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Ghaly M, Proulx J, Borgmann K, Park IW. Novel role of HIV-1 Nef in regulating the ubiquitination of cellular proteins. Front Cell Infect Microbiol 2023; 13:1106591. [PMID: 36968110 PMCID: PMC10031067 DOI: 10.3389/fcimb.2023.1106591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/16/2023] [Indexed: 03/10/2023] Open
Abstract
Our recent data established that HIV-1 Nef is pivotal in determining the fate of cellular proteins by modulating ubiquitination. However, it is unknown which proteins are ubiquitinated in the presence of Nef, a question critical for understanding the proliferation/restriction strategies of HIV-1 in infected cells. To identify cellular proteins ubiquitinated by Nef, we conducted a proteomic analysis of cellular proteins in the presence and absence of Nef. Proteomic analysis in HEK293T cells indicated that 93 proteins were upregulated and 232 were downregulated in their ubiquitination status by Nef. Computational analysis classified these proteins based on molecular function, biological process, subcellular localization, and biological pathway. Of those proteins, we found a majority of molecular functions to be involved in binding and catalytic activity. With respect to biological processes, a significant portion of the proteins identified were related to cellular and metabolic processes. Subcellular localization analysis showed the bulk of proteins to be localized to the cytosol and cytosolic compartments, which is consistent with the known function and location of Nef during HIV-1 infection. As for biological pathways, the wide range of affected proteins was denoted by the multiple modes to fulfill function, as distinguished from a strictly singular means, which was not detected. Among these ubiquitinated proteins, six were found to directly interact with Nef, wherein two were upregulated and four downregulated. We also identified 14 proteins involved in protein stability through directly participating in the Ubiquitin Proteasome System (UPS)-mediated proteasomal degradation pathway. Of those proteins, we found six upregulated and eight downregulated. Taken together, these analyses indicate that HIV-1 Nef is integral to regulating the stability of various cellular proteins via modulating ubiquitination. The molecular mechanisms directing Nef-triggered regulation of cellular protein ubiquitination are currently under investigation.
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Kumar A, Abbas W, Colin L, Khan KA, Bouchat S, Varin A, Larbi A, Gatot JS, Kabeya K, Vanhulle C, Delacourt N, Pasquereau S, Coquard L, Borch A, König R, Clumeck N, De Wit S, Rohr O, Rouzioux C, Fulop T, Van Lint C, Herbein G. Tuning of AKT-pathway by Nef and its blockade by protease inhibitors results in limited recovery in latently HIV infected T-cell line. Sci Rep 2016; 6:24090. [PMID: 27076174 PMCID: PMC4831010 DOI: 10.1038/srep24090] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/18/2016] [Indexed: 12/14/2022] Open
Abstract
Akt signaling plays a central role in many biological processes, which are key players in human immunodeficiency virus 1 (HIV-1) pathogenesis. We found that Akt interacts with HIV-1 Nef protein. In primary T cells treated with exogenous Nef or acutely infected with Nef-expressing HIV-1 in vitro, Akt became phosphorylated on serine473 and threonine308. In vitro, Akt activation mediated by Nef in T-cells was blocked by HIV protease inhibitors (PI), but not by reverse transcriptase inhibitors (RTI). Ex vivo, we found that the Akt pathway is hyperactivated in peripheral blood lymphocytes (PBLs) from cART naïve HIV-1-infected patients. PBLs isolated from PI-treated patients, but not from RTI-treated patients, exhibited decreased Akt activation, T-cell proliferation and IL-2 production. We found that PI but not RTI can block HIV-1 reactivation in latently infected J-Lat lymphoid cells stimulated with various stimuli. Using luciferase measurement, we further confirmed that Nef-mediated reactivation of HIV-1 from latency in 1G5 cells was blocked by PI parallel to decreased Akt activation. Our results indicate that PI-mediated blockade of Akt activation could impact the HIV-1 reservoir and support the need to further assess the therapeutic use of HIV-1 PI in order to curtail latently infected cells in HIV-1-infected patients.
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Affiliation(s)
- Amit Kumar
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Wasim Abbas
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Laurence Colin
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Kashif Aziz Khan
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Sophie Bouchat
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Audrey Varin
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Anis Larbi
- Department of Medicine, University of Sherbrooke, Sherbrooke, Canada
| | - Jean-Stéphane Gatot
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Kabamba Kabeya
- Department of Infectious Diseases, CHU St-Pierre, ULB, Bruxelles, Belgium
| | - Caroline Vanhulle
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Nadège Delacourt
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Sébastien Pasquereau
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Laurie Coquard
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
| | - Alexandra Borch
- Research Group "Host-Pathogen Interactions", Paul-Ehrlich-Institute, Langen, Germany
| | - Renate König
- Research Group "Host-Pathogen Interactions", Paul-Ehrlich-Institute, Langen, Germany.,Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Research Institute, La Jolla, CA; German Center for Infection Research (DZIF), Langen, Germany
| | - Nathan Clumeck
- Department of Infectious Diseases, CHU St-Pierre, ULB, Bruxelles, Belgium
| | - Stephane De Wit
- Department of Infectious Diseases, CHU St-Pierre, ULB, Bruxelles, Belgium
| | - Olivier Rohr
- Institut de Parasitologie et Pathologie Tropicale, University of Strasbourg, Strasbourg, France
| | - Christine Rouzioux
- Department of Virology, Paris University, EA7327 Paris Descartes, APHP Necker Hospital, Paris, France
| | - Tamas Fulop
- Department of Medicine, University of Sherbrooke, Sherbrooke, Canada
| | - Carine Van Lint
- Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Georges Herbein
- Department of Virology, Pathogens &Inflammation Laboratory, University of Franche-Comté and COMUE Bourgogne Franche-Comté University, UPRES EA4266, SFR FED 4234, CHRU Besançon, Besançon, France
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Luo X, Fan Y, Park IW, He JJ. Exosomes are unlikely involved in intercellular Nef transfer. PLoS One 2015; 10:e0124436. [PMID: 25919665 PMCID: PMC4412529 DOI: 10.1371/journal.pone.0124436] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 03/13/2015] [Indexed: 11/18/2022] Open
Abstract
HIV-1 Nef is an important pathogenic factor for HIV/AIDS pathogenesis. Several recent studies including ours have demonstrated that Nef can be transferred to neighboring cells and alters the function of these cells. However, how the intercellular Nef transfer occurs is in dispute. In the current study, we attempted to address this important issue using several complementary strategies, a panel of exosomal markers, and human CD4+ T lymphocyte cell line Jurkat and a commonly used cell line 293T. First, we showed that Nef was transferred from Nef-expressing or HIV-infected Jurkat to naïve Jurkat and other non-Jurkat cells and that the transfer required the membrane targeting function of Nef and was cell density-dependent. Then, we showed that Nef transfer was cell-cell contact-dependent, as exposure to culture supernatants or exosomes from HIV-infected Jurkat or Nef-expressing Jurkat and 293T led to little Nef detection in the target cells Jurkat. Thirdly, we demonstrated that Nef was only detected to be associated with HIV virions but not with acetylcholinesterase (AChE+) exosomes from HIV-infected Jurkat and not in the exosomes from Nef-expressing Jurkat. In comparison, when it was over-expressed in 293T, Nef was detected in detergent-insoluble AChE+/CD81low/TSG101low exosomes, but not in detergent-soluble AChE-/CD81high/TSG101high exosomes. Lastly, microscopic imaging showed no significant Nef detection in exosomal vesicle-like structures in and out 293T. Taken together, these results show that exosomes are unlikely involved in intercellular Nef transfer. In addition, this study reveals existence of two types of exosomes: AChE+/CD81low/TSG101low exosomes and AChE-/CD81high/TSG101high exosomes.
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Affiliation(s)
- Xiaoyu Luo
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, 76107, United States of America
| | - Yan Fan
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, 76107, United States of America
| | - In-Woo Park
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, 76107, United States of America
| | - Johnny J. He
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas, 76107, United States of America
- * E-mail:
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Pyeon D, Park IW. Interaction between Nef and INI1/SMARCB1 augments replicability of HIV-1 in resting human peripheral blood mononuclear cells. Arch Virol 2015; 160:727-37. [PMID: 25559666 DOI: 10.1007/s00705-014-2315-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/14/2014] [Indexed: 02/03/2023]
Abstract
A central feature of HIV-1 infection is the inability of entering virus to integrate into chromosomes of resting T lymphocytes unless they are mitogenically activated. In contrast, SIVpbj1.9 replicates in initially resting T lymphocytes by activating infected cells. Previous reports have shown that a difference in Nef-mediated T cell activation between HIV-1 and SIVpbj1.9 plays a critical role in the differing abilities of these viruses to replicate in resting lymphocytes. However, the molecular details of these differences are still unclear. Here, we show that infection with a chimeric virus, HSIVnef, which harbors the 5' 308 nucleotides of SIVpbj1.9 nef in place of the 5' 221 nucleotides of HIV-1 nef in the HIV-1 proviral backbone, resulted in integration of the provirus into host chromosomes without mitogenic activation and thereby replication in resting human PBMCs (hPBMCs). These results indicate that Nef is an essential viral determinant for the integration of provirus into host chromosomes in resting T cells. Using the yeast two-hybrid system, we identified integrase interactor-1 (INI1/SMARCB1) as a cellular factor that is involved in the integration process via interaction with Nef. Although INI1 interacted with both SIVpbj1.9 and HIV-1 Nefs, SIVpbj1.9 Nef, but not HIV-1 Nef, enhanced proviral integration into host DNA. Furthermore, mutational analysis revealed that the basic-amino-acid-rich amino-terminal domain in SIVpbj1.9 Nef is crucial for interaction with INI1 and virus replication in resting hPBMCs. Taken together, these data indicate that Nef is a critical viral protein for incorporating nascent proviral DNA into host chromosomes in resting PBMCs and that this occurs through interaction with INI1. This elucidates the basis for replication of the integrated provirus when the host cell is in a resting state.
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Affiliation(s)
- Dohun Pyeon
- Departments of Immunology and Microbiology, and Medicine, University of Colorado School of Medicine, 12800 E. 19th Ave. MS 8333, Aurora, CO, 80045, USA,
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