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Mauro E, Lapaillerie D, Tumiotto C, Charlier C, Martins F, Sousa SF, Métifiot M, Weigel P, Yamatsugu K, Kanai M, Munier-Lehmann H, Richetta C, Maisch M, Dutrieux J, Batisse J, Ruff M, Delelis O, Lesbats P, Parissi V. Modulation of the functional interfaces between retroviral intasomes and the human nucleosome. mBio 2023; 14:e0108323. [PMID: 37382440 PMCID: PMC10470491 DOI: 10.1128/mbio.01083-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 05/16/2023] [Indexed: 06/30/2023] Open
Abstract
Infection by retroviruses as HIV-1 requires the stable integration of their genome into the host cells. This process needs the formation of integrase (IN)-viral DNA complexes, called intasomes, and their interaction with the target DNA wrapped around nucleosomes within cell chromatin. To provide new tools to analyze this association and select drugs, we applied the AlphaLISA technology to the complex formed between the prototype foamy virus (PFV) intasome and nucleosome reconstituted on 601 Widom sequence. This system allowed us to monitor the association between both partners and select small molecules that could modulate the intasome/nucleosome association. Using this approach, drugs acting either on the DNA topology within the nucleosome or on the IN/histone tail interactions have been selected. Within these compounds, doxorubicin and histone binders calixarenes were characterized using biochemical, in silico molecular simulations and cellular approaches. These drugs were shown to inhibit both PFV and HIV-1 integration in vitro. Treatment of HIV-1-infected PBMCs with the selected molecules induces a decrease in viral infectivity and blocks the integration process. Thus, in addition to providing new information about intasome-nucleosome interaction determinants, our work also paves the way for further unedited antiviral strategies that target the final step of intasome/chromatin anchoring. IMPORTANCE In this work, we report the first monitoring of retroviral intasome/nucleosome interaction by AlphaLISA. This is the first description of the AlphaLISA application for large nucleoprotein complexes (>200 kDa) proving that this technology is suitable for molecular characterization and bimolecular inhibitor screening assays using such large complexes. Using this system, we have identified new drugs disrupting or preventing the intasome/nucleosome complex and inhibiting HIV-1 integration both in vitro and in infected cells. This first monitoring of the retroviral/intasome complex should allow the development of multiple applications including the analyses of the influence of cellular partners, the study of additional retroviral intasomes, and the determination of specific interfaces. Our work also provides the technical bases for the screening of larger libraries of drugs targeting specifically these functional nucleoprotein complexes, or additional nucleosome-partner complexes, as well as for their characterization.
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Affiliation(s)
- E. Mauro
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - D. Lapaillerie
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - C. Tumiotto
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - C. Charlier
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
- Nantes Université, CNRS, US2B, UMR 6286 and CHU Nantes, Inserm, CNRS, SFR Bonamy, IMPACT Platform, Nantes, France
| | - F. Martins
- UCIBIO@REQUIMTE, BioSIM Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal
| | - S. F. Sousa
- UCIBIO@REQUIMTE, BioSIM Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, Porto, Portugal
| | - M. Métifiot
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - P. Weigel
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
- Nantes Université, CNRS, US2B, UMR 6286 and CHU Nantes, Inserm, CNRS, SFR Bonamy, IMPACT Platform, Nantes, France
| | - K. Yamatsugu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - M. Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - H. Munier-Lehmann
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
- Institut Pasteur, Unité de Chimie et Biocatalyse, CNRS UMR 3523, Paris, France
| | - C. Richetta
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
- LBPA, ENS Paris-Saclay, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, Cachan, France
| | - M. Maisch
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS, UMR8104, Paris, France
| | - J. Dutrieux
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
- Université Paris Cité, Institut Cochin, INSERM U1016, CNRS, UMR8104, Paris, France
| | - J. Batisse
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
- Département de Biologie Structurale intégrative, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), UDS, U596 INSERM, UMR7104, CNRS, Strasbourg, France
| | - M. Ruff
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
- Département de Biologie Structurale intégrative, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), UDS, U596 INSERM, UMR7104, CNRS, Strasbourg, France
| | - O. Delelis
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
- LBPA, ENS Paris-Saclay, CNRS UMR8113, IDA FR3242, Université Paris-Saclay, Cachan, France
| | - P. Lesbats
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - V. Parissi
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
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2
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Pellaers E, Bhat A, Christ F, Debyser Z. Determinants of Retroviral Integration and Implications for Gene Therapeutic MLV-Based Vectors and for a Cure for HIV-1 Infection. Viruses 2022; 15:32. [PMID: 36680071 PMCID: PMC9861059 DOI: 10.3390/v15010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
To complete their replication cycle, retroviruses need to integrate a DNA copy of their RNA genome into a host chromosome. Integration site selection is not random and is driven by multiple viral and cellular host factors specific to different classes of retroviruses. Today, overwhelming evidence from cell culture, animal experiments and clinical data suggests that integration sites are important for retroviral replication, oncogenesis and/or latency. In this review, we will summarize the increasing knowledge of the mechanisms underlying the integration site selection of the gammaretrovirus MLV and the lentivirus HIV-1. We will discuss how host factors of the integration site selection of retroviruses may steer the development of safer viral vectors for gene therapy. Next, we will discuss how altering the integration site preference of HIV-1 using small molecules could lead to a cure for HIV-1 infection.
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Affiliation(s)
| | | | | | - Zeger Debyser
- Molecular Virology and Gene Therapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
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3
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HIV-1 Preintegration Complex Preferentially Integrates the Viral DNA into Nucleosomes Containing Trimethylated Histone 3-Lysine 36 Modification and Flanking Linker DNA. J Virol 2022; 96:e0101122. [PMID: 36094316 PMCID: PMC9517705 DOI: 10.1128/jvi.01011-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
HIV-1 DNA is preferentially integrated into chromosomal hot spots by the preintegration complex (PIC). To understand the mechanism, we measured the DNA integration activity of PICs-extracted from infected cells-and intasomes, biochemically assembled PIC substructures using a number of relevant target substrates. We observed that PIC-mediated integration into human chromatin is preferred compared to genomic DNA. Surprisingly, nucleosomes lacking histone modifications were not preferred integration compared to the analogous naked DNA. Nucleosomes containing the trimethylated histone 3 lysine 36 (H3K36me3), an epigenetic mark linked to active transcription, significantly stimulated integration, but the levels remained lower than the naked DNA. Notably, H3K36me3-modified nucleosomes with linker DNA optimally supported integration mediated by the PIC but not by the intasome. Interestingly, optimal intasome-mediated integration required the cellular cofactor LEDGF. Unexpectedly, LEDGF minimally affected PIC-mediated integration into naked DNA but blocked integration into nucleosomes. The block for the PIC-mediated integration was significantly relieved by H3K36me3 modification. Mapping the integration sites in the preferred substrates revealed that specific features of the nucleosome-bound DNA are preferred for integration, whereas integration into naked DNA was random. Finally, biochemical and genetic studies demonstrate that DNA condensation by the H1 protein dramatically reduces integration, providing further evidence that features inherent to the open chromatin are preferred for HIV-1 integration. Collectively, these results identify the optimal target substrate for HIV-1 integration, report a mechanistic link between H3K36me3 and integration preference, and importantly, reveal distinct mechanisms utilized by the PIC for integration compared to the intasomes. IMPORTANCE HIV-1 infection is dependent on integration of the viral DNA into the host chromosomes. The preintegration complex (PIC) containing the viral DNA, the virally encoded integrase (IN) enzyme, and other viral/host factors carries out HIV-1 integration. HIV-1 integration is not dependent on the target DNA sequence, and yet the viral DNA is selectively inserted into specific "hot spots" of human chromosomes. A growing body of literature indicates that structural features of the human chromatin are important for integration targeting. However, the mechanisms that guide the PIC and enable insertion of the PIC-associated viral DNA into specific hot spots of the human chromosomes are not fully understood. In this study, we describe a biochemical mechanism for the preference of the HIV-1 DNA integration into open chromatin. Furthermore, our study defines a direct role for the histone epigenetic mark H3K36me3 in HIV-1 integration preference and identify an optimal substrate for HIV-1 PIC-mediated viral DNA integration.
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4
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Rocchi C, Gouet P, Parissi V, Fiorini F. The C-Terminal Domain of HIV-1 Integrase: A Swiss Army Knife for the Virus? Viruses 2022; 14:v14071397. [PMID: 35891378 PMCID: PMC9316232 DOI: 10.3390/v14071397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 12/31/2022] Open
Abstract
Retroviral integrase is a multimeric enzyme that catalyzes the integration of reverse-transcribed viral DNA into the cellular genome. Beyond integration, the Human immunodeficiency virus type 1 (HIV-1) integrase is also involved in many other steps of the viral life cycle, such as reverse transcription, nuclear import, virion morphogenesis and proviral transcription. All these additional functions seem to depend on the action of the integrase C-terminal domain (CTD) that works as a molecular hub, interacting with many different viral and cellular partners. In this review, we discuss structural issues concerning the CTD, with particular attention paid to its interaction with nucleic acids. We also provide a detailed map of post-translational modifications and interaction with molecular partners.
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Affiliation(s)
- Cecilia Rocchi
- Molecular Microbiology and Structural Biochemistry (MMSB), CNRS, University of Lyon 1, UMR 5086, 69367 Lyon, France; (C.R.); (P.G.)
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), 33076 Bordeaux, France;
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry (MMSB), CNRS, University of Lyon 1, UMR 5086, 69367 Lyon, France; (C.R.); (P.G.)
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), 33076 Bordeaux, France;
| | - Vincent Parissi
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), 33076 Bordeaux, France;
- Fundamental Microbiology and Pathogenicity (MFP), CNRS, University of Bordeaux, UMR5234, 33405 Bordeaux, France
| | - Francesca Fiorini
- Molecular Microbiology and Structural Biochemistry (MMSB), CNRS, University of Lyon 1, UMR 5086, 69367 Lyon, France; (C.R.); (P.G.)
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), 33076 Bordeaux, France;
- Correspondence: ; Tel.: +33-4-72722624; Fax: +33-4-72722616
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5
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Targeting the Nucleosome Acidic Patch by Viral Proteins: Two Birds with One Stone? mBio 2022; 13:e0173321. [PMID: 35343785 PMCID: PMC9040877 DOI: 10.1128/mbio.01733-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The past decade illuminated the H2A-H2B acidic patch as a cornerstone for both nucleosome recognition and chromatin structure regulation. Higher-order folding of chromatin arrays is mediated by interactions of histone H4 tail with an adjacent nucleosome acidic patch. Dynamic chromatin folding ensures a proper regulation of nuclear functions fundamental to cellular homeostasis. Many cellular factors have been shown to act on chromatin by tethering nucleosomes via an arginine anchor binding to the acidic patch. This tethering mechanism has also been described for several viral proteins. In this minireview, we will discuss the structural basis for acidic patch engagement by viral proteins and the implications during respective viral infections. We will also discuss a model in which acidic patch occupancy by these non-self viral proteins alters the local chromatin state by preventing H4 tail-mediated higher-order chromatin folding.
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6
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Lapaillerie D, Lelandais B, Mauro E, Lagadec F, Tumiotto C, Miskey C, Ferran G, Kuschner N, Calmels C, Métifiot M, Rooryck C, Ivics Z, Ruff M, Zimmer C, Lesbats P, Toutain J, Parissi V. Modulation of the intrinsic chromatin binding property of HIV-1 integrase by LEDGF/p75. Nucleic Acids Res 2021; 49:11241-11256. [PMID: 34634812 PMCID: PMC8565322 DOI: 10.1093/nar/gkab886] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 09/06/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
The stable insertion of the retroviral genome into the host chromosomes requires the association between integration complexes and cellular chromatin via the interaction between retroviral integrase and the nucleosomal target DNA. This final association may involve the chromatin-binding properties of both the retroviral integrase and its cellular cofactor LEDGF/p75. To investigate this and better understand the LEDGF/p75-mediated chromatin tethering of HIV-1 integrase, we used a combination of biochemical and chromosome-binding assays. Our study revealed that retroviral integrase has an intrinsic ability to bind and recognize specific chromatin regions in metaphase even in the absence of its cofactor. Furthermore, this integrase chromatin-binding property was modulated by the interaction with its cofactor LEDGF/p75, which redirected the enzyme to alternative chromosome regions. We also better determined the chromatin features recognized by each partner alone or within the functional intasome, as well as the chronology of efficient LEDGF/p75-mediated targeting of HIV-1 integrase to chromatin. Our data support a new chromatin-binding function of integrase acting in concert with LEDGF/p75 for the optimal association with the nucleosomal substrate. This work also provides additional information about the behavior of retroviral integration complexes in metaphase chromatin and the mechanism of action of LEDGF/p75 in this specific context.
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Affiliation(s)
- Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Benoît Lelandais
- Imaging and modeling unit, Computational Biology Department, Institut Pasteur, Paris, France
| | - Eric Mauro
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Floriane Lagadec
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Camille Tumiotto
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Csaba Miskey
- Paul-Ehrlich-Institute, division of medical biotechnology, Langen, Germany
| | | | | | - Christina Calmels
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Mathieu Métifiot
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | | | - Zoltan Ivics
- Paul-Ehrlich-Institute, division of medical biotechnology, Langen, Germany
| | - Marc Ruff
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie Structurale intégrative, UDS, U596 INSERM, UMR7104, CNRS, Strasbourg, France
| | - Christophe Zimmer
- Imaging and modeling unit, Computational Biology Department, Institut Pasteur, Paris, France
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
| | - Jérôme Toutain
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France
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7
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Svensson JP. Targeting Epigenetics to Cure HIV-1: Lessons From (and for) Cancer Treatment. Front Cell Infect Microbiol 2021; 11:668637. [PMID: 34026665 PMCID: PMC8137950 DOI: 10.3389/fcimb.2021.668637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/21/2021] [Indexed: 11/17/2022] Open
Abstract
The Human Immunodeficiency Virus type 1 (HIV-1) integrates in the host genome as a provirus resulting in a long-lived reservoir of infected CD4 cells. As a provirus, HIV-1 has several aspects in common with an oncogene. Both the HIV-1 provirus and oncogenes only cause disease when expressed. A successful cure of both cancer and HIV-1 includes elimination of all cells with potential to regenerate the disease. For over two decades, epigenetic drugs developed against cancer have been used in the HIV-1 field to modulate the state of the proviral chromatin. Cells with an intact HIV-1 provirus exist in three states of infection: productive, inducible latent, and non-inducible latent. Here focus is on HIV-1, transcription control and chromatin structure; how the inducible proviruses are maintained in a chromatin structure that allows reactivation of transcription; and how transcription switches between different stages to allow for an abundance of different transcripts from a single promoter. Recently it was shown that a functional cure of HIV can be achieved by encapsulating all intact HIV-1 proviruses in heterochromatin, giving hope that epigenetic interventions may be used to end the HIV-1 epidemic.
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Affiliation(s)
- J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet (KI), Huddinge, Sweden
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8
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Bedwell GJ, Engelman AN. Factors that mold the nuclear landscape of HIV-1 integration. Nucleic Acids Res 2021; 49:621-635. [PMID: 33337475 PMCID: PMC7826272 DOI: 10.1093/nar/gkaa1207] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 11/26/2020] [Indexed: 12/17/2022] Open
Abstract
The integration of retroviral reverse transcripts into the chromatin of the cells that they infect is required for virus replication. Retroviral integration has far-reaching consequences, from perpetuating deadly human diseases to molding metazoan evolution. The lentivirus human immunodeficiency virus 1 (HIV-1), which is the causative agent of the AIDS pandemic, efficiently infects interphase cells due to the active nuclear import of its preintegration complex (PIC). To enable integration, the PIC must navigate the densely-packed nuclear environment where the genome is organized into different chromatin states of varying accessibility in accordance with cellular needs. The HIV-1 capsid protein interacts with specific host factors to facilitate PIC nuclear import, while additional interactions of viral integrase, the enzyme responsible for viral DNA integration, with cellular nuclear proteins and nucleobases guide integration to specific chromosomal sites. HIV-1 integration favors transcriptionally active chromatin such as speckle-associated domains and disfavors heterochromatin including lamina-associated domains. In this review, we describe virus-host interactions that facilitate HIV-1 PIC nuclear import and integration site targeting, highlighting commonalities among factors that participate in both of these steps. We moreover discuss how the nuclear landscape influences HIV-1 integration site selection as well as the establishment of active versus latent virus infection.
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Affiliation(s)
- Gregory J Bedwell
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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9
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Vansant G, Chen HC, Zorita E, Trejbalová K, Miklík D, Filion G, Debyser Z. The chromatin landscape at the HIV-1 provirus integration site determines viral expression. Nucleic Acids Res 2020; 48:7801-7817. [PMID: 32597987 PMCID: PMC7641320 DOI: 10.1093/nar/gkaa536] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/07/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
HIV-1 persists lifelong in memory cells of the immune system as latent provirus that rebounds upon treatment interruption. Therefore, the latent reservoir is the main target for an HIV cure. Here, we studied the direct link between integration site and transcription using LEDGINs and Barcoded HIV-ensembles (B-HIVE). LEDGINs are antivirals that inhibit the interaction between HIV-1 integrase and the chromatin-tethering factor LEDGF/p75. They were used as a tool to retarget integration, while the effect on HIV expression was measured with B-HIVE. B-HIVE tracks insert-specific HIV expression by tagging a unique barcode in the HIV genome. We confirmed that LEDGINs retarget integration out of gene-dense and actively transcribed regions. The distance to H3K36me3, the marker recognized by LEDGF/p75, clearly increased. LEDGIN treatment reduced viral RNA expression and increased the proportion of silent provirus. Finally, silent proviruses obtained after LEDGIN treatment were located further away from epigenetic marks associated with active transcription. Interestingly, proximity to enhancers stimulated transcription irrespective of LEDGIN treatment, while the distance to H3K36me3 only changed after treatment with LEDGINs. The fact that proximity to these markers are associated with RNA expression support the direct link between provirus integration site and viral expression.
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Affiliation(s)
- Gerlinde Vansant
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Flanders, Belgium
| | - Heng-Chang Chen
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalunya, Spain
| | - Eduard Zorita
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalunya, Spain
| | - Katerina Trejbalová
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska, Prague, Czech Republic
| | - Dalibor Miklík
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska, Prague, Czech Republic
| | - Guillaume Filion
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalunya, Spain.,University Pompeu Fabra, Barcelona, Catalunya, Spain
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Flanders, Belgium
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10
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Mauro E, Lesbats P, Lapaillerie D, Chaignepain S, Maillot B, Oladosu O, Robert X, Fiorini F, Kieffer B, Bouaziz S, Gouet P, Ruff M, Parissi V. Human H4 tail stimulates HIV-1 integration through binding to the carboxy-terminal domain of integrase. Nucleic Acids Res 2019; 47:3607-3618. [PMID: 30767014 PMCID: PMC6468294 DOI: 10.1093/nar/gkz091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/28/2019] [Accepted: 02/04/2019] [Indexed: 12/22/2022] Open
Abstract
The integration of the retroviral genome into the chromatin of the infected cell is catalysed by the integrase (IN)•viral DNA complex (intasome). This process requires functional association between the integration complex and the nucleosomes. Direct intasome/histone contacts have been reported to modulate the interaction between the integration complex and the target DNA (tDNA). Both prototype foamy virus (PFV) and HIV-1 integrases can directly bind histone amino-terminal tails. We have further investigated this final association by studying the effect of isolated histone tails on HIV-1 integration. We show here that the binding of HIV-1 IN to a peptide derived from the H4 tail strongly stimulates integration catalysis in vitro. This stimulation was not observed with peptide tails from other variants or with alpha-retroviral (RAV) and spuma-retroviral PFV integrases. Biochemical analyses show that the peptide tail induces both an increase in the IN oligomerization state and affinity for the target DNA, which are associated with substantial structural rearrangements in the IN carboxy-terminal domain (CTD) observed by NMR. Our data indicate that the H4 peptide tail promotes the formation of active strand transfer complexes (STCs) and support an activation step of the incoming intasome at the contact of the histone tail.
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Affiliation(s)
- Eric Mauro
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - Stephane Chaignepain
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,Université de Bordeaux, UMR CNRS 5248 CBMN (Chimie Biologie des Membranes et Nanoobjets), 33076 Bordeaux, France
| | - Benoit Maillot
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Strasbourg, France
| | - Oyindamola Oladosu
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Strasbourg, France
| | - Xavier Robert
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France
| | - Francesca Fiorini
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France
| | - Bruno Kieffer
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Strasbourg, France
| | - Serge Bouaziz
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,CiTCoM, CNRS, UMR 8038, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Patrice Gouet
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France
| | - Marc Ruff
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Strasbourg, France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
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11
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Structural Insights on Retroviral DNA Integration: Learning from Foamy Viruses. Viruses 2019; 11:v11090770. [PMID: 31443391 PMCID: PMC6784120 DOI: 10.3390/v11090770] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/28/2022] Open
Abstract
Foamy viruses (FV) are retroviruses belonging to the Spumaretrovirinae subfamily. They are non-pathogenic viruses endemic in several mammalian hosts like non-human primates, felines, bovines, and equines. Retroviral DNA integration is a mandatory step and constitutes a prime target for antiretroviral therapy. This activity, conserved among retroviruses and long terminal repeat (LTR) retrotransposons, involves a viral nucleoprotein complex called intasome. In the last decade, a plethora of structural insights on retroviral DNA integration arose from the study of FV. Here, we review the biochemistry and the structural features of the FV integration apparatus and will also discuss the mechanism of action of strand transfer inhibitors.
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12
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Vansant G, Vranckx LS, Zurnic I, Van Looveren D, Van de Velde P, Nobles C, Gijsbers R, Christ F, Debyser Z. Impact of LEDGIN treatment during virus production on residual HIV-1 transcription. Retrovirology 2019; 16:8. [PMID: 30940165 PMCID: PMC6444612 DOI: 10.1186/s12977-019-0472-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/23/2019] [Indexed: 11/24/2022] Open
Abstract
Background Persistence of latent, replication-competent provirus is the main impediment towards the cure of HIV infection. One of the critical questions concerning HIV latency is the role of integration site selection in HIV expression. Inhibition of the interaction between HIV integrase and its chromatin tethering cofactor LEDGF/p75 is known to reduce integration and to retarget residual provirus to regions resistant to reactivation. LEDGINs, small molecule inhibitors of the interaction between HIV integrase and LEDGF/p75, provide an interesting tool to study the underlying mechanisms. During early infection, LEDGINs block the interaction with LEDGF/p75 and allosterically inhibit the catalytic activity of IN (i.e. the early effect). When present during virus production, LEDGINs interfere with proper maturation due to enhanced IN oligomerization in the progeny virions (i.e. the late effect). Results We studied the effect of LEDGINs present during virus production on the transcriptional state of the residual virus. Infection of cells with viruses produced in the presence of LEDGINs resulted in a residual reservoir that was refractory to activation. Integration of residual provirus was less favored near epigenetic markers associated with active transcription. However, integration near H3K36me3 and active genes, both targeted by LEDGF/p75, was not affected. Also in primary cells, LEDGIN treatment induced a reservoir resistant to activation due to a combined early and late effect. Conclusion LEDGINs present a research tool to study the link between integration and transcription, an essential question in retrovirology. LEDGIN treatment during virus production altered integration of residual provirus in a LEDGF/p75-independent manner, resulting in a reservoir that is refractory to activation. Electronic supplementary material The online version of this article (10.1186/s12977-019-0472-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gerlinde Vansant
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium
| | - Lenard S Vranckx
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium
| | - Irena Zurnic
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium
| | - Dominique Van Looveren
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Belgium
| | - Paulien Van de Velde
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium
| | - Christopher Nobles
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Rik Gijsbers
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Belgium
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Box 1023, 3000, Leuven, Flanders, Belgium.
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