1
|
Abstract
The HIV genome encodes a small number of viral proteins (i.e., 16), invariably establishing cooperative associations among HIV proteins and between HIV and host proteins, to invade host cells and hijack their internal machineries. As a known example, the HIV envelope glycoprotein GP120 is closely associated with GP41 for viral entry. From a genome-wide perspective, a hypothesis can be worked out to determine whether 16 HIV proteins could develop 120 possible pairwise associations either by physical interactions or by functional associations mediated via HIV or host molecules. Here, we present the first systematic review of experimental evidence on HIV genome-wide protein associations using a large body of publications accumulated over the past 3 decades. Of 120 possible pairwise associations between 16 HIV proteins, at least 34 physical interactions and 17 functional associations have been identified. To achieve efficient viral replication and infection, HIV protein associations play essential roles (e.g., cleavage, inhibition, and activation) during the HIV life cycle. In either a dispensable or an indispensable manner, each HIV protein collaborates with another viral protein to accomplish specific activities that precisely take place at the proper stages of the HIV life cycle. In addition, HIV genome-wide protein associations have an impact on anti-HIV inhibitors due to the extensive cross talk between drug-inhibited proteins and other HIV proteins. Overall, this study presents for the first time a comprehensive overview of HIV genome-wide protein associations, highlighting meticulous collaborations between all viral proteins during the HIV life cycle.
Collapse
Affiliation(s)
- Guangdi Li
- Department of Metabolism and Endocrinology, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China KU Leuven-University of Leuven, Rega Institute for Medical Research, Department of Microbiology and Immunology, Leuven, Belgium
| | - Erik De Clercq
- KU Leuven-University of Leuven, Rega Institute for Medical Research, Department of Microbiology and Immunology, Leuven, Belgium
| |
Collapse
|
2
|
HIV Genome-Wide Protein Associations: a Review of 30 Years of Research. Microbiol Mol Biol Rev 2016; 80:679-731. [PMID: 27357278 DOI: 10.1128/mmbr.00065-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The HIV genome encodes a small number of viral proteins (i.e., 16), invariably establishing cooperative associations among HIV proteins and between HIV and host proteins, to invade host cells and hijack their internal machineries. As a known example, the HIV envelope glycoprotein GP120 is closely associated with GP41 for viral entry. From a genome-wide perspective, a hypothesis can be worked out to determine whether 16 HIV proteins could develop 120 possible pairwise associations either by physical interactions or by functional associations mediated via HIV or host molecules. Here, we present the first systematic review of experimental evidence on HIV genome-wide protein associations using a large body of publications accumulated over the past 3 decades. Of 120 possible pairwise associations between 16 HIV proteins, at least 34 physical interactions and 17 functional associations have been identified. To achieve efficient viral replication and infection, HIV protein associations play essential roles (e.g., cleavage, inhibition, and activation) during the HIV life cycle. In either a dispensable or an indispensable manner, each HIV protein collaborates with another viral protein to accomplish specific activities that precisely take place at the proper stages of the HIV life cycle. In addition, HIV genome-wide protein associations have an impact on anti-HIV inhibitors due to the extensive cross talk between drug-inhibited proteins and other HIV proteins. Overall, this study presents for the first time a comprehensive overview of HIV genome-wide protein associations, highlighting meticulous collaborations between all viral proteins during the HIV life cycle.
Collapse
|
3
|
Nkeze J, Li L, Benko Z, Li G, Zhao RY. Molecular characterization of HIV-1 genome in fission yeast Schizosaccharomyces pombe. Cell Biosci 2015; 5:47. [PMID: 26309721 PMCID: PMC4549081 DOI: 10.1186/s13578-015-0037-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/27/2015] [Indexed: 11/25/2022] Open
Abstract
Background The human immunodeficiency virus type 1 (HIV-1) genome (~9 kb RNA) is flanked by two long terminal repeats (LTR) promoter regions with nine open reading frames, which encode Gag, Pol and Env polyproteins, four accessory proteins (Vpu, Vif, Vpr, Nef) and two regulatory proteins (Rev, Tat). In this study, we carried out a genome-wide and functional analysis of the HIV-1 genome in fission yeast (Schizosaccharomyces pombe). Results Each one of the HIV-1 genes was cloned and expressed individually in fission yeast. Subcellular localization of each viral protein was first examined. The effect of protein expression on cellular proliferation and colony formations, an indication of cytotoxicity, were observed. Overall, there is a general correlation of subcellular localization of each viral protein between fission yeast and mammalian cells. Three viral proteins, viral protein R (Vpr), protease (PR) and regulator of expression of viral protein (Rev), were found to inhibit cellular proliferation. Rev was chosen for further analysis in fission yeast and mammalian cells. Consistent with the observation in fission yeast, expression of HIV-1 rev gene also caused growth retardation in mammalian cells. However, the observed growth delay was neither due to the cytotoxic effect nor due to alterations in cell cycling. Mechanistic testing of the Rev effect suggests it triggers transient induction of cellular oxidative stress. Conclusions Some of the behavioral and functional similarities of Rev between fission yeast and mammalian cells suggest fission yeast might be a useful model system for further studies of molecular functions of Rev and other HIV-1 viral proteins.
Collapse
Affiliation(s)
- Joseph Nkeze
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA
| | - Lin Li
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,AIDS Research Department, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Zsigmond Benko
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Ge Li
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA
| | - Richard Y Zhao
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA
| |
Collapse
|
4
|
Gautam A, Bhattacharya J. Evidence that Vpu modulates HIV-1 Gag-envelope interaction towards envelope incorporation and infectivity in a cell type dependent manner. PLoS One 2013; 8:e61388. [PMID: 23613843 PMCID: PMC3628852 DOI: 10.1371/journal.pone.0061388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 03/08/2013] [Indexed: 12/03/2022] Open
Abstract
The HIV-1 Vpu is required for efficient virus particle release from the plasma membrane and intracellular CD4 degradation in infected cells. In the present study, we found that the loss of virus infectivity as a result of envelope (Env) incorporation defect caused by a Gag matrix (MA) mutation (L30E) was significantly alleviated by introducing a start codon mutation in vpu. Inactivation of Vpu partially restored the Env incorporation defect imposed by L30E substitution in MA. This effect was found to be comparable in cell types such as 293T, HeLa, NP2 and GHOST as well as in peripheral blood mononuclear cells (PBMC) and monocyte-derived macrophages (MDM). However, in HeLa cells BST-2 knockdown was found to further alleviate the effect of Vpu inactivation on infectivity of L30E mutant. Our data demonstrated that the impaired infectivity of virus particles due to Env incorporation defect caused by MA mutation was modulated by start codon mutation in Vpu.
Collapse
Affiliation(s)
- Archana Gautam
- Department of Molecular Virology, National AIDS Research Institute, Bhosari, Pune, India
| | - Jayanta Bhattacharya
- Department of Molecular Virology, National AIDS Research Institute, Bhosari, Pune, India
| |
Collapse
|
5
|
Neil SJD, Eastman SW, Jouvenet N, Bieniasz PD. HIV-1 Vpu promotes release and prevents endocytosis of nascent retrovirus particles from the plasma membrane. PLoS Pathog 2006; 2:e39. [PMID: 16699598 PMCID: PMC1458960 DOI: 10.1371/journal.ppat.0020039] [Citation(s) in RCA: 218] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Accepted: 03/30/2006] [Indexed: 12/31/2022] Open
Abstract
The human immunodeficiency virus (HIV) type-1 viral protein U (Vpu) protein enhances the release of diverse retroviruses from human, but not monkey, cells and is thought to do so by ablating a dominant restriction to particle release. Here, we determined how Vpu expression affects the subcellular distribution of HIV-1 and murine leukemia virus (MLV) Gag proteins in human cells where Vpu is, or is not, required for efficient particle release. In HeLa cells, where Vpu enhances HIV-1 and MLV release approximately 10-fold, concentrations of HIV-1 Gag and MLV Gag fused to cyan fluorescent protein (CFP) were initially detected at the plasma membrane, but then accumulated over time in early and late endosomes. Endosomal accumulation of Gag-CFP was prevented by Vpu expression and, importantly, inhibition of plasma membrane to early endosome transport by dominant negative mutants of Rab5a, dynamin, and EPS-15. Additionally, accumulation of both HIV and MLV Gag in endosomes required a functional late-budding domain. In human HOS cells, where HIV-1 and MLV release was efficient even in the absence of Vpu, Gag proteins were localized predominantly at the plasma membrane, irrespective of Vpu expression or manipulation of endocytic transport. While these data indicated that Vpu inhibits nascent virion endocytosis, Vpu did not affect transferrin endocytosis. Moreover, inhibition of endocytosis did not restore Vpu-defective HIV-1 release in HeLa cells, but instead resulted in accumulation of mature virions that could be released from the cell surface by protease treatment. Thus, these findings suggest that a specific activity that is present in HeLa cells, but not in HOS cells, and is counteracted by Vpu, traps assembled retrovirus particles at the cell surface. This entrapment leads to subsequent endocytosis by a Rab5a- and clathrin-dependent mechanism and intracellular sequestration of virions in endosomes.
Collapse
Affiliation(s)
- Stuart J D Neil
- Aaron Diamond AIDS Research Center, Laboratory of Retrovirology, Rockefeller University, New York, New York, USA
| | | | | | | |
Collapse
|
6
|
Harila K, Prior I, Sjöberg M, Salminen A, Hinkula J, Suomalainen M. Vpu and Tsg101 regulate intracellular targeting of the human immunodeficiency virus type 1 core protein precursor Pr55gag. J Virol 2006; 80:3765-72. [PMID: 16571793 PMCID: PMC1440481 DOI: 10.1128/jvi.80.8.3765-3772.2006] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Assembly of human immunodeficiency virus type 1 (HIV-1) is directed by the viral core protein Pr55gag. Depending on the cell type, Pr55gag accumulates either at the plasma membrane or on late endosomes/multivesicular bodies. Intracellular localization of Pr55gag determines the site of virus assembly, but molecular mechanisms that define cell surface or endosomal targeting of Pr55gag are poorly characterized. We have analyzed targeting of newly synthesized Pr55gag in HeLa H1 cells by pulse-chase studies and subcellular fractionations. Our results indicated that Pr55gag was inserted into the plasma membrane and, when coexpressed with the viral accessory protein Vpu, Pr55gag remained at the plasma membrane and virions assembled at this site. In contrast, Pr55gag expressed in the absence of Vpu was initially inserted into the plasma membrane, but subsequently endocytosed, and virus assembly was partially shifted to internal membranes. This endocytosis of Pr55gag required the host protein Tsg101. These results identified a previously unknown role for Vpu and Tsg101 as regulators for the endocytic uptake of Pr55gag and suggested that the site of HIV-1 assembly is determined by factors that regulate the endocytosis of Pr55gag.
Collapse
Affiliation(s)
- Kirsi Harila
- Department of Virology, Haartman Institute, P.O. Box 21, FIN-00014 University of Helsinki, Finland
| | | | | | | | | | | |
Collapse
|
7
|
Wilson L, McKinlay C, Gage P, Ewart G. SARS coronavirus E protein forms cation-selective ion channels. Virology 2005; 330:322-31. [PMID: 15527857 PMCID: PMC7111769 DOI: 10.1016/j.virol.2004.09.033] [Citation(s) in RCA: 206] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Revised: 07/27/2004] [Accepted: 09/26/2004] [Indexed: 11/30/2022]
Abstract
Severe Acute Respiratory Syndrome (SARS) is caused by a novel coronavirus (SARS-CoV). Coronaviruses including SARS-CoV encode an envelope (E) protein, a small, hydrophobic membrane protein. We report that, in planar lipid bilayers, synthetic peptides corresponding to the SARS-CoV E protein forms ion channels that are more permeable to monovalent cations than to monovalent anions. Affinity-purified polyclonal antibodies recognizing the N-terminal 19 residues of SARS-CoV E protein were used to establish the specificity of channel formation by inhibiting the ion currents generated in the presence of the E protein peptides.
Collapse
Affiliation(s)
- Lauren Wilson
- Medical School, Frank Fenner Building 42, ANU, Canberra, ACT 2601, Australia.
| | | | | | | |
Collapse
|
8
|
Abstract
Vpu is an 81 amino acid protein encoded by HIV-1. Its role is to amplify viral release by two mechanisms: (i) docking to CD4 with the consequence of targeting CD4 for ubiquitine-mediated degradation, and (ii) formation of ion channels to enhance particle release. The intensive research on its in vivo function, combined with structural investigations, makes this viral membrane protein one of the better characterised membrane proteins. The wealth of structural information enables the use of computational methods to elucidate the mechanisms of function on an atomic scale. The discovery of Vpu and the development of structural models in a chronological order is summarised and first efforts on investigating the mechanics are outlined.
Collapse
Affiliation(s)
- W B Fischer
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
9
|
Abstract
After entry of the human immunodeficiency virus type 1 (HIV-1) into T cells and the subsequent synthesis of viral products, viral proteins and RNA must somehow find each other in the host cells and assemble on the plasma membrane to form the budding viral particle. In this general review of HIV-1 assembly, we present a brief overview of the HIV life cycle and then discuss assembly of the HIV Gag polyprotein on RNA and membrane substrates from a biochemical perspective. The role of the domains of Gag in targeting to the plasma membrane and the role of the cellular host protein cyclophilin are also reviewed.
Collapse
Affiliation(s)
- Suzanne Scarlata
- Department of Physiology and Biophysics, State University of New York at Stony Brook, Stony Brook, NY 11794-8661, USA.
| | | |
Collapse
|
10
|
Sramala I, Lemaitre V, Faraldo-Gómez JD, Vincent S, Watts A, Fischer WB. Molecular dynamics simulations on the first two helices of Vpu from HIV-1. Biophys J 2003; 84:3276-84. [PMID: 12719257 PMCID: PMC1302888 DOI: 10.1016/s0006-3495(03)70052-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Vpu is an 81 amino acid protein of HIV-1 with two phosphorylation sites. It consists of a short N-terminal end traversing the bilayer and a longer cytoplasmic part. The dual functional role of Vpu is attributed to these topological distinct regions of the protein. The first 52 amino acids of Vpu (HV1H2) have been simulated, which are thought to be embedded in a fully hydrated lipid bilayer and to consist of a transmembrane helix (helix-1) connected via a flexible linker region, including a Glu-Tyr-Arg (EYR) motif, with a second helix (helix-2) residing with its helix long axis on the bilayer surface. Repeated molecular dynamics simulations show that Glu-28 is involved in salt bridge formation with Lys-31 and Arg-34 establishing a kink between the two helices. Helix-2 remains in a helical conformation indicating its stability and function as a "peptide float," separating helix-1 from the rest of the protein. This leads to the conclusion that Vpu consists of three functional modules: helix-1, helix-2, and the remaining residues toward the C-terminal end.
Collapse
Affiliation(s)
- I Sramala
- Biomembrane Structure Unit, Department of Biochemistry, Oxford University, Oxford OX1 3QU, UK
| | | | | | | | | | | |
Collapse
|
11
|
Handley MA, Paddock S, Dall A, Panganiban AT. Association of Vpu-binding protein with microtubules and Vpu-dependent redistribution of HIV-1 Gag protein. Virology 2001; 291:198-207. [PMID: 11878889 DOI: 10.1006/viro.2001.1166] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The efficient exit of HIV-1 particles from cells requires the action of the viral encoded protein Vpu. Vpu-binding protein (Ubp) is a cellular protein that interacts with both Vpu and the major structural component of the viral capsid (Gag) and appears to affect the efficiency of particle exit. Elucidation of the function of Ubp and characterization of the spatial distribution of Ubp may provide information pertinent to understanding the role of Ubp in virus replication. To investigate the subcellular location of Ubp, and to see whether Vpu affects the intracellular distribution of Gag, we carried out immunofluorescence localization in conjunction with confocal microscopy. Based on this analysis Ubp is present in both the nucleus and the cytoplasm. In the cytoplasm, Ubp appeared to be associated with microtubules as evidenced by cofluorescence with tubulin in the absence and in the presence of colchicine. However, cytoskeletal isolation and detergent extraction of cells resulted in association of Ubp with the soluble fractions, indicating that Ubp is not in tight association with microtubules. Moreover, flotation gradient analysis demonstrated that Ubp is cytoplasmic and not stably associated with the plasma membrane. Interestingly, expression of Vpu in cells resulted in redistribution of both Ubp and Gag to a location near the periphery of the cell. The effect of Vpu on both Ubp and Gag protein has implications for Vpu-mediated particle exit from cells.
Collapse
Affiliation(s)
- M A Handley
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53706, USA
| | | | | | | |
Collapse
|
12
|
Deora A, Ratner L. Viral protein U (Vpu)-mediated enhancement of human immunodeficiency virus type 1 particle release depends on the rate of cellular proliferation. J Virol 2001; 75:6714-8. [PMID: 11413341 PMCID: PMC114397 DOI: 10.1128/jvi.75.14.6714-6718.2001] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viral protein U (Vpu) is a 17-kDa phosphoprotein that enhances the release of viral particles from human immunodeficiency virus type 1-infected cells. This study shows that the effect of Vpu on efficient particle release depends on the rate of cell proliferation. Cells arrested by contact inhibition, chemical arresting agents, or terminal differentiation (i.e., macrophages) all exhibited a striking dependence on Vpu for efficient particle release, as shown by examination of particle production from transfections with full-length clones, infections, and the vaccinia virus expression system. In contrast, actively proliferating cells did not exhibit enhanced particle release with Vpu expression. This study demonstrates the necessity of Vpu for efficient viral particle release from quiescent cells.
Collapse
Affiliation(s)
- A Deora
- Departments of Medicine, Pathology, and Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri 63110, USA
| | | |
Collapse
|