1
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Hardy J, Demecheleer E, Schauvliege M, Staelens D, Mortier V, Verhofstede C. Reverse transcription of plasma-derived HIV-1 RNA generates multiple artifacts through tRNA(Lys-3)-priming. Microbiol Spectr 2024; 12:e0387223. [PMID: 38442427 PMCID: PMC10986323 DOI: 10.1128/spectrum.03872-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
In vitro reverse transcription of full-length HIV-1 RNA extracted from the blood plasma of people living with HIV-1 remains challenging. Here, we describe the initiation of reverse transcription of plasma-derived viral RNA in the absence of an exogenous primer. Real-time PCR and Sanger sequencing were applied to identify the source and to monitor the outcome of this reaction. Results demonstrated that during purification of viral RNA from plasma, tRNA(Lys-3) is co-extracted in a complex with the viral RNA. In the presence of a reverse transcription enzyme, this tRNA(Lys-3) can induce reverse transcription, a reaction that is not confined to transcription of the 5' end of the viral RNA. A range of cDNA products is generated, most of them indicative for the occurrence of in vitro strand transfer events that involve translocation of cDNA from the 5' end to random positions on the viral RNA. This process results in the formation of cDNAs with large internal deletions. However, near full-length cDNA and cDNA with sequence patterns resembling multiple spliced HIV-1 RNA were also detected. Despite its potential to introduce significant bias in the interpretation of results across various applications, tRNA(Lys-3)-driven reverse transcription has been overlooked thus far. A more in-depth study of this tRNA-driven in vitro reaction may provide new insight into the complex process of in vivo HIV-1 replication.IMPORTANCEThe use of silica-based extraction methods for purifying HIV-1 RNA from viral particles is a common practice, but it involves co-extraction of human tRNA(Lys-3) due to the strong interactions between these molecules. This co-extraction becomes particularly significant when the extracted RNA is used in reverse transcription reactions, as the tRNA(Lys-3) then serves as a primer. Reverse transcription from tRNA(Lys-3) is not confined to cDNA synthesis of the 5' end of the viral RNA but extends across various regions of the viral genome through in vitro strand transfer events. Co-extraction of tRNA(Lys-3) has been overlooked thus far, despite its potential to introduce bias in downstream, reverse transcription-related applications. The observed events in the tRNA(Lys-3)-induced in vitro reverse transcription resemble in vivo replication processes. Therefore, these reactions may offer a unique model to better understand the replication dynamics of HIV-1.
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Affiliation(s)
- Jarryt Hardy
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Els Demecheleer
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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2
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Dragoni F, Kwaa AK, Traut CC, Veenhuis RT, Woldemeskel BA, Camilo-Contreras A, Raymond HE, Dykema AG, Scully EP, Rosecrans AM, Smith KN, Bushman FD, Simonetti FR, Blankson JN. Proviral location affects cognate peptide-induced virus production and immune recognition of HIV-1-infected T cell clones. J Clin Invest 2023; 133:e171097. [PMID: 37698927 PMCID: PMC10617777 DOI: 10.1172/jci171097] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUNDHIV-1-infected CD4+ T cells contribute to latent reservoir persistence by proliferating while avoiding immune recognition. Integration features of intact proviruses in elite controllers (ECs) and people on long-term therapy suggest that proviruses in specific chromosomal locations can evade immune surveillance. However, direct evidence of this mechanism is missing.METHODSIn this case report, we characterized integration sites and full genome sequences of expanded T cell clones in an EC before and after chemoradiation. We identified the cognate peptide of infected clones to investigate cell proliferation and virus production induced by T cell activation, and susceptibility to autologous CD8+ T cells.RESULTSThe proviral landscape was dominated by 2 large clones with replication-competent proviruses integrated into zinc finger (ZNF) genes (ZNF470 and ZNF721) in locations previously associated with deeper latency. A third nearly intact provirus, with a stop codon in Pol, was integrated into an intergenic site. Upon stimulation with cognate Gag peptides, infected clones proliferated extensively and produced virus, but the provirus in ZNF721 was 200-fold less inducible. While autologous CD8+ T cells decreased the proliferation of cells carrying the intergenic provirus, they had no effect on cells with the provirus in the ZNF721 gene.CONCLUSIONSWe provide direct evidence that upon activation of infected clones by cognate antigen, the lower inducibility of intact proviruses in ZNF genes can result in immune evasion and persistence.FUNDINGOffice of the NIH Director and National Institute of Dental & Craniofacial Research; NIAID, NIH; Johns Hopkins University Center for AIDS Research.
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Affiliation(s)
| | | | | | - Rebecca T. Veenhuis
- Department of Molecular and Comparative Pathobiology, and
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Hayley E. Raymond
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Arbor G. Dykema
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, and
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Kellie N. Smith
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, and
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Joel N. Blankson
- Department of Medicine
- Department of Molecular and Comparative Pathobiology, and
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3
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Gilmer O, Mailler E, Paillart JC, Mouhand A, Tisné C, Mak J, Smyth RP, Marquet R, Vivet-Boudou V. Structural maturation of the HIV-1 RNA 5' untranslated region by Pr55 Gag and its maturation products. RNA Biol 2022; 19:191-205. [PMID: 35067194 PMCID: PMC8786341 DOI: 10.1080/15476286.2021.2021677] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Maturation of the HIV-1 viral particles shortly after budding is required for infectivity. During this process, the Pr55Gag precursor undergoes a cascade of proteolytic cleavages, and whilst the structural rearrangements of the viral proteins are well understood, the concomitant maturation of the genomic RNA (gRNA) structure is unexplored, despite evidence that it is required for infectivity. To get insight into this process, we systematically analysed the interactions between Pr55Gag or its maturation products (NCp15, NCp9 and NCp7) and the 5ʹ gRNA region and their structural consequences, in vitro. We show that Pr55Gag and its maturation products mostly bind at different RNA sites and with different contributions of their two zinc knuckle domains. Importantly, these proteins have different transient and permanent effects on the RNA structure, the late NCp9 and NCp7 inducing dramatic structural rearrangements. Altogether, our results reveal the distinct contributions of the different Pr55Gag maturation products on the gRNA structural maturation.
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Affiliation(s)
- Orian Gilmer
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Elodie Mailler
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Jean-Christophe Paillart
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Assia Mouhand
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-chimique, Paris, France
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-chimique, Paris, France
| | - Johnson Mak
- Institute for Glycomics, Griffith University, Gold Coast, Australia
| | - Redmond P Smyth
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
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4
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Boyd PS, Brown JB, Brown JD, Catazaro J, Chaudry I, Ding P, Dong X, Marchant J, O’Hern CT, Singh K, Swanson C, Summers MF, Yasin S. NMR Studies of Retroviral Genome Packaging. Viruses 2020; 12:v12101115. [PMID: 33008123 PMCID: PMC7599994 DOI: 10.3390/v12101115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/03/2022] Open
Abstract
Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems—a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.
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5
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Mouhand A, Pasi M, Catala M, Zargarian L, Belfetmi A, Barraud P, Mauffret O, Tisné C. Overview of the Nucleic-Acid Binding Properties of the HIV-1 Nucleocapsid Protein in Its Different Maturation States. Viruses 2020; 12:v12101109. [PMID: 33003650 PMCID: PMC7601788 DOI: 10.3390/v12101109] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/17/2022] Open
Abstract
HIV-1 Gag polyprotein orchestrates the assembly of viral particles. Its C-terminus consists of the nucleocapsid (NC) domain that interacts with nucleic acids, and p1 and p6, two unstructured regions, p6 containing the motifs to bind ALIX, the cellular ESCRT factor TSG101 and the viral protein Vpr. The processing of Gag by the viral protease subsequently liberates NCp15 (NC-p1-p6), NCp9 (NC-p1) and NCp7, NCp7 displaying the optimal chaperone activity of nucleic acids. This review focuses on the nucleic acid binding properties of the NC domain in the different maturation states during the HIV-1 viral cycle.
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Affiliation(s)
- Assia Mouhand
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
| | - Marco Pasi
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
| | - Marjorie Catala
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
| | - Loussiné Zargarian
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
| | - Anissa Belfetmi
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
| | - Pierre Barraud
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
| | - Olivier Mauffret
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113 CNRS, Institut D’Alembert, École Normale Supérieure Paris-Saclay, Université Paris-Saclay, 4, Avenue des Sciences, 91190 Gif sur Yvette, France; (M.P.); (L.Z.); (A.B.)
- Correspondence: (O.M.); (C.T.)
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France; (A.M.); (M.C.); (P.B.)
- Correspondence: (O.M.); (C.T.)
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6
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Karnib H, Nadeem MF, Humbert N, Sharma KK, Grytsyk N, Tisné C, Boutant E, Lequeu T, Réal E, Boudier C, de Rocquigny H, Mély Y. The nucleic acid chaperone activity of the HIV-1 Gag polyprotein is boosted by its cellular partner RPL7: a kinetic study. Nucleic Acids Res 2020; 48:9218-9234. [PMID: 32797159 PMCID: PMC7498347 DOI: 10.1093/nar/gkaa659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 07/20/2020] [Accepted: 07/29/2020] [Indexed: 01/10/2023] Open
Abstract
The HIV-1 Gag protein playing a key role in HIV-1 viral assembly has recently been shown to interact through its nucleocapsid domain with the ribosomal protein L7 (RPL7) that acts as a cellular co-factor promoting Gag's nucleic acid (NA) chaperone activity. To further understand how the two proteins act together, we examined their mechanism individually and in concert to promote the annealing between dTAR, the DNA version of the viral transactivation element and its complementary cTAR sequence, taken as model HIV-1 sequences. Gag alone or complexed with RPL7 was found to act as a NA chaperone that destabilizes cTAR stem-loop and promotes its annealing with dTAR through the stem ends via a two-step pathway. In contrast, RPL7 alone acts as a NA annealer that through its NA aggregating properties promotes cTAR/dTAR annealing via two parallel pathways. Remarkably, in contrast to the isolated proteins, their complex promoted efficiently the annealing of cTAR with highly stable dTAR mutants. This was confirmed by the RPL7-promoted boost of the physiologically relevant Gag-chaperoned annealing of (+)PBS RNA to the highly stable tRNALys3 primer, favoring the notion that Gag recruits RPL7 to overcome major roadblocks in viral assembly.
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Affiliation(s)
- Hassan Karnib
- Laboratory of Bioimaging and Pathologies (LBP), UMR 7021, Faculty of pharmacy, University of Strasbourg, 67400 Illkirch, France
| | - Muhammad F Nadeem
- Laboratory of Bioimaging and Pathologies (LBP), UMR 7021, Faculty of pharmacy, University of Strasbourg, 67400 Illkirch, France
| | - Nicolas Humbert
- Laboratory of Bioimaging and Pathologies (LBP), UMR 7021, Faculty of pharmacy, University of Strasbourg, 67400 Illkirch, France
| | - Kamal K Sharma
- Laboratory of Bioimaging and Pathologies (LBP), UMR 7021, Faculty of pharmacy, University of Strasbourg, 67400 Illkirch, France
| | - Natalia Grytsyk
- Laboratory of Bioimaging and Pathologies (LBP), UMR 7021, Faculty of pharmacy, University of Strasbourg, 67400 Illkirch, France
| | - Carine Tisné
- Expression génétique microbienne, UMR 8261, CNRS, Université de Paris, Institut de biologie physico-chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Emmanuel Boutant
- Laboratory of Bioimaging and Pathologies (LBP), UMR 7021, Faculty of pharmacy, University of Strasbourg, 67400 Illkirch, France
| | - Thiebault Lequeu
- Laboratory of Bioimaging and Pathologies (LBP), UMR 7021, Faculty of pharmacy, University of Strasbourg, 67400 Illkirch, France
| | - Eleonore Réal
- Laboratory of Bioimaging and Pathologies (LBP), UMR 7021, Faculty of pharmacy, University of Strasbourg, 67400 Illkirch, France
| | - Christian Boudier
- Laboratory of Bioimaging and Pathologies (LBP), UMR 7021, Faculty of pharmacy, University of Strasbourg, 67400 Illkirch, France
| | - Hugues de Rocquigny
- Inserm – U1259 Morphogenesis and Antigenicity of HIV and Hepatitis Viruses (MAVIVH), 10 boulevard Tonnellé, BP 3223, 37032 Tours Cedex 1, France
| | - Yves Mély
- Laboratory of Bioimaging and Pathologies (LBP), UMR 7021, Faculty of pharmacy, University of Strasbourg, 67400 Illkirch, France
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7
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Boutant E, Bonzi J, Anton H, Nasim MB, Cathagne R, Réal E, Dujardin D, Carl P, Didier P, Paillart JC, Marquet R, Mély Y, de Rocquigny H, Bernacchi S. Zinc Fingers in HIV-1 Gag Precursor Are Not Equivalent for gRNA Recruitment at the Plasma Membrane. Biophys J 2020; 119:419-433. [PMID: 32574557 PMCID: PMC7376094 DOI: 10.1016/j.bpj.2020.05.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/15/2020] [Accepted: 05/06/2020] [Indexed: 01/16/2023] Open
Abstract
The human immunodeficiency virus type 1 Gag precursor specifically selects the unspliced viral genomic RNA (gRNA) from the bulk of cellular and spliced viral RNAs via its nucleocapsid (NC) domain and drives gRNA encapsidation at the plasma membrane (PM). To further identify the determinants governing the intracellular trafficking of Gag-gRNA complexes and their accumulation at the PM, we compared, in living and fixed cells, the interactions between gRNA and wild-type Gag or Gag mutants carrying deletions in NC zinc fingers (ZFs) or a nonmyristoylated version of Gag. Our data showed that the deletion of both ZFs simultaneously or the complete NC domain completely abolished intracytoplasmic Gag-gRNA interactions. Deletion of either ZF delayed the delivery of gRNA to the PM but did not prevent Gag-gRNA interactions in the cytoplasm, indicating that the two ZFs display redundant roles in this respect. However, ZF2 played a more prominent role than ZF1 in the accumulation of the ribonucleoprotein complexes at the PM. Finally, the myristate group, which is mandatory for anchoring the complexes at the PM, was found to be dispensable for the association of Gag with the gRNA in the cytosol.
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Affiliation(s)
- Emmanuel Boutant
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.
| | - Jeremy Bonzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Halina Anton
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Maaz Bin Nasim
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Raphael Cathagne
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Eléonore Réal
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Denis Dujardin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Philippe Carl
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Jean-Christophe Paillart
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Hugues de Rocquigny
- Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, Inserm - U1259 MAVIVH, Tours, France.
| | - Serena Bernacchi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France.
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8
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Gamba E, Sosic A, Saccone I, Magli E, Frecentese F, Gatto B. Multiple in Vitro Inhibition of HIV-1 Proteins by 2,6-Dipeptidyl-anthraquinone Conjugates Targeting the PBS RNA. ACS Med Chem Lett 2020; 11:949-955. [PMID: 32435410 DOI: 10.1021/acsmedchemlett.9b00682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/23/2020] [Indexed: 11/28/2022] Open
Abstract
We recently reported a series of 2,6-dipeptidyl-anthraquinone conjugates (AQs) as Trans-Activation Response element (TAR) RNA-binding agents able to inhibit in vitro the HIV-1 nucleocapsid (NC) protein-mediated processes. Because NC is a highly adaptable nucleic acid chaperone assisting several crucial steps along reverse transcription, in this study we investigate the ability of AQs to interact with other virus-derived nucleic acid structures thus potentially inhibiting multiple NC functions. Focusing on the HIV-1 Primer Binding Site (PBS) RNA sequence, we demonstrate that properly substituted dipeptidyl-anthraquinone conjugates efficiently inhibit the NC-mediated primer annealing in the low micromolar range. Similarly, we extended the analysis to the HIV-1 trans-activator of transcription (Tat) peptide, which has been recently shown to mimic the annealer functions of NC upon interacting with the same nucleic acid regulatory sequences. Our results highlight how RNA-targeting agents can act as multimode inhibitors of key viral proteins affecting their chaperone activity in reverse transcription processes.
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Affiliation(s)
- Elia Gamba
- Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - Alice Sosic
- Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - Irene Saccone
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Elisa Magli
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Francesco Frecentese
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Barbara Gatto
- Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
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9
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Asadi-Atoi P, Barraud P, Tisne C, Kellner S. Benefits of stable isotope labeling in RNA analysis. Biol Chem 2020; 400:847-865. [PMID: 30893050 DOI: 10.1515/hsz-2018-0447] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
RNAs are key players in life as they connect the genetic code (DNA) with all cellular processes dominated by proteins. They contain a variety of chemical modifications and many RNAs fold into complex structures. Here, we review recent progress in the analysis of RNA modification and structure on the basis of stable isotope labeling techniques. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy are the key tools and many breakthrough developments were made possible by the analysis of stable isotope labeled RNA. Therefore, we discuss current stable isotope labeling techniques such as metabolic labeling, enzymatic labeling and chemical synthesis. RNA structure analysis by NMR is challenging due to two major problems that become even more salient when the size of the RNA increases, namely chemical shift overlaps and line broadening leading to complete signal loss. Several isotope labeling strategies have been developed to provide solutions to these major issues, such as deuteration, segmental isotope labeling or site-specific labeling. Quantification of modified nucleosides in RNA by MS is only possible through the application of stable isotope labeled internal standards. With nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS), it is now possible to analyze the dynamic processes of post-transcriptional RNA modification and demodification. The trend, in both NMR and MS RNA analytics, is without doubt shifting from the analysis of snapshot moments towards the development and application of tools capable of analyzing the dynamics of RNA structure and modification profiles.
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Affiliation(s)
- Paria Asadi-Atoi
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Pierre Barraud
- Institut de Biologie Physico-Chimique (IBPC), UMR 8261, CNRS, Université Paris Diderot, 13 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Carine Tisne
- Institut de Biologie Physico-Chimique (IBPC), UMR 8261, CNRS, Université Paris Diderot, 13 rue Pierre et Marie Curie, F-75005 Paris, France
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, D-81377 Munich, Germany
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10
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Butovskaya E, Soldà P, Scalabrin M, Nadai M, Richter SN. HIV-1 Nucleocapsid Protein Unfolds Stable RNA G-Quadruplexes in the Viral Genome and Is Inhibited by G-Quadruplex Ligands. ACS Infect Dis 2019; 5:2127-2135. [PMID: 31646863 PMCID: PMC6909241 DOI: 10.1021/acsinfecdis.9b00272] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
The G-quadruplexes that form in the
HIV-1 RNA genome hinder progression
of reverse transcriptase
in vitro, but not in infected cells. We investigated the possibility
that the HIV-1 nucleocapsid protein NCp7, which remains associated
with the viral RNA during reverse transcription, modulated HIV-1 RNA
G-quadruplex stability. By electrophoresis, circular dichroism, mass
spectrometry, and reverse transcriptase stop assays, we demonstrated
that NCp7 binds and unfolds the HIV-1 RNA G-quadruplexes and promotes
DNA/RNA duplex formation, allowing reverse transcription to proceed.
The G-quadruplex ligand BRACO-19 was able to partially counteract
this effect. These results indicate NCp7 as the first known viral
protein able to unfold RNA G-quadruplexes, and they explain how the
extra-stable HIV-1 RNA G-quadruplexes are processed; they also point
out that the reverse transcription process is hindered by G-quadruplex
ligands at both reverse transcriptase and NCp7 level. This information
can lead to the development of more effective anti-HIV-1 drugs with
a new mechanism of action.
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Affiliation(s)
- Elena Butovskaya
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Paola Soldà
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
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11
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Mouhand A, Belfetmi A, Catala M, Larue V, Zargarian L, Brachet F, Gorelick RJ, Van Heijenoort C, Mirambeau G, Barraud P, Mauffret O, Tisné C. Modulation of the HIV nucleocapsid dynamics finely tunes its RNA-binding properties during virion genesis. Nucleic Acids Res 2019; 46:9699-9710. [PMID: 29986076 PMCID: PMC6182130 DOI: 10.1093/nar/gky612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/26/2018] [Indexed: 02/06/2023] Open
Abstract
During HIV-1 assembly and budding, Gag protein, in particular the C-terminal domain containing the nucleocapsid domain (NCd), p1 and p6, is the site of numerous interactions with viral and cellular factors. Most in vitro studies of Gag have used constructs lacking p1 and p6. Here, using NMR spectroscopy, we show that the p1-p6 region of Gag (NCp15) is largely disordered, but interacts transiently with the NCd. These interactions modify the dynamic properties of the NCd. Indeed, using isothermal titration calorimetry (ITC), we have measured a higher entropic penalty to RNA-binding for the NCd precursor, NCp15, than for the mature form, NCp7, which lacks p1 and p6. We propose that during assembly and budding of virions, concomitant with Gag oligomerization, transient interactions between NCd and p1-p6 become salient and responsible for (i) a higher level of structuration of p6, which favours recruitment of budding partners; and (ii) a higher entropic penalty to RNA-binding at specific sites that favours non-specific binding of NCd at multiple sites on the genomic RNA (gRNA). The contributions of p6 and p1 are sequentially removed via proteolysis during Gag maturation such that the RNA-binding specificity of the mature protein is governed by the properties of NCd.
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Affiliation(s)
- Assia Mouhand
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, IBPC, CNRS, Université Paris Diderot, USPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Anissa Belfetmi
- LBPA, CNRS UMR 8113, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du Pdt Wilson, F-94235 Cachan, France
| | - Marjorie Catala
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, IBPC, CNRS, Université Paris Diderot, USPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Valéry Larue
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Loussiné Zargarian
- LBPA, CNRS UMR 8113, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du Pdt Wilson, F-94235 Cachan, France
| | - Franck Brachet
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702-1201, USA
| | - Carine Van Heijenoort
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Gilles Mirambeau
- Infectious disease & AIDS Research unit, IDIBAPS, Barcelona, Barcelona, Spain.,Sorbonne Université, Faculté des Sciences et Ingénierie, UFR 927 des Sciences de la Vie, Paris, France
| | - Pierre Barraud
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, IBPC, CNRS, Université Paris Diderot, USPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivier Mauffret
- LBPA, CNRS UMR 8113, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du Pdt Wilson, F-94235 Cachan, France
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, IBPC, CNRS, Université Paris Diderot, USPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
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12
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Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A. Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA. Microorganisms 2018; 6:E110. [PMID: 30347855 PMCID: PMC6313347 DOI: 10.3390/microorganisms6040110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022] Open
Abstract
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takuya Kawamura
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takako Awai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
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13
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René B, Mauffret O, Fossé P. Retroviral nucleocapsid proteins and DNA strand transfers. BIOCHIMIE OPEN 2018; 7:10-25. [PMID: 30109196 PMCID: PMC6088434 DOI: 10.1016/j.biopen.2018.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/08/2018] [Indexed: 12/12/2022]
Abstract
An infectious retroviral particle contains 1000-1500 molecules of the nucleocapsid protein (NC) that cover the diploid RNA genome. NC is a small zinc finger protein that possesses nucleic acid chaperone activity that enables NC to rearrange DNA and RNA molecules into the most thermodynamically stable structures usually those containing the maximum number of base pairs. Thanks to the chaperone activity, NC plays an essential role in reverse transcription of the retroviral genome by facilitating the strand transfer reactions of this process. In addition, these reactions are involved in recombination events that can generate multiple drug resistance mutations in the presence of anti-HIV-1 drugs. The strand transfer reactions rely on base pairing of folded DNA/RNA structures. The molecular mechanisms responsible for NC-mediated strand transfer reactions are presented and discussed in this review. Antiretroviral strategies targeting the NC-mediated strand transfer events are also discussed.
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Affiliation(s)
- Brigitte René
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Olivier Mauffret
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Philippe Fossé
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
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14
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Larue V, Catala M, Belfetmi A, Zargarian L, Mauffret O, Tisné C. 1H, 13C and 15N backbone and partial side-chain resonance assignments of the C-terminal domain of HIV-1 Pr55 Gag encompassed in NCp15. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:139-143. [PMID: 29332151 DOI: 10.1007/s12104-017-9796-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/27/2017] [Indexed: 06/07/2023]
Abstract
During HIV-1 assembly, the Pr55Gag polyprotein precursor (Gag) interacts with the genomic RNA, with lipids of the plasma membrane, with host proteins (ALIX, TSG101) through the ESCRT complex, with the viral protein Vpr and are involved in intermolecular interactions with other Pr55Gag proteins. This network of interactions is responsible for the formation of the viral particle, the selection of genomic RNA and the packaging of Vpr. The C-terminal domain of Gag encompassed in NCp15 is involved in the majority of these interactions, either by its nucleocapsid or its p6 domains. We study the NCp15 protein as a model of the C-terminal domain of Gag to better understand the role of this domain in the assembly and budding of HIV-1. Here, we report the 1H, 13C and 15N chemical shift assignments of NCp15 obtained by heteronuclear multidimensional NMR spectroscopy as well as the analysis of its secondary structure in solution. These assignments of NCp15 pave the way for interaction studies with its numerous partners.
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Affiliation(s)
- Valéry Larue
- Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Faculté de Pharmacie, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006, Paris, France.
| | - Marjorie Catala
- Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Faculté de Pharmacie, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006, Paris, France
- Laboratoire d'Expression génétique microbienne, IBPC, CNRS UMR 8261, USPC, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Anissa Belfetmi
- LBPA, CNRS UMR 8113, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du Pdt Wilson, F-94235, Cachan, France
| | - Loussiné Zargarian
- LBPA, CNRS UMR 8113, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du Pdt Wilson, F-94235, Cachan, France
| | - Olivier Mauffret
- LBPA, CNRS UMR 8113, ENS Paris-Saclay, Université Paris-Saclay, 61 Avenue du Pdt Wilson, F-94235, Cachan, France
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Faculté de Pharmacie, Université Paris Descartes, USPC, 4 avenue de l'Observatoire, 75006, Paris, France.
- Laboratoire d'Expression génétique microbienne, IBPC, CNRS UMR 8261, USPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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15
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The multiple roles of the nucleocapsid in retroviral RNA conversion into proviral DNA by reverse transcriptase. Biochem Soc Trans 2017; 44:1427-1440. [PMID: 27911725 DOI: 10.1042/bst20160101-t] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 08/08/2016] [Accepted: 08/17/2016] [Indexed: 01/27/2023]
Abstract
Retroviruses are enveloped plus-strand RNA viruses that can cause cancer, immunodeficiency and neurological disorder in human and animals. Retroviruses have several unique properties, such as a genomic RNA in a dimeric form found in the virus, and a replication strategy called 'copy-and-paste' during which the plus-strand genomic RNA is converted into a double-stranded DNA, subsequently integrated into the cellular genome. Two essential viral enzymes, reverse transcriptase (RT) and integrase (IN), direct this 'copy-and-paste' replication. RT copies the genomic RNA generating the double-stranded proviral DNA, while IN catalyzes proviral DNA integration into the cellular DNA, then called the provirus. In that context, a major component of the virion core, the nucleocapsid protein (NC), was found to be a potent nucleic-acid chaperone that assists RT during the conversion of the genomic RNA into proviral DNA. Here we briefly review the interplay of NC with viral nucleic-acids, which enables rapid and faithful folding and hybridization of complementary sequences, and with active RT thus providing assistance to the synthesis of the complete proviral DNA. Because of its multiple roles in retrovirus replication, NC could be viewed as a two-faced Janus-chaperone acting on viral nucleic-acids and enzymes.
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16
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Virion-incorporated alpha-enolase suppresses the early stage of HIV-1 reverse transcription. Biochem Biophys Res Commun 2017; 484:278-284. [DOI: 10.1016/j.bbrc.2017.01.096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 01/19/2017] [Indexed: 11/22/2022]
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17
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Post K, Olson ED, Naufer MN, Gorelick RJ, Rouzina I, Williams MC, Musier-Forsyth K, Levin JG. Mechanistic differences between HIV-1 and SIV nucleocapsid proteins and cross-species HIV-1 genomic RNA recognition. Retrovirology 2016; 13:89. [PMID: 28034301 PMCID: PMC5198506 DOI: 10.1186/s12977-016-0322-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nucleocapsid (NC) domain of HIV-1 Gag is responsible for specific recognition and packaging of genomic RNA (gRNA) into new viral particles. This occurs through specific interactions between the Gag NC domain and the Psi packaging signal in gRNA. In addition to this critical function, NC proteins are also nucleic acid (NA) chaperone proteins that facilitate NA rearrangements during reverse transcription. Although the interaction with Psi and chaperone activity of HIV-1 NC have been well characterized in vitro, little is known about simian immunodeficiency virus (SIV) NC. Non-human primates are frequently used as a platform to study retroviral infection in vivo; thus, it is important to understand underlying mechanistic differences between HIV-1 and SIV NC. RESULTS Here, we characterize SIV NC chaperone activity for the first time. Only modest differences are observed in the ability of SIV NC to facilitate reactions that mimic the minus-strand annealing and transfer steps of reverse transcription relative to HIV-1 NC, with the latter displaying slightly higher strand transfer and annealing rates. Quantitative single molecule DNA stretching studies and dynamic light scattering experiments reveal that these differences are due to significantly increased DNA compaction energy and higher aggregation capability of HIV-1 NC relative to the SIV protein. Using salt-titration binding assays, we find that both proteins are strikingly similar in their ability to specifically interact with HIV-1 Psi RNA. In contrast, they do not demonstrate specific binding to an RNA derived from the putative SIV packaging signal. CONCLUSIONS Based on these studies, we conclude that (1) HIV-1 NC is a slightly more efficient NA chaperone protein than SIV NC, (2) mechanistic differences between the NA interactions of highly similar retroviral NC proteins are revealed by quantitative single molecule DNA stretching, and (3) SIV NC demonstrates cross-species recognition of the HIV-1 Psi RNA packaging signal.
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Affiliation(s)
- Klara Post
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780 USA
| | - Erik D. Olson
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - M. Nabuan Naufer
- Department of Physics, Northeastern University, Boston, MA 02115 USA
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201 USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115 USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Judith G. Levin
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780 USA
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18
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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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19
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Coey A, Larsen K, Puglisi JD, Viani Puglisi E. Heterogeneous structures formed by conserved RNA sequences within the HIV reverse transcription initiation site. RNA (NEW YORK, N.Y.) 2016; 22:1689-1698. [PMID: 27613581 PMCID: PMC5066621 DOI: 10.1261/rna.056804.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/03/2016] [Indexed: 06/06/2023]
Abstract
Reverse transcription is a key process in the early steps of HIV infection. This process initiates within a specific complex formed by the 5' UTR of the HIV genomic RNA (vRNA) and a host primer tRNALys3 Using nuclear magnetic resonance (NMR) spectroscopy and single-molecule fluorescence spectroscopy, we detect two distinct conformers adopted by the tRNA/vRNA initiation complex. We directly show that an interaction between the conserved 8-nucleotide viral RNA primer activation signal (PAS) and the primer tRNA occurs in one of these conformers. This intermolecular PAS interaction likely induces strain on a vRNA intramolecular helix, which must be broken for reverse transcription to initiate. We propose a mechanism by which this vRNA/tRNA conformer relieves the kinetic block formed by the vRNA intramolecular helix to initiate reverse transcription.
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Affiliation(s)
- Aaron Coey
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Kevin Larsen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
| | - Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
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20
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Racine PJ, Chamontin C, de Rocquigny H, Bernacchi S, Paillart JC, Mougel M. Requirements for nucleocapsid-mediated regulation of reverse transcription during the late steps of HIV-1 assembly. Sci Rep 2016; 6:27536. [PMID: 27273064 PMCID: PMC4895152 DOI: 10.1038/srep27536] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/13/2016] [Indexed: 12/19/2022] Open
Abstract
HIV-1 is a retrovirus replicating within cells by reverse transcribing its genomic RNA (gRNA) into DNA. Within cells, virus assembly requires the structural Gag proteins with few accessory proteins, notably the viral infectivity factor (Vif) and two copies of gRNA as well as cellular factors to converge to the plasma membrane. In this process, the nucleocapsid (NC) domain of Gag binds to the packaging signal of gRNA which consists of a series of stem-loops (SL1-SL3) ensuring gRNA selection and packaging into virions. Interestingly, mutating NC activates a late-occurring reverse transcription (RT) step in producer cells, leading to the release of DNA-containing HIV-1 particles. In order to decipher the molecular mechanism regulating this late RT, we explored the role of several key partners of NC, such as Vif, gRNA and the cellular cytidine deaminase APOBEC3G that restricts HIV-1 infection by targeting the RT. By studying combinations of deletions of these putative players, we revealed that NC, SL1-SL3 and in lesser extent Vif, but not APOBEC3G, interplay regulates the late RT.
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Affiliation(s)
- Pierre-Jean Racine
- Centre d'études d’agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Célia Chamontin
- Centre d'études d’agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Hugues de Rocquigny
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401, Illkirch Cedex, France
| | - Serena Bernacchi
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg, France
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg, France
| | - Marylène Mougel
- Centre d'études d’agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
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21
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Belfetmi A, Zargarian L, Tisné C, Sleiman D, Morellet N, Lescop E, Maskri O, René B, Mély Y, Fossé P, Mauffret O. Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein. RNA (NEW YORK, N.Y.) 2016; 22:506-517. [PMID: 26826129 PMCID: PMC4793207 DOI: 10.1261/rna.054445.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/06/2015] [Indexed: 06/05/2023]
Abstract
The mature HIV-1 nucleocapsid protein NCp7 (NC) plays a key role in reverse transcription facilitating the two obligatory strand transfers. Several properties contribute to its efficient chaperon activity: preferential binding to single-stranded regions, nucleic acid aggregation, helix destabilization, and rapid dissociation from nucleic acids. However, little is known about the relationships between these different properties, which are complicated by the ability of the protein to recognize particular HIV-1 stem-loops, such as SL1, SL2, and SL3, with high affinity and without destabilizing them. These latter properties are important in the context of genome packaging, during which NC is part of the Gag precursor. We used NMR to investigate destabilization of the full-length TAR (trans activating response element) RNA by NC, which is involved in the first strand transfer step of reverse transcription. NC was used at a low protein:nucleotide (nt) ratio of 1:59 in these experiments. NMR data for the imino protons of TAR identified most of the base pairs destabilized by NC. These base pairs were adjacent to the loops in the upper part of the TAR hairpin rather than randomly distributed. Gel retardation assays showed that conversion from the initial TAR-cTAR complex to the fully annealed form occurred much more slowly at the 1:59 ratio than at the higher ratios classically used. Nevertheless, NC significantly accelerated the formation of the initial complex at a ratio of 1:59.
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Affiliation(s)
- Anissa Belfetmi
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
| | - Loussiné Zargarian
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, Université Paris Descartes, CNRS UMR 8015, 75006 Paris Cedex, France
| | - Dona Sleiman
- Laboratoire de Cristallographie et RMN biologiques, Université Paris Descartes, CNRS UMR 8015, 75006 Paris Cedex, France
| | - Nelly Morellet
- Centre de Recherches de Gif, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, 91190 Gif sur Yvette Cedex, France
| | - Ewen Lescop
- Centre de Recherches de Gif, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, 91190 Gif sur Yvette Cedex, France
| | - Ouerdia Maskri
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
| | - Brigitte René
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, CNRS UMR 7213, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch Cedex, France
| | - Philippe Fossé
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
| | - Olivier Mauffret
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
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22
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Mori M, Kovalenko L, Lyonnais S, Antaki D, Torbett BE, Botta M, Mirambeau G, Mély Y. Nucleocapsid Protein: A Desirable Target for Future Therapies Against HIV-1. Curr Top Microbiol Immunol 2015; 389:53-92. [PMID: 25749978 PMCID: PMC7122173 DOI: 10.1007/82_2015_433] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The currently available anti-HIV-1 therapeutics is highly beneficial to infected patients. However, clinical failures occur as a result of the ability of HIV-1 to rapidly mutate. One approach to overcome drug resistance is to target HIV-1 proteins that are highly conserved among phylogenetically distant viral strains and currently not targeted by available therapies. In this respect, the nucleocapsid (NC) protein, a zinc finger protein, is particularly attractive, as it is highly conserved and plays a central role in virus replication, mainly by interacting with nucleic acids. The compelling rationale for considering NC as a viable drug target is illustrated by the fact that point mutants of this protein lead to noninfectious viruses and by the inability to select viruses resistant to a first generation of anti-NC drugs. In our review, we discuss the most relevant properties and functions of NC, as well as recent developments of small molecules targeting NC. Zinc ejectors show strong antiviral activity, but are endowed with a low therapeutic index due to their lack of specificity, which has resulted in toxicity. Currently, they are mainly being investigated for use as topical microbicides. Greater specificity may be achieved by using non-covalent NC inhibitors (NCIs) targeting the hydrophobic platform at the top of the zinc fingers or key nucleic acid partners of NC. Within the last few years, innovative methodologies have been developed to identify NCIs. Though the antiviral activity of the identified NCIs needs still to be improved, these compounds strongly support the druggability of NC and pave the way for future structure-based design and optimization of efficient NCIs.
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Affiliation(s)
- Mattia Mori
- Dipartimento di Biotecnologie Chimica e Farmacia, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy
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23
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Chamontin C, Rassam P, Ferrer M, Racine PJ, Neyret A, Lainé S, Milhiet PE, Mougel M. HIV-1 nucleocapsid and ESCRT-component Tsg101 interplay prevents HIV from turning into a DNA-containing virus. Nucleic Acids Res 2014; 43:336-47. [PMID: 25488808 PMCID: PMC4288153 DOI: 10.1093/nar/gku1232] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
HIV-1, the agent of the AIDS pandemic, is an RNA virus that reverse transcribes its RNA genome (gRNA) into DNA, shortly after its entry into cells. Within cells, retroviral assembly requires thousands of structural Gag proteins and two copies of gRNA as well as cellular factors, which converge to the plasma membrane in a finely regulated timeline. In this process, the nucleocapsid domain of Gag (GagNC) ensures gRNA selection and packaging into virions. Subsequent budding and virus release require the recruitment of the cellular ESCRT machinery. Interestingly, mutating GagNC results into the release of DNA-containing viruses, by promo-ting reverse transcription (RTion) prior to virus release, through an unknown mechanism. Therefore, we explored the biogenesis of these DNA-containing particles, combining live-cell total internal-reflection fluorescent microscopy, electron microscopy, trans-complementation assays and biochemical characterization of viral particles. Our results reveal that DNA virus production is the consequence of budding defects associated with Gag aggregation at the plasma membrane and deficiency in the recruitment of Tsg101, a key ESCRT-I component. Indeed, targeting Tsg101 to virus assembly sites restores budding, restricts RTion and favors RNA packaging into viruses. Altogether, our results highlight the role of GagNC in the spatiotemporal control of RTion, via an ESCRT-I-dependent mechanism.
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Affiliation(s)
- Célia Chamontin
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
| | - Patrice Rassam
- Centre de Biochimie Structurale, UMR5048 CNRS, University of Montpellier, 34090 Montpellier, France
| | - Mireia Ferrer
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
| | - Pierre-Jean Racine
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
| | - Aymeric Neyret
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
| | - Sébastien Lainé
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
| | - Pierre-Emmanuel Milhiet
- Centre de Biochimie Structurale, UMR5048 CNRS, University of Montpellier, 34090 Montpellier, France U1054 INSERM, 30090 Montpellier, France
| | - Marylène Mougel
- CPBS, UMR5236 CNRS, University of Montpellier, 34293 Montpellier, France
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24
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Wu T, Gorelick RJ, Levin JG. Selection of fully processed HIV-1 nucleocapsid protein is required for optimal nucleic acid chaperone activity in reverse transcription. Virus Res 2014; 193:52-64. [PMID: 24954787 PMCID: PMC4252486 DOI: 10.1016/j.virusres.2014.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/09/2014] [Accepted: 06/10/2014] [Indexed: 12/14/2022]
Abstract
The mature HIV-1 nucleocapsid protein (NCp7) is generated by sequential proteolytic cleavage of precursor proteins containing additional C-terminal peptides: NCp15 (NCp7-spacer peptide 2 (SP2)-p6); and NCp9 (NCp7-SP2). Here, we compare the nucleic acid chaperone activities of the three proteins, using reconstituted systems that model the annealing and elongation steps in tRNA(Lys3)-primed (-) strong-stop DNA synthesis and subsequent minus-strand transfer. The maximum levels of annealing are similar for all of the proteins, but there are important differences in their ability to facilitate reverse transcriptase (RT)-catalyzed DNA extension. Thus, at low concentrations, NCp9 has the greatest activity, but with increasing concentrations, DNA synthesis is significantly reduced. This finding reflects NCp9's strong nucleic acid binding affinity (associated with the highly basic SP2 domain) as well as its slow dissociation kinetics, which together limit the ability of RT to traverse the nucleic acid template. NCp15 has the poorest activity of the three proteins due to its acidic p6 domain. Indeed, mutants with alanine substitutions for the acidic residues in p6 have improved chaperone function. Collectively, these data can be correlated with the known biological properties of NCp9 and NCp15 mutant virions and help to explain why mature NC has evolved as the critical cofactor for efficient virus replication and long-term viral fitness.
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Affiliation(s)
- Tiyun Wu
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA
| | - Judith G Levin
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780, USA.
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25
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Garg D, Torbett BE. Advances in targeting nucleocapsid-nucleic acid interactions in HIV-1 therapy. Virus Res 2014; 193:135-43. [PMID: 25026536 PMCID: PMC4252855 DOI: 10.1016/j.virusres.2014.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/02/2014] [Accepted: 07/03/2014] [Indexed: 11/16/2022]
Abstract
The continuing challenge of HIV-1 treatment resistance in patients creates a need for the development of new antiretroviral inhibitors. The HIV nucleocapsid (NC) protein is a potential therapeutic target. NC is necessary for viral RNA packaging and in the early stages of viral infection. The high level of NC amino acid conservation among all HIV-1 clades suggests a low tolerance for mutations. Thus, NC mutations that could arise during inhibitor treatment to provide resistance may render the virus less fit. Disruption of NC function provides a unique opportunity to strongly dampen replication at multiple points during the viral life cycle with a single inhibitor. Although NC exhibits desirable features for a potential antiviral target, the structural flexibility, size, and the presence of two zinc fingers makes small molecule targeting of NC a challenging task. In this review, we discuss the recent advances in strategies to develop inhibitors of NC function and present a perspective on potential novel approaches that may help to overcome some of the current challenges in the field.
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Affiliation(s)
- Divita Garg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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26
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Sánchez-Luque FJ, Stich M, Manrubia S, Briones C, Berzal-Herranz A. Efficient HIV-1 inhibition by a 16 nt-long RNA aptamer designed by combining in vitro selection and in silico optimisation strategies. Sci Rep 2014; 4:6242. [PMID: 25175101 PMCID: PMC4150108 DOI: 10.1038/srep06242] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/04/2014] [Indexed: 02/08/2023] Open
Abstract
The human immunodeficiency virus type-1 (HIV-1) genome contains multiple, highly conserved structural RNA domains that play key roles in essential viral processes. Interference with the function of these RNA domains either by disrupting their structures or by blocking their interaction with viral or cellular factors may seriously compromise HIV-1 viability. RNA aptamers are amongst the most promising synthetic molecules able to interact with structural domains of viral genomes. However, aptamer shortening up to their minimal active domain is usually necessary for scaling up production, what requires very time-consuming, trial-and-error approaches. Here we report on the in vitro selection of 64 nt-long specific aptamers against the complete 5′-untranslated region of HIV-1 genome, which inhibit more than 75% of HIV-1 production in a human cell line. The analysis of the selected sequences and structures allowed for the identification of a highly conserved 16 nt-long stem-loop motif containing a common 8 nt-long apical loop. Based on this result, an in silico designed 16 nt-long RNA aptamer, termed RNApt16, was synthesized, with sequence 5′-CCCCGGCAAGGAGGGG-3′. The HIV-1 inhibition efficiency of such an aptamer was close to 85%, thus constituting the shortest RNA molecule so far described that efficiently interferes with HIV-1 replication.
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Affiliation(s)
- Francisco J Sánchez-Luque
- 1] Department of Molecular Biology. Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN-CSIC), PTS Granada. Avda. del Conocimiento s/n, Armilla (Granada 18016, Spain) [2]
| | - Michael Stich
- 1] Department of Molecular Evolution. Centro de Astrobiología (CAB-CSIC/INTA). Carretera Torrejón a Ajalvir km 4, Torrejón de Ardoz (Madrid 28850, Spain) [2]
| | - Susanna Manrubia
- Department of Molecular Evolution. Centro de Astrobiología (CAB-CSIC/INTA). Carretera Torrejón a Ajalvir km 4, Torrejón de Ardoz (Madrid 28850, Spain)
| | - Carlos Briones
- 1] Department of Molecular Evolution. Centro de Astrobiología (CAB-CSIC/INTA). Carretera Torrejón a Ajalvir km 4, Torrejón de Ardoz (Madrid 28850, Spain) [2] Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
| | - Alfredo Berzal-Herranz
- Department of Molecular Biology. Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN-CSIC), PTS Granada. Avda. del Conocimiento s/n, Armilla (Granada 18016, Spain)
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27
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Blond A, Ennifar E, Tisné C, Micouin L. The design of RNA binders: targeting the HIV replication cycle as a case study. ChemMedChem 2014; 9:1982-96. [PMID: 25100137 DOI: 10.1002/cmdc.201402259] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Indexed: 01/08/2023]
Abstract
The human immunodeficiency virus 1 (HIV-1) replication cycle is finely tuned with many important steps involving RNA-RNA or protein-RNA interactions, all of them being potential targets for the development of new antiviral compounds. This cycle can also be considered as a good benchmark for the evaluation of early-stage strategies aiming at designing drugs that bind to RNA, with the possibility to correlate in vitro activities with antiviral properties. In this review, we highlight different approaches developed to interfere with four important steps of the HIV-1 replication cycle: the early stage of reverse transcription, the transactivation of viral transcription, the nuclear export of partially spliced transcripts and the dimerization step.
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Affiliation(s)
- Aurélie Blond
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Fondamentales et Biomédicales, 45 Rue des Saints Pères, 75006 Paris (France)
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28
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Pachulska-Wieczorek K, Stefaniak AK, Purzycka KJ. Similarities and differences in the nucleic acid chaperone activity of HIV-2 and HIV-1 nucleocapsid proteins in vitro. Retrovirology 2014; 11:54. [PMID: 24992971 PMCID: PMC4227088 DOI: 10.1186/1742-4690-11-54] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/23/2014] [Indexed: 01/22/2023] Open
Abstract
Background The nucleocapsid domain of Gag and mature nucleocapsid protein (NC) act as nucleic acid chaperones and facilitate folding of nucleic acids at critical steps of retroviral replication cycle. The basic N-terminus of HIV-1 NC protein was shown most important for the chaperone activity. The HIV-2 NC (NCp8) and HIV-1 NC (NCp7) proteins possess two highly conserved zinc fingers, flanked by basic residues. However, the NCp8 N-terminal domain is significantly shorter and contains less positively charged residues. This study characterizes previously unknown, nucleic acid chaperone activity of the HIV-2 NC protein. Results We have comparatively investigated the in vitro nucleic acid chaperone properties of the HIV-2 and HIV-1 NC proteins. Using substrates derived from the HIV-1 and HIV-2 genomes, we determined the ability of both proteins to chaperone nucleic acid aggregation, annealing and strand exchange in duplex structures. Both NC proteins displayed comparable, high annealing activity of HIV-1 TAR DNA and its complementary nucleic acid. Interesting differences between the two NC proteins were discovered when longer HIV substrates, particularly those derived from the HIV-2 genome, were used in chaperone assays. In contrast to NCp7, NCp8 weakly facilitates annealing of HIV-2 TAR RNA to its complementary TAR (−) DNA. NCp8 is also unable to efficiently stimulate tRNALys3 annealing to its respective HIV-2 PBS motif. Using truncated NCp8 peptide, we demonstrated that despite the fact that the N-terminus of NCp8 differs from that of NCp7, this domain is essential for NCp8 activity. Conclusion Our data demonstrate that the HIV-2 NC protein displays reduced nucleic acid chaperone activity compared to that of HIV-1 NC. We found that NCp8 activity is limited by substrate length and stability to a greater degree than that of NCp7. This is especially interesting in light of the fact that the HIV-2 5′UTR is more structured than that of HIV-1. The reduced chaperone activity observed with NCp8 may influence the efficiency of reverse transcription and other key steps of the HIV-2 replication cycle.
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29
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Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 2014; 5:144. [PMID: 24904644 PMCID: PMC4033218 DOI: 10.3389/fgene.2014.00144] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/04/2014] [Indexed: 12/26/2022] Open
Abstract
To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Applied Chemistry, Graduate School of Science and Engineering, Ehime University Matsuyama, Japan
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30
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Kolomiets IN, Zarudnaya MI, Potyahaylo AL, Hovorun DM. Structural insight into HIV-1 reverse transcription initiation in MAL-like templates (CRF01_AE, subtype G and CRF02_AG). J Biomol Struct Dyn 2014; 33:418-33. [DOI: 10.1080/07391102.2014.884938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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31
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Sleiman D, Barraud P, Brachet F, Tisne C. The Interaction between tRNA(Lys) 3 and the primer activation signal deciphered by NMR spectroscopy. PLoS One 2013; 8:e64700. [PMID: 23762248 PMCID: PMC3675109 DOI: 10.1371/journal.pone.0064700] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/17/2013] [Indexed: 11/23/2022] Open
Abstract
The initiation of reverse transcription of the human immunodeficiency virus type 1 (HIV-1) requires the opening of the three-dimensional structure of the primer tRNALys3 for its annealing to the viral RNA at the primer binding site (PBS). Despite the fact that the result of this rearrangement is thermodynamically more stable, there is a high-energy barrier that requires the chaperoning activity of the viral nucleocapsid protein. In addition to the nucleotide complementarity to the PBS, several regions of tRNALys3 have been described as interacting with the viral genomic RNA. Among these sequences, a sequence of the viral genome called PAS for “primer activation signal” was proposed to interact with the T-arm of tRNALys3, this interaction stimulating the initiation of reverse transcription. In this report, we investigate the formation of this additional interaction with NMR spectroscopy, using a simple system composed of the primer tRNALys3, the 18 nucleotides of the PBS, the PAS (8 nucleotides) encompassed or not in a hairpin structure, and the nucleocapsid protein. Our NMR study provides molecular evidence of the existence of this interaction and highlights the role of the nucleocapsid protein in promoting this additional RNA-RNA annealing. This study presents the first direct observation at a single base-pair resolution of the PAS/anti-PAS association, which has been proposed to be involved in the chronological regulation of the reverse transcription.
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Affiliation(s)
- Dona Sleiman
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, Paris, France
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32
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Beerens N, Jepsen MD, Nechyporuk-Zloy V, Krüger AC, Darlix JL, Kjems J, Birkedal V. Role of the primer activation signal in tRNA annealing onto the HIV-1 genome studied by single-molecule FRET microscopy. RNA (NEW YORK, N.Y.) 2013; 19:517-526. [PMID: 23404895 PMCID: PMC3677262 DOI: 10.1261/rna.035733.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 12/13/2012] [Indexed: 06/01/2023]
Abstract
HIV-1 reverse transcription is primed by a cellular tRNAlys3 molecule that binds to the primer binding site (PBS) in the genomic RNA. An additional interaction between the tRNA molecule and the primer activation signal (PAS) is thought to regulate the initiation of reverse transcription. The mechanism of tRNA annealing onto the HIV-1 genome was examined using ensemble and single-molecule Förster Resonance Energy Transfer (FRET) assays, in which fluorescent donor and acceptor molecules were covalently attached to an RNA template mimicking the PBS region. The role of the viral nucleocapsid (NC) protein in tRNA annealing was studied. Both heat annealing and NC-mediated annealing of tRNAlys3 were found to change the FRET efficiency, and thus the conformation of the HIV-1 RNA template. The results are consistent with a model for tRNA annealing that involves an interaction between the tRNAlys3 molecule and the PAS sequence in the HIV-1 genome. The NC protein may stimulate the interaction of the tRNA molecule with the PAS, thereby regulating the initiation of reverse transcription.
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Affiliation(s)
- Nancy Beerens
- Department of Molecular Biology, Aarhus University, Aarhus 8000, Denmark
| | - Mette D.E. Jepsen
- Department of Molecular Biology, Aarhus University, Aarhus 8000, Denmark
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus 8000, Denmark
| | | | - Asger C. Krüger
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus 8000, Denmark
| | - Jean-Luc Darlix
- UMR 7213 CNRS, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, Illkirch 67401, France
| | - Jørgen Kjems
- Department of Molecular Biology, Aarhus University, Aarhus 8000, Denmark
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus 8000, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus 8000, Denmark
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33
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Lyonnais S, Gorelick RJ, Heniche-Boukhalfa F, Bouaziz S, Parissi V, Mouscadet JF, Restle T, Gatell JM, Le Cam E, Mirambeau G. A protein ballet around the viral genome orchestrated by HIV-1 reverse transcriptase leads to an architectural switch: from nucleocapsid-condensed RNA to Vpr-bridged DNA. Virus Res 2013; 171:287-303. [PMID: 23017337 PMCID: PMC3552025 DOI: 10.1016/j.virusres.2012.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 12/15/2022]
Abstract
HIV-1 reverse transcription is achieved in the newly infected cell before viral DNA (vDNA) nuclear import. Reverse transcriptase (RT) has previously been shown to function as a molecular motor, dismantling the nucleocapsid complex that binds the viral genome as soon as plus-strand DNA synthesis initiates. We first propose a detailed model of this dismantling in close relationship with the sequential conversion from RNA to double-stranded (ds) DNA, focusing on the nucleocapsid protein (NCp7). The HIV-1 DNA-containing pre-integration complex (PIC) resulting from completion of reverse transcription is translocated through the nuclear pore. The PIC nucleoprotein architecture is poorly understood but contains at least two HIV-1 proteins initially from the virion core, namely integrase (IN) and the viral protein r (Vpr). We next present a set of electron micrographs supporting that Vpr behaves as a DNA architectural protein, initiating multiple DNA bridges over more than 500 base pairs (bp). These complexes are shown to interact with NCp7 bound to single-stranded nucleic acid regions that are thought to maintain IN binding during dsDNA synthesis, concurrently with nucleocapsid complex dismantling. This unexpected binding of Vpr conveniently leads to a compacted but filamentous folding of the vDNA that should favor its nuclear import. Finally, nucleocapsid-like aggregates engaged in dsDNA synthesis appear to efficiently bind to F-actin filaments, a property that may be involved in targeting complexes to the nuclear envelope. More generally, this article highlights unique possibilities offered by in vitro reconstitution approaches combined with macromolecular imaging to gain insights into the mechanisms that alter the nucleoprotein architecture of the HIV-1 genome, ultimately enabling its insertion into the nuclear chromatin.
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MESH Headings
- DNA Packaging
- DNA, Viral/chemistry
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Genome, Viral
- HIV Integrase/genetics
- HIV Integrase/metabolism
- HIV Reverse Transcriptase/genetics
- HIV Reverse Transcriptase/metabolism
- HIV-1/chemistry
- HIV-1/enzymology
- HIV-1/genetics
- HIV-1/metabolism
- Humans
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Reverse Transcription
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/metabolism
- vpr Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program; SAIC-Frederick, Inc.; Frederick National Laboratory for Cancer Research; Frederick, MD USA
| | - Fatima Heniche-Boukhalfa
- Maintenance des génomes, Microscopies Moléculaire et Bionanosciences; UMR 8126 CNRS-Université Paris Sud, Villejuif, F-94805, France
| | - Serge Bouaziz
- Laboratoire de Cristallographie et RMN biologiques; UMR 8015 CNRS-Université Paris Descartes; Paris, F-75006, France
| | - Vincent Parissi
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, UMR5234 CNRS-Université Bordeaux Segalen, France
| | | | - Tobias Restle
- Institute of Molecular Medicine, University of Lübeck, Center for Structural and Cell Biology in Medicine (CSCM), D-23538 Lübeck, Germany
| | | | - Eric Le Cam
- Maintenance des génomes, Microscopies Moléculaire et Bionanosciences; UMR 8126 CNRS-Université Paris Sud, Villejuif, F-94805, France
| | - Gilles Mirambeau
- AIDS Research Group; IDIBAPS; E-08036 Barcelona, Spain
- Faculté de Biologie; UPMC Sorbonne Universités; Paris, F-75005, France
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