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Vicient CM. Retand LTR-retrotransposons in plants: a long way from pol to 3'LTR. Mob DNA 2025; 16:15. [PMID: 40176144 PMCID: PMC11963269 DOI: 10.1186/s13100-025-00354-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Accepted: 03/17/2025] [Indexed: 04/04/2025] Open
Abstract
BACKGROUND Plant Gypsy LTR-retrotransposons are classified into lineages according to the phylogenetic relationships of the reverse transcriptase. Retand is a lineage of non-chromovirus elements characterized by the presence of a long internal region compared to other lineages. RESULTS This work focuses on the identification and characterization of Potentially Recently Active Retand Elements (PRAREs) in 617 genomic sequence assemblies of Viridiplantae species. The Retand elements were considered PRAREs if their LTRs and insertion sequences were identical, and the sizes of their internal regions and LTRs did not differ by more than 2% from the consensus. A total of 2,735 PRAREs were identified, distributed in 122 clusters corresponding to 34 species, with copy numbers per cluster varying between 1 and 180. They are present in Eudicotyledons and Liliopsida but not in other groups of plants. Some PRAREs are non-autonomous elements, lacking some of the typical LTR retrotransposon coding domains. The size of the POL-3'LTR regions varies between 2,933 and 6,566 bp, and in all cases, includes potential coding regions oriented antisense to the gag and pol genes. 97% of the clusters contain antisense ORFs encoding the TRP28 protein domain of unknown function. The analysis of the consensus TRP28 domain indicates that it probably can bind DNA. About half of the PRAREs contain arrays of tandem repeats in the POL-3'LTR region. CONCLUSIONS The large internal region of the Retand elements is due to the presence of a long POL-3'LTR region. This region frequently contains arrays of tandem repeats that contribute to the expansion of this area. The presence of antisense ORFs in the POL-3'LTR region is also a common feature in these elements, many of which encode proteins with conserved domains, especially the TRP28 domain. The possible function of these TRP28-containing proteins is unknown, but their potential DNA binding capacity and the comparison with similar genes in some retroviruses suggest that they may play a regulatory role in the Retand transposition process.
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Affiliation(s)
- Carlos M Vicient
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
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2
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Vanegas-Torres CA, Schindler M. HIV-1 Vpr Functions in Primary CD4 + T Cells. Viruses 2024; 16:420. [PMID: 38543785 PMCID: PMC10975730 DOI: 10.3390/v16030420] [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: 01/31/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 05/23/2024] Open
Abstract
HIV-1 encodes four accesory proteins in addition to its structural and regulatory genes. Uniquely amongst them, Vpr is abundantly present within virions, meaning it is poised to exert various biological effects on the host cell upon delivery. In this way, Vpr contributes towards the establishment of a successful infection, as evidenced by the extent to which HIV-1 depends on this factor to achieve full pathogenicity in vivo. Although HIV infects various cell types in the host organism, CD4+ T cells are preferentially targeted since they are highly permissive towards productive infection, concomitantly bringing about the hallmark immune dysfunction that accompanies HIV-1 spread. The last several decades have seen unprecedented progress in unraveling the activities Vpr possesses in the host cell at the molecular scale, increasingly underscoring the importance of this viral component. Nevertheless, it remains controversial whether some of these advances bear in vivo relevance, since commonly employed cellular models significantly differ from primary T lymphocytes. One prominent example is the "established" ability of Vpr to induce G2 cell cycle arrest, with enigmatic physiological relevance in infected primary T lymphocytes. The objective of this review is to present these discoveries in their biological context to illustrate the mechanisms whereby Vpr supports HIV-1 infection in CD4+ T cells, whilst identifying findings that require validation in physiologically relevant models.
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Affiliation(s)
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, 72076 Tuebingen, Germany;
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3
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Liu X, Xu M, Li P, Zhang W, Zeng LH, Yang Y, Yang G. Roles of lncRNAs in the transcription regulation of HIV-1. Biomed J 2022; 45:580-593. [PMID: 35364293 PMCID: PMC9486250 DOI: 10.1016/j.bj.2022.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (LncRNAs) is a class of RNA molecules that are more than 200bp but cannot be translated into proteins. More and more studies have proved that lncRNA plays a crucial role in various biological functions and disease processes, including virus infection. It's worth noting that studies have also shown that lncRNAs play an essential role in the pathogenesis of human immunodeficiency virus 1 (HIV-1), one of the lethal virus that can destroy immune system. Although lncRNA-mediated gene regulation involves a variety of mechanisms, such as transcription regulation, translation regulation, protein modification, and the formation of RNA-protein complexes, in this review, we primarily focus on the role of lncRNAs in HIV-1 transcription regulation, which is one of the most important mechanisms that control the activation and development of HIV-1. This review also briefly summarizes the latest research progress of lncRNAs related to HIV-1 infection and its potential application in HIV-1 therapy. Although there are antiretroviral drugs that interfere with the function of HIV-1 virus-encoded proteins, this treatment for the HIV-1 virus is limited by its ability to produce drug resistance. Hence, a further understanding of HIV-1 transcription regulation by lncRNAs might help develop non-traditional antiviral therapy strategies.
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Affiliation(s)
- Xingzhu Liu
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Mengjiao Xu
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Ping Li
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Wenyuan Zhang
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Ling-Hui Zeng
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, 310015, China.
| | - Yadong Yang
- Institute of Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Geng Yang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, 310015, China.
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4
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Zeng X, Tsui JCC, Shi M, Peng J, Cao CY, Kan LLY, Lau CPY, Liang Y, Wang L, Liu L, Chen Z, Tsui SKW. Genome-Wide Characterization of Host Transcriptional and Epigenetic Alterations During HIV Infection of T Lymphocytes. Front Immunol 2020; 11:2131. [PMID: 33013899 PMCID: PMC7511662 DOI: 10.3389/fimmu.2020.02131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Background and methods: Host genomic alterations are closely related to dysfunction of CD4+ T lymphocytes in the HIV-host interplay. However, the roles of aberrant DNA methylation and gene expression in the response to HIV infection are not fully understood. We investigated the genome-wide DNA methylation and transcriptomic profiles in two HIV-infected T lymphocyte cell lines using high-throughput sequencing. Results: Based on DNA methylation data, we identified 3,060 hypomethylated differentially methylated regions (DMRs) and 2,659 hypermethylated DMRs in HIV-infected cells. Transcription-factor-binding motifs were significantly associated with methylation alterations, suggesting that DNA methylation modulates gene expression by affecting the binding to transcription factors during HIV infection. In support of this hypothesis, genes with promoters overlapping with DMRs were enriched in the biological function related to transcription factor activities. Furthermore, the analysis of gene expression data identified 1,633 upregulated genes and 2,142 downregulated genes on average in HIV-infected cells. These differentially expressed genes (DEGs) were significantly enriched in apoptosis-related pathways. Our results suggest alternative splicing as an additional mechanism that may contribute to T-cell apoptosis during HIV infection. We also demonstrated a genome-scale correlation between DNA methylation and gene expression in HIV-infected cells. We identified 831 genes with alterations in both DNA methylation and gene expression, which were enriched in apoptosis. Our results were validated using various experimental methods. In addition, consistent with our in silico results, a luciferase assay showed that the activity of the PDX1 and SMAD3 promoters was significantly decreased in the presence of HIV proteins, indicating the potential of these genes as genetic markers of HIV infection. Conclusions: Our results suggest important roles for DNA methylation and gene expression regulation in T-cell apoptosis during HIV infection. We propose a list of novel genes related to these processes for further investigation. This study also provides a comprehensive characterization of changes occurring at the transcriptional and epigenetic levels in T cells in response to HIV infection.
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Affiliation(s)
- Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Chi-Ching Tsui
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Peng
- Acquired Immunodeficiency Syndrome (AIDS) Institute, The University of Hong Kong, Hong Kong, China
| | - Cyanne Ye Cao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lea Ling-Yu Kan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Carol Po-Ying Lau
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yonghao Liang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lingyi Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Li Liu
- Acquired Immunodeficiency Syndrome (AIDS) Institute, The University of Hong Kong, Hong Kong, China
| | - Zhiwei Chen
- Acquired Immunodeficiency Syndrome (AIDS) Institute, The University of Hong Kong, Hong Kong, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China
- Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong, China
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5
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Wallet C, Rohr O, Schwartz C. Evolution of a concept: From accessory protein to key virulence factor, the case of HIV-1 Vpr. Biochem Pharmacol 2020; 180:114128. [PMID: 32619426 DOI: 10.1016/j.bcp.2020.114128] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 12/12/2022]
Abstract
Back in 1989 some studies have shown that the viral protein Vpr was dispensable for HIV-1 replication in vitro. From then the concept of accessory or auxiliary protein for Vpr has emerged and it is still used to date. However, Vpr soon appeared to be very important for in vivo virus spread and pathogenesis. Vpr has been involved in many biological functions including regulation of reverse transcriptase activity, the nuclear import of the pre-integration complex (PIC), HIV-1 transcription, gene splicing, apoptosis and in cell cycle arrest. Thus, we might rather consider Vpr as a true virulence factor instead of just an accessory factor. At present, Vpr can be regarded as a potential and promising target in different strategies aiming to fight infected cells including latently infected cells.
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Affiliation(s)
- Clémentine Wallet
- University of Strasbourg, Research Unit7292, DHPI, IUT Louis Pasteur, Schiltigheim, France
| | - Olivier Rohr
- University of Strasbourg, Research Unit7292, DHPI, IUT Louis Pasteur, Schiltigheim, France
| | - Christian Schwartz
- University of Strasbourg, Research Unit7292, DHPI, IUT Louis Pasteur, Schiltigheim, France.
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6
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Abstract
The discovery of long non-coding RNAs (lncRNAs) and the elucidation of the mechanisms by which they affect different disease states are providing researchers with a better understanding of a wide array of disease pathways. Moreover, lncRNAs are presenting themselves as both unique diagnostic biomarkers as well as novel targets against which to develop new therapeutics. Here we will explore the intricate network of non-coding RNAs associated with infection by the human immunodeficiency virus (HIV). Non-coding RNAs derived from both the human host as well as those from HIV itself are emerging as important regulatory elements. We discuss here the various mechanisms through which both small and long non-coding RNAs impact viral replication, pathogenesis and disease progression. Given the lack of an effective vaccine or cure for HIV and the scale of the current pandemic, a deeper understanding of the complex interplay between non-coding RNAs and HIV will support the development of innovative strategies for the treatment of HIV/acquired immunodeficiency disease (AIDS).
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Affiliation(s)
- Daniel C Lazar
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA; School of Biotechnology and Biomedical Sciences, University of New South Wales, Kensington, NSW, Australia.
| | - Sheena M Saayman
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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7
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Abstract
Dinucleotide usage is known to vary in the genomes of organisms. The dinucleotide usage profiles or genome signatures are similar for sequence samples taken from the same genome, but are different for taxonomically distant species. This concept of genome signatures has been used to study several organisms including viruses, to elucidate the signatures of evolutionary processes at the genome level. Genome signatures assume greater importance in the case of host-pathogen interactions, where molecular interactions between the two species take place continuously, and can influence their genomic composition. In this study, analyses of whole genome sequences of the HIV-1 subtype B, a retrovirus that caused global pandemic of AIDS, have been carried out to analyse the variation in genome signatures of the virus from 1983 to 2007. We show statistically significant temporal variations in some dinucleotide patterns highlighting the selective evolution of the dinucleotide profiles of HIV-1 subtype B, possibly a consequence of host specific selection.
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8
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Abstract
Numerous viral vectors have been developed for the delivery of transgenes to specific target cells. For persistent transgene expression, vectors based on retroviruses are attractive delivery vehicles because of their ability to stably integrate their DNA into the host cell genome. Initially, vectors based on simple retroviruses were the vector of choice for such applications. However, these vectors can only transduce actively dividing cells. Therefore, much interest has turned to retroviral vectors based on the lentivirus genus because of their ability to transduce both dividing and non-dividing cells. The best characterized lentiviral vectors are derived from the human immunodeficiency virus type 1 (HIV-1). This chapter describes the basic features of the HIV-1 replication cycle and the many improvements reported for the lentiviral vector systems to increase the safety and efficiency. We also provide practical information on the production of HIV-1 derived lentiviral vectors, the cell transduction protocol and a method to determine the transduction titers of a lentiviral vector.
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Affiliation(s)
- Ying Poi Liu
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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9
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Xue B, Mizianty MJ, Kurgan L, Uversky VN. Protein intrinsic disorder as a flexible armor and a weapon of HIV-1. Cell Mol Life Sci 2012; 69:1211-59. [PMID: 22033837 PMCID: PMC11114566 DOI: 10.1007/s00018-011-0859-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/28/2011] [Accepted: 10/03/2011] [Indexed: 01/19/2023]
Abstract
Many proteins and protein regions are disordered in their native, biologically active states. These proteins/regions are abundant in different organisms and carry out important biological functions that complement the functional repertoire of ordered proteins. Viruses, with their highly compact genomes, small proteomes, and high adaptability for fast change in their biological and physical environment utilize many of the advantages of intrinsic disorder. In fact, viral proteins are generally rich in intrinsic disorder, and intrinsically disordered regions are commonly used by viruses to invade the host organisms, to hijack various host systems, and to help viruses in accommodation to their hostile habitats and to manage their economic usage of genetic material. In this review, we focus on the structural peculiarities of HIV-1 proteins, on the abundance of intrinsic disorder in viral proteins, and on the role of intrinsic disorder in their functions.
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Affiliation(s)
- Bin Xue
- Department of Molecular Medicine, University of South Florida, College of Medicine, 12901 Bruce B. Downs Blvd, MDC07, Tampa, FL 33612 USA
| | - Marcin J. Mizianty
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4 Canada
| | - Lukasz Kurgan
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4 Canada
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, College of Medicine, 12901 Bruce B. Downs Blvd, MDC07, Tampa, FL 33612 USA
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region Russia
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10
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Pandit A, Sinha S. Differential trends in the codon usage patterns in HIV-1 genes. PLoS One 2011; 6:e28889. [PMID: 22216135 PMCID: PMC3245234 DOI: 10.1371/journal.pone.0028889] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 11/16/2011] [Indexed: 12/27/2022] Open
Abstract
Host-pathogen interactions underlie one of the most complex evolutionary phenomena resulting in continual adaptive genetic changes, where pathogens exploit the host's molecular resources for growth and survival, while hosts try to eliminate the pathogen. Deciphering the molecular basis of host-pathogen interactions is useful in understanding the factors governing pathogen evolution and disease propagation. In host-pathogen context, a balance between mutation, selection, and genetic drift is known to maintain codon bias in both organisms. Studies revealing determinants of the bias and its dynamics are central to the understanding of host-pathogen evolution. We considered the Human Immunodeficiency Virus (HIV) type 1 and its human host to search for evolutionary signatures in the viral genome. Positive selection is known to dominate intra-host evolution of HIV-1, whereas high genetic variability underlies the belief that neutral processes drive inter-host differences. In this study, we analyze the codon usage patterns of HIV-1 genomes across all subtypes and clades sequenced over a period of 23 years. We show presence of unique temporal correlations in the codon bias of three HIV-1 genes illustrating differential adaptation of the HIV-1 genes towards the host preferred codons. Our results point towards gene-specific translational selection to be an important force driving the evolution of HIV-1 at the population level.
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Affiliation(s)
- Aridaman Pandit
- Mathematical Modeling and Computational Biology Group, Centre for Cellular & Molecular Biology (CSIR), Hyderabad, Andhra Pradesh, India
| | - Somdatta Sinha
- Mathematical Modeling and Computational Biology Group, Centre for Cellular & Molecular Biology (CSIR), Hyderabad, Andhra Pradesh, India
- Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
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11
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The HIV-1 Vpu viroporin inhibitor BIT225 does not affect Vpu-mediated tetherin antagonism. PLoS One 2011; 6:e27660. [PMID: 22110710 PMCID: PMC3215742 DOI: 10.1371/journal.pone.0027660] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 10/21/2011] [Indexed: 12/14/2022] Open
Abstract
Among its many roles, the HIV-1 accessory protein Vpu performs a viroporin function and also antagonizes the host cell restriction factor tetherin through its transmembrane domain. BIT225 is a small molecule inhibitor that specifically targets the Vpu viroporin function, which, in macrophages, resulted in late stage inhibition of virus release and decreased infectivity of released virus, a phenotype similar to tetherin-mediated restriction. Here, we investigated whether BIT225 might mediate its antiviral function, at least in part, via inhibition of Vpu-mediated tetherin antagonism. Using T-cell lines inducible for tetherin expression, we found that BIT225 does not exert its antiviral function by inhibiting Vpu-mediated tetherin downmodulation from the cell surface, the main site of action of tetherin activity. In addition, results from a bioluminescence resonance energy transfer (BRET) assay showed that the Vpu-tetherin interaction was not affected by BIT225. Our data provide support for the concept that tetherin antagonism and viroporin function are separable on the Vpu transmembrane and that viroporin function might be cell-type dependent. Further, this work contributes to the characterization of BIT225 as an inhibitor that specifically targets the viroporin function of Vpu.
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12
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Kuhl BD, Cheng V, Wainberg MA, Liang C. Tetherin and its viral antagonists. J Neuroimmune Pharmacol 2011; 6:188-201. [PMID: 21222046 PMCID: PMC3087111 DOI: 10.1007/s11481-010-9256-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 12/27/2010] [Indexed: 12/13/2022]
Abstract
Restriction factors comprise an important layer of host defense to fight against viral infection. Some restriction factors are constitutively expressed whereas the majority is induced by interferon to elicit innate immunity. In addition to a number of well-characterized interferon-inducible antiviral factors such as RNaseL/OAS, ISG15, Mx, PKR, and ADAR, tetherin (BST-2/CD317/HM1.24) was recently discovered to block the release of enveloped viruses from the cell surface, which is regarded as a novel antiviral mechanism induced by interferon. Here, we briefly review the history of tetherin discovery, discuss how tetherin blocks virus production, and highlight the viral countermeasures to evade tetherin restriction.
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Affiliation(s)
- Björn D Kuhl
- McGill AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montréal, Quebec, Canada H3T 1E2
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13
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Hauser H, Lopez LA, Yang SJ, Oldenburg JE, Exline CM, Guatelli JC, Cannon PM. HIV-1 Vpu and HIV-2 Env counteract BST-2/tetherin by sequestration in a perinuclear compartment. Retrovirology 2010; 7:51. [PMID: 20529266 PMCID: PMC2890665 DOI: 10.1186/1742-4690-7-51] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2010] [Accepted: 06/07/2010] [Indexed: 12/30/2022] Open
Abstract
Background In the absence of the Vpu protein, newly formed HIV-1 particles can remain attached to the surface of human cells due to the action of an interferon-inducible cellular restriction factor, BST-2/tetherin. Tetherin also restricts the release of other enveloped viral particles and is counteracted by a several viral anti-tetherin factors including the HIV-2 Env, SIV Nef and KSHV K5 proteins. Results We observed that a fraction of tetherin is located at the surface of restricting cells, and that co-expression of both HIV-1 Vpu and HIV-2 Env reduced this population. In addition, Vpu, but not the HIV-2 Env, reduced total cellular levels of tetherin. An additional effect observed for both Vpu and the HIV-2 Env was to redirect tetherin to an intracellular perinuclear compartment that overlapped with markers for the TGN (trans-Golgi network). Sequestration of tetherin in this compartment was independent of tetherin's normal endocytosis trafficking pathway. Conclusions Both HIV-1 Vpu and HIV-2 Env redirect tetherin away from the cell surface and sequester the protein in a perinuclear compartment, which likely blocks the action of this cellular restriction factor. Vpu also promotes the degradation of tetherin, suggesting that it uses more than one mechanism to counteract tetherin restriction.
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Affiliation(s)
- Heiko Hauser
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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14
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Romani B, Engelbrecht S, Glashoff RH. Antiviral roles of APOBEC proteins against HIV-1 and suppression by Vif. Arch Virol 2009; 154:1579-88. [DOI: 10.1007/s00705-009-0481-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Accepted: 07/22/2009] [Indexed: 01/18/2023]
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15
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Romani B, Engelbrecht S. Human immunodeficiency virus type 1 Vpr: functions and molecular interactions. J Gen Virol 2009; 90:1795-1805. [PMID: 19458171 DOI: 10.1099/vir.0.011726-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) viral protein R (Vpr) is an accessory protein that interacts with a number of cellular and viral proteins. The functions of many of these interactions in the pathogenesis of HIV-1 have been identified. Deletion of the vpr gene reduces the virulence of HIV-1 dramatically, indicating the importance of this protein for the virus. This review describes the current findings on several established functions of HIV-1 Vpr and some possible roles proposed for this protein. Because Vpr exploits cellular proteins and pathways to influence the biology of HIV-1, understanding the functions of Vpr usually involves the study of cellular pathways. Several functions of Vpr are attributed to the virion-incorporated protein, but some of them are attributed to the expression of Vpr in HIV-1-infected cells. The structure of Vpr may be key to understanding the variety of its interactions. Due to the critical role of Vpr in HIV-1 pathogenicity, study of the interactions between Vpr and cellular proteins may help us to understand the mechanism(s) of HIV-1 pathogenicity.
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Affiliation(s)
- Bizhan Romani
- Department of Pathology, Division of Medical Virology, University of Stellenbosch, Tygerberg 7505, South Africa
| | - Susan Engelbrecht
- National Health Laboratory Services, Tygerberg 7505, South Africa.,Department of Pathology, Division of Medical Virology, University of Stellenbosch, Tygerberg 7505, South Africa
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16
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Keriel A, Mahuteau-Betzer F, Jacquet C, Plays M, Grierson D, Sitbon M, Tazi J. Protection against retrovirus pathogenesis by SR protein inhibitors. PLoS One 2009; 4:e4533. [PMID: 19225570 PMCID: PMC2640060 DOI: 10.1371/journal.pone.0004533] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 12/12/2008] [Indexed: 11/18/2022] Open
Abstract
Indole derivatives compounds (IDC) are a new class of splicing inhibitors that have a selective action on exonic splicing enhancers (ESE)-dependent activity of individual serine-arginine-rich (SR) proteins. Some of these molecules have been shown to compromise assembly of HIV infectious particles in cell cultures by interfering with the activity of the SR protein SF2/ASF and by subsequently suppressing production of splicing-dependent retroviral accessory proteins. For all replication-competent retroviruses, a limiting requirement for infection and pathogenesis is the expression of the envelope glycoprotein which strictly depends on the host splicing machinery. Here, we have evaluated the efficiency of IDC on an animal model of retroviral pathogenesis using a fully replication-competent retrovirus. In this model, all newborn mice infected with a fully replicative murine leukemia virus (MLV) develop erythroleukemia within 6 to 8 weeks of age. We tested several IDC for their ability to interfere ex vivo with MLV splicing and virus spreading as well as for their protective effect in vivo. We show here that two of these IDC, IDC13 and IDC78, selectively altered splicing-dependent production of the retroviral envelope gene, thus inhibiting early viral replication in vivo, sufficiently to protect mice from MLV-induced pathogenesis. The apparent specificity and clinical safety observed here for both IDC13 and IDC78 strongly support further assessment of inhibitors of SR protein splicing factors as a new class of antiretroviral therapeutic agents.
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Affiliation(s)
- Anne Keriel
- Université Montpellier 2 Université Montpellier 1 CNRS, Institut de Génétique Moléculaire de Montpellier (IGMM), UMR5535, IFR122, Montpellier, France
| | - Florence Mahuteau-Betzer
- Laboratoire de Pharmaco-chimie, CNRS-Institut Curie, UMR 176 Bat 110 Centre Universitaire, Orsay, France
| | - Chantal Jacquet
- Université Montpellier 2 Université Montpellier 1 CNRS, Institut de Génétique Moléculaire de Montpellier (IGMM), UMR5535, IFR122, Montpellier, France
| | - Marc Plays
- Université Montpellier 2 Université Montpellier 1 CNRS, Institut de Génétique Moléculaire de Montpellier (IGMM), UMR5535, IFR122, Montpellier, France
| | - David Grierson
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc Sitbon
- Université Montpellier 2 Université Montpellier 1 CNRS, Institut de Génétique Moléculaire de Montpellier (IGMM), UMR5535, IFR122, Montpellier, France
- * E-mail: (MS); (JT)
| | - Jamal Tazi
- Université Montpellier 2 Université Montpellier 1 CNRS, Institut de Génétique Moléculaire de Montpellier (IGMM), UMR5535, IFR122, Montpellier, France
- * E-mail: (MS); (JT)
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17
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Biesinger T, Kimata JT. HIV-1 Transmission, Replication Fitness and Disease Progression. Virology (Auckl) 2008. [DOI: 10.4137/vrt.s860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Upon transmission, human immunodeficiency virus type 1 (HIV-1) establishes infection of the lymphatic reservoir, leading to profound depletion of the memory CD4+ T cell population despite the induction of the adaptive immune response. The rapid evolution and association of viral variants having distinct characteristics during different stages of infection, the level of viral burden, and rate of disease progression suggest a role for viral variants in this process. Here, we review the literature on HIV-1 variants and disease and discuss the importance of viral fitness for transmission and disease.
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Affiliation(s)
- Tasha Biesinger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030. U.S.A
| | - Jason T. Kimata
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030. U.S.A
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Nef-mediated enhancement of virion infectivity and stimulation of viral replication are fundamental properties of primate lentiviruses. J Virol 2007; 81:13852-64. [PMID: 17928336 DOI: 10.1128/jvi.00904-07] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Nef is a multifunctional accessory protein of primate lentiviruses. Recently, it has been shown that the ability of Nef to downmodulate CD4, CD28, and class I major histocompatibility complex is highly conserved between most or all primate lentiviruses, whereas Nef-mediated downregulation of T-cell receptor-CD3 was lost in the lineage that gave rise to human immunodeficiency virus type 1 (HIV-1). Whether or not other Nef activities are preserved between different groups of primate lentiviruses remained to be determined. Here, we show that nef genes from a large variety of HIVs and simian immunodeficiency viruses (SIVs) enhance virion infectivity and stimulate viral replication in human cells and/or in ex vivo infected human lymphoid tissue (HLT). Notably, nef alleles from unpassaged SIVcpz and SIVsmm enhanced viral infectivity, replication, and cytopathicity in cell culture and in ex vivo infected HLT as efficiently as those from HIV-1 and HIV-2, their human counterparts. Furthermore, nef genes from several highly divergent SIVs that have not been found in humans were also highly active in human cells and/or tissues. Thus, most primate lentiviral Nefs enhance virion infectivity and stimulate viral replication. Moreover, our data show that SIVcpz and SIVsmm Nefs do not require adaptive changes to perform these functions in human cells or tissues and support the idea that nef alleles from other primate lentiviruses would also be capable of promoting efficient virus spread in humans.
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Schindler M, Rajan D, Specht A, Ritter C, Pulkkinen K, Saksela K, Kirchhoff F. Association of Nef with p21-activated kinase 2 is dispensable for efficient human immunodeficiency virus type 1 replication and cytopathicity in ex vivo-infected human lymphoid tissue. J Virol 2007; 81:13005-14. [PMID: 17881449 PMCID: PMC2169106 DOI: 10.1128/jvi.01436-07] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Interaction of the human immunodeficiency virus type 1 (HIV-1) Nef protein with p21-activated kinase 2 (PAK2) has been proposed to play a role in T-cell activation, viral replication, apoptosis, and progression to AIDS. However, these hypotheses were based on results obtained using Nef mutants impaired in multiple functions. Recently, it was reported that Nef residue F191 is specifically involved in PAK2 binding. However, only a limited number of Nef activities were investigated in these studies. To further evaluate the role of F191 in Nef function and to elucidate the biological relevance of Nef-PAK2 interaction, we performed a comprehensive analysis of HIV-1 Nef mutants carrying F191H and F191R mutations. We found that the F191H mutation reduces and the F191R mutation disrupts the association of Nef with PAK2. Both mutants upregulated the major histocompatibility complex II (MHC-II)-associated invariant chain and downregulated CD4, MHC-I, and CD28, although with reduced efficiency for the latter. Furthermore, the F191H/R changes neither affected the levels of interleukin-2 receptor expression and apoptosis of HIV-1-infected primary T cells nor reduced Nef-mediated induction of NFAT. Unexpectedly, the F191H change markedly reduced and the F191R mutation disrupted the ability of Nef to enhance virion infectivity in P4-CCR5 indicator cells but not in TZM-bl cells or peripheral blood mononuclear cells. Most importantly, all HIV-1 Nef mutants replicated efficiently and caused CD4+ T-cell depletion in ex vivo-infected human lymphoid tissue. Altogether, our data show that the interaction of Nef with PAK2 does not play a major role in T-cell activation, viral replication, and apoptosis.
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20
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Wolfrum N, Mühlebach MD, Schüle S, Kaiser JK, Kloke BP, Cichutek K, Schweizer M. Impact of viral accessory proteins of SIVsmmPBj on early steps of infection of quiescent cells. Virology 2007; 364:330-41. [PMID: 17418360 DOI: 10.1016/j.virol.2007.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 12/21/2006] [Accepted: 03/05/2007] [Indexed: 11/24/2022]
Abstract
Although lentiviruses like HIV-1 are able to infect non-dividing cells, particular resting cells such as non-stimulated primary peripheral blood mononuclear cells (PBMC) are resistant to infection. In contrast to other lentiviruses, SIVsmmPBj can replicate in non-stimulated PBMC. Moreover, SIVsmmPBj-derived, but not HIV-1-derived, replication-incompetent vectors enable gene transfer into G(0)-arrested human cell lines and primary human monocytes. Here, we demonstrate that transduction of G(0)-arrested cell lines by SIVsmmPBj-derived vectors is independent of the viral accessory proteins Vif, Vpx, Vpr, or Nef. In contrast, for the transduction of primary human monocytes, the Vpx protein proved to be essential. However, trans-complementation of HIV-1 vectors with SIVsmmPBj Vpx did not provide the property of gene transfer into monocytes. Taken together, these data indicate that Vpx is essential for the infection of primary monocytes by SIVsmmPBj. Additionally, further genome functions besides the accessory proteins are required for the particular capacity of SIVsmmPBj in transduction or infection events.
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Affiliation(s)
- Nina Wolfrum
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Strasse 51-59, Langen, Germany
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21
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Anderson JL, Johnson AT, Howard JL, Purcell DFJ. Both linear and discontinuous ribosome scanning are used for translation initiation from bicistronic human immunodeficiency virus type 1 env mRNAs. J Virol 2007; 81:4664-76. [PMID: 17329338 PMCID: PMC1900145 DOI: 10.1128/jvi.01028-06] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) generates 16 alternatively spliced isoforms of env mRNA that contain the same overlapping open reading frames for Vpu and Env proteins but differ in their 5' untranslated regions (UTR). A subset of env mRNAs carry the extra upstream Rev initiation codon in the 5' UTR. We explored the effect of the alternative UTR on the translation of Vpu and Env proteins from authentic env mRNAs expressed from cDNA constructs. Vpu expression from the subset of env mRNA isoforms with exons containing an upstream Rev AUG codon was minimal. However, every env mRNA isoform expressed similar levels of Env protein. Mutations that removed, altered the strength of, or introduced upstream AUG codons dramatically altered Vpu expression but had little impact on the consistent expression of Env. These data show that the different isoforms of env mRNA are not redundant but instead regulate Vpu production in HIV-1-infected cells. Furthermore, while the initiation of Vpu translation conforms to the leaky ribosome-scanning model, the consistent Env synthesis infers a novel, discontinuous ribosome-scanning mechanism to translate Env.
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Affiliation(s)
- Jenny L Anderson
- Department of Microbiology and Immunology, The University of Melbourne, Parkville 3010, Victoria, Australia
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22
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Venkatachari NJ, Majumder B, Ayyavoo V. Human immunodeficiency virus (HIV) type 1 Vpr induces differential regulation of T cell costimulatory molecules: Direct effect of Vpr on T cell activation and immune function. Virology 2007; 358:347-56. [PMID: 17023015 DOI: 10.1016/j.virol.2006.08.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 07/18/2006] [Accepted: 08/22/2006] [Indexed: 10/24/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) viral proteins disrupt the normal host cellular immune pathways thus exploiting the cellular machinery for replication, survival and to escape host immune attack. Here we evaluated the direct effects of HIV-1 Vpr-mediated immune modulation of infected T cells. Vpr specifically downregulated the expression of CD28 and increased the expression of CTLA-4, whereas no significant difference in the expression of CD25 and HLA-DR was observed. Interferon gamma (IFN-gamma) production in T cells was evaluated as a measure of the downstream effector functions. Results indicate that Vpr significantly inhibited IFN-gamma production and this may, in part, due to Vpr's ability to inhibit the nuclear translocation of NF-kappaB, and its transcriptional regulation. Together these results support that HIV-1 Vpr selectively dysregulates the immune functions at multiple levels and exerts its inhibitory effects in the presence of other viral proteins.
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Affiliation(s)
- Narasimhan J Venkatachari
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, 130 Desoto Street, Pittsburgh, PA 15261, USA
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23
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Abstract
Several innate immune mechanisms exist in mammalian cells that prevent the replication of viruses. These cellular factors influence the tropism of retroviruses in mammalian cells by inducing a dominant restriction that acts after viral entry but before integration into the host genome. The identification of several cellular factors involved with the post entry block of HIV has recently been revealed. These recent advances identified the tripartite motif protein 5alpha (Trim5alpha) and the apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3G (APOBEC3G), which work to inactivate several retroviruses including HIV-1. The mechanism of restriction by these cellular proteins is unknown. Therefore, this review highlights recent advances in understanding the function of Trim5alpha and APOBEC3G.
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Affiliation(s)
- Omar Perez
- Department of Cell and Molecular Biology, Northwestern University, 303 East Chicago Avenue, Chicago, Illinois 60611-3008, USA
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24
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Abstract
Retroviruses are efficient vehicles for delivering transgenes in vivo. Their ability to integrate into the host genome, providing a permanent imprint of their genes in the host, is a key asset for gene therapy. Furthermore, the lentivirus subset of retroviruses can infect nondividing as well as dividing cells. This expands the cell types capable of gene therapy, driving the development of lentiviral vectors. However, the precise mechanisms used by different retroviruses to efficiently deliver their genes into cell nuclei remains largely unclear. Understanding these molecular mechanisms may reveal features to improve the efficacy of current retroviral vectors. Moreover, this knowledge may expose elements pliable to other gene therapy vehicles to improve their in vivo performance and circumvent the biosafety concerns of using retroviral vectors. Therefore, the mechanisms underlying the early trafficking of retroviral vectors in host cells are reviewed here, as understood from studying the native retroviruses. Events after virus entry up to nuclear delivery of the viral cDNA are discussed. Cellular obstacles faced by these retroviral vectors and how they advance beyond these barriers is emphasized.
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Affiliation(s)
- J L Anderson
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611-3093, USA
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