viral life cycle. Through a novel assay we had recently developed, we reported on the necessary and sufficient region for RNA dimerization in the HIV-1 virion. Using this system, we performed further detailed mapping of the functional base pairs necessary for HIV-1 DLS structure. Interestingly, the study revealed a previously unnoticed stem formation between two distantly positioned regions. Based on this and other findings on functional base pairing in vivo, we propose new 3D models of the HIV-1 DLS which contain a unique pseudoknot-like conformation. Since this pseudoknot-like conformation appears to be thermodynamically stable, forms a foundational skeleton for the DLS and sterically restricts the spontaneous diversification of DLS conformations, its unique shape may contribute to the viral life cycle and potentially serve as a novel target for anti-HIV-1 therapies.
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Affiliation(s)
- Jun-ichi Sakuragi
- Department of Viral Infections, RIMD, Osaka Univ. 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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13
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Identification of a minimal region of the HIV-1 5'-leader required for RNA dimerization, NC binding, and packaging. J Mol Biol 2012; 417:224-39. [PMID: 22306406 DOI: 10.1016/j.jmb.2012.01.033] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/13/2012] [Accepted: 01/21/2012] [Indexed: 11/23/2022]
Abstract
Assembly of human immunodeficiency virus type 1 (HIV-1) particles is initiated in the cytoplasm by the formation of a ribonucleoprotein complex comprising the dimeric RNA genome and a small number of viral Gag polyproteins. Genomes are recognized by the nucleocapsid (NC) domains of Gag, which interact with packaging elements believed to be located primarily within the 5'-leader (5'-L) of the viral RNA. Recent studies revealed that the native 5'-L exists as an equilibrium of two conformers, one in which dimer-promoting residues and NC binding sites are sequestered and packaging is attenuated, and one in which these sites are exposed and packaging is promoted. To identify the elements within the dimeric 5'-L that are important for packaging, we generated HIV-1 5'-L RNAs containing mutations and deletions designed to eliminate substructures without perturbing the overall structure of the leader and examined effects of the mutations on RNA dimerization, NC binding, and packaging. Our findings identify a 159-residue RNA packaging signal that possesses dimerization and NC binding properties similar to those of the intact 5'-L and contains elements required for efficient RNA packaging.
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14
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Miyazaki Y, Miyake A, Nomaguchi M, Adachi A. Structural dynamics of retroviral genome and the packaging. Front Microbiol 2011; 2:264. [PMID: 22232618 PMCID: PMC3247676 DOI: 10.3389/fmicb.2011.00264] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 12/11/2011] [Indexed: 12/17/2022] Open
Abstract
Retroviruses can cause diseases such as AIDS, leukemia, and tumors, but are also used as vectors for human gene therapy. All retroviruses, except foamy viruses, package two copies of unspliced genomic RNA into their progeny viruses. Understanding the molecular mechanisms of retroviral genome packaging will aid the design of new anti-retroviral drugs targeting the packaging process and improve the efficacy of retroviral vectors. Retroviral genomes have to be specifically recognized by the cognate nucleocapsid domain of the Gag polyprotein from among an excess of cellular and spliced viral mRNA. Extensive virological and structural studies have revealed how retroviral genomic RNA is selectively packaged into the viral particles. The genomic area responsible for the packaging is generally located in the 5′ untranslated region (5′ UTR), and contains dimerization site(s). Recent studies have shown that retroviral genome packaging is modulated by structural changes of RNA at the 5′ UTR accompanied by the dimerization. In this review, we focus on three representative retroviruses, Moloney murine leukemia virus, human immunodeficiency virus type 1 and 2, and describe the molecular mechanism of retroviral genome packaging.
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Affiliation(s)
- Yasuyuki Miyazaki
- Department of Microbiology, Institute of Health Biosciences, The University of Tokushima Graduate School Tokushima, Japan
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15
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Didierlaurent L, Racine PJ, Houzet L, Chamontin C, Berkhout B, Mougel M. Role of HIV-1 RNA and protein determinants for the selective packaging of spliced and unspliced viral RNA and host U6 and 7SL RNA in virus particles. Nucleic Acids Res 2011; 39:8915-27. [PMID: 21791531 PMCID: PMC3203606 DOI: 10.1093/nar/gkr577] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/27/2011] [Accepted: 06/28/2011] [Indexed: 01/22/2023] Open
Abstract
HIV-1 particles contain RNA species other than the unspliced viral RNA genome. For instance, viral spliced RNAs and host 7SL and U6 RNAs are natural components that are non-randomly incorporated. To understand the mechanism of packaging selectivity, we analyzed the content of a large panel of HIV-1 variants mutated either in the 5'UTR structures of the viral RNA or in the Gag-nucleocapsid protein (GagNC). In parallel, we determined whether the selection of host 7SL and U6 RNAs is dependent or not on viral RNA and/or GagNC. Our results reveal that the polyA hairpin in the 5'UTR is a major packaging determinant for both spliced and unspliced viral RNAs. In contrast, 5'UTR RNA structures have little influence on the U6 and 7SL RNAs, indicating that packaging of these host RNAs is independent of viral RNA packaging. Experiments with GagNC mutants indicated that the two zinc-fingers and N-terminal basic residues restrict the incorporation of the spliced RNAs, while favoring unspliced RNA packaging. GagNC through the zinc-finger motifs also restricts the packaging of 7SL and U6 RNAs. Thus, GagNC is a major contributor to the packaging selectivity. Altogether our results provide new molecular insight on how HIV selects distinct RNA species for incorporation into particles.
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Affiliation(s)
- L. Didierlaurent
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - P. J. Racine
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - L. Houzet
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - C. Chamontin
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - B. Berkhout
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - M. Mougel
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
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16
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Lu K, Heng X, Summers MF. Structural determinants and mechanism of HIV-1 genome packaging. J Mol Biol 2011; 410:609-33. [PMID: 21762803 DOI: 10.1016/j.jmb.2011.04.029] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/11/2011] [Accepted: 04/11/2011] [Indexed: 11/30/2022]
Abstract
Like all retroviruses, the human immunodeficiency virus selectively packages two copies of its unspliced RNA genome, both of which are utilized for strand-transfer-mediated recombination during reverse transcription-a process that enables rapid evolution under environmental and chemotherapeutic pressures. The viral RNA appears to be selected for packaging as a dimer, and there is evidence that dimerization and packaging are mechanistically coupled. Both processes are mediated by interactions between the nucleocapsid domains of a small number of assembling viral Gag polyproteins and RNA elements within the 5'-untranslated region of the genome. A number of secondary structures have been predicted for regions of the genome that are responsible for packaging, and high-resolution structures have been determined for a few small RNA fragments and protein-RNA complexes. However, major questions regarding the RNA structures (and potentially the structural changes) that are responsible for dimeric genome selection remain unanswered. Here, we review efforts that have been made to identify the molecular determinants and mechanism of human immunodeficiency virus type 1 genome packaging.
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Affiliation(s)
- Kun Lu
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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Jaballah SA, Aktar SJ, Ali J, Phillip PS, Al Dhaheri NS, Jabeen A, Rizvi TA. A G-C-rich palindromic structural motif and a stretch of single-stranded purines are required for optimal packaging of Mason-Pfizer monkey virus (MPMV) genomic RNA. J Mol Biol 2010; 401:996-1014. [PMID: 20600114 DOI: 10.1016/j.jmb.2010.06.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 06/21/2010] [Accepted: 06/21/2010] [Indexed: 01/17/2023]
Abstract
During retroviral RNA packaging, two copies of genomic RNA are preferentially packaged into the budding virus particles whereas the spliced viral RNAs and the cellular RNAs are excluded during this process. Specificity towards retroviral RNA packaging is dependent upon sequences at the 5' end of the viral genome, which at times extend into Gag sequences. It has earlier been suggested that the Mason-Pfizer monkey virus (MPMV) contains packaging sequences within the 5' untranslated region (UTR) and Gag. These studies have also suggested that the packaging determinants of MPMV that lie in the UTR are bipartite and are divided into two regions both upstream and downstream of the major splice donor. However, the precise boundaries of these discontinuous regions within the UTR and the role of the intervening sequences between these dipartite sequences towards MPMV packaging have not been investigated. Employing a combination of genetic and structural prediction analyses, we have shown that region "A", immediately downstream of the primer binding site, is composed of 50 nt, whereas region "B" is composed of the last 23 nt of UTR, and the intervening 55 nt between these two discontinuous regions do not contribute towards MPMV RNA packaging. In addition, we have identified a 14-nt G-C-rich palindromic sequence (with 100% autocomplementarity) within region A that has been predicted to fold into a structural motif and is essential for optimal MPMV RNA packaging. Furthermore, we have also identified a stretch of single-stranded purines (ssPurines) within the UTR and 8 nt of these ssPurines are duplicated in region B. The native ssPurines or its repeat in region B when predicted to refold as ssPurines has been shown to be essential for RNA packaging, possibly functioning as a potential nucleocapsid binding site. Findings from this study should enhance our understanding of the steps involved in MPMV replication including RNA encapsidation process.
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Affiliation(s)
- Soumeya Ali Jaballah
- Department of Microbiology and Immunology, Faculty of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al Ain, United Arab Emirates
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18
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Sinck L, Richer D, Howard J, Alexander M, Purcell DFJ, Marquet R, Paillart JC. In vitro dimerization of human immunodeficiency virus type 1 (HIV-1) spliced RNAs. RNA (NEW YORK, N.Y.) 2007; 13:2141-2150. [PMID: 17925344 PMCID: PMC2080610 DOI: 10.1261/rna.678307] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Accepted: 08/28/2007] [Indexed: 05/25/2023]
Abstract
The human immunodeficiency virus type 1 (HIV-1) packages its genomic RNA as a dimer of homologous RNA molecules that has to be selected among a multitude of cellular and viral RNAs. Interestingly, spliced viral mRNAs are packaged into viral particles with a relatively low efficiency despite the fact that they contain most of the extended packaging signal found in the 5' untranslated region of the genomic RNA, including the dimerization initiation site (DIS). As a consequence, HIV-1 spliced viral RNAs can theoretically homodimerize and heterodimerize with the genomic RNA, and thus they should directly compete with genomic RNA for packaging. To shed light on this issue, we investigated for the first time the in vitro dimerization properties of spliced HIV-1 RNAs. We found that singly spliced (env, vpr) and multispliced (tat, rev, and nef) RNA fragments are able to dimerize in vitro, and to efficiently form heterodimers with genomic RNA. Chemical probing experiments and inhibition of RNA dimerization by an antisense oligonucleotide directed against the DIS indicated that the DIS is structurally functional in spliced HIV-1 RNA, and that RNA dimerization occurs through a loop-loop interaction. In addition, by combining in vitro transcription and dimerization assays, we show that heterodimers can be efficiently formed only when the two RNA fragments are synthesized simultaneously, in the same environment. Together, our results support a model in which RNA dimerization would occur during transcription in the nucleus and could thus play a major role in splicing, transport, and localization of HIV-1 RNA.
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Affiliation(s)
- Lucile Sinck
- Architecture et Réactivité de l'ARN, Université Louis Pasteur, CNRS, IBMC, 67084, Strasbourg cedex, France
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19
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Laham-Karam N, Bacharach E. Transduction of human immunodeficiency virus type 1 vectors lacking encapsidation and dimerization signals. J Virol 2007; 81:10687-98. [PMID: 17652403 PMCID: PMC2045463 DOI: 10.1128/jvi.00653-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The encapsidation signal (Psi) and the nested dimerization initiation site are important for efficient packaging of human immunodeficiency virus type 1 (HIV-1) genomic RNA dimers. Consequently, these signals are included in all HIV-1 vectors. Here, we provide evidence demonstrating that these elements in such vectors are not absolutely required for vector transduction. In single-cycle infection assays, vectors with Psi deleted (DeltaPsi) were transduced with only a two- to fivefold reduction compared to the wild type. The transduction of DeltaPsi showed typical products of reverse transcription and vector integration; however, in vitro and in vivo dimerization assays demonstrated the lack of normal dimerization of the DeltaPsi vector. The reduction in transduction reflected a similar reduction in packaging. Nevertheless, a relatively high specificity of packaging was retained, as the DeltaPsi vector was encapsidated at a level 4 orders of magnitude higher than that for overexpressed, nonretroviral cellular mRNA and 15 orders of magnitude higher than that for a murine leukemia virus (MLV)-based vector, all containing the same reporter gene, suggesting a Psi-independent mechanism of packaging. The fact that HIV-1 and MLV vectors were encapsidated with a much higher level of efficiency than the cellular RNA suggests that the genomic RNAs of different retroviruses share common features and/or pathways that target them to encapsidation. Overall, these results formally demonstrate that packaging and dimerization signals are not required for the early stages of infection and can be deleted without risking a total loss of vector transduction. Deletion of these signals should enhance the safety of these vectors.
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Affiliation(s)
- Nihay Laham-Karam
- Department of Cell Research and Immunology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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20
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Houzet L, Paillart JC, Smagulova F, Maurel S, Morichaud Z, Marquet R, Mougel M. HIV controls the selective packaging of genomic, spliced viral and cellular RNAs into virions through different mechanisms. Nucleic Acids Res 2007; 35:2695-704. [PMID: 17426127 PMCID: PMC1885669 DOI: 10.1093/nar/gkm153] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In addition to genomic RNA, HIV-1 particles package cellular and spliced viral RNAs. In order to determine the encapsidation mechanisms of these RNAs, we determined the packaging efficiencies and specificities of genomic RNA, singly and fully spliced HIV mRNAs and different host RNAs species: 7SL RNA, U6 snRNA and GAPDH mRNA using RT-QPCR. Except GAPDH mRNA, all RNAs are selectively encapsidated. Singly spliced RNAs, harboring the Rev-responsible element, and fully spliced viral RNAs, which do not contain this motif, are enriched in virions to similar levels, even though they are exported from the nucleus by different routes. Deletions of key motifs (SL1 and/or SL3) of the packaging signal of genomic RNA indicate that HIV and host RNAs are encapsidated through independent mechanisms, while genomic and spliced viral RNA compete for the same trans-acting factor due to the presence of the 5′ common exon containing the TAR, poly(A) and U5-PBS hairpins. Surprisingly, the RNA dimerization initiation site (DIS/SL1) appears to be the main packaging determinant of genomic RNA, but is not involved in packaging of spliced viral RNAs, suggesting a functional interaction with intronic sequences. Active and selective packaging of host and spliced viral RNAs provide new potential functions to these RNAs in the early stages of the virus life cycle.
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Affiliation(s)
- Laurent Houzet
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Jean Christophe Paillart
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Fatima Smagulova
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Stephan Maurel
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Zakia Morichaud
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Roland Marquet
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Marylène Mougel
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
- *To whom correspondence should be addressed +33 4 67 60 02 32+33 4 67 60 44 20
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21
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Affiliation(s)
- Andrew M L Lever
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
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22
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Fisher RJ, Fivash MJ, Stephen AG, Hagan NA, Shenoy SR, Medaglia MV, Smith LR, Worthy KM, Simpson JT, Shoemaker R, McNitt KL, Johnson DG, Hixson CV, Gorelick RJ, Fabris D, Henderson LE, Rein A. Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides. Nucleic Acids Res 2006; 34:472-84. [PMID: 16434700 PMCID: PMC1351370 DOI: 10.1093/nar/gkj442] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Revised: 12/23/2005] [Accepted: 12/23/2005] [Indexed: 11/20/2022] Open
Abstract
The HIV-1 nucleocapsid (NC) protein is a small, basic protein containing two retroviral zinc fingers. It is a highly active nucleic acid chaperone; because of this activity, it plays a crucial role in virus replication as a cofactor during reverse transcription, and is probably important in other steps of the replication cycle as well. We previously reported that NC binds with high-affinity to the repeating sequence d(TG)n. We have now analyzed the interaction between NC and d(TG)4 in considerable detail, using surface plasmon resonance (SPR), tryptophan fluorescence quenching (TFQ), fluorescence anisotropy (FA), isothermal titration calorimetry (ITC) and electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). Our results show that the interactions between these two molecules are surprisngly complex: while the K(d) for binding of a single d(TG)4 molecule to NC is only approximately 5 nM in 150 mM NaCl, a single NC molecule is capable of interacting with more than one d(TG)4 molecule, and conversely, more than one NC molecule can bind to a single d(TG)4 molecule. The strengths of these additional binding reactions are quantitated. The implications of this multivalency for the functions of NC in virus replication are discussed.
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Affiliation(s)
- Robert J Fisher
- Protein Chemistry Laboratory, SAIC-Frederick, Inc. NCI Frederick, Frederick, MD 21702, USA.
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23
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Ghazawi A, Mustafa F, Phillip PS, Jayanth P, Ali J, Rizvi TA. Both the 5' and 3' LTRs of FIV contain minor RNA encapsidation determinants compared to the two core packaging determinants within the 5' untranslated region and gag. Microbes Infect 2006; 8:767-78. [PMID: 16513389 DOI: 10.1016/j.micinf.2005.09.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 09/08/2005] [Accepted: 09/27/2005] [Indexed: 11/17/2022]
Abstract
This study was undertaken to address the role of feline immunodeficiency virus (FIV) long terminal repeats (LTR) as potential packaging determinants. A number of studies in the recent past have clearly demonstrated that the core packaging determinants of FIV reside within at least two distinct regions at the 5' end of the viral genome, from R in the 5' LTR to approximately 150 bp within the 5' untranslated region (5' UTR) and within the first 100 bp of gag; however, there have been conflicting observations as to the role of the LTR regions in packaging and whether they contain the principal packaging determinants of FIV. Using a semi-quantitative RT-PCR approach on heterologous non-viral vector RNAs in an in vivo packaging assay, this study demonstrates that the principal packaging determinants of FIV reside within the first 150 bp of 5' UTR and 100 bp of gag (the two core regions) and not the viral 5' LTR. Furthermore, it shows that in addition to the 5' LTR, the 3' LTR also contains packaging determinants, but of a less significant nature compared to the core packaging determinants. This study defines the relative contribution of the various regions implicated in FIV genomic RNA packaging, and reveals that like other primate lentiviruses, the packaging determinants of FIV are multipartite and spread out, an observation that has implications for safer and more streamlined design of FIV-based gene transfer vectors.
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Affiliation(s)
- Akela Ghazawi
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences (FMHS), United Arab Emirates University (UAEU), P.O. Box 17666, Al Ain, United Arab Emirates
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Roy BB, Russell RS, Turner D, Liang C. The T12I mutation within the SP1 region of Gag restricts packaging of spliced viral RNA into human immunodeficiency virus type 1 with mutated RNA packaging signals and mutated nucleocapsid sequence. Virology 2006; 344:304-14. [PMID: 16226779 DOI: 10.1016/j.virol.2005.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 08/10/2005] [Accepted: 09/12/2005] [Indexed: 10/25/2022]
Abstract
Specific packaging of human immunodeficiency virus type 1 (HIV-1) RNA is attributable to the high affinity of nucleocapsid (NC) sequence of Gag for the cis-acting RNA packaging signals located within the 5' un-translated region (5' UTR). Interestingly, we have previously reported that the T12I mutation (named MP2) within SP1 of Gag prevented incorporation of spliced viral RNA into mutated viruses that lacked the stem-loop 1 (SL1) RNA element (also named dimerization initiation site, DIS), suggesting a role for the SP1 sequence in viral RNA packaging. In this study, we have further tested this activity of MP2 in the context of a variety of mutations that affect viral RNA incorporation. The results showed that MP2 was able to effectively restrict packaging of spliced viral RNA into viruses containing either NC mutations R10A and K11A or mutated 5' UTR sequence, such as DeltaGU3 that lacked the 112-GUCUGUUGUGUG-123 sequence of U5, D1 that was deleted of a 27 nt fragment immediately downstream of the primer binding site (PBS), Delta(306-325) that had the SL3 RNA element removed and MD2 that was missing the 328-GGAG-331 sequence. As a result, MP2 contributed increased infectivity to the related viruses. Therefore, the MP2 mutation demonstrates a distinct role in HIV-1 RNA packaging that is neither pertained to the specific viral RNA packaging signal nor to the NC sequence.
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Affiliation(s)
- Bibhuti Bhusan Roy
- McGill AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
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25
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Guo X, Roy BB, Hu J, Roldan A, Wainberg MA, Liang C. The R362A mutation at the C-terminus of CA inhibits packaging of human immunodeficiency virus type 1 RNA. Virology 2005; 343:190-200. [PMID: 16183096 DOI: 10.1016/j.virol.2005.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 07/11/2005] [Accepted: 08/22/2005] [Indexed: 12/15/2022]
Abstract
The capsid (CA) sequence of human immunodeficiency virus type 1 (HIV-1) Gag protein consists of two independently folded domains named the N-terminal domain (NTD) and C-terminal domain (CTD) that are connected by a flexible linker. Most of the CTD sequence adopts rigid structure except for the last 11 amino acids (positions 354 to 364) that are disordered even in the context of the downstream SP1 and nucleocapsid (NC) sequence. Although disordered, this short peptide region plays a crucial role in HIV-1 replication. In this study, we identified three second-site mutations within Gag named A238T, G358S, and N373K that rescued a deleterious mutation R362A located at the C-terminus of CA. A238T is located within the NTD of CA, G358S and N373K are positioned proximal to R362A. One of the mechanisms underlying this compensation event is correction of reduced packaging of viral RNA into the R362A mutated viruses, as shown by the results of RNase protection assays, native Northern blots experiments as well as filter-binding assays. These data suggest that one potential function for the C-terminal disordered sequence of CA in HIV-1 replication is to regulate HIV-1 RNA packaging.
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Affiliation(s)
- Xiaofeng Guo
- McGill AIDS Centre, Lady Davis Institute-Jewish General Hospital, 3755 Cote Ste-Catherine Road, Montreal, Quebec, Canada H3T 1E2
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Abstract
As retroviruses assemble in infected cells, two copies of their full-length, unspliced RNA genomes are selected for packaging from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Understanding the molecular details of genome packaging is important for the development of new antiviral strategies and to enhance the efficacy of retroviral vectors used in human gene therapy. Recent studies of viral RNA structure in vitro and in vivo and high-resolution studies of RNA fragments and protein-RNA complexes are helping to unravel the mechanism of genome packaging and providing the first glimpses of the initial stages of retrovirus assembly.
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Affiliation(s)
- Victoria D'Souza
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
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27
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Russell RS, Liang C, Wainberg MA. Is HIV-1 RNA dimerization a prerequisite for packaging? Yes, no, probably? Retrovirology 2004; 1:23. [PMID: 15345057 PMCID: PMC516451 DOI: 10.1186/1742-4690-1-23] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 09/02/2004] [Indexed: 01/14/2023] Open
Abstract
During virus assembly, all retroviruses specifically encapsidate two copies of full-length viral genomic RNA in the form of a non-covalently linked RNA dimer. The absolute conservation of this unique genome structure within the Retroviridae family is strong evidence that a dimerized genome is of critical importance to the viral life cycle. An obvious hypothesis is that retroviruses have evolved to preferentially package two copies of genomic RNA, and that dimerization ensures the proper packaging specificity for such a genome. However, this implies that dimerization must be a prerequisite for genome encapsidation, a notion that has been debated for many years. In this article, we review retroviral RNA dimerization and packaging, highlighting the research that has attempted to dissect the intricate relationship between these two processes in the context of HIV-1, and discuss the therapeutic potential of these putative antiretroviral targets.
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Affiliation(s)
- Rodney S Russell
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, 3755 Cote Ste-Catherine Road Montreal, Quebec, Canada H3T 1E2
- Department of Microbiology & Immunology Montreal, Quebec, Canada H3A 2B4
| | - Chen Liang
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, 3755 Cote Ste-Catherine Road Montreal, Quebec, Canada H3T 1E2
- Department of Medicine, McGill University, Montreal, Quebec, Canada H3A 2B4
| | - Mark A Wainberg
- McGill AIDS Centre, Lady Davis Institute, Jewish General Hospital, 3755 Cote Ste-Catherine Road Montreal, Quebec, Canada H3T 1E2
- Department of Microbiology & Immunology Montreal, Quebec, Canada H3A 2B4
- Department of Medicine, McGill University, Montreal, Quebec, Canada H3A 2B4
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28
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Paillart JC, Shehu-Xhilaga M, Marquet R, Mak J. Dimerization of retroviral RNA genomes: an inseparable pair. Nat Rev Microbiol 2004; 2:461-72. [PMID: 15152202 DOI: 10.1038/nrmicro903] [Citation(s) in RCA: 232] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Jean-Christophe Paillart
- UPR 9002 du CNRS affiliée à l'Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France
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Russell RS, Roldan A, Detorio M, Hu J, Wainberg MA, Liang C. Effects of a single amino acid substitution within the p2 region of human immunodeficiency virus type 1 on packaging of spliced viral RNA. J Virol 2004; 77:12986-95. [PMID: 14645555 PMCID: PMC296066 DOI: 10.1128/jvi.77.24.12986-12995.2003] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 encapsidates two copies of viral genomic RNA in the form of a dimer. The dimerization process initiates via a 6-nucleotide palindrome that constitutes the loop of a viral RNA stem-loop structure (i.e., stem loop 1 [SL1], also termed the dimerization initiation site [DIS]) located within the 5' untranslated region of the viral genome. We have now shown that deletion of the entire DIS sequence virtually eliminated viral replication but that this impairment was overcome by four second-site mutations located within the matrix (MA), capsid (CA), p2, and nucleocapsid (NC) regions of Gag. Interestingly, defective viral RNA dimerization caused by the DeltaDIS deletion was not significantly corrected by these compensatory mutations, which did, however, allow the mutated viruses to package wild-type levels of this DIS-deleted viral RNA while excluding spliced viral RNA from encapsidation. Further studies demonstrated that the compensatory mutation T12I located within p2, termed MP2, sufficed to prevent spliced viral RNA from being packaged into the DeltaDIS virus. Consistently, the DeltaDIS-MP2 virus displayed significantly higher levels of infectiousness than did the DeltaDIS virus. The importance of position T12 in p2 was further demonstrated by the identification of four point mutations,T12D, T12E, T12G, and T12P, that resulted in encapsidation of spliced viral RNA at significant levels. Taken together, our data demonstrate that selective packaging of viral genomic RNA is influenced by the MP2 mutation and that this represents a major mechanism for rescue of viruses containing the DeltaDIS deletion.
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Affiliation(s)
- Rodney S Russell
- McGill AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
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Lanchy JM, Ivanovitch JD, Lodmell JS. A structural linkage between the dimerization and encapsidation signals in HIV-2 leader RNA. RNA (NEW YORK, N.Y.) 2003; 9:1007-1018. [PMID: 12869711 PMCID: PMC1370466 DOI: 10.1261/rna.5590603] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2003] [Accepted: 04/30/2003] [Indexed: 05/24/2023]
Abstract
The 5' untranslated leader region of retroviral RNAs contains noncoding information that is essential for viral replication, including signals for transcriptional transactivation, splicing, primer binding for reverse transcription, dimerization of the genomic RNA, and encapsidation of the viral RNA into virions. These RNA motifs have considerable structural and functional overlap. In this study, we investigate the conformational dynamics associated with the use and silencing of a sequence in HIV-2 RNA that is involved in genomic RNA dimerization called stem-loop 1 (SL1) and its relationship with a flanking sequence that is known to be important for encapsidation of viral RNAs. We demonstrate that a long-distance intramolecular interaction between nucleotides located upstream of the primer-binding site domain and nucleotides encompassing the Gag translation start codon functionally silences SL1 as a dimerization element. This silencing can be relieved by mutation or by hybridization of an oligonucleotide that disrupts the long-distance interaction. Furthermore, we identify a palindrome within the packaging/encapsidation signal Psi (just 5' of SL1) that can either serve as an efficient dimerization signal itself, or can mediate SL1 silencing through base pairing with SL1. These results provide a tangible link between the functions of genomic RNA dimerization and encapsidation, which are known to be related, but whose physical relationship has been unclear. A model is proposed that accounts for observations of dimerization, packaging, and translation of viral RNAs during different phases of the viral replication cycle.
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Affiliation(s)
- Jean-Marc Lanchy
- Division of Biological Sciences, The University of Montana, Missoula, Montana 59812, USA
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