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Krishnan A, Ali LM, Prabhu SG, Pillai VN, Chameettachal A, Vivet-Boudou V, Bernacchi S, Mustafa F, Marquet R, Rizvi TA. Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging. RNA (NEW YORK, N.Y.) 2023; 30:68-88. [PMID: 37914398 PMCID: PMC10726167 DOI: 10.1261/rna.079840.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023]
Abstract
The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous regions within the 5' end of the gRNA that assumes a higher order structure harboring several structural motifs. To better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ sequences using genetic, biochemical, and structure-function relationship approaches. Our mutational analysis revealed that the unpaired U85CUG88 stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput selective 2' hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences, with substitutions in the U85CUG88 stretch, revealed that these mutations had limited structural impact and maintained nucleotides 80-92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our data suggest that the single-stranded U85CUG88 sequence is important during FIV RNA packaging. Filter-binding assays performed using purified FIV Pr50Gag on WT and mutant U85CUG88 ψ RNAs led to reduced levels of Pr50Gag binding to mutant U85CUG88 ψ RNAs, indicating that the U85CUG88 stretch is crucial for ψ RNA-Pr50Gag interactions. Delineating sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of FIV-based vectors for human gene therapy.
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Affiliation(s)
- Anjana Krishnan
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Lizna M Ali
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Suresha G Prabhu
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Vineeta N Pillai
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Akhil Chameettachal
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67084 Strasbourg cedex, France
| | - Serena Bernacchi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67084 Strasbourg cedex, France
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Research Institute in Precision Medicine, Abu Dhabi, United Arab Emirates
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67084 Strasbourg cedex, France
| | - Tahir A Rizvi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Research Institute in Precision Medicine, Abu Dhabi, United Arab Emirates
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2
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Akkawi C, Feuillard J, Diaz FL, Belkhir K, Godefroy N, Peloponese JM, Mougel M, Laine S. Murine leukemia virus (MLV) P50 protein induces cell transformation via transcriptional regulatory function. Retrovirology 2023; 20:16. [PMID: 37700325 PMCID: PMC10496198 DOI: 10.1186/s12977-023-00631-w] [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: 04/10/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND The murine leukemia virus (MLV) has been a powerful model of pathogenesis for the discovery of genes involved in cancer. Its splice donor (SD')-associated retroelement (SDARE) is important for infectivity and tumorigenesis, but the mechanism remains poorly characterized. Here, we show for the first time that P50 protein, which is produced from SDARE, acts as an accessory protein that transregulates transcription and induces cell transformation. RESULTS By infecting cells with MLV particles containing SDARE transcript alone (lacking genomic RNA), we show that SDARE can spread to neighbouring cells as shown by the presence of P50 in infected cells. Furthermore, a role for P50 in cell transformation was demonstrated by CCK8, TUNEL and anchorage-independent growth assays. We identified the integrase domain of P50 as being responsible for transregulation of the MLV promoter using luciferase assay and RTqPCR with P50 deleted mutants. Transcriptomic analysis furthermore revealed that the expression of hundreds of cellular RNAs involved in cancerogenesis were deregulated in the presence of P50, suggesting that P50 induces carcinogenic processes via its transcriptional regulatory function. CONCLUSION We propose a novel SDARE-mediated mode of propagation of the P50 accessory protein in surrounding cells. Moreover, due to its transforming properties, P50 expression could lead to a cellular and tissue microenvironment that is conducive to cancer development.
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Affiliation(s)
- Charbel Akkawi
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Jerome Feuillard
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Felipe Leon Diaz
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France
| | - Khalid Belkhir
- ISEM, CNRS, EPHE, Université Montpellier, IRD, Montpellier, France
| | - Nelly Godefroy
- ISEM, CNRS, EPHE, Université Montpellier, IRD, Montpellier, France
| | | | - Marylene Mougel
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France.
| | - Sebastien Laine
- Team R2D2: Retroviral RNA Dynamics and Delivery, IRIM, UMR9004, CNRS, University of Montpellier, Montpellier, France.
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3
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Huang Y, Liao Z, Dang P, Queen S, Abreu CM, Gololobova O, Zheng L, Witwer KW. Longitudinal characterization of circulating extracellular vesicles and small RNA during simian immunodeficiency virus infection and antiretroviral therapy. AIDS 2023; 37:733-744. [PMID: 36779477 PMCID: PMC9994802 DOI: 10.1097/qad.0000000000003487] [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: 09/06/2022] [Accepted: 01/11/2023] [Indexed: 02/14/2023]
Abstract
OBJECTIVES Latent infection by HIV hinders viral eradication despite effective antiretroviral treatment (ART). Among proposed contributors to viral latency are cellular small RNAs that have also been proposed to shuttle between cells in extracellular vesicles. Thus, we profiled extracellular vesicle small RNAs during different infection phases to understand the potential relationship between these extracellular vesicle associated small RNAs and viral infection. DESIGN A well characterized simian immunodeficiency virus (SIV)/macaque model of HIV was used to profile extracellular vesicle enriched blood plasma fractions harvested during preinfection, acute infection, latent infection/ART treatment, and rebound after ART interruption. METHODS Measurement of extracellular vesicle concentration, size distribution, and morphology was complemented with qPCR array for small RNA expression, followed by individual qPCR validations. Iodixanol density gradients were used to separate extracellular vesicle subtypes and virions. RESULTS Plasma extracellular vesicle particle counts correlated with viral load and peaked during acute infection. However, SIV gag RNA detection showed that virions did not fully explain this peak. Extracellular vesicle microRNAs miR-181a, miR-342-3p, and miR-29a decreased with SIV infection and remained downregulated in latency. Interestingly, small nuclear RNA U6 had a tight association with viral load peak. CONCLUSION This study is the first to monitor how extracellular vesicle concentration and extracellular vesicle small RNA expression change dynamically in acute viral infection, latency, and rebound in a carefully controlled animal model. These changes may also reveal regulatory roles in retroviral infection and latency.
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Affiliation(s)
- Yiyao Huang
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhaohao Liao
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Phuong Dang
- College of Pharmacy, University of Texas, Houston, Texas, USA
| | - Suzanne Queen
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Celina Monteiro Abreu
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Olesia Gololobova
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Kenneth W. Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Neurology
- Richman Family Precision Medicine Center of Excellence in Alzheimer's Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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4
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Chameettachal A, Mustafa F, Rizvi TA. Understanding Retroviral Life Cycle and its Genomic RNA Packaging. J Mol Biol 2023; 435:167924. [PMID: 36535429 DOI: 10.1016/j.jmb.2022.167924] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Members of the family Retroviridae are important animal and human pathogens. Being obligate parasites, their replication involves a series of steps during which the virus hijacks the cellular machinery. Additionally, many of the steps of retrovirus replication are unique among viruses, including reverse transcription, integration, and specific packaging of their genomic RNA (gRNA) as a dimer. Progress in retrovirology has helped identify several molecular mechanisms involved in each of these steps, but many are still unknown or remain controversial. This review summarizes our present understanding of the molecular mechanisms involved in various stages of retrovirus replication. Furthermore, it provides a comprehensive analysis of our current understanding of how different retroviruses package their gRNA into the assembling virions. RNA packaging in retroviruses holds a special interest because of the uniqueness of packaging a dimeric genome. Dimerization and packaging are highly regulated and interlinked events, critical for the virus to decide whether its unspliced RNA will be packaged as a "genome" or translated into proteins. Finally, some of the outstanding areas of exploration in the field of RNA packaging are highlighted, such as the role of epitranscriptomics, heterogeneity of transcript start sites, and the necessity of functional polyA sequences. An in-depth knowledge of mechanisms that interplay between viral and cellular factors during virus replication is critical in understanding not only the virus life cycle, but also its pathogenesis, and development of new antiretroviral compounds, vaccines, as well as retroviral-based vectors for human gene therapy.
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Affiliation(s)
- Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates. https://twitter.com/chameettachal
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University, Al Ain, United Arab Emirates; Zayed bin Sultan Center for Health Sciences (ZCHS), United Arab Emirates University, Al Ain, United Arab Emirates.
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5
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Lei X, Gonçalves-Carneiro D, Zang TM, Bieniasz PD. Initiation of HIV-1 Gag lattice assembly is required for recognition of the viral genome packaging signal. eLife 2023; 12:e83548. [PMID: 36688533 PMCID: PMC9908077 DOI: 10.7554/elife.83548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
The encapsidation of HIV-1 gRNA into virions is enabled by the binding of the nucleocapsid (NC) domain of the HIV-1 Gag polyprotein to the structured viral RNA packaging signal (Ψ) at the 5' end of the viral genome. However, the subcellular location and oligomeric status of Gag during the initial Gag-Ψ encounter remain uncertain. Domains other than NC, such as capsid (CA), may therefore indirectly affect RNA recognition. To investigate the contribution of Gag domains to Ψ recognition in a cellular environment, we performed protein-protein crosslinking and protein-RNA crosslinking immunoprecipitation coupled with sequencing (CLIP-seq) experiments. We demonstrate that NC alone does not bind specifically to Ψ in living cells, whereas full-length Gag and a CANC subdomain bind to Ψ with high specificity. Perturbation of the Ψ RNA structure or NC zinc fingers affected CANC:Ψ binding specificity. Notably, CANC variants with substitutions that disrupt CA:CA dimer, trimer, or hexamer interfaces in the immature Gag lattice also affected RNA binding, and mutants that were unable to assemble a nascent Gag lattice were unable to specifically bind to Ψ. Artificially multimerized NC domains did not specifically bind Ψ. CA variants with substitutions in inositol phosphate coordinating residues that prevent CA hexamerization were also deficient in Ψ binding and second-site revertant mutants that restored CA assembly also restored specific binding to Ψ. Overall, these data indicate that the correct assembly of a nascent immature CA lattice is required for the specific interaction between Gag and Ψ in cells.
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Affiliation(s)
- Xiao Lei
- Laboratory of Retrovirology, Rockefeller UniversityNew YorkUnited States
| | | | - Trinity M Zang
- Laboratory of Retrovirology, Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute, The Rockefeller UniversityNew York, New YorkUnited States
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute, The Rockefeller UniversityNew York, New YorkUnited States
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6
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HIV UTR, LTR, and Epigenetic Immunity. Viruses 2022; 14:v14051084. [PMID: 35632825 PMCID: PMC9146425 DOI: 10.3390/v14051084] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/05/2022] [Accepted: 05/13/2022] [Indexed: 02/06/2023] Open
Abstract
The duel between humans and viruses is unending. In this review, we examine the HIV RNA in the form of un-translated terminal region (UTR), the viral DNA in the form of long terminal repeat (LTR), and the immunity of human DNA in a format of epigenetic regulation. We explore the ways in which the human immune responses to invading pathogenic viral nucleic acids can inhibit HIV infection, exemplified by a chromatin vaccine (cVaccine) to elicit the immunity of our genome—epigenetic immunity towards a cure.
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7
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Moonmuang S, Maniratanachote R, Chetprayoon P, Sornsuwan K, Thongkum W, Chupradit K, Tayapiwatana C. Specific Interaction of DARPin with HIV-1 CA NTD Disturbs the Distribution of Gag, RNA Packaging, and Tetraspanin Remodelling in the Membrane. Viruses 2022; 14:v14040824. [PMID: 35458554 PMCID: PMC9025900 DOI: 10.3390/v14040824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022] Open
Abstract
A designed repeat scaffold protein (AnkGAG1D4) recognizing the human immunodeficiency virus-1 (HIV-1) capsid (CA) was formerly established with antiviral assembly. Here, we investigated the molecular mechanism of AnkGAG1D4 function during the late stages of the HIV-1 replication cycle. By applying stimulated emission-depletion (STED) microscopy, Gag polymerisation was interrupted at the plasma membrane. Disturbance of Gag polymerisation triggered Gag accumulation inside producer cells and trapping of the CD81 tetraspanin on the plasma membrane. Moreover, reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) experiments were performed to validate the packaging efficiency of RNAs. Our results advocated that AnkGAG1D4 interfered with the Gag precursor protein from selecting HIV-1 and cellular RNAs for encapsidation into viral particles. These findings convey additional information on the antiviral activity of AnkGAG1D4 at late stages of the HIV-1 life cycle, which is potential for an alternative anti-HIV molecule.
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Affiliation(s)
- Sutpirat Moonmuang
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Department of Medical Technology, Division of Clinical Immunology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Rawiwan Maniratanachote
- Toxicology and Bio Evaluation Service Center (TBES), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (R.M.); (P.C.)
| | - Paninee Chetprayoon
- Toxicology and Bio Evaluation Service Center (TBES), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (R.M.); (P.C.)
| | - Kanokporn Sornsuwan
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
| | - Weeraya Thongkum
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Koollawat Chupradit
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Siriraj Center for Regenerative Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chatchai Tayapiwatana
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Department of Medical Technology, Division of Clinical Immunology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence:
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8
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Abstract
Genetically-characterizing full-length HIV-1 RNA is critical for identifying genetically-intact genomes and for comparing these RNA genomes to proviral DNA. We have developed a method for sequencing plasma-derived RNA using long-range sequencing (PRLS assay; ∼8.3 kb from gag to the 3′ end or ∼5 kb from integrase to the 3′ end). We employed the gag-3′ PRLS assay to sequence HIV-1 RNA genomes from ART-naive participants during acute/early infection (n = 6) or chronic infection (n = 2). On average, only 65% of plasma-derived genomes were genetically-intact. Defects were found in all genomic regions but were concentrated in env and pol. We compared these genomes to near-full-length proviral sequences from paired peripheral blood mononuclear cell (PBMC) samples for the acute/early group and found that near-identical (>99.98% identical) sequences were identified only during acute infection. For three participants who initiated therapy during acute infection, we used the int-3′ PRLS assay to sequence plasma-derived genomes from an analytical treatment interruption and identified 100% identical genomes between pretherapy and rebound time points. The PRLS assay provides a new level of sensitivity for understanding the genetic composition of plasma-derived HIV-1 RNA from viremic individuals either pretherapy or after treatment interruption, which will be invaluable in assessing possible HIV-1 curative strategies. IMPORTANCE We developed novel plasma-derived RNA using long-range sequencing assays (PRLS assay; 8.3 kb, gag-3′, and 5.0 kb, int-3′). Employing the gag-3′ PRLS assay, we found that 26% to 51% of plasma-derived genomes are genetically-defective, largely as a result of frameshift mutations and deletions. These genetic defects were concentrated in the env region compared to gag and pol, likely a reflection of viral immune escape in env during untreated HIV-1 infection. Employing the int-3′ PRLS assay, we found that analytical treatment interruption (ATI) plasma-derived sequences were identical and genetically-intact. Several sequences from the ATI plasma samples were identical to viral sequences from pretherapy plasma and PBMC samples, indicating that HIV-1 reservoirs established prior to therapy contribute to viral rebound during an ATI. Therefore, near-full-length sequencing of HIV-1 particles is required to gain an accurate picture of the genetic landscape of plasma HIV-1 virions in studies of HIV-1 replication and persistence.
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9
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Pereira-Montecinos C, Toro-Ascuy D, Ananías-Sáez C, Gaete-Argel A, Rojas-Fuentes C, Riquelme-Barrios S, Rojas-Araya B, García-de-Gracia F, Aguilera-Cortés P, Chnaiderman J, Acevedo ML, Valiente-Echeverría F, Soto-Rifo R. Epitranscriptomic regulation of HIV-1 full-length RNA packaging. Nucleic Acids Res 2022; 50:2302-2318. [PMID: 35137199 PMCID: PMC8887480 DOI: 10.1093/nar/gkac062] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 12/27/2022] Open
Abstract
During retroviral replication, the full-length RNA serves both as mRNA and genomic RNA. However, the mechanisms by which the HIV-1 Gag protein selects the two RNA molecules that will be packaged into nascent virions remain poorly understood. Here, we demonstrate that deposition of N6-methyladenosine (m6A) regulates full-length RNA packaging. While m6A deposition by METTL3/METTL14 onto the full-length RNA was associated with increased Gag synthesis and reduced packaging, FTO-mediated demethylation promoted the incorporation of the full-length RNA into viral particles. Interestingly, HIV-1 Gag associates with the RNA demethylase FTO in the nucleus and contributes to full-length RNA demethylation. We further identified two highly conserved adenosines within the 5'-UTR that have a crucial functional role in m6A methylation and packaging of the full-length RNA. Together, our data propose a novel epitranscriptomic mechanism allowing the selection of the HIV-1 full-length RNA molecules that will be used as viral genomes.
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Affiliation(s)
- Camila Pereira-Montecinos
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Daniela Toro-Ascuy
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Catarina Ananías-Sáez
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aracelly Gaete-Argel
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Cecilia Rojas-Fuentes
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Sebastián Riquelme-Barrios
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Bárbara Rojas-Araya
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Francisco García-de-Gracia
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Paulina Aguilera-Cortés
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Jonás Chnaiderman
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Mónica L Acevedo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup (CHAIR), Faculty of Medicine, Universidad de Chile, Santiago, Chile
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10
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Durand S, Seigneuret F, Burlaud-Gaillard J, Lemoine R, Tassi MF, Moreau A, Mougel M, Roingeard P, Tauber C, de Rocquigny H. Quantitative analysis of the formation of nucleoprotein complexes between HIV-1 Gag protein and genomic RNA using transmission electron microscopy. J Biol Chem 2022; 298:101500. [PMID: 34929171 PMCID: PMC8760521 DOI: 10.1016/j.jbc.2021.101500] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 01/06/2023] Open
Abstract
In HIV, the polyprotein precursor Gag orchestrates the formation of the viral capsid. In the current view of this viral assembly, Gag forms low-order oligomers that bind to the viral genomic RNA triggering the formation of high-ordered ribonucleoprotein complexes. However, this assembly model was established using biochemical or imaging methods that do not describe the cellular location hosting Gag-gRNA complex nor distinguish gRNA packaging in single particles. Here, we studied the intracellular localization of these complexes by electron microscopy and monitored the distances between the two partners by morphometric analysis of gold beads specifically labeling Gag and gRNA. We found that formation of these viral clusters occurred shortly after the nuclear export of the gRNA. During their transport to the plasma membrane, the distance between Gag and gRNA decreases together with an increase of gRNA packaging. Point mutations in the zinc finger patterns of the nucleocapsid domain of Gag caused an increase in the distance between Gag and gRNA as well as a sharp decrease of gRNA packaged into virions. Finally, we show that removal of stem loop 1 of the 5'-untranslated region does not interfere with gRNA packaging, whereas combined with the removal of stem loop 3 is sufficient to decrease but not abolish Gag-gRNA cluster formation and gRNA packaging. In conclusion, this morphometric analysis of Gag-gRNA cluster formation sheds new light on HIV-1 assembly that can be used to describe at nanoscale resolution other viral assembly steps involving RNA or protein-protein interactions.
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Affiliation(s)
- Stéphanie Durand
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Florian Seigneuret
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Julien Burlaud-Gaillard
- Microscopy IBiSA Platform, PPF ASB, University of Tours and CHRU of Tours, Tours Cedex 1, France
| | - Roxane Lemoine
- B Cell Ressources Platform, EA4245 "Transplantation, Immunology and Inflammation", University of Tours, Tours Cedex 1, France
| | - Marc-Florent Tassi
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Alain Moreau
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France
| | - Marylène Mougel
- Équipe R2D2 Retroviral RNA Dynamics and Delivery, IRIM, CNRS UMR9004, University of Montpellier, Montpellier, France
| | - Philippe Roingeard
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France; Microscopy IBiSA Platform, PPF ASB, University of Tours and CHRU of Tours, Tours Cedex 1, France
| | - Clovis Tauber
- UMR U1253 iBrain, Inserm, University of Tours, Tours Cedex 1, France
| | - Hugues de Rocquigny
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, Inserm - U1259 MAVIVH, Bretonneau Hospital, Tours Cedex 1, France.
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11
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Selective packaging of HIV-1 RNA genome is guided by the stability of 5' untranslated region polyA stem. Proc Natl Acad Sci U S A 2021; 118:2114494118. [PMID: 34873042 DOI: 10.1073/pnas.2114494118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2021] [Indexed: 01/08/2023] Open
Abstract
To generate infectious virus, HIV-1 must package two copies of its full-length RNA into particles. HIV-1 transcription initiates from multiple, neighboring sites, generating RNA species that only differ by a few nucleotides at the 5' end, including those with one (1G) or three (3G) 5' guanosines. Strikingly, 1G RNA is preferentially packaged into virions over 3G RNA. We investigated how HIV-1 distinguishes between these nearly identical RNAs using in-gel chemical probing combined with recently developed computational tools for determining RNA conformational ensembles, as well as cell-based assays to quantify the efficiency of RNA packaging into viral particles. We found that 1G and 3G RNAs fold into distinct structural ensembles. The 1G RNA, but not the 3G RNA, primarily adopts conformations with an intact polyA stem, exposed dimerization initiation site, and multiple, unpaired guanosines known to mediate Gag binding. Furthermore, we identified mutants that exhibited altered genome selectivity and packaged 3G RNA efficiently. In these mutants, both 1G and 3G RNAs fold into similar conformational ensembles, such that they can no longer be distinguished. Our findings demonstrate that polyA stem stability guides RNA-packaging selectivity. These studies also uncover the mechanism by which HIV-1 selects its genome for packaging: 1G RNA is preferentially packaged because it exposes structural elements that promote RNA dimerization and Gag binding.
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12
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A Stretch of Unpaired Purines in the Leader Region of Simian Immunodeficiency Virus (SIV) Genomic RNA is Critical for its Packaging into Virions. J Mol Biol 2021; 433:167293. [PMID: 34624298 DOI: 10.1016/j.jmb.2021.167293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 11/22/2022]
Abstract
Simian immunodeficiency virus (SIV) is an important lentivirus used as a non-human primate model to study HIV replication, and pathogenesis of human AIDS, as well as a potential vector for human gene therapy. This study investigated the role of single-stranded purines (ssPurines) as potential genomic RNA (gRNA) packaging determinants in SIV replication. Similar ssPurines have been implicated as important motifs for gRNA packaging in many retroviruses like, HIV-1, MPMV, and MMTV by serving as Gag binding sites during virion assembly. In examining the secondary structure of the SIV 5' leader region, as recently deduced using SHAPE methodology, we identified four specific stretches of ssPurines (I-IV) in the region that harbors major packaging determinants of SIV. The significance of these ssPurine motifs were investigated by mutational analysis coupled with a biologically relevant single round of replication assay. These analyses revealed that while ssPurine II was essential, the others (ssPurines I, III, & IV) did not significantly contribute to SIV gRNA packaging. Any mutation in the ssPurine II, such as its deletion or substitution, or other mutations that caused base pairing of ssPurine II loop resulted in near abrogation of RNA packaging, further substantiating the crucial role of ssPurine II and its looped conformation in SIV gRNA packaging. Structure prediction analysis of these mutants further corroborated the biological results and further revealed that the unpaired nature of ssPurine II is critical for its function during SIV RNA packaging perhaps by enabling it to function as a specific binding site for SIV Gag.
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13
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5'-Cap sequestration is an essential determinant of HIV-1 genome packaging. Proc Natl Acad Sci U S A 2021; 118:2112475118. [PMID: 34493679 PMCID: PMC8449379 DOI: 10.1073/pnas.2112475118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/05/2021] [Indexed: 12/14/2022] Open
Abstract
HIV-1 selectively packages two copies of its 5'-capped RNA genome (gRNA) during virus assembly, a process mediated by the nucleocapsid (NC) domain of the viral Gag polyprotein and encapsidation signals located within the dimeric 5' leader of the viral RNA. Although residues within the leader that promote packaging have been identified, the determinants of authentic packaging fidelity and efficiency remain unknown. Here, we show that a previously characterized 159-nt region of the leader that possesses all elements required for RNA dimerization, high-affinity NC binding, and packaging in a noncompetitive RNA packaging assay (ΨCES) is unexpectedly poorly packaged when assayed in competition with the intact 5' leader. ΨCES lacks a 5'-tandem hairpin element that sequesters the 5' cap, suggesting that cap sequestration may be important for packaging. Consistent with this hypothesis, mutations within the intact leader that expose the cap without disrupting RNA structure or NC binding abrogated RNA packaging, and genetic addition of a 5' ribozyme to ΨCES to enable cotranscriptional shedding of the 5' cap promoted ΨCES-mediated RNA packaging to wild-type levels. Additional mutations that either block dimerization or eliminate subsets of NC binding sites substantially attenuated competitive packaging. Our studies indicate that packaging is achieved by a bipartite mechanism that requires both sequestration of the 5' cap and exposure of NC binding sites that reside fully within the ΨCES region of the dimeric leader. We speculate that cap sequestration prevents irreversible capture by the cellular RNA processing and translation machinery, a mechanism likely employed by other viruses that package 5'-capped RNA genomes.
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14
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Faoro C, Ataide SF. Noncanonical Functions and Cellular Dynamics of the Mammalian Signal Recognition Particle Components. Front Mol Biosci 2021; 8:679584. [PMID: 34113652 PMCID: PMC8185352 DOI: 10.3389/fmolb.2021.679584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/29/2021] [Indexed: 12/24/2022] Open
Abstract
The signal recognition particle (SRP) is a ribonucleoprotein complex fundamental for co-translational delivery of proteins to their proper membrane localization and secretory pathways. Literature of the past two decades has suggested new roles for individual SRP components, 7SL RNA and proteins SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72, outside the SRP cycle. These noncanonical functions interconnect SRP with a multitude of cellular and molecular pathways, including virus-host interactions, stress response, transcriptional regulation and modulation of apoptosis in autoimmune diseases. Uncovered novel properties of the SRP components present a new perspective for the mammalian SRP as a biological modulator of multiple cellular processes. As a consequence of these findings, SRP components have been correlated with a growing list of diseases, such as cancer progression, myopathies and bone marrow genetic diseases, suggesting a potential for development of SRP-target therapies of each individual component. For the first time, here we present the current knowledge on the SRP noncanonical functions and raise the need of a deeper understanding of the molecular interactions between SRP and accessory cellular components. We examine diseases associated with SRP components and discuss the development and feasibility of therapeutics targeting individual SRP noncanonical functions.
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Affiliation(s)
- Camilla Faoro
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Sandro F Ataide
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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15
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Chameettachal A, Vivet-Boudou V, Pitchai F, Pillai V, Ali L, Krishnan A, Bernacchi S, Mustafa F, Marquet R, Rizvi T. A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag. Nucleic Acids Res 2021; 49:4668-4688. [PMID: 33836091 PMCID: PMC8096270 DOI: 10.1093/nar/gkab223] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 12/22/2022] Open
Abstract
Retroviral RNA genome (gRNA) harbors cis-acting sequences that facilitate its specific packaging from a pool of other viral and cellular RNAs by binding with high-affinity to the viral Gag protein during virus assembly. However, the molecular intricacies involved during selective gRNA packaging are poorly understood. Binding and footprinting assays on mouse mammary tumor virus (MMTV) gRNA with purified Pr77Gag along with in cell gRNA packaging study identified two Pr77Gag binding sites constituting critical, non-redundant packaging signals. These included: a purine loop in a bifurcated stem-loop containing the gRNA dimerization initiation site, and the primer binding site (PBS). Despite these sites being present on both unspliced and spliced RNAs, Pr77Gag specifically bound to unspliced RNA, since only that could adopt the native bifurcated stem-loop structure containing looped purines. These results map minimum structural elements required to initiate MMTV gRNA packaging, distinguishing features that are conserved amongst divergent retroviruses from those perhaps unique to MMTV. Unlike purine-rich motifs frequently associated with packaging signals, direct involvement of PBS in gRNA packaging has not been documented in retroviruses. These results enhance our understanding of retroviral gRNA packaging/assembly, making it not only a target for novel therapeutic interventions, but also development of safer gene therapy vectors.
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Affiliation(s)
- Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Fathima Nuzra Nagoor Pitchai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Vineeta N Pillai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Lizna Mohamed Ali
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Anjana Krishnan
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Serena Bernacchi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, United Arab Emirates
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Strasbourg, France
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences (CMHS), United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, United Arab Emirates
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16
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Ali LM, Pitchai FNN, Vivet-Boudou V, Chameettachal A, Jabeen A, Pillai VN, Mustafa F, Marquet R, Rizvi TA. Role of Purine-Rich Regions in Mason-Pfizer Monkey Virus (MPMV) Genomic RNA Packaging and Propagation. Front Microbiol 2020; 11:595410. [PMID: 33250884 PMCID: PMC7674771 DOI: 10.3389/fmicb.2020.595410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
A distinguishing feature of the Mason-Pfizer monkey virus (MPMV) packaging signal RNA secondary structure is a single-stranded purine-rich sequence (ssPurines) in close vicinity to a palindromic stem loop (Pal SL) that functions as MPMV dimerization initiation site (DIS). However, unlike other retroviruses, MPMV contains a partially base-paired repeat sequence of ssPurines (bpPurines) in the adjacent region. Both purine-rich sequences have earlier been proposed to act as potentially redundant Gag binding sites to initiate the process of MPMV genomic RNA (gRNA) packaging. The objective of this study was to investigate the biological significance of ssPurines and bpPurines in MPMV gRNA packaging by systematic mutational and biochemical probing analyses. Deletion of either ssPurines or bpPurines individually had no significant effect on MPMV gRNA packaging, but it was severely compromised when both sequences were deleted simultaneously. Selective 2′ hydroxyl acylation analyzed by primer extension (SHAPE) analysis of the mutant RNAs revealed only mild effects on structure by deletion of either ssPurines or bpPurines, while the structure was dramatically affected by the two simultaneous deletions. This suggests that ssPurines and bpPurines play a redundant role in MPMV gRNA packaging, probably as Gag binding sites to facilitate gRNA capture and encapsidation. Interestingly, the deletion of bpPurines revealed an additional severe defect on RNA propagation that was independent of the presence or absence of ssPurines or the gRNA structure of the region. These findings further suggest that the bpPurines play an additional role in the early steps of MPMV replication cycle that is yet to be identified.
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Affiliation(s)
- Lizna Mohamed Ali
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Fathima Nuzra Nagoor Pitchai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Valérie Vivet-Boudou
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ayesha Jabeen
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Vineeta N Pillai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Roland Marquet
- Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS, Université de Strasbourg, Strasbourg, France
| | - Tahir A Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.,Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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17
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Chen S, Xu J, Liu M, Rao ALN, Zandi R, Gill SS, Mohideen U. Investigation of HIV-1 Gag binding with RNAs and lipids using Atomic Force Microscopy. PLoS One 2020; 15:e0228036. [PMID: 32015565 PMCID: PMC6996966 DOI: 10.1371/journal.pone.0228036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/06/2020] [Indexed: 11/22/2022] Open
Abstract
Atomic Force Microscopy was utilized to study the morphology of Gag, ΨRNA, and their binding complexes with lipids in a solution environment with 0.1Å vertical and 1nm lateral resolution. TARpolyA RNA was used as a RNA control. The lipid used was phospha-tidylinositol-(4,5)-bisphosphate (PI(4,5)P2). The morphology of specific complexes Gag-ΨRNA, Gag-TARpolyA RNA, Gag-PI(4,5)P2 and PI(4,5)P2-ΨRNA-Gag were studied. They were imaged on either positively or negatively charged mica substrates depending on the net charges carried. Gag and its complexes consist of monomers, dimers and tetramers, which was confirmed by gel electrophoresis. The addition of specific ΨRNA to Gag is found to increase Gag multimerization. Non-specific TARpolyA RNA was found not to lead to an increase in Gag multimerization. The addition PI(4,5)P2 to Gag increases Gag multimerization, but to a lesser extent than ΨRNA. When both ΨRNA and PI(4,5)P2 are present Gag undergoes comformational changes and an even higher degree of multimerization.
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Affiliation(s)
- Shaolong Chen
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Jun Xu
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Mingyue Liu
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - A. L. N. Rao
- Department of Plant Pathology & Microbiology, University of California, Riverside, California, United States of America
| | - Roya Zandi
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
| | - Sarjeet S. Gill
- Department of Cell Biology & Neuroscience, University of California, Riverside, California, United States of America
| | - Umar Mohideen
- Department of Physics & Astronomy, University of California, Riverside, California, United States of America
- * E-mail:
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18
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Purification and Functional Characterization of a Biologically Active Full-Length Feline Immunodeficiency Virus (FIV) Pr50 Gag. Viruses 2019; 11:v11080689. [PMID: 31357656 PMCID: PMC6723490 DOI: 10.3390/v11080689] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 01/01/2023] Open
Abstract
The feline immunodeficiency virus (FIV) full-length Pr50Gag precursor is a key player in the assembly of new viral particles. It is also a critical component of the efficient selection and packaging of two copies of genomic RNA (gRNA) into the newly formed virus particles from a wide pool of cellular and spliced viral RNA. To understand the molecular mechanisms involved during FIV gRNA packaging, we expressed the His6-tagged and untagged recombinant FIV Pr50Gag protein both in eukaryotic and prokaryotic cells. The recombinant Pr50Gag-His6-tag fusion protein was purified from soluble fractions of prokaryotic cultures using immobilized metal affinity chromatography (IMAC). This purified protein was able to assemble in vitro into virus-like particles (VLPs), indicating that it preserved its ability to oligomerize/multimerize. Furthermore, VLPs formed in eukaryotic cells by the FIV full-length Pr50Gag both in the presence and absence of His6-tag could package FIV sub-genomic RNA to similar levels, suggesting that the biological activity of the recombinant full-length Pr50Gag fusion protein was retained in the presence of His6-tag at the carboxy terminus. Successful expression and purification of a biologically active, recombinant full-length Pr50Gag-His6-tag fusion protein will allow study of the intricate RNA-protein interactions involved during FIV gRNA encapsidation.
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19
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Pitchai FNN, Ali L, Pillai VN, Chameettachal A, Ashraf SS, Mustafa F, Marquet R, Rizvi TA. Expression, purification, and characterization of biologically active full-length Mason-Pfizer monkey virus (MPMV) Pr78 Gag. Sci Rep 2018; 8:11793. [PMID: 30087395 PMCID: PMC6081465 DOI: 10.1038/s41598-018-30142-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
MPMV precursor polypeptide Pr78Gag orchestrates assembly and packaging of genomic RNA (gRNA) into virus particles. Therefore, we have expressed recombinant full-length Pr78Gag either with or without His6-tag in bacterial as well as eukaryotic cultures and purified the recombinant protein from soluble fractions of the bacterial cultures. The recombinant Pr78Gag protein has the intrinsic ability to assemble in vitro to form virus like particles (VLPs). Consistent with this observation, the recombinant protein could form VLPs in both prokaryotes and eukaryotes. VLPs formed in eukaryotic cells by recombinant Pr78Gag with or without His6-tag can encapsidate MPMV transfer vector RNA, suggesting that the inclusion of the His6-tag to the full-length Pr78Gag did not interfere with its expression or biological function. This study demonstrates the expression and purification of a biologically active, recombinant Pr78Gag, which should pave the way to study RNA-protein interactions involved in the MPMV gRNA packaging process.
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Affiliation(s)
- Fathima Nuzra Nagoor Pitchai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Lizna Ali
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Vineeta Narayana Pillai
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Akhil Chameettachal
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Syed Salman Ashraf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Farah Mustafa
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR, 9002, Strasbourg, France.
| | - Tahir Aziz Rizvi
- Department of Microbiology & Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.
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20
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Dubois N, Khoo KK, Ghossein S, Seissler T, Wolff P, McKinstry WJ, Mak J, Paillart JC, Marquet R, Bernacchi S. The C-terminal p6 domain of the HIV-1 Pr55 Gag precursor is required for specific binding to the genomic RNA. RNA Biol 2018; 15:923-936. [PMID: 29954247 DOI: 10.1080/15476286.2018.1481696] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The Pr55Gag precursor specifically selects the HIV-1 genomic RNA (gRNA) from a large excess of cellular and partially or fully spliced viral RNAs and drives the virus assembly at the plasma membrane. During these processes, the NC domain of Pr55Gag interacts with the gRNA, while its C-terminal p6 domain binds cellular and viral factors and orchestrates viral particle release. Gag∆p6 is a truncated form of Pr55Gag lacking the p6 domain usually used as a default surrogate for wild type Pr55Gag for in vitro analysis. With recent advance in production of full-length recombinant Pr55Gag, here, we tested whether the p6 domain also contributes to the RNA binding specificity of Pr55Gag by systematically comparing binding of Pr55Gag and Gag∆p6 to a panel of viral and cellular RNAs. Unexpectedly, our fluorescence data reveal that the p6 domain is absolutely required for specific binding of Pr55Gag to the HIV-1 gRNA. Its deletion resulted not only in a decreased affinity for gRNA, but also in an increased affinity for spliced viral and cellular RNAs. In contrast Gag∆p6 displayed a similar affinity for all tested RNAs. Removal of the C-terminal His-tag from Pr55Gag and Gag∆p6 uniformly increased the Kd values of the RNA-protein complexes by ~ 2.5 fold but did not affect the binding specificities of these proteins. Altogether, our results demonstrate a novel role of the p6 domain in the specificity of Pr55Gag-RNA interactions, and strongly suggest that the p6 domain contributes to the discrimination of HIV-1 gRNA from cellular and spliced viral mRNAs, which is necessary for its selective encapsidation.
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Affiliation(s)
- Noé Dubois
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
| | - Keith K Khoo
- b School of Medicine , Deakin University , Geelong , Australia.,c CSIRO Manufacturing , Parkville , Australia
| | - Shannon Ghossein
- b School of Medicine , Deakin University , Geelong , Australia.,c CSIRO Manufacturing , Parkville , Australia
| | - Tanja Seissler
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
| | - Philippe Wolff
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France.,d Plateforme protéomique Strasbourg-Esplanade, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
| | | | - Johnson Mak
- b School of Medicine , Deakin University , Geelong , Australia.,e Institute for Glycomics, Griffith University , Southport , Australia
| | - Jean-Christophe Paillart
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
| | - Roland Marquet
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
| | - Serena Bernacchi
- a Architecture et Réactivité de l'ARN, UPR 9002, IBMC, CNRS , Université de Strasbourg , Strasbourg , France
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21
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Bieniasz P, Telesnitsky A. Multiple, Switchable Protein:RNA Interactions Regulate Human Immunodeficiency Virus Type 1 Assembly. Annu Rev Virol 2018; 5:165-183. [PMID: 30048218 DOI: 10.1146/annurev-virology-092917-043448] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) particle assembly requires several protein:RNA interactions that vary widely in their character, from specific recognition of highly conserved and structured viral RNA elements to less specific interactions with variable RNA sequences. Genetic, biochemical, biophysical, and structural studies have illuminated how virion morphogenesis is accompanied by dramatic changes in the interactions among the protein and RNA virion components. The 5' leader RNA element drives RNA recognition by Gag upon initiation of HIV-1 assembly and can assume variable conformations that influence translation, dimerization, and Gag recognition. As Gag multimerizes on the plasma membrane, forming immature particles, its RNA binding specificity transiently changes, enabling recognition of the A-rich composition of the viral genome. Initiation of assembly may also be regulated by occlusion of the membrane binding surface of Gag by tRNA. Finally, recent work has suggested that RNA interactions with viral enzymes may activate and ensure the accuracy of virion maturation.
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Affiliation(s)
- Paul Bieniasz
- Laboratory of Retrovirology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA;
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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22
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Smyth RP, Smith MR, Jousset AC, Despons L, Laumond G, Decoville T, Cattenoz P, Moog C, Jossinet F, Mougel M, Paillart JC, von Kleist M, Marquet R. In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging. Nucleic Acids Res 2018; 46:e57. [PMID: 29514260 PMCID: PMC5961354 DOI: 10.1093/nar/gky152] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/02/2018] [Accepted: 03/01/2018] [Indexed: 12/28/2022] Open
Abstract
Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5' region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5' PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production.
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Affiliation(s)
- Redmond P Smyth
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Maureen R Smith
- Freie Universität Berlin, Department of Mathematics and Computer Science, Arnimallee 6, 14195 Berlin, Germany
| | - Anne-Caroline Jousset
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Laurence Despons
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Géraldine Laumond
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Thomas Decoville
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Pierre Cattenoz
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Christiane Moog
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Fabrice Jossinet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Marylène Mougel
- IRIM CNRS UMR9004, Université de Montpellier, Montpellier, France
| | - Jean-Christophe Paillart
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Max von Kleist
- Freie Universität Berlin, Department of Mathematics and Computer Science, Arnimallee 6, 14195 Berlin, Germany
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
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Itano MS, Arnion H, Wolin SL, Simon SM. Recruitment of 7SL RNA to assembling HIV-1 virus-like particles. Traffic 2017; 19:36-43. [PMID: 29044909 DOI: 10.1111/tra.12536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 11/28/2022]
Abstract
Retroviruses incorporate specific host cell RNAs into virions. In particular, the host noncoding 7SL RNA is highly abundant in all examined retroviruses compared with its cellular levels or relative to common mRNAs such as actin. Using live cell imaging techniques, we have determined that the 7SL RNA does not arrive with the HIV-1 RNA genome. Instead, it is recruited contemporaneously with assembly of the protein HIV-1 Gag at the plasma membrane. Further, we demonstrate that complexes of 7SL RNA and Gag can be immunoprecipitated from both cytosolic and plasma membrane fractions. This indicates that 7SL RNAs likely interact with Gag prior to high-order Gag multimerization at the plasma membrane. Thus, the interactions between Gag and the host RNA 7SL occur independent of the interactions between Gag and the host endosomal sorting complex required for transport (ESCRT) proteins, which are recruited temporarily at late stages of assembly. The interactions of 7SL and Gag are also independent of interactions of Gag and the HIV-1 genome which are seen on the plasma membrane prior to assembly of Gag.
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Affiliation(s)
- Michelle S Itano
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
| | - Helene Arnion
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
| | - Sandra L Wolin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York
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24
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Subcellular Localization of HIV-1 gag-pol mRNAs Regulates Sites of Virion Assembly. J Virol 2017; 91:JVI.02315-16. [PMID: 28053097 DOI: 10.1128/jvi.02315-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/23/2016] [Indexed: 02/07/2023] Open
Abstract
Full-length unspliced human immunodeficiency virus type 1 (HIV-1) RNAs serve dual roles in the cytoplasm as mRNAs encoding the Gag and Gag-Pol capsid proteins as well as genomic RNAs (gRNAs) packaged by Gag into virions undergoing assembly at the plasma membrane (PM). Because Gag is sufficient to drive the assembly of virus-like particles even in the absence of gRNA binding, whether viral RNA trafficking plays an active role in the native assembly pathway is unknown. In this study, we tested the effects of modulating the cytoplasmic abundance or distribution of full-length viral RNAs on Gag trafficking and assembly in the context of single cells. Increasing full-length viral RNA abundance or distribution had little-to-no net effect on Gag assembly competency when provided in trans In contrast, artificially tethering full-length viral RNAs or surrogate gag-pol mRNAs competent for Gag synthesis to non-PM membranes or the actin cytoskeleton severely reduced net virus particle production. These effects were explained, in large part, by RNA-directed changes to Gag's distribution in the cytoplasm, yielding aberrant subcellular sites of virion assembly. Interestingly, RNA-dependent disruption of Gag trafficking required either of two cis-acting RNA regulatory elements: the 5' packaging signal (Psi) bound by Gag during genome encapsidation or, unexpectedly, the Rev response element (RRE), which regulates the nuclear export of gRNAs and other intron-retaining viral RNAs. Taken together, these data support a model for native infection wherein structural features of the gag-pol mRNA actively compartmentalize Gag to preferred sites within the cytoplasm and/or PM.IMPORTANCE The spatial distribution of viral mRNAs within the cytoplasm can be a crucial determinant of efficient translation and successful virion production. Here we provide direct evidence that mRNA subcellular trafficking plays an important role in regulating the assembly of human immunodeficiency virus type 1 (HIV-1) virus particles at the plasma membrane (PM). Artificially tethering viral mRNAs encoding Gag capsid proteins (gag-pol mRNAs) to distinct non-PM subcellular locales, such as cytoplasmic vesicles or the actin cytoskeleton, markedly alters Gag subcellular distribution, relocates sites of assembly, and reduces net virus particle production. These observations support a model for native HIV-1 assembly wherein HIV-1 gag-pol mRNA localization helps to confine interactions between Gag, viral RNAs, and host determinants in order to ensure virion production at the right place and right time. Direct perturbation of HIV-1 mRNA subcellular localization may represent a novel antiviral strategy.
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25
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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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Comas-Garcia M, Davis SR, Rein A. On the Selective Packaging of Genomic RNA by HIV-1. Viruses 2016; 8:v8090246. [PMID: 27626441 PMCID: PMC5035960 DOI: 10.3390/v8090246] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/16/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022] Open
Abstract
Like other retroviruses, human immunodeficiency virus type 1 (HIV-1) selectively packages genomic RNA (gRNA) during virus assembly. However, in the absence of the gRNA, cellular messenger RNAs (mRNAs) are packaged. While the gRNA is selected because of its cis-acting packaging signal, the mechanism of this selection is not understood. The affinity of Gag (the viral structural protein) for cellular RNAs at physiological ionic strength is not much higher than that for the gRNA. However, binding to the gRNA is more salt-resistant, implying that it has a higher non-electrostatic component. We have previously studied the spacer 1 (SP1) region of Gag and showed that it can undergo a concentration-dependent conformational transition. We proposed that this transition represents the first step in assembly, i.e., the conversion of Gag to an assembly-ready state. To explain selective packaging of gRNA, we suggest here that binding of Gag to gRNA, with its high non-electrostatic component, triggers this conversion more readily than binding to other RNAs; thus we predict that a Gag-gRNA complex will nucleate particle assembly more efficiently than other Gag-RNA complexes. New data shows that among cellular mRNAs, those with long 3'-untranslated regions (UTR) are selectively packaged. It seems plausible that the 3'-UTR, a stretch of RNA not occupied by ribosomes, offers a favorable binding site for Gag.
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Affiliation(s)
- Mauricio Comas-Garcia
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| | - Sean R Davis
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Alan Rein
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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27
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The Life-Cycle of the HIV-1 Gag-RNA Complex. Viruses 2016; 8:v8090248. [PMID: 27626439 PMCID: PMC5035962 DOI: 10.3390/v8090248] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/16/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) replication is a highly regulated process requiring the recruitment of viral and cellular components to the plasma membrane for assembly into infectious particles. This review highlights the recent process of understanding the selection of the genomic RNA (gRNA) by the viral Pr55Gag precursor polyprotein, and the processes leading to its incorporation into viral particles.
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28
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Ferrer M, Henriet S, Chamontin C, Lainé S, Mougel M. From Cells to Virus Particles: Quantitative Methods to Monitor RNA Packaging. Viruses 2016; 8:v8080239. [PMID: 27556480 PMCID: PMC4997601 DOI: 10.3390/v8080239] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/16/2016] [Accepted: 08/16/2016] [Indexed: 02/07/2023] Open
Abstract
In cells, positive strand RNA viruses, such as Retroviridae, must selectively recognize their full-length RNA genome among abundant cellular RNAs to assemble and release particles. How viruses coordinate the intracellular trafficking of both RNA and protein components to the assembly sites of infectious particles at the cell surface remains a long-standing question. The mechanisms ensuring packaging of genomic RNA are essential for viral infectivity. Since RNA packaging impacts on several essential functions of retroviral replication such as RNA dimerization, translation and recombination events, there are many studies that require the determination of RNA packaging efficiency and/or RNA packaging ability. Studies of RNA encapsidation rely upon techniques for the identification and quantification of RNA species packaged by the virus. This review focuses on the different approaches available to monitor RNA packaging: Northern blot analysis, ribonuclease protection assay and quantitative reverse transcriptase-coupled polymerase chain reaction as well as the most recent RNA imaging and sequencing technologies. Advantages, disadvantages and limitations of these approaches will be discussed in order to help the investigator to choose the most appropriate technique. Although the review was written with the prototypic simple murine leukemia virus (MLV) and complex human immunodeficiency virus type 1 (HIV-1) in mind, the techniques were described in order to benefit to a larger community.
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Affiliation(s)
- Mireia Ferrer
- CPBS, CNRS, Université de Montpellier, 1919 Route de Mende, Montpellier 34293, France.
| | - Simon Henriet
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5018, Norway.
| | - Célia Chamontin
- CPBS, CNRS, Université de Montpellier, 1919 Route de Mende, Montpellier 34293, France.
| | - Sébastien Lainé
- CPBS, CNRS, Université de Montpellier, 1919 Route de Mende, Montpellier 34293, France.
| | - Marylène Mougel
- CPBS, CNRS, Université de Montpellier, 1919 Route de Mende, Montpellier 34293, France.
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29
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Telesnitsky A, Wolin SL. The Host RNAs in Retroviral Particles. Viruses 2016; 8:v8080235. [PMID: 27548206 PMCID: PMC4997597 DOI: 10.3390/v8080235] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 12/15/2022] Open
Abstract
As they assemble, retroviruses encapsidate both their genomic RNAs and several types of host RNA. Whereas limited amounts of messenger RNA (mRNA) are detectable within virion populations, the predominant classes of encapsidated host RNAs do not encode proteins, but instead include endogenous retroelements and several classes of non-coding RNA (ncRNA), some of which are packaged in significant molar excess to the viral genome. Surprisingly, although the most abundant host RNAs in retroviruses are also abundant in cells, unusual forms of these RNAs are packaged preferentially, suggesting that these RNAs are recruited early in their biogenesis: before associating with their cognate protein partners, and/or from transient or rare RNA populations. These RNAs' packaging determinants differ from the viral genome's, and several of the abundantly packaged host ncRNAs serve cells as the scaffolds of ribonucleoprotein particles. Because virion assembly is equally efficient whether or not genomic RNA is available, yet RNA appears critical to the structural integrity of retroviral particles, it seems possible that the selectively encapsidated host ncRNAs might play roles in assembly. Indeed, some host ncRNAs appear to act during replication, as some transfer RNA (tRNA) species may contribute to nuclear import of human immunodeficiency virus 1 (HIV-1) reverse transcription complexes, and other tRNA interactions with the viral Gag protein aid correct trafficking to plasma membrane assembly sites. However, despite high conservation of packaging for certain host RNAs, replication roles for most of these selectively encapsidated RNAs-if any-have remained elusive.
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Affiliation(s)
- Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Sandra L Wolin
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06536, USA.
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30
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Hellmund C, Lever AML. Coordination of Genomic RNA Packaging with Viral Assembly in HIV-1. Viruses 2016; 8:E192. [PMID: 27428992 PMCID: PMC4974527 DOI: 10.3390/v8070192] [Citation(s) in RCA: 8] [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: 06/16/2016] [Revised: 07/04/2016] [Accepted: 07/07/2016] [Indexed: 12/15/2022] Open
Abstract
The tremendous progress made in unraveling the complexities of human immunodeficiency virus (HIV) replication has resulted in a library of drugs to target key aspects of the replication cycle of the virus. Yet, despite this accumulated wealth of knowledge, we still have much to learn about certain viral processes. One of these is virus assembly, where the viral genome and proteins come together to form infectious progeny. Here we review this topic from the perspective of how the route to production of an infectious virion is orchestrated by the viral genome, and we compare and contrast aspects of the assembly mechanisms employed by HIV-1 with those of other RNA viruses.
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Affiliation(s)
- Chris Hellmund
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
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31
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Ferrer M, Clerté C, Chamontin C, Basyuk E, Lainé S, Hottin J, Bertrand E, Margeat E, Mougel M. Imaging HIV-1 RNA dimerization in cells by multicolor super-resolution and fluctuation microscopies. Nucleic Acids Res 2016; 44:7922-34. [PMID: 27280976 PMCID: PMC5027490 DOI: 10.1093/nar/gkw511] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/27/2016] [Indexed: 11/15/2022] Open
Abstract
Dimerization is a unique and vital characteristic of retroviral genomes. It is commonly accepted that genomic RNA (gRNA) must be dimeric at the plasma membrane of the infected cells to be packaged during virus assembly. However, where, when and how HIV-1 gRNA find each other and dimerize in the cell are long-standing questions that cannot be answered using conventional approaches. Here, we combine two state-of-the-art, multicolor RNA labeling strategies with two single-molecule microscopy technologies to address these questions. We used 3D-super-resolution structured illumination microscopy to analyze and quantify the spatial gRNA association throughout the cell and monitored the dynamics of RNA-RNA complexes in living-cells by cross-correlation fluctuation analysis. These sensitive and complementary approaches, combined with trans-complementation experiments, reveal for the first time the presence of interacting gRNA in the cytosol, a challenging observation due to the low frequency of these events and their dilution among the bulk of other RNAs, and allow the determination of the subcellular orchestration of the HIV-1 dimerization process.
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Affiliation(s)
- Mireia Ferrer
- Centre d'études d'agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Caroline Clerté
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U1054, 34090 Montpellier, France Université de Montpellier, 34090 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
| | - Eugenia Basyuk
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Sébastien Lainé
- Centre d'études d'agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Jérome Hottin
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U1054, 34090 Montpellier, France Université de Montpellier, 34090 Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Emmanuel Margeat
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U1054, 34090 Montpellier, France Université de Montpellier, 34090 Montpellier, 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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32
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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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Sakaguchi N, Maeda K. Germinal Center B-Cell-Associated Nuclear Protein (GANP) Involved in RNA Metabolism for B Cell Maturation. Adv Immunol 2016; 131:135-86. [PMID: 27235683 DOI: 10.1016/bs.ai.2016.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Germinal center B-cell-associated nuclear protein (GANP) is upregulated in germinal center B cells against T-cell-dependent antigens in mice and humans. In mice, GANP depletion in B cells impairs antibody affinity maturation. Conversely, its transgenic overexpression augments the generation of high-affinity antigen-specific B cells. GANP associates with AID in the cytoplasm, shepherds AID into the nucleus, and augments its access to the rearranged immunoglobulin (Ig) variable (V) region of the genome in B cells, thereby precipitating the somatic hypermutation of V region genes. GANP is also upregulated in human CD4(+) T cells and is associated with APOBEC3G (A3G). GANP interacts with A3G and escorts it to the virion cores to potentiate its antiretroviral activity by inactivating HIV-1 genomic cDNA. Thus, GANP is characterized as a cofactor associated with AID/APOBEC cytidine deaminase family molecules in generating diversity of the IgV region of the genome and genetic alterations of exogenously introduced viral targets. GANP, encoded by human chromosome 21, as well as its mouse equivalent on chromosome 10, contains a region homologous to Saccharomyces Sac3 that was characterized as a component of the transcription/export 2 (TREX-2) complex and was predicted to be involved in RNA export and metabolism in mammalian cells. The metabolism of RNA during its maturation, from the transcription site at the chromosome within the nucleus to the cytoplasmic translation apparatus, needs to be elaborated with regard to acquired and innate immunity. In this review, we summarize the current knowledge on GANP as a component of TREX-2 in mammalian cells.
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Affiliation(s)
- N Sakaguchi
- WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan; Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
| | - K Maeda
- WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan; Laboratory of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
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Tran T, Liu Y, Marchant J, Monti S, Seu M, Zaki J, Yang AL, Bohn J, Ramakrishnan V, Singh R, Hernandez M, Vega A, Summers MF. Conserved determinants of lentiviral genome dimerization. Retrovirology 2015; 12:83. [PMID: 26420212 PMCID: PMC4588261 DOI: 10.1186/s12977-015-0209-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 09/18/2015] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Retroviruses selectively package two copies of their unspliced genomes by what appears to be a dimerization-dependent RNA packaging mechanism. Dimerization of human immunodeficiency virus Type-1 (HIV-1) genomes is initiated by "kissing" interactions between GC-rich palindromic loop residues of a conserved hairpin (DIS), and is indirectly promoted by long-range base pairing between residues overlapping the gag start codon (AUG) and an upstream Unique 5' element (U5). The DIS and U5:AUG structures are phylogenetically conserved among divergent retroviruses, suggesting conserved functions. However, some studies suggest that the DIS of HIV-2 does not participate in dimerization, and that U5:AUG pairing inhibits, rather than promotes, genome dimerization. We prepared RNAs corresponding to native and mutant forms of the 5' leaders of HIV-1 (NL4-3 strain), HIV-2 (ROD strain), and two divergent strains of simian immunodeficiency virus (SIV; cpz-TAN1 and -US strains), and probed for potential roles of the DIS and U5:AUG base pairing on intrinsic and NC-dependent dimerization by mutagenesis, gel electrophoresis, and NMR spectroscopy. RESULTS Dimeric forms of the native HIV-2 and SIV leaders were only detectable using running buffers that contained Mg(2+), indicating that these dimers are more labile than that of the HIV-1 leader. Mutations designed to promote U5:AUG base pairing promoted dimerization of the HIV-2 and SIV RNAs, whereas mutations that prevented U5:AUG pairing inhibited dimerization. Chimeric HIV-2 and SIV leader RNAs containing the dimer-promoting loop of HIV-1 (DIS) exhibited HIV-1 leader-like dimerization properties, whereas an HIV-1NL4-3 mutant containing the SIVcpzTAN1 DIS loop behaved like the SIVcpzTAN1 leader. The cognate NC proteins exhibited varying abilities to promote dimerization of the retroviral leader RNAs, but none were able to convert labile dimers to non-labile dimers. CONCLUSIONS The finding that U5:AUG formation promotes dimerization of the full-length HIV-1, HIV-2, SIVcpzUS, and SIVcpzTAN1 5' leaders suggests that these retroviruses utilize a common RNA structural switch mechanism to modulate function. Differences in native and NC-dependent dimerization propensity and lability are due to variations in the compositions of the DIS loop residues rather than other sequences within the leader RNAs. Although NC is a well-known RNA chaperone, its role in dimerization has the hallmarks of a classical riboswitch.
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Affiliation(s)
- Thao Tran
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Yuanyuan Liu
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Jan Marchant
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Sarah Monti
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Michelle Seu
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Jessica Zaki
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Ae Lim Yang
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Jennifer Bohn
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Venkateswaran Ramakrishnan
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Rashmi Singh
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Mateo Hernandez
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Alexander Vega
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
| | - Michael F Summers
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
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HIV-1 RNAs: sense and antisense, large mRNAs and small siRNAs and miRNAs. Curr Opin HIV AIDS 2015; 10:103-9. [PMID: 25565176 DOI: 10.1097/coh.0000000000000135] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW This review summarizes recent findings concerning the ever-growing HIV-1 RNA population. RECENT FINDINGS The retrovirus HIV-1 has an RNA genome that is converted into DNA and is integrated into the genome of the infected host cell. Transcription from the long terminal repeat-encoded promoter results in the production of a full-length genomic RNA and multiple spliced mRNAs. Recent experiments, mainly based on next-generation sequencing, provided evidence for several additional HIV-encoded RNAs, including antisense RNAs and virus-encoded microRNAs. SUMMARY We will survey recent findings related to HIV-1 RNA biosynthesis, especially regulatory mechanisms that control initiation of transcription, capping and polyadenylation. We zoom in on the diversity of HIV-1 derived RNA transcripts, their mode of synthesis and proposed functions in the infected cell. Special attention is paid to the viral transacting responsive RNA hairpin motif that has been suggested to encode microRNAs.
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van Bel N, Ghabri A, Das AT, Berkhout B. The HIV-1 leader RNA is exquisitely sensitive to structural changes. Virology 2015; 483:236-52. [DOI: 10.1016/j.virol.2015.03.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/05/2015] [Accepted: 03/27/2015] [Indexed: 01/14/2023]
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Xu R, El-Hage N, Dever SM. Fluorescently-labeled RNA packaging into HIV-1 particles: Direct examination of infectivity across central nervous system cell types. J Virol Methods 2015; 224:20-9. [PMID: 26272129 DOI: 10.1016/j.jviromet.2015.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 07/05/2015] [Accepted: 07/10/2015] [Indexed: 12/29/2022]
Abstract
HIV penetrates the central nervous system (CNS), and although it is clear that microglia and to a lesser extent astrocytes are infected, whether certain other cell types such as neurons are infected remains unclear. Here, we confirmed the finding that RNAs of both cellular and viral origins are present in native HIV-1 particles and exploited this phenomenon to directly examine HIV-1 infectivity of CNS cell types. Using in vitro transcribed mRNAs that were labeled with a fluorescent dye, we showed that these fluorescent mRNAs were packaged into HIV-1 particles by directly examining infected cells using fluorescence microscopy. Cells in culture infected with these labeled virions showed the fluorescent signals of mRNA labels by a distinct pattern of punctate, focal signals within the cells which was used to demonstrate that the CXCR4-tropic NL4-3 strain was able to enter microglia and to a lesser extent astrocytes, but not neurons. The strategy used in the present study may represent a novel approach of simplicity, robustness and reliability for versatile applications in HIV studies, such as the determination of infectivity across a broad range of cell types and within sub-populations of an individual cell type by direct visualization of viral entry into cells.
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Affiliation(s)
- Ruqiang Xu
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA; School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Nazira El-Hage
- Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA; Department of Immunology, Florida International University Herbert Wertheim College of Medicine, Miami, FL 33199, USA
| | - Seth M Dever
- Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA; Department of Immunology, Florida International University Herbert Wertheim College of Medicine, Miami, FL 33199, USA.
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38
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Mutational interference mapping experiment (MIME) for studying RNA structure and function. Nat Methods 2015; 12:866-72. [PMID: 26237229 DOI: 10.1038/nmeth.3490] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 06/16/2015] [Indexed: 11/08/2022]
Abstract
RNA regulates many biological processes; however, identifying functional RNA sequences and structures is complex and time-consuming. We introduce a method, mutational interference mapping experiment (MIME), to identify, at single-nucleotide resolution, the primary sequence and secondary structures of an RNA molecule that are crucial for its function. MIME is based on random mutagenesis of the RNA target followed by functional selection and next-generation sequencing. Our analytical approach allows the recovery of quantitative binding parameters and permits the identification of base-pairing partners directly from the sequencing data. We used this method to map the binding site of the human immunodeficiency virus-1 (HIV-1) Pr55(Gag) protein on the viral genomic RNA in vitro, and showed that, by analyzing permitted base-pairing patterns, we could model RNA structure motifs that are crucial for protein binding.
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39
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Specific recognition of the HIV-1 genomic RNA by the Gag precursor. Nat Commun 2014; 5:4304. [PMID: 24986025 DOI: 10.1038/ncomms5304] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 06/05/2014] [Indexed: 11/08/2022] Open
Abstract
During assembly of HIV-1 particles in infected cells, the viral Pr55(Gag) protein (or Gag precursor) must select the viral genomic RNA (gRNA) from a variety of cellular and viral spliced RNAs. However, there is no consensus on how Pr55(Gag) achieves this selection. Here, by using RNA binding and footprinting assays, we demonstrate that the primary Pr55(Gag) binding site on the gRNA consists of the internal loop and the lower part of stem-loop 1 (SL1), the upper part of which initiates gRNA dimerization. A double regulation ensures specific binding of Pr55(Gag) to the gRNA despite the fact that SL1 is also present in spliced viral RNAs. The region upstream of SL1, which is present in all HIV-1 RNAs, prevents binding to SL1, but this negative effect is counteracted by sequences downstream of SL4, which are unique to the gRNA.
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40
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Maeda K, Almofty SA, Singh SK, Eid MMA, Shimoda M, Ikeda T, Koito A, Pham P, Goodman MF, Sakaguchi N. GANP interacts with APOBEC3G and facilitates its encapsidation into the virions to reduce HIV-1 infectivity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2013; 191:6030-6039. [PMID: 24198285 PMCID: PMC4086635 DOI: 10.4049/jimmunol.1302057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The ssDNA-dependent deoxycytidine deaminase apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like 3G (A3G) is a potent restrictive factor against HIV-1 virus lacking viral-encoded infectivity factor (Vif) in CD4(+) T cells. A3G antiretroviral activity requires its encapsulation into HIV-1 virions. In this study, we show that germinal center-associated nuclear protein (GANP) is induced in activated CD4(+) T cells and physically interacts with A3G. Overexpression of GANP augments the A3G encapsidation into the virion-like particles and ΔVif HIV-1 virions. GANP is encapsidated in HIV-1 virion and modulates A3G packaging into the cores together with cellular RNAs, including 7SL RNA, and with unspliced HIV-1 genomic RNA. GANP upregulation leads to a significant increase in A3G-catalyzed G→A hypermutation in the viral genome and suppression of HIV-1 infectivity in a single-round viral infection assay. Conversely, GANP knockdown caused a marked increase in HIV-1 infectivity in a multiple-round infection assay. The data suggest that GANP is a cellular factor that facilitates A3G encapsidation into HIV-1 virions to inhibit viral infectivity.
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MESH Headings
- APOBEC-3G Deaminase
- Acetyltransferases/antagonists & inhibitors
- Acetyltransferases/biosynthesis
- Acetyltransferases/chemistry
- Acetyltransferases/genetics
- Acetyltransferases/physiology
- CD4-Positive T-Lymphocytes/immunology
- Cells, Cultured
- Cytidine Deaminase/chemistry
- Cytidine Deaminase/physiology
- Genes, vif
- HIV-1/physiology
- HIV-1/ultrastructure
- Humans
- Intracellular Signaling Peptides and Proteins/antagonists & inhibitors
- Intracellular Signaling Peptides and Proteins/biosynthesis
- Intracellular Signaling Peptides and Proteins/chemistry
- Intracellular Signaling Peptides and Proteins/genetics
- Intracellular Signaling Peptides and Proteins/physiology
- Lymphocyte Activation
- Mutation
- Protein Interaction Mapping
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Small Cytoplasmic/metabolism
- RNA, Small Interfering/pharmacology
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Signal Recognition Particle/metabolism
- Up-Regulation
- Virion/metabolism
- Virion/ultrastructure
- Virulence
- Virus Replication
- vif Gene Products, Human Immunodeficiency Virus/deficiency
- RNA, Small Untranslated
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Affiliation(s)
- Kazuhiko Maeda
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Sarah Ameen Almofty
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Shailendra Kumar Singh
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Mohammed Mansour Abbas Eid
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Mayuko Shimoda
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Terumasa Ikeda
- Department of Retrovirology and Self-Defense, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Atsushi Koito
- Department of Retrovirology and Self-Defense, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
| | - Phuong Pham
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910
| | - Myron F. Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910
| | - Nobuo Sakaguchi
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
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Brameier M, Ibing W, Höfer K, Montag J, Stahl-Hennig C, Motzkus D. Mapping the small RNA content of simian immunodeficiency virions (SIV). PLoS One 2013; 8:e75063. [PMID: 24086438 PMCID: PMC3781035 DOI: 10.1371/journal.pone.0075063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 08/09/2013] [Indexed: 12/30/2022] Open
Abstract
Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodeficiency virions (SIV), which were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIV mac239 genome sequence. Among these we could identify 12 virus-derived small RNAs (vsRNAs) that were highly abundant. Beside known retrovirus-enriched small RNAs, like 7SL-RNA, tRNALys3 and tRNALys isoacceptors, we also identified defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50 fold in SIV. We also found evidence that small nucleolar RNAs U2 and U12 were underrepresented in the SIV preparation, indicating that the relative number or the content of co-isolated exosomes was changed upon infection. Our comprehensive atlas of SIV-incorporated small RNAs provides a refined picture of the composition of retrovirions, which gives novel insights into viral packaging.
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MESH Headings
- Base Sequence
- Cell Line
- Exosomes/metabolism
- High-Throughput Nucleotide Sequencing
- Humans
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Sequence Data
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Cytoplasmic/genetics
- RNA, Small Cytoplasmic/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- RNA, Untranslated/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Signal Recognition Particle/genetics
- Signal Recognition Particle/metabolism
- Simian Immunodeficiency Virus/genetics
- Virion/genetics
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Affiliation(s)
- Markus Brameier
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
| | - Wiebke Ibing
- Unit of Infection Models, German Primate Center, Göttingen, Germany
| | - Katharina Höfer
- Unit of Infection Models, German Primate Center, Göttingen, Germany
| | - Judith Montag
- Unit of Infection Models, German Primate Center, Göttingen, Germany
| | | | - Dirk Motzkus
- Unit of Infection Models, German Primate Center, Göttingen, Germany
- * E-mail:
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Webb JA, Jones CP, Parent LJ, Rouzina I, Musier-Forsyth K. Distinct binding interactions of HIV-1 Gag to Psi and non-Psi RNAs: implications for viral genomic RNA packaging. RNA (NEW YORK, N.Y.) 2013; 19:1078-88. [PMID: 23798665 PMCID: PMC3708528 DOI: 10.1261/rna.038869.113] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/13/2013] [Indexed: 05/02/2023]
Abstract
Despite the vast excess of cellular RNAs, precisely two copies of viral genomic RNA (gRNA) are selectively packaged into new human immunodeficiency type 1 (HIV-1) particles via specific interactions between the HIV-1 Gag and the gRNA psi (ψ) packaging signal. Gag consists of the matrix (MA), capsid, nucleocapsid (NC), and p6 domains. Binding of the Gag NC domain to ψ is necessary for gRNA packaging, but the mechanism by which Gag selectively interacts with ψ is unclear. Here, we investigate the binding of NC and Gag variants to an RNA derived from ψ (Psi RNA), as well as to a non-ψ region (TARPolyA). Binding was measured as a function of salt to obtain the effective charge (Zeff) and nonelectrostatic (i.e., specific) component of binding, Kd(1M). Gag binds to Psi RNA with a dramatically reduced Kd(1M) and lower Zeff relative to TARPolyA. NC, GagΔMA, and a dimerization mutant of Gag bind TARPolyA with reduced Zeff relative to WT Gag. Mutations involving the NC zinc finger motifs of Gag or changes to the G-rich NC-binding regions of Psi RNA significantly reduce the nonelectrostatic component of binding, leading to an increase in Zeff. These results show that Gag interacts with gRNA using different binding modes; both the NC and MA domains are bound to RNA in the case of TARPolyA, whereas binding to Psi RNA involves only the NC domain. Taken together, these results suggest a novel mechanism for selective gRNA encapsidation.
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Affiliation(s)
- Joseph A. Webb
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- Center for Retrovirus Research, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Christopher P. Jones
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- Center for Retrovirus Research, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Leslie J. Parent
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- Center for Retrovirus Research, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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Chamontin C, Yu B, Racine PJ, Darlix JL, Mougel M. MoMuLV and HIV-1 nucleocapsid proteins have a common role in genomic RNA packaging but different in late reverse transcription. PLoS One 2012; 7:e51534. [PMID: 23236513 PMCID: PMC3517543 DOI: 10.1371/journal.pone.0051534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 11/05/2012] [Indexed: 11/25/2022] Open
Abstract
Retroviral nucleocapsid proteins harbor nucleic acid chaperoning activities that mostly rely on the N-terminal basic residues and the CCHC zinc finger motif. Such chaperoning is essential for virus replication, notably for genomic RNA selection and packaging in virions, and for reverse transcription of genomic RNA into DNA. Recent data revealed that HIV-1 nucleocapsid restricts reverse transcription during virus assembly--a process called late reverse transcription--suggesting a regulation between RNA packaging and late reverse transcription. Indeed, mutating the HIV-1 nucleocapsid basic residues or the two zinc fingers caused a reduction in RNA incorporated and an increase in newly made viral DNA in the mutant virions. MoMuLV nucleocapsid has an N-terminal basic region similar to HIV-1 nucleocapsid but a unique zinc finger. This prompted us to investigate whether the N-terminal basic residues and the zinc finger of MoMuLV and HIV-1 nucleocapsids play a similar role in genomic RNA packaging and late reverse transcription. To this end, we analyzed the genomic RNA and viral DNA contents of virions produced by cells transfected with MoMuLV molecular clones where the zinc finger was mutated or completely deleted or with a deletion of the N-terminal basic residues of nucleocapsid. All mutant virions showed a strong defect in genomic RNA content indicating that the basic residues and zinc finger are important for genomic RNA packaging. In contrast to HIV-1 nucleocapsid-mutants, the level of viral DNA in mutant MoMuLV virions was only slightly increased. These results confirm that the N-terminal basic residues and zinc finger of MoMuLV nucleocapsid are critical for genomic RNA packaging but, in contrast to HIV-1 nucleocapsid, they most probably do not play a role in the control of late reverse transcription. In addition, these results suggest that virus formation and late reverse transcription proceed according to distinct mechanisms for MuLV and HIV-1.
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Affiliation(s)
| | - Bing Yu
- UMR5236 CNRS, UM1,UM2, CPBS, Montpellier, France
| | | | - Jena-Luc Darlix
- UMR 7213 CNRS, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, Illkirch, France
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Schopman NC, van Montfort T, Willemsen M, Knoepfel SA, Pollakis G, van Kampen A, Sanders RW, Haasnoot J, Berkhout B. Selective packaging of cellular miRNAs in HIV-1 particles. Virus Res 2012; 169:438-47. [DOI: 10.1016/j.virusres.2012.06.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/07/2012] [Accepted: 06/12/2012] [Indexed: 01/21/2023]
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45
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Grewe B, Ehrhardt K, Hoffmann B, Blissenbach M, Brandt S, Uberla K. The HIV-1 Rev protein enhances encapsidation of unspliced and spliced, RRE-containing lentiviral vector RNA. PLoS One 2012; 7:e48688. [PMID: 23133650 PMCID: PMC3486793 DOI: 10.1371/journal.pone.0048688] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 09/28/2012] [Indexed: 11/25/2022] Open
Abstract
Background During the RNA encapsidation process of human immunodeficiency virus (HIV) viral genomic, unspliced RNA (gRNA) is preferentially incorporated into assembling virions. However, a certain amount of spliced viral transcripts can also be detected in viral particles. Recently, we observed that nuclear export of HIV and lentiviral vector gRNA by Rev is required for efficient encapsidation. Since singly-spliced HIV transcripts also contain the Rev-response element (RRE), we investigated if the encapsidation efficiency of RRE-containing spliced HIV-vector transcripts is also increased by the viral Rev protein. Findings Starting with a lentiviral vector imitating the splicing pattern of HIV, we constructed vectors that express an unspliced transcript either identical in sequence to the singly-spliced or the fully-spliced RNA of the parental construct. After transfection of the different lentiviral vectors cytoplasmic and virion-associated RNA levels and vector titers were determined in the presence and absence of Rev. Rev enhanced the infectious titer of vectors containing an RRE 6 to 37-fold. Furthermore, Rev strongly increased encapsidation efficiencies of all RRE-containing transcripts up to 200-fold. However, a good correlation between encapsidation efficiency and lentiviral vector titer could only be observed for the gRNA. The infectious titer of the vector encoding the fully-spliced RNA without RRE as well as the encapsidation efficiency of all transcripts lacking the RRE was not influenced by Rev. Interestingly, the splicing process itself did not seem to interfere with packaging, since the encapsidation efficiencies of the same RNA expressed either by splicing or as an unspliced transcript did not differ significantly. Conclusions Rev-mediated nuclear export enhances the encapsidation efficiency of RRE-containing lentiviral vector RNAs independently of whether they have been spliced or not.
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Affiliation(s)
- Bastian Grewe
- Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany.
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46
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Das AT, Vrolijk MM, Harwig A, Berkhout B. Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging. Retrovirology 2012; 9:59. [PMID: 22828074 PMCID: PMC3432602 DOI: 10.1186/1742-4690-9-59] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 07/04/2012] [Indexed: 01/29/2023] Open
Abstract
Background The TAR hairpin is present at both the 5′ and 3′ end of the HIV-1 RNA genome. The 5′ element binds the viral Tat protein and is essential for Tat-mediated activation of transcription. We recently observed that complete TAR deletion is allowed in the context of an HIV-1 variant that does not depend on this Tat-TAR axis for transcription. Mutations that open the 5′ stem-loop structure did however affect the leader RNA conformation and resulted in a severe replication defect. In this study, we set out to analyze which step of the HIV-1 replication cycle is affected by this conformational change of the leader RNA. Results We demonstrate that opening the 5′ TAR structure through a deletion in either side of the stem region caused aberrant dimerization and reduced packaging of the unspliced viral RNA genome. In contrast, truncation of the TAR hairpin through deletions in both sides of the stem did not affect RNA dimer formation and packaging. Conclusions These results demonstrate that, although the TAR hairpin is not essential for RNA dimerization and packaging, mutations in TAR can significantly affect these processes through misfolding of the relevant RNA signals.
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Affiliation(s)
- Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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Abstract
The host noncoding RNA 7SL is highly enriched in the virions of retroviruses. We examined the regions of 7SL that mediate packaging by HIV-1. Both the Alu domain and the S domain were sufficient to mediate specific packaging when expressed separately as truncations of 7SL. However, while the Alu domain competed with endogenous 7SL for packaging in proportion to Gag, the S domain was packaged additively, implying that the Alu and S domains are packaged via separate mechanisms and that the Alu domain is packaged by the same mechanism as endogenous 7SL. Further truncations of the Alu domain or mutation of the Alu domain helix 5c region significantly reduced packaging efficiency, implicating helix 5c as critical for packaging, reinforcing the finding that 7SL packaging is highly selective, and confirming that 7SL is not passively acquired. Surprisingly, when the Alu domain was mutated so that it no longer contained a binding site for the SRP protein heterodimer SRP9/14, it was no longer packaged in a competitive manner but instead was packaged additively with endogenous 7SL. These data support a model in which 7SL RNA is packaged via interactions between Gag and a 7SL RNA structure that exists transiently at a discrete stage of SRP biogenesis. Our data further indicate that a secondary "additive" pathway exists that can result in the packaging of certain 7SL derivatives in molar excess to endogenously packaged 7SL.
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Jalalirad M, Saadatmand J, Laughrea M. Dominant role of the 5' TAR bulge in dimerization of HIV-1 genomic RNA, but no evidence of TAR-TAR kissing during in vivo virus assembly. Biochemistry 2012; 51:3744-58. [PMID: 22482513 DOI: 10.1021/bi300111p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The 5' untranslated region of HIV-1 genomic RNA (gRNA) contains two stem-loop structures that appear to be equally important for gRNA dimerization: the 57-nucleotide 5' TAR, at the very 5' end, and the 35-nucleotide SL1 (nucleotides 243-277). SL1 is well-known for containing the dimerization initiation site (DIS) in its apical loop. The DIS is a six-nucleotide palindrome. Here, we investigated the mechanism of TAR-directed gRNA dimerization. We found that the trinucleotide bulge (UCU24) of the 5' TAR has dominant impacts on both formation of HIV-1 RNA dimers and maturation of the formed dimers. The ΔUCU trinucleotide deletion strongly inhibited the first process and blocked the other, thus impairing gRNA dimerization as severely as deletion of the entire 5' TAR, and more severely than deletion of the DIS, inactivation of the viral protease, or most severe mutations in the nucleocapsid protein. The apical loop of TAR contains a 10-nucleotide palindrome that has been postulated to stimulate gRNA dimerization by a TAR-TAR kissing mechanism analogous to the one used by SL1 to stimulate dimerization. Using mutations that strongly destabilize formation of the TAR palindrome duplex, as well as compensatory mutations that restore duplex formation to a wild-type-like level, we found no evidence of TAR-TAR kissing, even though mutations nullifying the kissing potential of the TAR palindrome could impair dimerization by a mechanism other than hindering of SL1. However, nullifying the kissing potential of TAR had much less severe effects than ΔUCU. By not uncovering a dimerization mechanism intrinsic to TAR, our data suggest that TAR mutations exert their effect 3' of TAR, yet not on SL1, because TAR and SL1 mutations have synergistic effects on gRNA dimerization.
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Affiliation(s)
- Mohammad Jalalirad
- McGill AIDS Center, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
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van der Kuyl AC. HIV infection and HERV expression: a review. Retrovirology 2012; 9:6. [PMID: 22248111 PMCID: PMC3311604 DOI: 10.1186/1742-4690-9-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 01/16/2012] [Indexed: 12/24/2022] Open
Abstract
The human genome contains multiple copies of retrovirus genomes known as endogenous retroviruses (ERVs) that have entered the germ-line at some point in evolution. Several of these proviruses have retained (partial) coding capacity, so that a number of viral proteins or even virus particles are expressed under various conditions. Human ERVs (HERVs) belong to the beta-, gamma-, or spuma- retrovirus groups. Endogenous delta- and lenti- viruses are notably absent in humans, although endogenous lentivirus genomes have been found in lower primates. Exogenous retroviruses that currently form a health threat to humans intriguingly belong to those absent groups. The best studied of the two infectious human retroviruses is the lentivirus human immunodeficiency virus (HIV) which has an overwhelming influence on its host by infecting cells of the immune system. One HIV-induced change is the induction of HERV transcription, often leading to induced HERV protein expression. This review will discuss the potential HIV-HERV interactions. Several studies have suggested that HERV proteins are unlikely to complement defective HIV virions, nor is HIV able to package HERV transcripts, probably due to low levels of sequence similarity. It is unclear whether the expression of HERVs has a negative, neutral, or positive influence on HIV-AIDS disease progression. A positive effect was recently reported by the specific expression of HERVs in chronically HIV-infected patients, which results in the presentation of HERV-derived peptides to CD8+ T-cells. These cytotoxic T-cells were not tolerant to HERV peptides, as would be expected for self-antigens, and consequently lysed the HIV-infected, HERV-presenting cells. This novel mechanism could control HIV replication and result in a low plasma viral load. The possibility of developing a vaccination strategy based on these HERV peptides will be discussed.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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