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Rashid F, Zaongo SD, Iqbal H, Harypursat V, Song F, Chen Y. Interactions between HIV proteins and host restriction factors: implications for potential therapeutic intervention in HIV infection. Front Immunol 2024; 15:1390650. [PMID: 39221250 PMCID: PMC11361988 DOI: 10.3389/fimmu.2024.1390650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Different host proteins target different HIV proteins and antagonize their functions, depending on the stage of the HIV life cycle and the stage of infection. Concurrently, HIV proteins also target and antagonize various different host proteins to facilitate HIV replication within host cells. The preceding quite specific area of knowledge in HIV pathogenesis, however, remains insufficiently understood. We therefore propose, in this review article, to examine and discuss the HIV proteins that counteract those host restriction proteins which results directly in increased infectivity of HIV. We elaborate on HIV proteins that antagonize host cellular proteins to promote HIV replication, and thus HIV infection. We examine the functions and mechanisms via which Nef, Vif, Vpu, Env, Vpr, and Vpx counteract host proteins such as Ser5, PSGL-1, IFITMS, A3G, tetherin, GBP5, SAMHD1, STING, HUSH, REAF, and TET2 to increase HIV infectivity. Nef antagonizes three host proteins, viz., Ser5, PSGL1, and IFITIMs, while Vpx also antagonizes three host restriction factors, viz., SAMHD1, STING, and HUSH complex; therefore, these proteins may be potential candidates for therapeutic intervention in HIV infection. Tetherin is targeted by Vpu and Env, PSGL1 is targeted by Nef and Vpu, while Ser5 is targeted by Nef and Env proteins. Finally, conclusive remarks and future perspectives are also presented.
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Affiliation(s)
- Farooq Rashid
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Silvere D. Zaongo
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Hifza Iqbal
- School of science, University of Management and Technology, Lahore, Pakistan
| | - Vijay Harypursat
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Fangzhou Song
- Basic Medicine College, Chongqing Medical University, Chongqing, China
| | - Yaokai Chen
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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2
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Sonela N, Mann J, Godwe C, Goni OH, Tchakoute M, Nkoue N, de Oliveira T, Brockman MA, Brumme ZL, Ndung'u T, Tongo M. No detectable differences in Nef-mediated downregulation of HLA-I and CD4 molecules among HIV-1 group M lineages circulating in Cameroon, where the pandemic originated. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2024; 4:fviro.2024.1379217. [PMID: 38883214 PMCID: PMC7616105 DOI: 10.3389/fviro.2024.1379217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
HIV-1 group M (HIV-1M) lineages downregulate HLA-I and CD4 expression via their Nef proteins. We hypothesized that these Nef functions may be partially responsible for the differences in prevalence of viruses from different lineages that co-circulate within an epidemic. Here, we characterized these two Nef activities in HIV-1M isolates from Cameroon, where multiple variants have been circulating since the pandemic's origin. Single HIV-1 Nef clones from 234 HIV-1-ART naïve individuals living in remote villages and two cosmopolitan cities of Cameroon, sampled between 2000 and 2013, were isolated from plasma HIV RNA and analyzed for their capacity to downregulate HLA-I and CD4 molecules. We found that, despite a large degree of within- and inter- lineage variation, the ability of Nef to downregulate HLA-I was similar across these different viruses. Moreover, Nef-mediated CD4 downregulation activity was also well conserved across the different lineages found in Cameroon. In addition, we observed a trend towards higher HLA-I downregulation activity of viruses circulating in the cosmopolitan cities versus the remote villages, whereas the CD4 downregulation activities were similar across the two settings. Furthermore, we noted a significant decline of HLA-I downregulation activity from 2000 to 2013, providing additional evidence supporting the attenuation of the global HIV-1M population over time. Finally, we identified 18 amino acids associated with differential HLA-I downregulation and 13 amino acids associated with differential CD4 downregulation within the dominant CRF02_AG lineage. Our lack of observation of HIV lineage-related differences in Nef-mediated HLA-I and CD4 downregulation function suggests that these activities do not substantively influence the prevalence of different HIV-1M lineages in Cameroon.
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Affiliation(s)
- Nelson Sonela
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Chantal BIYA International Reference Centre for Research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, NY, United States
| | - Jaclyn Mann
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | - Celestin Godwe
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Départment of Biochemistry, University of Douala, Douala, Cameroon
| | - Oumarou H Goni
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
- Départment of Microbiology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Mérime Tchakoute
- Programmes de Santé et développement au sein du Groupement de la Filière Bois du Cameroun, Yaoundé, Cameroon
| | - Nathalie Nkoue
- Programmes de Santé et développement au sein du Groupement de la Filière Bois du Cameroun, Yaoundé, Cameroon
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Mark A Brockman
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- Africa Health Research Institute (AHRI), Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Marcel Tongo
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
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Sid Ahmed S, Bajak K, Fackler OT. Beyond Impairment of Virion Infectivity: New Activities of the Anti-HIV Host Cell Factor SERINC5. Viruses 2024; 16:284. [PMID: 38400059 PMCID: PMC10892966 DOI: 10.3390/v16020284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Members of the serine incorporator (SERINC) protein family exert broad antiviral activity, and many viruses encode SERINC antagonists to circumvent these restrictions. Significant new insight was recently gained into the mechanisms that mediate restriction and antagonism. In this review, we summarize our current understanding of the mode of action and relevance of SERINC proteins in HIV-1 infection. Particular focus will be placed on recent findings that provided important new mechanistic insights into the restriction of HIV-1 virion infectivity, including the discovery of SERINC's lipid scramblase activity and its antagonism by the HIV-1 pathogenesis factor Nef. We also discuss the identification and implications of several additional antiviral activities by which SERINC proteins enhance pro-inflammatory signaling and reduce viral gene expression in myeloid cells. SERINC proteins emerge as versatile and multifunctional regulators of cell-intrinsic immunity against HIV-1 infection.
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Affiliation(s)
- Samy Sid Ahmed
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany; (S.S.A.); (K.B.)
| | - Kathrin Bajak
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany; (S.S.A.); (K.B.)
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, 38124 Heidelberg, Germany
| | - Oliver T. Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany; (S.S.A.); (K.B.)
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, 38124 Heidelberg, Germany
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Cano-Ortiz L, Luedde T, Münk C. HIV-1 restriction by SERINC5. Med Microbiol Immunol 2023; 212:133-140. [PMID: 35333966 PMCID: PMC10085909 DOI: 10.1007/s00430-022-00732-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/08/2022] [Indexed: 11/25/2022]
Abstract
Serine incorporator 5 (SERINC5 or SER5) is a multipass transmembrane protein with ill-defined cellular activities. SER5 was recently described as a human immunodeficiency virus 1 (HIV-1) restriction factor capable of inhibiting HIV-1 that does not express its accessory protein Nef (Δ Nef). SER5 incorporated into the viral membrane impairs the entry of HIV-1 by disrupting the fusion between the viral and the plasma membrane after envelope receptor interaction induced the first steps of the fusion process. The mechanisms of how SER5 prevents membrane fusion are not fully understood and viral envelope proteins were identified that escape the SER5-mediated restriction. Primate lentiviruses, such as HIV-1 and simian immunodeficiency viruses (SIVs), use their accessory protein Nef to downregulate SER5 from the plasma membrane by inducing an endocytic pathway. In addition to being directly antiviral, recent data suggest that SER5 is an important adapter protein in innate signaling pathways leading to the induction of inflammatory cytokines. This review discusses the current knowledge about HIV-1 restriction by SER5.
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Affiliation(s)
- Lucía Cano-Ortiz
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Tom Luedde
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany.
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Naicker D, Sonela N, Jin SW, Mulaudzi T, Ojwach D, Reddy T, Brockman MA, Brumme ZL, Ndung'u T, Mann JK. HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity. Retrovirology 2023; 20:3. [PMID: 37004071 PMCID: PMC10067162 DOI: 10.1186/s12977-023-00618-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Nef performs multiple cellular activities that enhance HIV-1 pathogenesis. The role of Nef-mediated down-regulation of the host restriction factor SERINC5 in HIV-1 pathogenesis is not well-defined. We aimed to investigate if SERINC5 down-regulation activity contributes to HIV-1 subtype C disease progression, to assess the relative contribution of this activity to overall Nef function, and to identify amino acids required for optimal activity. We measured the SERINC5 down-regulation activity of 106 subtype C Nef clones, isolated from individuals in early infection, for which the Nef activities of CD4 and HLA-I down-regulation as well as alteration of TCR signalling were previously measured. The relationship between SERINC5 down-regulation and markers of disease progression, and the relative contribution of SERINC5 down-regulation to a Nef fitness model-derived E value (a proxy for overall Nef fitness in vivo), were assessed. RESULTS No overall relationship was found between SERINC5 down-regulation and viral load set point (p = 0.28) or rate of CD4+ T cell decline (p = 0.45). CD4 down-regulation (p = 0.02) and SERINC5 down-regulation (p = 0.003) were significant determinants of E values in univariate analyses, with the greatest relative contribution for SERINC5 down-regulation, and only SERINC5 down-regulation remained significant in the multivariate analysis (p = 0.003). Using a codon-by-codon analysis, several amino acids were significantly associated with increased (10I, 11V, 38D, 51T, 65D, 101V, 188H and, 191H) or decreased (10K, 38E, 65E, 135F, 173T, 176T and, 191R) SERINC5 down-regulation activity. Site-directed mutagenesis experiments of selected mutants confirmed a substantial reduction in SERINC5 down-regulation activity associated with the mutation 173T, while mutations 10K, 135F, and 176T were associated with more modest reductions in activity that were not statistically significant. CONCLUSIONS These results suggest that SERINC5 down-regulation is a significant contributor to overall Nef function and identify potential genetic determinants of this Nef function that may have relevance for vaccines or therapeutics.
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Affiliation(s)
- Delon Naicker
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Nelson Sonela
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), P.O. Box 3077, Yaoundé, Cameroon
| | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Takalani Mulaudzi
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Doty Ojwach
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Tarylee Reddy
- Medical Research Council, Biostatistics Unit, Durban, 4001, South Africa
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa
- Africa Health Research Institute, Durban, 4001, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, 4001, South Africa.
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Firrito C, Bertelli C, Rosa A, Chande A, Ananth S, van Dijk H, Fackler OT, Stoneham C, Singh R, Guatelli J, Pizzato M. A Conserved Acidic Residue in the C-Terminal Flexible Loop of HIV-1 Nef Contributes to the Activity of SERINC5 and CD4 Downregulation. Viruses 2023; 15:652. [PMID: 36992361 PMCID: PMC10057511 DOI: 10.3390/v15030652] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
The host transmembrane protein SERINC5 is incorporated into retrovirus particles and inhibits HIV-1 infectivity. The lentiviral Nef protein counteracts SERINC5 by downregulating it from the cell surface and preventing its incorporation into virions. The ability of Nef to antagonize the host factor varies in magnitude between different HIV-1 isolates. After having identified a subtype H nef allele unable to promote HIV-1 infectivity in the presence of SERINC5, we investigated the molecular determinants responsible for the defective counteraction of the host factor. Chimeric molecules with a subtype C Nef highly active against SERINC5 were constructed to locate Nef residues crucial for the activity against SERINC5. An Asn at the base of the C-terminal loop of the defective nef allele was found in place of a highly conserved acidic residue (D/E 150). The conversion of Asn to Asp restored the ability of the defective Nef to downregulate SERINC5 and promote HIV-1 infectivity. The substitution was also found to be crucial for the ability of Nef to downregulate CD4, but not for Nef activities that do not rely on the internalization of receptors from the cell surface, suggesting a general implication in promoting clathrin-mediated endocytosis. Accordingly, bimolecular fluorescence complementation revealed that the conserved acidic residue contributes to the recruitment of AP2 by Nef. Altogether, our results confirm that Nef downregulates SERINC5 and CD4 by engaging a similar machinery and indicates that, in addition to the di-leucine motif, other residues in the C-terminal flexible loop are important for the ability of the protein to sustain clathrin-mediated endocytosis.
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Affiliation(s)
- Claudia Firrito
- Department of Cellular, Computational and integrative Biology, University of Trento, 38123 Trento, Italy
| | - Cinzia Bertelli
- Department of Cellular, Computational and integrative Biology, University of Trento, 38123 Trento, Italy
| | - Annachiara Rosa
- Department of Cellular, Computational and integrative Biology, University of Trento, 38123 Trento, Italy
| | - Ajit Chande
- Department of Cellular, Computational and integrative Biology, University of Trento, 38123 Trento, Italy
| | - Swetha Ananth
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Hannah van Dijk
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Oliver T. Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Center for Infection Research (DZIF), 69120 Heidelberg, Germany
| | - Charlotte Stoneham
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Rajendra Singh
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - John Guatelli
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Massimo Pizzato
- Department of Cellular, Computational and integrative Biology, University of Trento, 38123 Trento, Italy
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7
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Wilson KM, He JJ. HIV Nef Expression Down-modulated GFAP Expression and Altered Glutamate Uptake and Release and Proliferation in Astrocytes. Aging Dis 2023; 14:152-169. [PMID: 36818564 PMCID: PMC9937695 DOI: 10.14336/ad.2022.0712] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/12/2022] [Indexed: 11/18/2022] Open
Abstract
HIV infection of astrocytes leads to restricted gene expression and replication but abundant expression of HIV early genes Tat, Nef and Rev. A great deal of neuroHIV research has so far been focused on Tat protein, its effects on astrocytes, and its roles in neuroHIV. In the current study, we aimed to determine effects of Nef expression on astrocytes and their function. Using transfection or infection of VSVG-pseudotyped HIV viruses, we showed that Nef expression down-modulated glial fibrillary acidic protein (GFAP) expression. We then showed that Nef expression also led to decreased GFAP mRNA expression. The transcriptional regulation was further confirmed using a GFAP promoter-driven reporter gene assay. We performed transcription factor profiling array to compare the expression of transcription factors between Nef-intact and Nef-deficient HIV-infected cells and identified eight transcription factors with expression changes of 1.5-fold or higher: three up-regulated by Nef (Stat1, Stat5, and TFIID), and five down-regulated by Nef (AR, GAS/ISRE, HIF, Sp1, and p53). We then demonstrated that removal of the Sp1 binding sites from the GFAP promoter resulted in a much lower level of the promoter activity and reversal of Nef effects on the GFAP promoter, confirming important roles of Sp1 in the GFAP promoter activity and for Nef-induced GFAP expression. Lastly, we showed that Nef expression led to increased glutamate uptake and decreased glutamate release by astrocytes and increased astrocyte proliferation. Taken together, these results indicate that Nef leads to down-modulation of GFAP expression and alteration of glutamate metabolism in astrocytes, and astrocyte proliferation and could be an important contributor to neuroHIV.
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Affiliation(s)
- Kelly M Wilson
- Department of Microbiology and Immunology, Center for Cancer Cell Biology, Immunology and Infection, School of Graduate and Postdoctoral Studies, Rosalind Franklin University, Chicago Medical School, North Chicago, IL 60064, USA
| | - Johnny J He
- Department of Microbiology and Immunology, Center for Cancer Cell Biology, Immunology and Infection, School of Graduate and Postdoctoral Studies, Rosalind Franklin University, Chicago Medical School, North Chicago, IL 60064, USA
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8
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Li S, Li R, Ahmad I, Liu X, Johnson SF, Sun L, Zheng YH. Cul3-KLHL20 E3 ubiquitin ligase plays a key role in the arms race between HIV-1 Nef and host SERINC5 restriction. Nat Commun 2022; 13:2242. [PMID: 35474067 PMCID: PMC9042822 DOI: 10.1038/s41467-022-30026-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
HIV-1 must counteract various host restrictions to establish productive infection. SERINC5 is a potent restriction factor that blocks HIV-1 entry from virions, but its activity is counteracted by Nef. The SERINC5 and Nef activities are both initiated from the plasma membrane, where SERINC5 is packaged into virions for viral inhibition or downregulated by Nef via lysosomal degradation. However, it is still unclear how SERINC5 is localized to and how its expression is regulated on the plasma membrane. We now report that Cullin 3-KLHL20, a trans-Golgi network (TGN)-localized E3 ubiquitin ligase, polyubiquitinates SERINC5 at lysine 130 via K33/K48-linked ubiquitination. The K33-linked polyubiquitination determines SERINC5 expression on the plasma membrane, and the K48-linked polyubiquitination contributes to SERINC5 downregulation from the cell surface. Our study reveals an important role of K130 polyubiquitination and K33/K48-linked ubiquitin chains in HIV-1 infection by regulating SERINC5 post-Golgi trafficking and degradation. SERINC5 is a host-restriction factor preventing HIV progeny entry, which is counteracted by interactions with HIV Nef. Here, Li et al. show that E3 ubiquitin ligase Cullin 3 polyubiquitinates SERINC5 at Lys 130 via K48- and K33-linked ubiquitin chains and provide evidence that this modification is not only required for its membrane localization and anti-viral activity but also relevant for Nef counteractive activity.
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Affiliation(s)
- Sunan Li
- Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Rongrong Li
- Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Iqbal Ahmad
- Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaomeng Liu
- Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Silas F Johnson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Yong-Hui Zheng
- Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin, China. .,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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9
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Chai Q, Li S, Collins MK, Li R, Ahmad I, Johnson SF, Frabutt DA, Yang Z, Shen X, Sun L, Hu J, Hultquist JF, Peterlin BM, Zheng YH. HIV-1 Nef interacts with the cyclin K/CDK13 complex to antagonize SERINC5 for optimal viral infectivity. Cell Rep 2021; 36:109514. [PMID: 34380030 PMCID: PMC8385645 DOI: 10.1016/j.celrep.2021.109514] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/17/2021] [Accepted: 07/20/2021] [Indexed: 11/03/2022] Open
Abstract
HIV-1-negative factor (Nef) protein antagonizes serine incorporator 5 (SERINC5) by redirecting this potent restriction factor to the endosomes and lysosomes for degradation. However, the precise mechanism remains unclear. Using affinity purification/mass spectrometry, we identify cyclin K (CycK) and cyclin-dependent kinase 13 (CDK13) as a Nef-associated kinase complex. CycK/CDK13 phosphorylates the serine at position 360 (S360) in SERINC5, which is required for Nef downregulation of SERINC5 from the cell surface and its counteractivity of the SERINC5 antiviral activity. To understand the role of S360 phosphorylation, we generate chimeric proteins between CD8 and SERINC5 to study their response to Nef. Nef not only downregulates but, importantly, also binds to this chimera in an S360-dependent manner. Thus, S360 phosphorylation increases interactions between Nef and SERINC5 and initiates the destruction of SERINC5 by the endocytic machinery.
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Affiliation(s)
- Qingqing Chai
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Sunan Li
- Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Morgan K Collins
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Rongrong Li
- Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Iqbal Ahmad
- Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Silas F Johnson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA; Department of Biology, Hillsdale College, Hillsdale, MI, USA
| | - Dylan A Frabutt
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Jian Hu
- Department of Chemistry, Michigan State University, East Lansing, MI, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Judd F Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - B Matija Peterlin
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Yong-Hui Zheng
- Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin, China; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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10
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An Amino Acid Polymorphism within the HIV-1 Nef Dileucine Motif Functionally Uncouples Cell Surface CD4 and SERINC5 Downregulation. J Virol 2021; 95:e0058821. [PMID: 34037423 DOI: 10.1128/jvi.00588-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serine incorporator 5 (SERINC5) reduces the infectivity of progeny HIV-1 virions by incorporating into the outer host-derived viral membrane during egress. To counter SERINC5, the HIV-1 accessory protein Nef triggers SERINC5 internalization by engaging the adaptor protein 2 (AP-2) complex using the [D/E]xxxL[L/I]167 Nef dileucine motif. Nef also engages AP-2 via its dileucine motif to downregulate the CD4 receptor. Although these two Nef functions are related, the mechanisms governing SERINC5 downregulation are incompletely understood. Here, we demonstrate that two primary Nef isolates, referred to as 2410 and 2391 Nef, acquired from acutely HIV-1 infected women from Zimbabwe, both downregulate CD4 from the cell surface. However, only 2410 Nef retains the ability to downregulate cell surface SERINC5. Using a series of Nef chimeras, we mapped the region of 2391 Nef responsible for the functional uncoupling of these two antagonistic pathways to the dileucine motif. Modifications of the first and second x positions of the 2410 Nef dileucine motif to asparagine and aspartic acid residues, respectively (ND164), impaired cell surface SERINC5 downregulation, which resulted in reduced infectious virus yield in the presence of SERINC5. The ND164 mutation additionally partially impaired, but did not completely abrogate, Nef-mediated cell surface CD4 downregulation. Furthermore, the patient infected with HIV-1 encoding 2391 Nef had stable CD4+ T cell counts, whereas infection with HIV-1 encoding 2410 Nef resulted in CD4+ T cell decline and disease progression. IMPORTANCE A contributing factor to HIV-1 persistence is evasion of the host immune response. HIV-1 uses the Nef accessory protein to evade the antiviral roles of the adaptive and intrinsic innate immune responses. Nef targets SERINC5, a restriction factor which potently impairs HIV-1 infection by triggering SERINC5 removal from the cell surface. The molecular determinants underlying this Nef function remain incompletely understood. Recent studies have found a correlation between the extent of Nef-mediated SERINC5 downregulation and the rate of disease progression. Furthermore, single-residue polymorphisms outside the known Nef functional motifs can modulate SERINC5 downregulation. The identification of a naturally occurring Nef polymorphism impairing SERINC5 downregulation in this study supports a link between Nef downregulation of SERINC5 and the rate of plasma CD4+ T cell decline. Moreover, the observed functional impairments of this polymorphism could provide clues to further elucidate unknown aspects of the SERINC5 antagonistic pathway via Nef.
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11
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Molnar S, Wieczorek L, Zemil M, Schulte B, Martinez E, Gift S, Tang L, Streeck H, Gramzinski RA, Michael NL, Joyce G, Polonis VR. Novel monoclonal antibodies to the SERINC5 HIV-1 restriction factor detect endogenous andvirion-associated SERINC5. MAbs 2021; 12:1802187. [PMID: 32835602 PMCID: PMC7531522 DOI: 10.1080/19420862.2020.1802187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
SERINC5 is a multi-pass transmembrane protein that is thought to play a role in serine incorporation during cellular membrane biosynthesis. This protein has also been identified as a human immunodeficiency virus Type 1 (HIV-1) restriction factor. The paucity of monoclonal antibodies (mAbs) against SERINC5 has posed a challenge for the study of the endogenous protein. Here we report the development of novel anti-SERINC5 mAbs that target three distinct loops on the protein. We demonstrate that these SERINC5 mAbs can be used to detect endogenously expressed SERINC5 protein in various cell lines using Western blot, whole-cell ELISA, flow cytometry, and immunocytochemistry. We further show that some of these antibodies can detect SERINC5 that is present in HIV-1 viral stocks. These antibodies will aid in the characterization of the functions and mechanisms of action of SERINC5 in different cell types.
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Affiliation(s)
- Sebastian Molnar
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Lindsay Wieczorek
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Michelle Zemil
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Bianca Schulte
- Institute for Virology, University Hospital Bonn , Bonn, Germany
| | - Elizabeth Martinez
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Syna Gift
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Lan Tang
- Biologics Department, GenScript , Piscataway, NJ, USA
| | - Hendrik Streeck
- Institute for Virology, University Hospital Bonn , Bonn, Germany
| | - Robert A Gramzinski
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA
| | - Nelson L Michael
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA
| | - Gordon Joyce
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine , Bethesda, MD, USA
| | - Victoria R Polonis
- Military HIV Research Program, Walter Reed Army Institute of Research , Silver Spring, MD, USA
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12
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Kruize Z, van Nuenen AC, van Wijk SW, Girigorie AF, van Dort KA, Booiman T, Kootstra NA. Nef Obtained from Individuals with HIV-1 Vary in Their Ability to Antagonize SERINC3- and SERINC5-Mediated HIV-1 Restriction. Viruses 2021; 13:v13030423. [PMID: 33800773 PMCID: PMC8000780 DOI: 10.3390/v13030423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/14/2022] Open
Abstract
Nef is a multifunctional viral protein that has the ability to downregulate cell surface molecules, including CD4 and major histocompatibility complex class I (MHC-I) and, as recently shown, also members of the serine incorporator family (SERINC). Here, we analyzed the impact of naturally occurring mutations in HIV-1 Nef on its ability to counteract SERINC restriction and the clinical course of infection. HIV-1 Nef sequences were obtained from 123 participants of the Amsterdam Cohort Studies and showed multiple amino acid variations and mutations. Most of the primary Nef proteins showed increased activity to counteract SERINC3 and SERINC5 as compared to NL4-3 Nef. Several mutations in Nef were associated with either an increased or decreased infectivity of Bal26-pseudotyped HIV-1 produced in the presence of SERINC3 or SERINC5. The 8R, 157N and R178G Nef mutations were shown to have an effect on disease progression. Survival analysis showed an accelerated disease progression of individuals infected with HIV-1 carrying arginine or asparagine at position 8 or 157 in Nef, respectively, or the R178G Nef mutation. Here, we observed that naturally occurring mutations in Nef affect the ability of Nef to counteract SERINC3- and SERINC5-mediated inhibition of viral infectivity. The majority of these Nef mutations had no significant effect on HIV-1 pathogenesis and only the 8R, 157N and R178G mutations were associated with disease course.
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13
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Zhang HG, Guo J, Yuan Y, Zuo Y, Liu J, Zhu L, Miao Y, Chen X, Jin L, Huang F, Ren T, He J, Shi W, Wen Z, Zhu C, Zheng H, Dong C, Qian F. Ubiquitin E3 Ligase c-Cbl Is a Host Negative Regulator of Nef Protein of HIV-1. Front Microbiol 2020; 11:597972. [PMID: 33329486 PMCID: PMC7710902 DOI: 10.3389/fmicb.2020.597972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/28/2020] [Indexed: 11/23/2022] Open
Abstract
Nef is an accessory protein encoded by human immunodeficiency virus type-1 (HIV-1) and plays important roles in regulating HIV-1 infection and viral replication. Interestingly, HIV-1 Nef can promote degradation of numerous host proteins to disrupt cellular antiviral immune response. However, how HIV-1 Nef is degraded by host factors remains largely unexplored. Here, we identified c-Cbl as a host ubiquitin E3 ligase of HIV-1 Nef. We found that c-Cbl interacts with Nef and reduces protein levels of HIV-1 Nef. Further studies demonstrated that c-Cbl promoted Lys48-linked polyubiquitination of HIV-1 Nef, thus attenuating protein stability of HIV-1 Nef. Importantly, cellular c-Cbl ubiquitinated and degraded Nef proteins produced by HIV-1 NL4-3 virions, and ultimately attenuated HIV-1 virulence for infection of THP1 cells. This study reveals a ubiquitination and proteasome-dependent degradation mechanism of HIV-1 Nef protein, and could provide potential strategies for fighting against HIV-1.
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Affiliation(s)
- Hong-Guang Zhang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Jing Guo
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Yukang Yuan
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Yibo Zuo
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Jin Liu
- The Second Affiliated Hospital of Soochow University, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Li Zhu
- The Second Affiliated Hospital of Soochow University, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Ying Miao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Xiangjie Chen
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Lincong Jin
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Fan Huang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Tengfei Ren
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Jiuyi He
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Weifeng Shi
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Zhenke Wen
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Chuanwu Zhu
- The Second Affiliated Hospital of Soochow University, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Hui Zheng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Chunsheng Dong
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Feng Qian
- The Second Affiliated Hospital of Soochow University, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
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14
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Impaired ability of Nef to counteract SERINC5 is associated with reduced plasma viremia in HIV-infected individuals. Sci Rep 2020; 10:19416. [PMID: 33173092 PMCID: PMC7656250 DOI: 10.1038/s41598-020-76375-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/28/2020] [Indexed: 01/23/2023] Open
Abstract
HIV-1 Nef plays an essential role in enhancing virion infectivity by antagonizing the host restriction molecule SERINC5. Because Nef is highly polymorphic due to the selective forces of host cellular immunity, we hypothesized that certain immune-escape polymorphisms may impair Nef’s ability to antagonize SERINC5 and thereby influence viral fitness in vivo. To test this hypothesis, we identified 58 Nef polymorphisms that were overrepresented in HIV-infected patients in Japan sharing the same HLA genotypes. The number of immune-associated Nef polymorphisms was inversely correlated with the plasma viral load. By breaking down the specific HLA allele-associated mutations, we found that a number of the HLA-B*51:01-associated Y120F and Q125H mutations were most significantly associated with a reduced plasma viral load. A series of biochemical experiments showed that the double mutations Y120F/Q125H, but not either single mutation, impaired Nef’s ability to antagonize SERINC5 and was associated with decreasing virion infectivity and viral replication in primary lymphocytes. In contrast, other Nef functions such as CD4, CCR5, CXCR4 and HLA class I downregulation and CD74 upregulation remained unchanged. Taken together, our results suggest that the differential ability of Nef to counteract SERINC5 by naturally occurring immune-associated mutations was associated with the plasma viral load in vivo.
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15
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Arantes I, Ribeiro-Alves M, S. D. de Azevedo S, Delatorre E, Bello G. Few amino acid signatures distinguish HIV-1 subtype B pandemic and non-pandemic strains. PLoS One 2020; 15:e0238995. [PMID: 32960906 PMCID: PMC7508567 DOI: 10.1371/journal.pone.0238995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/27/2020] [Indexed: 11/26/2022] Open
Abstract
The Human Immunodeficiency Virus Type I (HIV-1) subtype B comprises approximately 10% of all HIV infections in the world. The HIV-1 subtype B epidemic comprehends a pandemic variant (named BPANDEMIC) disseminated worldwide and non-pandemic variants (named BCAR) that are mostly restricted to the Caribbean. The goal of this work was the identification of amino acid signatures (AAs) characteristic to the BCAR and BPANDEMIC variants. To this end, we analyzed HIV-1 subtype B full-length (n = 486) and partial (n = 814) genomic sequences from the Americas classified within the BCAR and BPANDEMIC clades and reconstructed the sequences of their most recent common ancestors (MRCA). Analysis of contemporary HIV-1 sequences revealed 13 AAs between BCAR and BPANDEMIC variants (four on Gag, three on Pol, three on Rev, and one in Vif, Vpu, and Tat) of which only two (one on Gag and one on Pol) were traced to the MRCA. All AAs correspond to polymorphic sites located outside essential functional proteins domains, except the AAs in Tat. The absence of stringent AAs inherited from their ancestors between modern BCAR and BPANDEMIC variants support that ecological factors, rather than viral determinants, were the main driving force behind the successful spread of the BPANDEMIC strain.
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Affiliation(s)
- Ighor Arantes
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, Brazil
| | - Marcelo Ribeiro-Alves
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Pesquisa Clínica em DST-AIDS, Rio de Janeiro, Brazil
| | - Suwellen S. D. de Azevedo
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, Brazil
| | - Edson Delatorre
- Universidade Federal do Espírito Santo, Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Alegre, Brazil
| | - Gonzalo Bello
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, Brazil
- * E-mail: ,
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16
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Jin SW, Mwimanzi FM, Mann JK, Bwana MB, Lee GQ, Brumme CJ, Hunt PW, Martin JN, Bangsberg DR, Ndung’u T, Brumme ZL, Brockman MA. Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5. PLoS Pathog 2020; 16:e1008813. [PMID: 32925973 PMCID: PMC7515180 DOI: 10.1371/journal.ppat.1008813] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 09/24/2020] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
HIV Nef counteracts cellular host restriction factors SERINC3 and SERINC5, but our understanding of how naturally occurring global Nef sequence diversity impacts these activities is limited. Here, we quantify SERINC3 and SERINC5 internalization function for 339 Nef clones, representing the major pandemic HIV-1 group M subtypes A, B, C and D. We describe distinct subtype-associated hierarchies for Nef-mediated internalization of SERINC5, for which subtype B clones display the highest activities on average, and of SERINC3, for which subtype B clones display the lowest activities on average. We further identify Nef polymorphisms that modulate its ability to counteract SERINC proteins, including substitutions in the N-terminal domain that selectively impair SERINC3 internalization. Our findings demonstrate that the SERINC antagonism activities of HIV Nef differ markedly among major viral subtypes and between individual isolates within a subtype, suggesting that variation in these functions may contribute to global differences in viral pathogenesis.
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Affiliation(s)
- Steven W. Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | | | - Jaclyn K. Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Mwebesa Bosco Bwana
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Guinevere Q. Lee
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Peter W. Hunt
- School of Medicine, University of California, San Francisco, United States of America
| | - Jeff N. Martin
- School of Medicine, University of California, San Francisco, United States of America
| | - David R. Bangsberg
- School of Public Health, Oregon Health Science University, Portland, United States of America
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, United States of America
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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17
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Differential Pressures of SERINC5 and IFITM3 on HIV-1 Envelope Glycoprotein over the Course of HIV-1 Infection. J Virol 2020; 94:JVI.00514-20. [PMID: 32493821 DOI: 10.1128/jvi.00514-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 05/25/2020] [Indexed: 12/23/2022] Open
Abstract
Infection of human immunodeficiency virus type 1 (HIV-1) is subject to restriction by cellular factors. Serine incorporator 5 (SERINC5) and interferon-inducible transmembrane 3 (IFITM3) proteins represent two of these restriction factors, which inhibit HIV-1 entry into target cells. Both proteins impede fusion of the viral membrane with the cellular membrane and the formation of a viral fusion pore, and both are countered by the HIV-1 envelope glycoprotein (Env). Given the immense and lasting pressure which Env endures from host adaptive immune responses, it is important to understand whether and how HIV-1 Env is able to maintain the resistance to SERINC5 and IFITM3 throughout the course of infection. We have thus examined a panel of HIV-1 Env clones that were isolated at different stages of viral infection-transmission, acute, and chronic. While HIV-1 Env clones from the transmission stage are resistant to both SERINC5 and IFITM3, as infection progresses into the acute and chronic stages, the resistance to IFITM3 but not to SERINC5 is gradually lost. We further discovered a significant correlation between the resistance of HIV-1 Env to soluble CD4 inhibition and the resistance to SERINC5 but not to IFITM3. Interestingly, the miniprotein CD4 mimetic M48U1 sensitizes HIV-1 Env to the inhibition by SERINC5 but not IFITM3. Together, these data indicate that SERINC5 and IFITM3 exert differential inhibitory pressures on HIV-1 Env over different stages of HIV-1 infection and that HIV-1 Env uses varied strategies to resist these two restriction factors.IMPORTANCE HIV-1 Env protein is exposed to the inhibition not only by humoral response, but also by host restriction factors, including serine incorporator 5 (SERINC5) and interferon-inducible transmembrane 3 (IFITM3). This study investigates how HIV-1 envelope glycoprotein (Env) manages to overcome the pressures from all these different host inhibition mechanisms over the long course of viral infection. HIV-1 Env preserves the resistance to SERINC5 but becomes sensitive to IFITM3 when infection progresses into the chronic stage. Our study also supports the possibility of using CD4 mimetic compounds to sensitize HIV-1 Env to the inhibition by SERINC5 as a potential therapeutic strategy.
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18
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Mann JK, Rajkoomar E, Jin SW, Mkhize Q, Baiyegunhi O, Mbona P, Brockman MA, Ndung'u T. Consequences of HLA-associated mutations in HIV-1 subtype C Nef on HLA-I downregulation ability. J Med Virol 2020; 92:1182-1190. [PMID: 31944317 DOI: 10.1002/jmv.25676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/07/2020] [Indexed: 11/10/2022]
Abstract
Identification of CD8+ T lymphocyte (CTL) escape mutations that compromise the pathogenic functions of the Nef protein may be relevant for an HIV-1 attenuation-based vaccine. Previously, HLA-associated mutations 102H, 105R, 108D, and 199Y were individually statistically associated with decreased Nef-mediated HLA-I downregulation ability in a cohort of 298 HIV-1 subtype C infected individuals. In the present study, these mutations were introduced by site-directed mutagenesis into different patient-derived Nef sequence backgrounds of high similarity to the consensus C Nef sequence, and their ability to downregulate HLA-I was measured by flow cytometry in a CEM-derived T cell line. A substantial negative effect of 199Y on HLA-I downregulation and Nef expression was observed, while 102H and 105R displayed negative effects on HLA-I downregulation ability and Nef expression to a lesser extent. The total magnitude of CTL responses in individuals harboring the 199Y mutation was lower than those without the mutation, although this was not statistically significant. Overall, a modest positive relationship between Nef-mediated HLA-I downregulation ability and total magnitude of CTL responses was observed, suggesting that there is a higher requirement for HLA-I downregulation with increased CTL pressure. These results highlight a region of Nef that could be targeted by vaccine-induced CTL to reduce HLA-I downregulation and maximize CTL efficacy.
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Affiliation(s)
- Jaclyn K Mann
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | - Erasha Rajkoomar
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Burnaby, BC, Canada
| | - Qiniso Mkhize
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | | | - Pholisiwe Mbona
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Burnaby, BC, Canada.,Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute, Durban, South Africa.,Ragon Institute of MGH, MIT and Harvard University, Cambridge, Maryland.,Max Planck Institute for Infection Biology, Berlin, Germany.,Division of Infection and Immunity, University College London, London, United Kingdom
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19
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Sudderuddin H, Kinloch NN, Jin SW, Miller RL, Jones BR, Brumme CJ, Joy JB, Brockman MA, Brumme ZL. Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study. Retrovirology 2020; 17:3. [PMID: 31918727 PMCID: PMC6953280 DOI: 10.1186/s12977-019-0510-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/26/2019] [Indexed: 11/29/2022] Open
Abstract
The HIV accessory protein Nef downregulates the viral entry receptor CD4, the Human Leukocyte Antigen (HLA)-A and -B molecules, the Serine incorporator 5 (SERINC5) protein and other molecules from the infected cell surface, thereby promoting viral infectivity, replication and immune evasion. The nef locus also represents one of the most genetically variable regions in the HIV genome, and nef sequences undergo substantial evolution within a single individual over the course of infection. Few studies however have simultaneously characterized the impact of within-host nef sequence evolution on Nef protein function over prolonged timescales. Here, we isolated 50 unique Nef clones by single-genome amplification over an 11-year period from the plasma of an individual who was largely naïve to antiretroviral treatment during this time. Together, these clones harbored nonsynonymous substitutions at 13% of nef’s codons. We assessed their ability to downregulate cell-surface CD4, HLA and SERINC5 and observed that all three Nef functions declined modestly over time, where the reductions in CD4 and HLA downregulation (an average of 0.6% and 2.0% per year, respectively) achieved statistical significance. The results from this case study support all three Nef activities as being important to maintain throughout untreated HIV infection, but nevertheless suggest that, despite nef’s mutational plasticity, within-host viral evolution can compromise Nef function, albeit modestly, over prolonged periods.
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Affiliation(s)
- Hanwei Sudderuddin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Rachel L Miller
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | | | - Chanson J Brumme
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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