Visualizing Interactions Between HIV-1 Nef and Host Cellular Proteins Using Ground-State Depletion Microscopy

Brennan S. Dirk; Bryan Heit; Jimmy D. Dikeakos

doi:10.1089/aid.2014.0333

Vpr Enhances Tumor Necrosis Factor Production by HIV-1-Infected T Cells

Journal of Virology ◽

10.1128/jvi.02098-15 ◽

2015 ◽

Vol 89 (23) ◽

pp. 12118-12130 ◽

Cited By ~ 16

Author(s):

Ferdinand Roesch ◽

Léa Richard ◽

Réjane Rua ◽

Françoise Porrot ◽

Nicoletta Casartelli ◽

...

Keyword(s):

Immune Responses ◽

Proinflammatory Cytokine ◽

Tumor Necrosis ◽

Cellular Proteins ◽

Accessory Protein ◽

Infected Cells ◽

Hiv 1 ◽

Necrosis Factor ◽

Stimulation Of

ABSTRACTThe HIV-1 accessory protein Vpr displays different activities potentially impacting viral replication, including the arrest of the cell cycle in the G2phase and the stimulation of apoptosis and DNA damage response pathways. Vpr also modulates cytokine production by infected cells, but this property remains partly characterized. Here, we investigated the effect of Vpr on the production of the proinflammatory cytokine tumor necrosis factor (TNF). We report that Vpr significantly increases TNF secretion by infected lymphocytes.De novoproduction of Vpr is required for this effect. Vpr mutants known to be defective for G2cell cycle arrest induce lower levels of TNF secretion, suggesting a link between these two functions. Silencing experiments and the use of chemical inhibitors further implicated the cellular proteins DDB1 and TAK1 in this activity of Vpr. TNF secreted by HIV-1-infected cells triggers NF-κB activity in bystander cells and allows viral reactivation in a model of latently infected cells. Thus, the stimulation of the proinflammatory pathway by Vpr may impact HIV-1 replicationin vivo.IMPORTANCEThe role of the HIV-1 accessory protein Vpr remains only partially characterized. This protein is important for viral pathogenesis in infected individuals but is dispensable for viral replication in most cell culture systems. Some of the functions described for Vpr remain controversial. In particular, it remains unclear whether Vpr promotes or instead prevents proinflammatory and antiviral immune responses. In this report, we show that Vpr promotes the release of TNF, a proinflammatory cytokine associated with rapid disease progression. Using Vpr mutants or inhibiting selected cellular genes, we show that the cellular proteins DDB1 and TAK1 are involved in the release of TNF by HIV-infected cells. This report provides novel insights into how Vpr manipulates TNF production and helps clarify the role of Vpr in innate immune responses and inflammation.

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Focus on Translation Initiation of the HIV-1 mRNAs

International Journal of Molecular Sciences ◽

10.3390/ijms20010101 ◽

2018 ◽

Vol 20 (1) ◽

pp. 101 ◽

Cited By ~ 11

Author(s):

Sylvain de Breyne ◽

Théophile Ohlmann

Keyword(s):

Translation Initiation ◽

Translational Control ◽

Translation Initiation Factor ◽

Initiation Factor ◽

Cellular Proteins ◽

Internal Ribosome Entry ◽

Eukaryotic Translation ◽

Cellular Environment ◽

Key Steps ◽

Hiv 1

To replicate and disseminate, viruses need to manipulate and modify the cellular machinery for their own benefit. We are interested in translation, which is one of the key steps of gene expression and viruses that have developed several strategies to hijack the ribosomal complex. The type 1 human immunodeficiency virus is a good paradigm to understand the great diversity of translational control. Indeed, scanning, leaky scanning, internal ribosome entry sites, and adenosine methylation are used by ribosomes to translate spliced and unspliced HIV-1 mRNAs, and some require specific cellular factors, such as the DDX3 helicase, that mediate mRNA export and translation. In addition, some viral and cellular proteins, including the HIV-1 Tat protein, also regulate protein synthesis through targeting the protein kinase PKR, which once activated, is able to phosphorylate the eukaryotic translation initiation factor eIF2α, which results in the inhibition of cellular mRNAs translation. Finally, the infection alters the integrity of several cellular proteins, including initiation factors, that directly or indirectly regulates translation events. In this review, we will provide a global overview of the current situation of how the HIV-1 mRNAs interact with the host cellular environment to produce viral proteins.

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Flow Cytometry Analysis of HIV-1 Env Conformations at the Surface of Infected Cells and Virions: Role of Nef, CD4, and SERINC5

Journal of Virology ◽

10.1128/jvi.01783-19 ◽

2019 ◽

Vol 94 (6) ◽

Cited By ~ 3

Author(s):

Isabelle Staropoli ◽

Jérémy Dufloo ◽

Anaïs Ducher ◽

Pierre-Henri Commere ◽

Anna Sartori-Rupp ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Cellular Proteins ◽

Viral Infectivity ◽

Viral Particles ◽

Immunodeficiency Virus ◽

Infected Cells ◽

Env Protein ◽

The Impact ◽

Hiv 1

ABSTRACT The HIV-1 Env protein is exposed at the surface of virions and infected cells. Env fluctuates between different closed and open structural states and these conformations influence both viral infectivity and sensitivity to antibody binding and neutralization. We established a flow virometry assay to visualize Env proteins at the surface of human immunodeficiency virus type 1 (HIV-1) virions. The assay is performed on ultracentrifuged fluorescent viral particles that are stained with a panel of broadly neutralizing antibodies (bNAbs) and nonneutralizing antibodies (nnAbs) that probe different epitopes of Env. We used this assay to compare Env at the surface of producer cells and viral particles and to analyze the effect of Nef, CD4, and SERINC5 on Env accessibility to antibodies. We studied the laboratory-adapted strain NL4-3 and two transmitted/founder viruses, THRO and CH058. We confirm that antibody accessibility varies between viral strains and show that Nef, CD4, and SERINC5 additively impact Env conformations. We further demonstrate that the Env accessibility profile on virions is globally similar to that observed on HIV-1-infected cells, with some noticeable differences. For instance, nnAbs bind to virions more efficiently than to producer cells, likely reflecting changes in Env conformational states on mature viral particles. This test complements other techniques and provides a convenient and simple tool for quantifying and probing the structure of Env at the virion surface and to analyze the impact of viral and cellular proteins on these parameters. IMPORTANCE HIV-1 Env conformation is one of the key parameters determining viral infectivity. The flow virometry-based assay developed in this study allows for the characterization of proteins incorporated in HIV-1 particles. We studied the conformation of HIV-1 Env and the impact that the viral protein Nef and the cellular proteins CD4 and SERINC5 have on Env accessibility to antibodies. Our assay permitted us to highlight some noticeable differences in the conformation of Env between producer cells and viral particles. It contributes to a better understanding of the actual composition of HIV-1 particles.

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Effects of Tat proteins and Tat mutants of different human immunodeficiency virus type 1 clades on glial JC virus early and late gene transcription

Journal of General Virology ◽

10.1099/vir.0.047902-0 ◽

2013 ◽

Vol 94 (3) ◽

pp. 514-523 ◽

Cited By ~ 4

Author(s):

Clayton A. Wright ◽

Jonas A. Nance ◽

Edward M. Johnson

Keyword(s):

Human Immunodeficiency Virus ◽

Dna Replication ◽

Gene Transcription ◽

Cellular Proteins ◽

Late Gene ◽

Clade B ◽

Immunodeficiency Virus ◽

The Brain ◽

Hiv 1

Polyomavirus JC (JCV) is the aetiological agent of progressive multifocal leukoencephalopathy (PML), a frequently fatal infection of the brain afflicting nearly 4 % of AIDS patients in the USA. Human immunodeficiency virus type 1 (HIV-1) Tat, acting together with cellular proteins at the JCV non-coding control region (NCCR), can stimulate JCV DNA transcription and replication. Tat in the brain is secreted by HIV-1-infected cells and incorporated by oligodendroglia, cells capable of infection by JCV. Thus far the effects of Tat on JCV have been studied primarily with protein encoded by the HIV-1 B clade most common in North America. Here, we determine the abilities of Tat from different HIV-1 clades to alter JCV early and late gene transcription and DNA replication initiated at the JCV origin. Tat from all clades tested stimulates both JCV early and late gene promoters, with clade B Tat being significantly most effective. Tat proteins from the HIV-1 clades display parallel patterns of differences in their effects on HIV-1 and JCV transcription, suggesting that Tat effects in both cases are mediated by the same cellular proteins. Clade B Tat is most effective at directing Smad mediators of tumour growth factor beta and cellular partner Purα to the NCCR. Tat proteins from all non-B clades inhibit initiation of JCV DNA replication. The effectiveness of HIV-1 clade B Tat at promoting JCV transcriptional and replicative processes highlights a need for further investigation to determine which molecular aspects of Tat from distinct HIV-1 substrains can contribute to the course of PML development in neuroAIDS.

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Analysis of HIV-1 Gag Protein Interactions via Biotin Ligase Tagging

Journal of Virology ◽

10.1128/jvi.03584-14 ◽

2015 ◽

Vol 89 (7) ◽

pp. 3988-4001 ◽

Cited By ~ 25

Author(s):

Christopher Ritchie ◽

Isabel Cylinder ◽

Emily J. Platt ◽

Eric Barklis

Keyword(s):

Lipid Metabolism ◽

Rna Processing ◽

Protein Trafficking ◽

Cellular Proteins ◽

Wild Type ◽

Gag Protein ◽

Gag Proteins ◽

Biotin Ligase ◽

Close Proximity ◽

Hiv 1

ABSTRACTWe have examined the interactions of wild-type (WT) and matrix protein-deleted (ΔMA) HIV-1 precursor Gag (PrGag) proteins in virus-producing cells using a biotin ligase-tagging approach. To do so, WT and ΔMA PrGag proteins were tagged with theEscherichia colipromiscuous biotin ligase (BirA*), expressed in cells, and examined. Localization patterns of PrGag proteins and biotinylated proteins overlapped, consistent with observations that BirA*-tagged proteins biotinylate neighbor proteins that are in close proximity. Results indicate that BirA*-tagged PrGag proteins biotinylated themselves as well as WT PrGag proteins intrans. Previous data have shown that the HIV-1 Envelope (Env) protein requires an interaction with MA for assembly into virions. Unexpectedly, ΔMA proteins biotinylated Env, whereas WT BirA*-tagged proteins did not, suggesting that the presence of MA made Env inaccessible to biotinylation. We also identified over 50 cellular proteins that were biotinylated by BirA*-tagged PrGag proteins. These included membrane proteins, cytoskeleton-associated proteins, nuclear transport factors, lipid metabolism regulators, translation factors, and RNA-processing proteins. The identification of these biotinylated proteins offers new insights into HIV-1 Gag protein trafficking and activities and provides new potential targets for antiviral interference.IMPORTANCEWe have employed a novel strategy to analyze the interactions of the HIV-1 structural Gag proteins, which involved tagging wild-type and mutant Gag proteins with a biotin ligase. Expression of the tagged proteins in cells allowed us to analyze proteins that came in close proximity to the Gag proteins as they were synthesized, transported, assembled, and released from cells. The tagged proteins biotinylated proteins encoded by the HIV-1polgene and neighbor Gag proteins, but, surprisingly, only the mutant Gag protein biotinylated the HIV-1 Envelope protein. We also identified over 50 cellular proteins that were biotinylated, including membrane and cytoskeletal proteins and proteins involved in lipid metabolism, nuclear import, translation, and RNA processing. Our results offer new insights into HIV-1 Gag protein trafficking and activities and provide new potential targets for antiviral interference.

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HIV-1 Vpr Induces the K48-Linked Polyubiquitination and Proteasomal Degradation of Target Cellular Proteins To Activate ATR and Promote G2 Arrest

Journal of Virology ◽

10.1128/jvi.02590-09 ◽

2010 ◽

Vol 84 (7) ◽

pp. 3320-3330 ◽

Cited By ~ 36

Author(s):

Jean-Philippe Belzile ◽

Jonathan Richard ◽

Nicole Rougeau ◽

Yong Xiao ◽

Éric A. Cohen

Keyword(s):

Ubiquitin Ligase ◽

Affinity Purification ◽

E3 Ubiquitin Ligase ◽

E3 Ligase ◽

Proteasomal Degradation ◽

Dominant Negative ◽

Cellular Proteins ◽

Dominant Negative Mutant ◽

M Phase ◽

Hiv 1

ABSTRACT HIV-1 viral protein R (Vpr) induces cell cycle arrest at the G2/M phase by a mechanism involving the activation of the DNA damage sensor ATR. We and others recently showed that Vpr performs this function by subverting the activity of the DDB1-CUL4A (VPRBP) E3 ubiquitin ligase. Vpr could thus act as a connector between the E3 ligase and an unknown cellular factor whose ubiquitination would induce G2 arrest. While attractive, this model is based solely on the indirect observation that some mutants of Vpr retain their interaction with the E3 ligase but fail to induce G2 arrest. Using a tandem affinity purification approach, we observed that Vpr interacts with ubiquitinated cellular proteins and that this association requires the recruitment of an active E3 ligase given that the depletion of VPRBP by RNA interference or the overexpression of a dominant negative mutant of CUL4A decreased this association. Importantly, G2-arrest-defective mutants of Vpr in the C-terminal putative substrate-interacting domain displayed a decreased association with ubiquitinated proteins. We also found that the inhibition of proteasomal activity increased this association and that the ubiquitin chains were at least in part constituted of classical K48 linkages. Interestingly, the inhibition of K48 polyubiquitination specifically impaired the Vpr-induced phosphorylation of H2AX, an early target of ATR, but did not affect UV-induced H2AX phosphorylation. Overall, our results provide direct evidence that the association of Vpr with the DDB1-CUL4A (VPRBP) E3 ubiquitin ligase induces the K48-linked polyubiquitination of as-yet-unknown cellular proteins, resulting in their proteasomal degradation and ultimately leading to the activation of ATR and G2 arrest.

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Structure-Function Analysis of the HIV-1 Integrase in Complex With Two Cellular Proteins: Ledgf and INI1

Biophysical Journal ◽

10.1016/j.bpj.2009.12.053 ◽

2010 ◽

Vol 98 (3) ◽

pp. 9a

Author(s):

Benoit Maillot ◽

Corinne Crucifix ◽

Florence Granger ◽

Sylvia Eiler ◽

Dino Moras ◽

...

Keyword(s):

Structure Function ◽

Function Analysis ◽

Cellular Proteins ◽

Hiv 1

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The E3 Ubiquitin-Protein Ligase Cullin 3 Regulates HIV-1 Transcription

Cells ◽

10.3390/cells9092010 ◽

2020 ◽

Vol 9 (9) ◽

pp. 2010 ◽

Cited By ~ 1

Author(s):

Simon Langer ◽

Xin Yin ◽

Arturo Diaz ◽

Alex J. Portillo ◽

David E. Gordon ◽

...

Keyword(s):

Gene Expression ◽

T Cells ◽

Life Cycle ◽

Viral Replication ◽

Viral Gene Expression ◽

Viral Life Cycle ◽

Cellular Proteins ◽

Viral Gene ◽

Cullin 3 ◽

Hiv 1

The infectious life cycle of the human immunodeficiency virus type 1 (HIV-1) is characterized by an ongoing battle between a compendium of cellular proteins that either promote or oppose viral replication. On the one hand, HIV-1 utilizes dependency factors to support and sustain infection and complete the viral life cycle. On the other hand, both inducible and constitutively expressed host factors mediate efficient and functionally diverse antiviral processes that counteract an infection. To shed light into the complex interplay between HIV-1 and cellular proteins, we previously performed a targeted siRNA screen to identify and characterize novel regulators of viral replication and identified Cullin 3 (Cul3) as a previously undescribed factor that negatively regulates HIV-1 replication. Cul3 is a component of E3-ubiquitin ligase complexes that target substrates for ubiquitin-dependent proteasomal degradation. In the present study, we show that Cul3 is expressed in HIV-1 target cells, such as CD4+ T cells, monocytes, and macrophages and depletion of Cul3 using siRNA or CRISPR/Cas9 increases HIV-1 infection in immortalized cells and primary CD4+ T cells. Conversely, overexpression of Cul3 reduces HIV-1 infection in single replication cycle assays. Importantly, the antiviral effect of Cul3 was mapped to the transcriptional stage of the viral life cycle, an effect which is independent of its role in regulating the G1/S cell cycle transition. Using isogenic viruses that only differ in their promotor region, we find that the NF-κB/NFAT transcription factor binding sites in the LTR are essential for Cul3-dependent regulation of viral gene expression. Although Cul3 effectively suppresses viral gene expression, HIV-1 does not appear to antagonize the antiviral function of Cul3 by targeting it for degradation. Taken together, these results indicate that Cul3 is a negative regulator of HIV-1 transcription which governs productive viral replication in infected cells.

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Functional Interactions of Human Immunodeficiency Virus Type 1 Integrase with Human and Yeast HSP60

Journal of Virology ◽

10.1128/jvi.75.23.11344-11353.2001 ◽

2001 ◽

Vol 75 (23) ◽

pp. 11344-11353 ◽

Cited By ~ 35

Author(s):

Vincent Parissi ◽

Christina Calmels ◽

Vaea Richard De Soultrait ◽

Anne Caumont ◽

Michel Fournier ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Human Immunodeficiency Virus Type ◽

Virus Type ◽

Nuclear Genome ◽

Cellular Proteins ◽

Immunodeficiency Virus ◽

Hiv 1

ABSTRACT Integration of human immunodeficiency virus type 1 (HIV-1) proviral DNA in the nuclear genome is catalyzed by the retroviral integrase (IN). In addition to IN, viral and cellular proteins associated in the high-molecular-weight preintegration complex have been suggested to be involved in this process. In an attempt to define host factors interacting with IN, we used an in vitro system to identify cellular proteins in interaction with HIV-1 IN. The yeast Saccharomyces cerevisiae was chosen since (i) its complete sequence has been established and the primary structure of all the putative proteins from this eucaryote has been deduced, (ii) there is a significant degree of homology between human and yeast proteins, and (iii) we have previously shown that the expression of HIV-1 IN in yeast induces a lethal phenotype. Strong evidences suggest that this lethality is linked to IN activity in infected human cells where integration requires the cleavage of genomic DNA. Using IN-affinity chromatography we identified four yeast proteins interacting with HIV-1 IN, including the yeast chaperonin yHSP60, which is the counterpart of human hHSP60. Yeast lethality induced by HIV-1 IN was abolished when a mutated HSP60 was coexpressed, therefore suggesting that both proteins interact in vivo. Besides interacting with HIV-1 IN, the hHSP60 was able to stimulate the in vitro processing and joining activities of IN and protected this enzyme from thermal denaturation. In addition, the functional human HSP60-HSP10 complex in the presence of ATP was able to recognize the HIV-1 IN as a substrate.

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