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Hardy J, Demecheleer E, Schauvliege M, Staelens D, Mortier V, Verhofstede C. Reverse transcription of plasma-derived HIV-1 RNA generates multiple artifacts through tRNA(Lys-3)-priming. Microbiol Spectr 2024; 12:e0387223. [PMID: 38442427 PMCID: PMC10986323 DOI: 10.1128/spectrum.03872-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
In vitro reverse transcription of full-length HIV-1 RNA extracted from the blood plasma of people living with HIV-1 remains challenging. Here, we describe the initiation of reverse transcription of plasma-derived viral RNA in the absence of an exogenous primer. Real-time PCR and Sanger sequencing were applied to identify the source and to monitor the outcome of this reaction. Results demonstrated that during purification of viral RNA from plasma, tRNA(Lys-3) is co-extracted in a complex with the viral RNA. In the presence of a reverse transcription enzyme, this tRNA(Lys-3) can induce reverse transcription, a reaction that is not confined to transcription of the 5' end of the viral RNA. A range of cDNA products is generated, most of them indicative for the occurrence of in vitro strand transfer events that involve translocation of cDNA from the 5' end to random positions on the viral RNA. This process results in the formation of cDNAs with large internal deletions. However, near full-length cDNA and cDNA with sequence patterns resembling multiple spliced HIV-1 RNA were also detected. Despite its potential to introduce significant bias in the interpretation of results across various applications, tRNA(Lys-3)-driven reverse transcription has been overlooked thus far. A more in-depth study of this tRNA-driven in vitro reaction may provide new insight into the complex process of in vivo HIV-1 replication.IMPORTANCEThe use of silica-based extraction methods for purifying HIV-1 RNA from viral particles is a common practice, but it involves co-extraction of human tRNA(Lys-3) due to the strong interactions between these molecules. This co-extraction becomes particularly significant when the extracted RNA is used in reverse transcription reactions, as the tRNA(Lys-3) then serves as a primer. Reverse transcription from tRNA(Lys-3) is not confined to cDNA synthesis of the 5' end of the viral RNA but extends across various regions of the viral genome through in vitro strand transfer events. Co-extraction of tRNA(Lys-3) has been overlooked thus far, despite its potential to introduce bias in downstream, reverse transcription-related applications. The observed events in the tRNA(Lys-3)-induced in vitro reverse transcription resemble in vivo replication processes. Therefore, these reactions may offer a unique model to better understand the replication dynamics of HIV-1.
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Affiliation(s)
- Jarryt Hardy
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Els Demecheleer
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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Li CW, Chen BS. Investigating HIV-Human Interaction Networks to Unravel Pathogenic Mechanism for Drug Discovery: A Systems Biology Approach. Curr HIV Res 2019; 16:77-95. [PMID: 29468972 DOI: 10.2174/1570162x16666180219155324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 01/18/2018] [Accepted: 02/14/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND Two big issues in the study of pathogens are determining how pathogens infect hosts and how the host defends itself against infection. Therefore, investigating host-pathogen interactions is important for understanding pathogenicity and host defensive mechanisms and treating infections. METHODS In this study, we used omics data, including time-course data from high-throughput sequencing, real-time polymerase chain reaction, and human microRNA (miRNA) and protein-protein interaction to construct an interspecies protein-protein and miRNA interaction (PPMI) network of human CD4+ T cells during HIV-1 infection through system modeling and identification. RESULTS By applying a functional annotation tool to the identified PPMI network at each stage of HIV infection, we found that repressions of three miRNAs, miR-140-5p, miR-320a, and miR-941, are involved in the development of autoimmune disorders, tumor proliferation, and the pathogenesis of T cells at the reverse transcription stage. Repressions of miR-331-3p and miR-320a are involved in HIV-1 replication, replicative spread, anti-apoptosis, cell proliferation, and dysregulation of cell cycle control at the integration/replication stage. Repression of miR-341-5p is involved in carcinogenesis at the late stage of HIV-1 infection. CONCLUSION By investigating the common core proteins and changes in specific proteins in the PPMI network between the stages of HIV-1 infection, we obtained pathogenic insights into the functional core modules and identified potential drug combinations for treating patients with HIV-1 infection, including thalidomide, oxaprozin, and metformin, at the reverse transcription stage; quercetin, nifedipine, and fenbendazole, at the integration/replication stage; and staurosporine, quercetin, prednisolone, and flufenamic acid, at the late stage.
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Affiliation(s)
- Cheng-Wei Li
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Bor-Sen Chen
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
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3
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Tokarev A, Creegan M, Eller MA, Roederer M, Bolton DL. Single-cell Quantitation of mRNA and Surface Protein Expression in Simian Immunodeficiency Virus-infected CD4+ T Cells Isolated from Rhesus macaques. J Vis Exp 2018. [PMID: 30320741 DOI: 10.3791/57776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Single-cell analysis is an important tool for dissecting heterogeneous populations of cells. The identification and isolation of rare cells can be difficult. To overcome this challenge, a methodology combining indexed flow cytometry and high-throughput multiplexed quantitative polymerase chain reaction (qPCR) was developed. The objective was to identify and characterize simian immunodeficiency virus (SIV)-infected cells present within rhesus macaques. Through quantitation of surface protein by fluorescence-activated cell sorting (FACS) and mRNA by qPCR, virus-infected cells are identified by viral gene expression, which is combined with host gene and protein measurements to create a multidimensional profile. We term the approach, targeted Single-Cell Proteo-transcriptional Evaluation, or tSCEPTRE. To perform the method, viable cells are stained with fluorescent antibodies specific for surface markers used for FACS isolation of a cell subset and/or downstream phenotypic analysis. Single cells are sorted followed by immediate lysis, multiplex reverse transcription (RT), PCR pre-amplification, and high throughput qPCR of up to 96 transcripts. FACS measurements are recorded at the time of sorting and subsequently linked to the gene expression data by well position to create a combined protein and transcriptional profile. To study SIV-infected cells directly ex vivo, cells were identified by qPCR detection of multiple viral RNA species. The combination of viral transcripts and the quantity of each provide a framework for classifying cells into distinct stages of the viral life cycle (e.g., productive versus non-productive). Moreover, tSCEPTRE of SIV+ cells were compared to uninfected cells isolated from the same specimen to assess differentially expressed host genes and proteins. The analysis revealed previously unappreciated viral RNA expression heterogeneity among infected cells as well as in vivo SIV-mediated post-transcriptional gene regulation with single-cell resolution. The tSCEPTRE method is relevant for the analysis of any cell population amenable to identification by expression of surface protein marker(s), host or pathogen gene(s), or combinations thereof.
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Affiliation(s)
- Andrey Tokarev
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research
| | - Matthew Creegan
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research
| | - Michael A Eller
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research
| | | | - Diane L Bolton
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research;
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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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Bolton DL, McGinnis K, Finak G, Chattopadhyay P, Gottardo R, Roederer M. Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells. PLoS Pathog 2017; 13:e1006445. [PMID: 28654687 PMCID: PMC5507340 DOI: 10.1371/journal.ppat.1006445] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/10/2017] [Accepted: 06/04/2017] [Indexed: 12/27/2022] Open
Abstract
CD4 T cells harboring HIV-1/SIV represent a formidable hurdle to eradicating infection, and yet their detailed phenotype remains unknown. Here we integrate two single-cell technologies, flow cytometry and highly multiplexed quantitative RT-PCR, to characterize SIV-infected CD4 T cells directly ex vivo. Within individual cells, we correlate the cellular phenotype, in terms of host protein and RNA expression, with stages of the viral life cycle defined by combinatorial expression of viral RNAs. Spliced RNA+ infected cells display multiple memory and activation phenotypes, indicating virus production by diverse CD4 T cell subsets. In most (but not all) cells, progressive infection accompanies post-transcriptional downregulation of CD4 protein, while surface MHC class I is largely retained. Interferon-stimulated genes were also commonly upregulated. Thus, we demonstrate that combined quantitation of transcriptional and post-transcriptional regulation at the single-cell level informs in vivo mechanisms of viral replication and immune evasion. HIV-1, and its simian counterpart, SIV, infect and kill CD4 T cells, resulting in their massive depletion that ultimately leads to AIDS in the absence of antiretroviral therapy. With effective therapy, these cells are largely preserved, but a subset harbors latent virus that can persist for decades and reemerge upon therapy interruption, preventing HIV-1 cure. To prevent or eliminate productive cellular infection, there is tremendous demand to identify host factors expressed by these cells in vivo, which may serve as unique biomarkers or drug targets. Here we provide the first detailed combined transcriptomic and protein expression profile of SIV-infected cells directly ex vivo using novel single-cell technologies. Our survey of activation markers, interferon-stimulated genes, and viral restriction factors identified multiple host genes differentially expressed by SIV-infected cells and will inform future therapeutic strategies.
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Affiliation(s)
- Diane L. Bolton
- US Military HIV Research Program, Henry M. Jackson Foundation, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- * E-mail:
| | - Kathleen McGinnis
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Greg Finak
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Pratip Chattopadhyay
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Raphael Gottardo
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
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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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7
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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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8
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Didierlaurent L, Racine PJ, Houzet L, Chamontin C, Berkhout B, Mougel M. Role of HIV-1 RNA and protein determinants for the selective packaging of spliced and unspliced viral RNA and host U6 and 7SL RNA in virus particles. Nucleic Acids Res 2011; 39:8915-27. [PMID: 21791531 PMCID: PMC3203606 DOI: 10.1093/nar/gkr577] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/27/2011] [Accepted: 06/28/2011] [Indexed: 01/22/2023] Open
Abstract
HIV-1 particles contain RNA species other than the unspliced viral RNA genome. For instance, viral spliced RNAs and host 7SL and U6 RNAs are natural components that are non-randomly incorporated. To understand the mechanism of packaging selectivity, we analyzed the content of a large panel of HIV-1 variants mutated either in the 5'UTR structures of the viral RNA or in the Gag-nucleocapsid protein (GagNC). In parallel, we determined whether the selection of host 7SL and U6 RNAs is dependent or not on viral RNA and/or GagNC. Our results reveal that the polyA hairpin in the 5'UTR is a major packaging determinant for both spliced and unspliced viral RNAs. In contrast, 5'UTR RNA structures have little influence on the U6 and 7SL RNAs, indicating that packaging of these host RNAs is independent of viral RNA packaging. Experiments with GagNC mutants indicated that the two zinc-fingers and N-terminal basic residues restrict the incorporation of the spliced RNAs, while favoring unspliced RNA packaging. GagNC through the zinc-finger motifs also restricts the packaging of 7SL and U6 RNAs. Thus, GagNC is a major contributor to the packaging selectivity. Altogether our results provide new molecular insight on how HIV selects distinct RNA species for incorporation into particles.
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Affiliation(s)
- L. Didierlaurent
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - P. J. Racine
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - L. Houzet
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - C. Chamontin
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - B. Berkhout
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
| | - M. Mougel
- UMR5236 CNRS, UMI&II, CPBS, 1919 Rte de Mende, Montpellier, France, LMM, NIAID, NIH Bethesda, MD, USA and Laboratory of Experimental Virology, Department of Medical Microbiology (CINIMA), Amsterdam, The Netherlands
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9
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Jouvenet N, Lainé S, Pessel-Vivares L, Mougel M. Cell biology of retroviral RNA packaging. RNA Biol 2011; 8:572-80. [PMID: 21691151 DOI: 10.4161/rna.8.4.16030] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Generation of infectious retroviral particles rely on the targeting of all structural components to the correct cellular sites at the correct time. Gag, the main structural protein, orchestrates the assembly process and the mechanisms that trigger its targeting to assembly sites are well described. Gag is also responsible for the packaging of the viral genome and the molecular details of the Gag/RNA interaction are well characterized. Until recently, much less was understood about the cell biology of retrovirus RNA packaging. However, novel biochemical and live-cell microscopic approaches have identified where in the cell the initial events of genome recognition by Gag occur. These recent developments have shed light on the role played by the viral genome during virion assembly. Other central issues of the cell biology of RNA packaging, such as how the Gag-RNA complex traffics through the cytoplasm towards assembly sites, await characterization.
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10
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Khatua AK, Taylor HE, Hildreth JEK, Popik W. Non-productive HIV-1 infection of human glomerular and urinary podocytes. Virology 2010; 408:119-27. [PMID: 20937511 DOI: 10.1016/j.virol.2010.09.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 07/28/2010] [Accepted: 09/04/2010] [Indexed: 01/02/2023]
Abstract
Podocyte damage induced by HIV-1 is critical to the pathogenesis of HIV-1 associated nephropathy (HIVAN) and is believed to result from productive replication of the virus. Here we demonstrate that HIV-1 readily enters human podocytes by a dynamin-mediated endocytosis but does not establish productive infection. We provide evidence suggesting that viral nucleic acids and proteins detected in podocytes are delivered by viral particles internalized by the cells. Endocytosed HIV-1 is only transiently harbored by podocytes and is subsequently released to the extracellular milieu as fully infectious virus. Similarly, primary podocytes established from normal human urine do not support productive infection by HIV-1 but sustain replication of VSV-G pseudotyped virus that bypasses HIV-1 entry receptors. Moreover, transfected podocytes expressing CD4 and CXCR4 receptors support productive replication of HIV-1. This further confirms that lack of HIV-1 entry receptors is the major barrier preventing productive infection of podocytes in vitro.
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Affiliation(s)
- Atanu K Khatua
- Center for AIDS Health Disparities Research, Meharry Medical College, 1005 D. B. Todd Blvd., Nashville, TN 37208, USA
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11
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Maurel S, Mougel M. Murine leukemia virus RNA dimerization is coupled to transcription and splicing processes. Retrovirology 2010; 7:64. [PMID: 20687923 PMCID: PMC2925334 DOI: 10.1186/1742-4690-7-64] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 08/05/2010] [Indexed: 11/16/2022] Open
Abstract
Most of the cell biological aspects of retroviral genome dimerization remain unknown. Murine leukemia virus (MLV) constitutes a useful model to study when and where dimerization occurs within the cell. For instance, MLV produces a subgenomic RNA (called SD') that is co-packaged with the genomic RNA predominantly as FLSD' heterodimers. This SD' RNA is generated by splicing of the genomic RNA and also by direct transcription of a splice-associated retroelement of MLV (SDARE). We took advantage of these two SD' origins to study the effects of transcription and splicing events on RNA dimerization. Using genetic approaches coupled to capture of RNA heterodimer in virions, we determined heterodimerization frequencies in different cellular contexts. Several cell lines were stably established in which SD' RNA was produced by either splicing or transcription from SDARE. Moreover, SDARE was integrated into the host chromosome either concomitantly or sequentially with the genomic provirus. Our results showed that transcribed genomic and SD' RNAs preferentially formed heterodimers when their respective proviruses were integrated together. In contrast, heterodimerization was strongly affected when the two proviruses were integrated independently. Finally, dimerization was enhanced when the transcription sites were expected to be physically close. For the first time, we report that splicing and RNA dimerization appear to be coupled. Indeed, when the RNAs underwent splicing, the FLSD' dimerization reached a frequency similar to co-transcriptional heterodimerization. Altogether, our results indicate that randomness of heterodimerization increases when RNAs are co-expressed during either transcription or splicing. Our results strongly support the notion that dimerization occurs in the nucleus, at or near the transcription and splicing sites, at areas of high viral RNA concentration.
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Affiliation(s)
- Stéphan Maurel
- Université Montpellier 1, Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS, UMR 5236, 4 Bd Henri IV, 34965 Montpellier, France
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12
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Mougel M, Cimarelli A, Darlix JL. Implications of the nucleocapsid and the microenvironment in retroviral reverse transcription. Viruses 2010; 2:939-960. [PMID: 21994662 PMCID: PMC3185662 DOI: 10.3390/v2040939] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 03/03/2010] [Accepted: 04/01/2010] [Indexed: 01/21/2023] Open
Abstract
This mini-review summarizes the process of reverse-transcription, an obligatory step in retrovirus replication during which the retroviral RNA/DNA-dependent DNA polymerase (RT) copies the single-stranded genomic RNA to generate the double-stranded viral DNA while degrading the genomic RNA via its associated RNase H activity. The hybridization of complementary viral sequences by the nucleocapsid protein (NC) receives a special focus, since it acts to chaperone the strand transfers obligatory for synthesis of the complete viral DNA and flanking long terminal repeats (LTR). Since the physiological microenvironment can impact on reverse-transcription, this mini-review also focuses on factors present in the intra-cellular or extra-cellular milieu that can drastically influence both the timing and the activity of reverse-transcription and hence virus infectivity.
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Affiliation(s)
- Marylène Mougel
- CPBS, UMR5236 CNRS, UMI, 4 bd Henri IV, 34965 Montpellier, France; E-Mail:
| | - Andrea Cimarelli
- LaboRetro Unité de Virologie humaine INSERM #758, IFR128, ENS Lyon, 46 Allée d’Italie, 69364 Lyon, France; E-Mail:
| | - Jean-Luc Darlix
- LaboRetro Unité de Virologie humaine INSERM #758, IFR128, ENS Lyon, 46 Allée d’Italie, 69364 Lyon, France; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33 472728169; Fax: +33 472728137
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13
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Kharytonchyk S, Pedersen FS. A unique, thermostable dimer linkage structure of RD114 retroviral RNA. RNA (NEW YORK, N.Y.) 2010; 16:572-584. [PMID: 20075164 PMCID: PMC2822922 DOI: 10.1261/rna.1495110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 11/13/2009] [Indexed: 05/28/2023]
Abstract
Retroviruses package their genome as RNA dimers linked together primarily by base-pairing between palindromic stem-loop (psl) sequences at the 5' end of genomic RNA. Retroviral RNA dimers usually melt in the range of 55 degrees C-70 degrees C. However, RNA dimers from virions of the feline endogenous gammaretrovirus RD114 were reported to melt only at 87 degrees C. We here report that the high thermal stability of RD114 RNA dimers generated from in vitro synthesized RNA is an effect of multiple dimerization sites located in the 5' region from the R region to sequences downstream from the splice donor (SD) site. By antisense oligonucleotide probing we were able to map at least five dimerization sites. Computational prediction revealed a possibility to form stems with autocomplementary loops for all of the mapped dimerization sites. Three of them were located upstream of the SD site. Mutant analysis supported a role of all five loop sequences in the formation and thermal stability of RNA dimers. Four of the five psls were also predicted in the RNA of two baboon endogenous retroviruses proposed to be ancestors of RD114. RNA fragments of the 5' R region or prolonged further downstream could be efficiently dimerized in vitro. However, this was not the case for the 3' R region linked to upstream U3 sequences, suggesting a specific mechanism of negative regulation of dimerization at the 3' end of the genome, possibly explained by a long double-stranded RNA region at the U3-R border. Altogether, these data point to determinants of the high thermostability of the dimer linkage structure of the RD114 genome and reveal differences from other retroviruses.
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14
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Steinbauerová V, Neumann P, Macas J. Experimental evidence for splicing of intron-containing transcripts of plant LTR retrotransposon Ogre. Mol Genet Genomics 2008; 280:427-36. [PMID: 18762986 PMCID: PMC2596294 DOI: 10.1007/s00438-008-0376-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 08/19/2008] [Indexed: 02/05/2023]
Abstract
Ogre elements are a distinct group of plant Ty3/gypsy-like retrotransposons characterized by several specific features, one of which is a separation of the gag-pol region into two non-overlapping open reading frames: ORF2 coding for Gag-Pro, and ORF3 coding for RT/RH-INT proteins. Previous characterization of Ogre elements from several plant species revealed that part of their transcripts lacks the region between ORF2 and ORF3, carrying one uninterrupted ORF instead. In this work, we investigated a hypothesis that this region represents an intron that is spliced out from part of the Ogre transcripts as a means for preferential production of ORF2-encoded proteins over those encoded by the complete ORF2-ORF3 region. The experiments involved analysis of transcription patterns of well-defined Ogre populations in a model plant Medicago truncatula and examination of transcripts carrying dissected pea Ogre intron expressed within a coding sequence of chimeric reporter gene. Both experimental approaches proved that the region between ORF2 and ORF3 is spliced from Ogre transcripts and showed that this process is only partial, probably due to weak splice signals. This is one of very few known cases of spliced LTR retrotransposons and the only one where splicing does not involve parts of the element's coding sequences, thus resembling intron splicing found in most cellular genes.
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Affiliation(s)
- Veronika Steinbauerová
- Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, 37005 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Pavel Neumann
- Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jiří Macas
- Institute of Plant Molecular Biology, Biology Centre ASCR, Branišovská 31, 37005 České Budějovice, Czech Republic
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15
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Sinck L, Richer D, Howard J, Alexander M, Purcell DFJ, Marquet R, Paillart JC. In vitro dimerization of human immunodeficiency virus type 1 (HIV-1) spliced RNAs. RNA (NEW YORK, N.Y.) 2007; 13:2141-2150. [PMID: 17925344 PMCID: PMC2080610 DOI: 10.1261/rna.678307] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Accepted: 08/28/2007] [Indexed: 05/25/2023]
Abstract
The human immunodeficiency virus type 1 (HIV-1) packages its genomic RNA as a dimer of homologous RNA molecules that has to be selected among a multitude of cellular and viral RNAs. Interestingly, spliced viral mRNAs are packaged into viral particles with a relatively low efficiency despite the fact that they contain most of the extended packaging signal found in the 5' untranslated region of the genomic RNA, including the dimerization initiation site (DIS). As a consequence, HIV-1 spliced viral RNAs can theoretically homodimerize and heterodimerize with the genomic RNA, and thus they should directly compete with genomic RNA for packaging. To shed light on this issue, we investigated for the first time the in vitro dimerization properties of spliced HIV-1 RNAs. We found that singly spliced (env, vpr) and multispliced (tat, rev, and nef) RNA fragments are able to dimerize in vitro, and to efficiently form heterodimers with genomic RNA. Chemical probing experiments and inhibition of RNA dimerization by an antisense oligonucleotide directed against the DIS indicated that the DIS is structurally functional in spliced HIV-1 RNA, and that RNA dimerization occurs through a loop-loop interaction. In addition, by combining in vitro transcription and dimerization assays, we show that heterodimers can be efficiently formed only when the two RNA fragments are synthesized simultaneously, in the same environment. Together, our results support a model in which RNA dimerization would occur during transcription in the nucleus and could thus play a major role in splicing, transport, and localization of HIV-1 RNA.
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Affiliation(s)
- Lucile Sinck
- Architecture et Réactivité de l'ARN, Université Louis Pasteur, CNRS, IBMC, 67084, Strasbourg cedex, France
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16
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Houzet L, Morichaud Z, Mougel M. Fully-spliced HIV-1 RNAs are reverse transcribed with similar efficiencies as the genomic RNA in virions and cells, but more efficiently in AZT-treated cells. Retrovirology 2007; 4:30. [PMID: 17474982 PMCID: PMC1868081 DOI: 10.1186/1742-4690-4-30] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 05/02/2007] [Indexed: 11/10/2022] Open
Abstract
We have shown previously that HIV actively and selectively packages the spliced HIV RNAs into progeny virions. In the present study, by using a RT-QPCR and QPCR strategies, we show that spliced viral RNAs are present in infectious particles and consequently participate, along with the unspliced genomic RNA, to some of the early steps of infection such as the reverse transcription step. This work provides the first quantitative data on reverse transcription of the fully spliced viral RNAs, also called the early transcripts, in target cells but also inside virions. The latter results were obtained by measuring the natural endogenous reverse transcription activity directly on intact HIV-1 particles. Our study reveals that spliced HIV RNAs are reverse transcribed as efficiently as the genomic RNA, both in cells and virions. Interestingly, we also show that reverse transcription of spliced RNAs is 56-fold less sensitive to the inhibitor AZT than reverse transcription of the genomic RNA. Therefore, the selection mediated by inhibitors of reverse transcription used to treat patients could lead to increased representativeness of spliced forms of HIV, thus favoring recombination between the HIV DNA species and facilitating HIV recovery.
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Affiliation(s)
- Laurent Houzet
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France
| | - Zakia Morichaud
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France
| | - Marylène Mougel
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France
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17
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Houzet L, Paillart JC, Smagulova F, Maurel S, Morichaud Z, Marquet R, Mougel M. HIV controls the selective packaging of genomic, spliced viral and cellular RNAs into virions through different mechanisms. Nucleic Acids Res 2007; 35:2695-704. [PMID: 17426127 PMCID: PMC1885669 DOI: 10.1093/nar/gkm153] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In addition to genomic RNA, HIV-1 particles package cellular and spliced viral RNAs. In order to determine the encapsidation mechanisms of these RNAs, we determined the packaging efficiencies and specificities of genomic RNA, singly and fully spliced HIV mRNAs and different host RNAs species: 7SL RNA, U6 snRNA and GAPDH mRNA using RT-QPCR. Except GAPDH mRNA, all RNAs are selectively encapsidated. Singly spliced RNAs, harboring the Rev-responsible element, and fully spliced viral RNAs, which do not contain this motif, are enriched in virions to similar levels, even though they are exported from the nucleus by different routes. Deletions of key motifs (SL1 and/or SL3) of the packaging signal of genomic RNA indicate that HIV and host RNAs are encapsidated through independent mechanisms, while genomic and spliced viral RNA compete for the same trans-acting factor due to the presence of the 5′ common exon containing the TAR, poly(A) and U5-PBS hairpins. Surprisingly, the RNA dimerization initiation site (DIS/SL1) appears to be the main packaging determinant of genomic RNA, but is not involved in packaging of spliced viral RNAs, suggesting a functional interaction with intronic sequences. Active and selective packaging of host and spliced viral RNAs provide new potential functions to these RNAs in the early stages of the virus life cycle.
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Affiliation(s)
- Laurent Houzet
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Jean Christophe Paillart
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Fatima Smagulova
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Stephan Maurel
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Zakia Morichaud
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Roland Marquet
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
| | - Marylène Mougel
- CPBS, UMI, CNRS, 4 bd Henri IV, CS 69033, 34965 Montpellier, France and Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue R. Descartes, 67084 Strabourg, France
- *To whom correspondence should be addressed +33 4 67 60 02 32+33 4 67 60 44 20
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18
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Aguiar RS, Pereira HS, Costa LJ, Brindeiro RM, Tanuri A. Gag-Pol bearing a reverse transcriptase drug-resistant mutation influences viral genomic RNA incorporation into human immunodeficiency virus type 1 particles. J Gen Virol 2006; 87:2669-2677. [PMID: 16894207 DOI: 10.1099/vir.0.82046-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The unspliced human immunodeficiency virus type 1 (HIV-1) RNA is both the messenger for Gag and Gag-Pol and the viral genomic RNA (vRNA) that is packaged into the virion. Although Gag alone is sufficient for the incorporation of vRNA into virus particles, Gag-Pol molecules play an important role in vRNA dimerization and virion maturation. Here, a cis model for vRNA packaging was demonstrated, in which nascent Gag-Pol molecules were preferentially co-encapsulated with their cognate RNA used as the template. Genome-incorporation frequencies were evaluated for two distinct HIV-1 proviral clones differing in their ability to respond to nevirapine (NVP) treatment in one round of infection. It was shown that, under NVP selection, there was a twofold-higher incorporation of vRNAs and integration of provirus genome carrying NVP resistance when compared with the wild-type counterpart. Although cis incorporation has been already demonstrated for Gag, the novelty of these findings is that newly acquired resistant mutations in Gag-Pol will select their specific genomic RNA during virus replication, thus rapidly increasing the chance of the emergence of resistant viruses during the course of anti-retroviral treatment.
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Affiliation(s)
- Renato S Aguiar
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS Bloco A2 sala 121, Cidade Universitária, Ilha do Fundão, 2194421944-970 Rio de Janeiro, Brazil
| | - Helena S Pereira
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS Bloco A2 sala 121, Cidade Universitária, Ilha do Fundão, 2194421944-970 Rio de Janeiro, Brazil
| | - Luciana J Costa
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS Bloco A2 sala 121, Cidade Universitária, Ilha do Fundão, 2194421944-970 Rio de Janeiro, Brazil
| | - Rodrigo M Brindeiro
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS Bloco A2 sala 121, Cidade Universitária, Ilha do Fundão, 2194421944-970 Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS Bloco A2 sala 121, Cidade Universitária, Ilha do Fundão, 2194421944-970 Rio de Janeiro, Brazil
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19
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Clarke JN, Lake JA, Burrell CJ, Wesselingh SL, Gorry PR, Li P. Novel pathway of human immunodeficiency virus type 1 uptake and release in astrocytes. Virology 2006; 348:141-55. [PMID: 16445956 DOI: 10.1016/j.virol.2005.12.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Revised: 10/06/2005] [Accepted: 12/05/2005] [Indexed: 01/08/2023]
Abstract
Astrocytes persistently infected with HIV-1 can transmit virus to CD4+ cells, suggesting that astrocytes may be a source of viral persistence and dissemination in the brain. In the present study, we investigated the fate of HIV-1 upon infection of astrocytes. HIV-1 was observed in vesicle-like structures. Unspliced genomic RNA and extrachromosomal HIV-1 DNA were detected in astrocytes, with levels declining over time. The extrachromosomal viral DNA was not de novo reverse transcribed in astrocytes but most likely the products of intravirion reverse transcription present in the virus inoculum. Integrated HIV-1 DNA was not detected in assays sensitive to detect 2 integrated copies of provirus. However, the majority of astrocyte cultures released infectious virus that could be transmitted to CD4+ cells. Our findings suggest a novel pathway of HIV-1 uptake and release in astrocytes that does not necessarily require virus replication, which may contribute to persistence and spread of HIV-1 in the brain.
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Affiliation(s)
- Jennifer N Clarke
- Australian Centre for HIV and Hepatitis Virology Research, Infectious Diseases Laboratories, Institute of Medical and Veterinary Science, Adelaide, Australia.
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20
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Lavie L, Medstrand P, Schempp W, Meese E, Mayer J. Human endogenous retrovirus family HERV-K(HML-5): status, evolution, and reconstruction of an ancient betaretrovirus in the human genome. J Virol 2004; 78:8788-98. [PMID: 15280487 PMCID: PMC479102 DOI: 10.1128/jvi.78.16.8788-8798.2004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human genome harbors numerous distinct families of so-called human endogenous retroviruses (HERV) which are remnants of exogenous retroviruses that entered the germ line millions of years ago. We describe here the hitherto little-characterized betaretrovirus HERV-K(HML-5) family (named HERVK22 in Repbase) in greater detail. Out of 139 proviruses, only a few loci represent full-length proviruses, and many lack gag protease and/or env gene regions. We generated a consensus sequence from multiple alignment of 62 HML-5 loci that displays open reading frames for the four major retroviral proteins. Four HML-5 long terminal repeat (LTR) subfamilies were identified that are associated with monophyletic proviral bodies, implying different evolution of HML-5 LTRs and genes. Sequence analysis indicated that the proviruses formed approximately 55 million years ago. Accordingly, HML-5 proviral sequences were detected in Old World and New World primates but not in prosimians. No recent activity is associated with this HERV family. We also conclude that the HML-5 consensus sequence primer binding site is identical to methionine tRNA. Therefore, the family should be designated HERV-M. Our study provides important insights into the structure and evolution of the oldest betaretrovirus in the primate genome known to date.
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Affiliation(s)
- Laurence Lavie
- Department of Human Genetics, Building 60, University of Saarland, Medical Faculty, 66421 Homburg, Germany
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