1
|
Kölling R. Interaction between ESCRT-III proteins and the yeast SERINC homolog Tms1. Genetics 2024:iyae132. [PMID: 39271159 DOI: 10.1093/genetics/iyae132] [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: 03/07/2024] [Accepted: 07/30/2024] [Indexed: 09/15/2024] Open
Abstract
The endosomal sorting complex required for transport (ESCRT)-III is involved in membrane remodeling and abscission during intraluminal vesicle (ILV) formation at endosomes. Our data now suggest that ESCRT-III function could be connected to lipid remodeling of the endosomal membrane. This notion is based on our finding that ESCRT-III proteins bind to the yeast serine incorporator (SERINC) homolog Tms1. Human SERINC3 and SERINC5 are HIV-1 restriction factors and have been shown to act as scramblases, flipping phospholipids between membrane leaflets. Due to the extraordinarily high sequence conservation between Tms1 and human SERINCs, it is likely that Tms1 is also a scramblase. While deletion of TMS1 had only a moderate effect on the sorting of multivesicular body (MVB) cargo proteins, the simultaneous deletion of a component of the Vps55/Vps68 complex led to a strong synergistic phenotype. This pronounced synergism suggests that Tms1 and Vps55/Vps68 perform a parallel function at endosomes. Vps55/Vps68 loosely resembles Tms1 in its overall structure. Thus, it is possible that Vps55/Vps68 is also a scramblase. Since both Vps55 and Tms1 physically interact with ESCRT-III proteins, we propose that the recruitment of a scramblase plays a crucial role in ESCRT-III-dependent membrane remodeling at endosomes.
Collapse
Affiliation(s)
- Ralf Kölling
- Institut für Lebensmittelwissenschaft und Biotechnologie, Fg. Hefegenetik und Gärungstechnologie, Universität Hohenheim, 70599 Stuttgart, Germany
| |
Collapse
|
2
|
Raghunath G, Abbott EH, Marin M, Wu H, Reyes Ballista JM, Brindley MA, Melikyan GB. Disruption of Transmembrane Phosphatidylserine Asymmetry by HIV-1 Incorporated SERINC5 Is Not Responsible for Virus Restriction. Biomolecules 2024; 14:570. [PMID: 38785977 PMCID: PMC11118262 DOI: 10.3390/biom14050570] [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: 03/22/2024] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Host restriction factor SERINC5 (SER5) incorporates into the HIV-1 membrane and inhibits infectivity by a poorly understood mechanism. Recently, SER5 was found to exhibit scramblase-like activity leading to the externalization of phosphatidylserine (PS) on the viral surface, which has been proposed to be responsible for SER5's antiviral activity. This and other reports that document modulation of HIV-1 infectivity by viral lipid composition prompted us to investigate the role of PS in regulating SER5-mediated HIV-1 restriction. First, we show that the level of SER5 incorporation into virions correlates with an increase in PS levels in the outer leaflet of the viral membrane. We developed an assay to estimate the PS distribution across the viral membrane and found that SER5, but not SER2, which lacks antiviral activity, abrogates PS asymmetry by externalizing this lipid. Second, SER5 incorporation diminished the infectivity of pseudoviruses produced from cells lacking a flippase subunit CDC50a and, therefore, exhibited a higher baseline level of surface-accessible PS. Finally, exogenous manipulation of the viral PS levels utilizing methyl-alpha-cyclodextrin revealed a lack of correlation between external PS and virion infectivity. Taken together, our study implies that the increased PS exposure to SER5-containing virions itself is not directly linked to HIV-1 restriction.
Collapse
Affiliation(s)
- Gokul Raghunath
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Elizabeth H. Abbott
- Emory College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Mariana Marin
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Hui Wu
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (M.M.); (H.W.)
| | - Judith Mary Reyes Ballista
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (J.M.R.B.); (M.A.B.)
| | - Melinda A. Brindley
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (J.M.R.B.); (M.A.B.)
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Gregory B. Melikyan
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Leonhardt SA, Purdy MD, Grover JR, Yang Z, Poulos S, McIntire WE, Tatham EA, Erramilli SK, Nosol K, Lai KK, Ding S, Lu M, Uchil PD, Finzi A, Rein A, Kossiakoff AA, Mothes W, Yeager M. Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry. Nat Commun 2023; 14:4368. [PMID: 37474505 PMCID: PMC10359404 DOI: 10.1038/s41467-023-39262-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/06/2023] [Indexed: 07/22/2023] Open
Abstract
The host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of SERINCs via binding to intracellular loop 4 (ICL4). Here, we determine cryoEM maps of full-length human SERINC3 and an ICL4 deletion construct, which reveal that hSERINC3 is comprised of two α-helical bundles connected by a ~ 40-residue, highly tilted, "crossmember" helix. The design resembles non-ATP-dependent lipid transporters. Consistently, purified hSERINCs reconstituted into proteoliposomes induce flipping of phosphatidylserine (PS), phosphatidylethanolamine and phosphatidylcholine. Furthermore, SERINC3, SERINC5 and the scramblase TMEM16F expose PS on the surface of HIV-1 and reduce infectivity, with similar results in MLV. SERINC effects in HIV-1 and MLV are counteracted by Nef and GlycoGag, respectively. Our results demonstrate that SERINCs are membrane transporters that flip lipids, resulting in a loss of membrane asymmetry that is strongly correlated with changes in Env conformation and loss of infectivity.
Collapse
Grants
- P01 AI150471 NIAID NIH HHS
- P41 GM103311 NIGMS NIH HHS
- G20 RR031199 NCRR NIH HHS
- R01 GM117372 NIGMS NIH HHS
- U54 AI170856 NIAID NIH HHS
- S10 OD018149 NIH HHS
- U24 GM129539 NIGMS NIH HHS
- S10 RR025067 NCRR NIH HHS
- This work was supported by the National Institutes of Health (NIH) grants P50 AI15046 and U54 AI170856-01 (M.Y., W.M. and A.K.K.), R01 AI154092 (M.Y.), R01 GM117372 (A.A.K.) and P01 AI150471 (W.M.)., by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research, and in part by the NIH Intramural AIDS Targeted Antiviral Program. S.D. and A.F. were supported by the CIHR grant 352417 and a Canada Research Chair. Some molecular graphics and analyses were performed with the University of California, San Francisco Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by the National Institute of General Medical Sciences Grant P41 GM103311).
Collapse
Affiliation(s)
- Susan A Leonhardt
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael D Purdy
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Molecular Electron Microscopy Core, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jonathan R Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ziwei Yang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Sandra Poulos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - William E McIntire
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Elizabeth A Tatham
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Kamil Nosol
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, P.O. Box B, Building 535, Frederick, MD, 21702, USA
| | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC, Canada
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
- Department of Cellular and Molecular Biology, University of Texas Health Science Center, Tyler, TX, USA
| | - Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Alan Rein
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, P.O. Box B, Building 535, Frederick, MD, 21702, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA.
| | - Mark Yeager
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA.
- Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Medicine, Division of Cardiovascular Medicine, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| |
Collapse
|
5
|
Ramdas P, Chande A. SERINC5 Mediates a Postintegration Block to HIV-1 Gene Expression in Macrophages. mBio 2023; 14:e0016623. [PMID: 36976020 PMCID: PMC10127607 DOI: 10.1128/mbio.00166-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/01/2023] [Indexed: 03/29/2023] Open
Abstract
HIV-1 antagonizes SERINC5 by redundant mechanisms, primarily through Nef and additionally via envelope glycoprotein. Paradoxically, HIV-1 preserves Nef function to ensure the exclusion of SERINC5 from virion incorporation regardless of the availability of envelope that can confer resistance, suggesting additional roles of the virion-incorporated host factor. Here, we report an unusual mode of SERINC5 action in inhibiting viral gene expression. This inhibition is observed only in the myeloid lineage cells but not in the cells of epithelial or lymphoid origin. We found that SERINC5-bearing viruses induce the expression of RPL35 and DRAP1 in macrophages, and these host proteins intercept HIV-1 Tat from binding to and recruiting a mammalian capping enzyme (MCE1) to the HIV-1 transcriptional complex. As a result, uncapped viral transcripts are synthesized, leading to the inhibition of viral protein synthesis and subsequent progeny virion biogenesis. Cell-type-specific inhibition of HIV-1 gene expression thus exemplifies a novel antiviral function of virion-incorporated SERINC5. IMPORTANCE In addition to Nef, HIV-1 envelope glycoprotein has been shown to modulate SERINC5-mediated inhibition. Counterintuitively, Nef from the same isolates preserves the ability to prevent SERINC5 incorporation into virions, implying additional functions of the host protein. We identify that virion-associated SERINC5 can manifest an antiviral mechanism independent of the envelope glycoprotein to regulate HIV-1 gene expression in macrophages. This mechanism is exhibited by affecting the viral RNA capping and is plausibly adopted by the host to overcome the envelope glycoprotein-mediated resistance to SERINC5 restriction.
Collapse
Affiliation(s)
- Pavitra Ramdas
- Molecular Virology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Ajit Chande
- Molecular Virology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| |
Collapse
|
6
|
Ward AE, Sokovikova D, Waxham MN, Heberle FA, Levental I, Levental KR, Kiessling V, White JM, Tamm LK. Serinc5 Restricts HIV Membrane Fusion by Altering Lipid Order and Heterogeneity in the Viral Membrane. ACS Infect Dis 2023; 9:773-784. [PMID: 36946615 PMCID: PMC10366416 DOI: 10.1021/acsinfecdis.2c00478] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The host restriction factor, Serinc5, incorporates into budding HIV particles and inhibits their infection by an incompletely understood mechanism. We have previously reported that Serinc5 but not its paralogue, Serinc2, blocks HIV cell entry by membrane fusion, specifically by inhibiting fusion pore formation and dilation. A body of work suggests that Serinc5 may alter the conformation and clustering of the HIV fusion protein, Env. To contribute an additional perspective to the developing model of Serinc5 restriction, we assessed Serinc2 and Serinc5's effects on HIV pseudoviral membranes. By measuring pseudoviral membrane thickness via cryo-electron microscopy and order via the fluorescent dye, FLIPPER-TR, Serinc5 was found to increase membrane heterogeneity, skewing the distribution toward a larger fraction of the viral membrane in an ordered phase. We also directly observed for the first time the coexistence of membrane domains within individual viral membrane envelopes. Using a total internal reflection fluorescence-based single particle fusion assay, we found that treatment of HIV pseudoviral particles with phosphatidylethanolamine (PE) rescued HIV pseudovirus fusion from restriction by Serinc5, which was accompanied by decreased membrane heterogeneity and order. This effect was specific for PE and did not depend on acyl chain length or saturation. Together, these data suggest that Serinc5 alters multiple interrelated properties of the viral membrane─lipid chain order, rigidity, line tension, and lateral pressure─which decrease the accessibility of fusion intermediates and disfavor completion of fusion. These biophysical insights into Serinc5 restriction of HIV infectivity could contribute to the development of novel antivirals that exploit the same weaknesses.
Collapse
Affiliation(s)
- Amanda E. Ward
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA 22908
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908
| | - Daria Sokovikova
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA 22908
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908
| | - Melvin Neal Waxham
- Department of Neurobiology and Anatomy, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
| | | | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA 22908
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908
| | - Kandice R. Levental
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA 22908
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908
| | - Volker Kiessling
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA 22908
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908
| | - Judith M. White
- Department of Cell Biology, University of Virginia Health System, Charlottesville, VA 22908
| | - Lukas K. Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA 22908
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Affiliation(s)
- Uddhav Timilsina
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, New York, United States of America
| | - Spyridon Stavrou
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, New York, United States of America
- * E-mail:
| |
Collapse
|
9
|
Meseguer S, Rubio MP, Lainez B, Pérez-Benavente B, Pérez-Moraga R, Romera-Giner S, García-García F, Martinez-Macias O, Cremades A, Iborra FJ, Candelas-Rivera O, Almazan F, Esplugues E. SARS-CoV-2-encoded small RNAs are able to repress the host expression of SERINC5 to facilitate viral replication. Front Microbiol 2023; 14:1066493. [PMID: 36876111 PMCID: PMC9978209 DOI: 10.3389/fmicb.2023.1066493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
Serine incorporator protein 5 (SERINC5) is a key innate immunity factor that operates in the cell to restrict the infectivity of certain viruses. Different viruses have developed strategies to antagonize SERINC5 function but, how SERINC5 is controlled during viral infection is poorly understood. Here, we report that SERINC5 levels are reduced in COVID-19 patients during the infection by SARS-CoV-2 and, since no viral protein capable of repressing the expression of SERINC5 has been identified, we hypothesized that SARS-CoV-2 non-coding small viral RNAs (svRNAs) could be responsible for this repression. Two newly identified svRNAs with predicted binding sites in the 3'-untranslated region (3'-UTR) of the SERINC5 gene were characterized and we found that the expression of both svRNAs during the infection was not dependent on the miRNA pathway proteins Dicer and Argonaute-2. By using svRNAs mimic oligonucleotides, we demonstrated that both viral svRNAs can bind the 3'UTR of SERINC5 mRNA, reducing SERINC5 expression in vitro. Moreover, we found that an anti-svRNA treatment to Vero E6 cells before SARS-CoV-2 infection recovered the levels of SERINC5 and reduced the levels of N and S viral proteins. Finally, we showed that SERINC5 positively controls the levels of Mitochondrial Antiviral Signalling (MAVS) protein in Vero E6. These results highlight the therapeutic potential of targeting svRNAs based on their action on key proteins of the innate immune response during SARS-CoV-2 viral infection.
Collapse
Affiliation(s)
- Salvador Meseguer
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Mari-Paz Rubio
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Begoña Lainez
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Beatriz Pérez-Benavente
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Raúl Pérez-Moraga
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Sergio Romera-Giner
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Francisco García-García
- Bioinformatics and Biostatistics Unit, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | | | | | - Francisco J Iborra
- Biological Noise and Cell Plasticity Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Associated Unit to Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain
| | - Oscar Candelas-Rivera
- Molecular and Cellular Biology Department, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Fernando Almazan
- Molecular and Cellular Biology Department, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Enric Esplugues
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, United States
| |
Collapse
|
10
|
Ramirez PW, Vollbrecht T, Acosta FM, Suarez M, Angerstein AO, Wallace J, O' Connell RM, Guatelli J. Nef enhances HIV-1 replication and infectivity independently of SERINC5 in CEM T cells. Virology 2023; 578:154-162. [PMID: 36577173 PMCID: PMC10484624 DOI: 10.1016/j.virol.2022.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022]
Abstract
A primary function of HIV-1 Nef is the enhancement of viral infectivity and replication. Whether counteraction of the antiretroviral proteins SERINC3 and SERINC5 is the cause of this positive influence on viral growth-rate and infectivity remains unclear. Here, we utilized CRISPR/Cas9 to knockout SERINC3 and SERINC5 in a leukemic CD4-positive T cell line (CEM) that displays nef-related infectivity and growth-rate phenotypes. Viral replication was attenuated in CEM cells infected with HIV-1 lacking Nef (HIV-1ΔNef). This attenuated growth-rate phenotype was observed regardless of whether the coding regions of the serinc3 or serinc5 genes were intact. Moreover, knockout of serinc5 alone or of both serinc5 and serinc3 together failed to restore the infectivity of HIV1ΔNef virions produced from infected CEM cells. Our results corroborate a similar study using another T-lymphoid cell line (MOLT-3) and indicate that the antagonism of SERINC3 and SERINC5 does not fully explain the virology of HIV-1 lacking Nef.
Collapse
Affiliation(s)
- Peter W Ramirez
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA, USA.
| | - Thomas Vollbrecht
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; VA San Diego Healthcare System, San Diego, CA, USA
| | - Francisco M Acosta
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA, USA
| | | | - Aaron O Angerstein
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; VA San Diego Healthcare System, San Diego, CA, USA
| | - Jared Wallace
- Division of Microbiology and Immunology, Department of Pathology, The University of Utah, Salt Lake City, UT, USA
| | - Ryan M O' Connell
- Division of Microbiology and Immunology, Department of Pathology, The University of Utah, Salt Lake City, UT, USA
| | - John Guatelli
- Department of Medicine, University of California San Diego, La Jolla, CA, USA; VA San Diego Healthcare System, San Diego, CA, USA
| |
Collapse
|
11
|
Negi G, Sharma A, Dey M, Dhanawat G, Parveen N. Membrane attachment and fusion of HIV-1, influenza A, and SARS-CoV-2: resolving the mechanisms with biophysical methods. Biophys Rev 2022; 14:1109-1140. [PMID: 36249860 PMCID: PMC9552142 DOI: 10.1007/s12551-022-00999-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022] Open
Abstract
Attachment to and fusion with cell membranes are two major steps in the replication cycle of many human viruses. We focus on these steps for three enveloped viruses, i.e., HIV-1, IAVs, and SARS-CoV-2. Viral spike proteins drive the membrane attachment and fusion of these viruses. Dynamic interactions between the spike proteins and membrane receptors trigger their specific attachment to the plasma membrane of host cells. A single virion on cell membranes can engage in binding with multiple receptors of the same or different types. Such dynamic and multivalent binding of these viruses result in an optimal attachment strength which in turn leads to their cellular entry and membrane fusion. The latter process is driven by conformational changes of the spike proteins which are also class I fusion proteins, providing the energetics of membrane tethering, bending, and fusion. These viruses exploit cellular and membrane factors in regulating the conformation changes and membrane processes. Herein, we describe the major structural and functional features of spike proteins of the enveloped viruses including highlights on their structural dynamics. The review delves into some of the case studies in the literature discussing the findings on multivalent binding, membrane hemifusion, and fusion of these viruses. The focus is on applications of biophysical tools with an emphasis on single-particle methods for evaluating mechanisms of these processes at the molecular and cellular levels.
Collapse
Affiliation(s)
- Geetanjali Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Anurag Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Manorama Dey
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Garvita Dhanawat
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Nagma Parveen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| |
Collapse
|
12
|
Raghunath G, Chen YC, Marin M, Wu H, Melikyan GB. SERINC5-Mediated Restriction of HIV-1 Infectivity Correlates with Resistance to Cholesterol Extraction but Not with Lipid Order of Viral Membrane. Viruses 2022; 14:v14081636. [PMID: 35893701 PMCID: PMC9332783 DOI: 10.3390/v14081636] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/19/2022] [Accepted: 07/23/2022] [Indexed: 12/13/2022] Open
Abstract
Serine incorporator 5 (SER5) is a protein that upon incorporation into virions inhibits HIV-1 infectivity by interfering with the ability of the Env glycoprotein to promote viral fusion. The mechanisms by which SER5 antagonizes HIV-1 fusion are not well understood. A recent study of SER5's structure revealed a lipid-binding pocket, suggesting the ability to sequester lipids. This finding, along with the well-documented modulation of HIV-1 infectivity by viral lipids, especially cholesterol, prompted our examination of SER5's effect on the general lipid order of the HIV-1 membrane. Pseudoviruses bearing the SER5-sensitive HXB2-Env and containing SER5 or SER2, a control protein that lacks antiviral activity, were analyzed using two distinct lipid-order probes. We show that SER5 incorporation does not noticeably affect the lipid order of pseudoviruses. Although viral cholesterol extraction reduces HIV-1 infectivity, SER5+ viruses are less sensitive to cholesterol extraction than the control samples. In contrast, the virus' sensitivity to cholesterol oxidation was not affected by SER5 incorporation. The hydrolytic release of sphingomyelin-sequestered cholesterol had a minimal impact on the apparent resistance to cholesterol extraction. Based on these results, we propose that a subpopulation of more stable Env glycoproteins responsible for the residual infectivity of SER5+ viruses is less sensitive to the cholesterol content of the viral membrane.
Collapse
Affiliation(s)
- Gokul Raghunath
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (Y.-C.C.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Yen-Cheng Chen
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (Y.-C.C.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Mariana Marin
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (Y.-C.C.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Hui Wu
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (Y.-C.C.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Gregory B. Melikyan
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (Y.-C.C.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Correspondence:
| |
Collapse
|
13
|
Kirschman J, Marin M, Chen YC, Chen J, Herschhorn A, Smith AB, Melikyan GB. SERINC5 Restricts HIV-1 Infectivity by Promoting Conformational Changes and Accelerating Functional Inactivation of Env. Viruses 2022; 14:1388. [PMID: 35891369 PMCID: PMC9323560 DOI: 10.3390/v14071388] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/18/2022] [Accepted: 06/23/2022] [Indexed: 12/16/2022] Open
Abstract
SERINC5 incorporates into HIV-1 particles and inhibits the ability of Env glycoprotein to mediate virus-cell fusion. SERINC5-resistance maps to Env, with primary isolates generally showing greater resistance than laboratory-adapted strains. Here, we examined a relationship between the inhibition of HIV-1 infectivity and the rate of Env inactivation using a panel of SERINC5-resistant and -sensitive HIV-1 Envs. SERINC5 incorporation into pseudoviruses resulted in a faster inactivation of sensitive compared to resistant Env strains. A correlation between fold reduction in infectivity and the rate of inactivation was also observed for multiple Env mutants known to stabilize and destabilize the closed Env structure. Unexpectedly, most mutations disfavoring the closed Env conformation rendered HIV-1 less sensitive to SERINC5. In contrast, functional inactivation of SERINC5-containing viruses was significantly accelerated in the presence of a CD4-mimetic compound, suggesting that CD4 binding sensitizes Env to SERINC5. Using a small molecule inhibitor that selectively targets the closed Env structure, we found that, surprisingly, SERINC5 increases the potency of this compound against a laboratory-adapted Env which prefers a partially open conformation, indicating that SERINC5 may stabilize the closed trimeric Env structure. Our results reveal a complex effect of SERINC5 on Env conformational dynamics that promotes Env inactivation and is likely responsible for the observed restriction phenotype.
Collapse
Affiliation(s)
- Junghwa Kirschman
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA; (J.K.); (M.M.); (Y.-C.C.)
| | - Mariana Marin
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA; (J.K.); (M.M.); (Y.-C.C.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Yen-Cheng Chen
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA; (J.K.); (M.M.); (Y.-C.C.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Junhua Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.C.); (A.B.S.III)
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.C.); (A.B.S.III)
| | - Gregory B. Melikyan
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA; (J.K.); (M.M.); (Y.-C.C.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| |
Collapse
|
14
|
Xu S, Zheng Z, Pathak JL, Cheng H, Zhou Z, Chen Y, Wu Q, Wang L, Zeng M, Wu L. The Emerging Role of the Serine Incorporator Protein Family in Regulating Viral Infection. Front Cell Dev Biol 2022; 10:856468. [PMID: 35433679 PMCID: PMC9010877 DOI: 10.3389/fcell.2022.856468] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/09/2022] [Indexed: 11/25/2022] Open
Abstract
Serine incorporator (SERINC) proteins 1–5 (SERINC1-5) are involved in the progression of several diseases. SERINC2-4 are carrier proteins that incorporate the polar amino acid serine into membranes to facilitate the synthesis of phosphatidylserine and sphingolipids. SERINC genes are also differentially expressed in tumors. Abnormal expression of SERINC proteins occurs in human cancers of the breast, lung, colon, liver, and various glands, as well as in mouse testes. SERINC proteins also affect cleft lip and palate and nerve-related diseases, such as seizure Parkinsonism and borderline personality. Moreover, SERINC proteins have garnered significant interest as retroviral restriction factors, spurring efforts to define their function and elucidate the mechanisms through which they operate when associated with viruses. Human SERINC proteins possess antiviral potential against human immunodeficiency virus (HIV), SARS-COV-2, murine leukemia virus (MLV), equine infectious anemia virus (EIAV), and hepatitis B virus (HBV). Furthermore, the crystal structure is known, and the critical residues of SERINC5 that act against HIV have been identified. In this review, we discuss the most prevalent mechanisms by which SERINC3 and SERINC5 antagonize viruses and focus on the potential therapeutic applications of SERINC5/3 against HIV.
Collapse
Affiliation(s)
- Shaofen Xu
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhichao Zheng
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Basic Oral Medicine, Guangzhou Medical University School and Hospital of Stomatology, Guangzhou, China
| | - Janak L. Pathak
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haoyu Cheng
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ziliang Zhou
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanping Chen
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Qiuyu Wu
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lijing Wang
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
- Vascular Biology Research Institute, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, China
- *Correspondence: Lihong Wu, ; Mingtao Zeng, ; Lijing Wang,
| | - Mingtao Zeng
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
- *Correspondence: Lihong Wu, ; Mingtao Zeng, ; Lijing Wang,
| | - Lihong Wu
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Basic Oral Medicine, Guangzhou Medical University School and Hospital of Stomatology, Guangzhou, China
- *Correspondence: Lihong Wu, ; Mingtao Zeng, ; Lijing Wang,
| |
Collapse
|
15
|
Bryer AJ, Reddy T, Lyman E, Perilla JR. Full scale structural, mechanical and dynamical properties of HIV-1 liposomes. PLoS Comput Biol 2022; 18:e1009781. [PMID: 35041642 PMCID: PMC8797243 DOI: 10.1371/journal.pcbi.1009781] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 01/28/2022] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
Enveloped viruses are enclosed by a lipid membrane inside of which are all of the components necessary for the virus life cycle; viral proteins, the viral genome and metabolites. Viral envelopes are lipid bilayers that adopt morphologies ranging from spheres to tubes. The envelope is derived from the host cell during viral replication. Thus, the composition of the bilayer depends on the complex constitution of lipids from the host-cell's organelle(s) where assembly and/or budding of the viral particle occurs. Here, molecular dynamics (MD) simulations of authentic, asymmetric HIV-1 liposomes are used to derive a unique level of resolution of its full-scale structure, mechanics and dynamics. Analysis of the structural properties reveal the distribution of thicknesses of the bilayers over the entire liposome as well as its global fluctuations. Moreover, full-scale mechanical analyses are employed to derive the global bending rigidity of HIV-1 liposomes. Finally, dynamical properties of the lipid molecules reveal important relationships between their 3D diffusion, the location of lipid-rafts and the asymmetrical composition of the envelope. Overall, our simulations reveal complex relationships between the rich lipid composition of the HIV-1 liposome and its structural, mechanical and dynamical properties with critical consequences to different stages of HIV-1's life cycle.
Collapse
Affiliation(s)
- Alexander J. Bryer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
| | - Tyler Reddy
- CCS-7 Applied Computer Science, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Edward Lyman
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, United States of America
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
| |
Collapse
|
16
|
Cano-Ortiz L, Gu Q, de Sousa-Pereira P, Zhang Z, Chiapella C, Penda Twizerimana A, Lin C, Cláudia Franco A, VandeWoude S, Luedde T, Baldauf HM, Münk C. Feline Leukemia Virus-B Envelope together with its GlycoGag and Human Immunodeficiency Virus-1 Nef Mediate Resistance to Feline SERINC5. J Mol Biol 2021; 434:167421. [DOI: 10.1016/j.jmb.2021.167421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 11/29/2022]
|
17
|
Rausch L, Lutz K, Schifferer M, Winheim E, Gruber R, Oesterhaus EF, Rinke L, Hellmuth JC, Scherer C, Muenchhoff M, Mandel C, Bergwelt‐Baildon M, Simons M, Straub T, Krug AB, Kranich J, Brocker T. Binding of phosphatidylserine-positive microparticles by PBMCs classifies disease severity in COVID-19 patients. J Extracell Vesicles 2021; 10:e12173. [PMID: 34854246 PMCID: PMC8636722 DOI: 10.1002/jev2.12173] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/02/2021] [Indexed: 01/08/2023] Open
Abstract
Infection with SARS-CoV-2 is associated with thromboinflammation, involving thrombotic and inflammatory responses, in many COVID-19 patients. In addition, immune dysfunction occurs in patients characterised by T cell exhaustion and severe lymphopenia. We investigated the distribution of phosphatidylserine (PS), a marker of dying cells, activated platelets and platelet-derived microparticles (PMP), during the clinical course of COVID-19. We found an unexpectedly high amount of blood cells loaded with PS+ PMPs for weeks after the initial COVID-19 diagnosis. Elevated frequencies of PS+ PMP+ PBMCs correlated strongly with increasing disease severity. As a marker, PS outperformed established laboratory markers for inflammation, leucocyte composition and coagulation, currently used for COVID-19 clinical scoring. PS+ PMPs preferentially bound to CD8+ T cells with gene expression signatures of proliferating effector rather than memory T cells. As PS+ PMPs carried programmed death-ligand 1 (PD-L1), they may affect T cell expansion or function. Our data provide a novel marker for disease severity and show that PS, which can trigger the blood coagulation cascade, the complement system, and inflammation, resides on activated immune cells. Therefore, PS may serve as a beacon to attract thromboinflammatory processes towards lymphocytes and cause immune dysfunction in COVID-19.
Collapse
Affiliation(s)
- Lisa Rausch
- Institute for ImmunologyBiomedical Center (BMC), Faculty of Medicine, LMU MunichMunichGermany
| | - Konstantin Lutz
- Institute for ImmunologyBiomedical Center (BMC), Faculty of Medicine, LMU MunichMunichGermany
| | - Martina Schifferer
- German Center for Neurodegenerative Diseases (DZNE)MunichGermany
- Munich Cluster of Systems Neurology (Synergy)MunichGermany
| | - Elena Winheim
- Institute for ImmunologyBiomedical Center (BMC), Faculty of Medicine, LMU MunichMunichGermany
| | - Rudi Gruber
- bene pharmaChem GmbH & Co.KG., GeretsriedGermany
| | - Elina F. Oesterhaus
- COVID‐19 Registry of the LMU Munich (CORKUM)University Hospital, LMU MunichMunichGermany
- Max von Pettenkofer Institute & Gene CenterVirologyNational Reference Center for RetrovirusesLMU MünchenMunichGermany
| | - Linus Rinke
- Institute for ImmunologyBiomedical Center (BMC), Faculty of Medicine, LMU MunichMunichGermany
| | - Johannes C. Hellmuth
- COVID‐19 Registry of the LMU Munich (CORKUM)University Hospital, LMU MunichMunichGermany
- Department of Medicine IIIUniversity Hospital, LMU MunichMunichGermany
| | - Clemens Scherer
- COVID‐19 Registry of the LMU Munich (CORKUM)University Hospital, LMU MunichMunichGermany
- Department of Medicine IUniversity Hospital, LMU MunichMunichGermany
| | - Maximilian Muenchhoff
- COVID‐19 Registry of the LMU Munich (CORKUM)University Hospital, LMU MunichMunichGermany
- Max von Pettenkofer Institute & Gene CenterVirologyNational Reference Center for RetrovirusesLMU MünchenMunichGermany
- German Center for Infection Research (DZIF)partner site MunichGermany
| | - Christopher Mandel
- COVID‐19 Registry of the LMU Munich (CORKUM)University Hospital, LMU MunichMunichGermany
- Department of Medicine IVUniversity Hospital, LMU MunichMunichGermany
| | - Michael Bergwelt‐Baildon
- COVID‐19 Registry of the LMU Munich (CORKUM)University Hospital, LMU MunichMunichGermany
- Department of Medicine IIIUniversity Hospital, LMU MunichMunichGermany
| | - Mikael Simons
- German Center for Neurodegenerative Diseases (DZNE)MunichGermany
- Munich Cluster of Systems Neurology (Synergy)MunichGermany
- Institute of Neuronal Cell BiologyTechnical University of MunichMunichGermany
| | - Tobias Straub
- Core facility BioinformaticsBiomedical Center (BMC)Faculty of MedicineLMU MunichMunichGermany
| | - Anne B. Krug
- Institute for ImmunologyBiomedical Center (BMC), Faculty of Medicine, LMU MunichMunichGermany
| | - Jan Kranich
- Institute for ImmunologyBiomedical Center (BMC), Faculty of Medicine, LMU MunichMunichGermany
| | - Thomas Brocker
- Institute for ImmunologyBiomedical Center (BMC), Faculty of Medicine, LMU MunichMunichGermany
| |
Collapse
|
18
|
Hadpech S, Moonmuang S, Chupradit K, Yasamut U, Tayapiwatana C. Updating on Roles of HIV Intrinsic Factors: A Review of Their Antiviral Mechanisms and Emerging Functions. Intervirology 2021; 65:67-79. [PMID: 34464956 DOI: 10.1159/000519241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 08/24/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Host restriction factors are cellular proteins that inhibit specific steps of the viral life cycle. Since the 1970s, several new factors have been identified, including human immunodeficiency virus-1 (HIV-1) replication restriction. Evidence accumulated in the last decade has substantially broadened our understanding of the molecular mechanisms utilized to abrogate the HIV-1 life cycle. SUMMARY In this review, we focus on the interaction between host restriction factors participating in the early phase of HIV-1 infection, particularly CA-targeting proteins. Host factors involved in the late phase of the replication cycle, such as viral assembly and egress factors, are also described. Additionally, current reports on well-known antiviral intrinsic factors, as well as other viral restriction factors with their emerging roles, are included. CONCLUSION A comprehensive understanding of the interactions between viruses and hosts is expected to provide insight into the design of novel HIV-1 therapeutic interventions.
Collapse
Affiliation(s)
- Sudarat Hadpech
- Division of Pharmacology and Biopharmacy, Faculty of Pharmaceutical Sciences, Burapha University, Chon Buri, Thailand
| | - Sutpirat Moonmuang
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Koollawat Chupradit
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Siriraj Center for Regenerative Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Umpa Yasamut
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| |
Collapse
|
19
|
HIV-1 entry: Duels between Env and host antiviral transmembrane proteins on the surface of virus particles. Curr Opin Virol 2021; 50:59-68. [PMID: 34390925 DOI: 10.1016/j.coviro.2021.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 12/18/2022]
Abstract
Human Immunodeficiency Virus type-1 (HIV-1) is the causative agent of AIDS. Its entry step is mediated by the envelope glycoprotein (Env). During the entry process, Env vastly changes its conformation. While non-liganded Env tends to have a closed structure, receptor-binding of Env opens its conformation, which leads to virus-cell membrane fusion. Single-molecule fluorescence resonance energy transfer (smFRET) imaging allows observation of these conformational changes on the virion surface. Nascent HIV-1 particles incorporate multiple host transmembrane proteins, some of which inhibit the entry process. The Env structure or its dynamics may determine the effectiveness of these antiviral mechanisms. Here, we review recent findings about the Env conformation changes on virus particles and inhibition of Env activities by virion-incorporated host transmembrane proteins.
Collapse
|
20
|
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.
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Influence of Different Glycoproteins and of the Virion Core on SERINC5 Antiviral Activity. Viruses 2021; 13:v13071279. [PMID: 34209034 PMCID: PMC8310182 DOI: 10.3390/v13071279] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 11/25/2022] Open
Abstract
Host plasma membrane protein SERINC5 is incorporated into budding retrovirus particles where it blocks subsequent entry into susceptible target cells. Three structurally unrelated proteins encoded by diverse retroviruses, human immunodeficiency virus type 1 (HIV-1) Nef, equine infectious anemia virus (EIAV) S2, and ecotropic murine leukemia virus (MLV) GlycoGag, disrupt SERINC5 antiviral activity by redirecting SERINC5 from the site of virion assembly on the plasma membrane to an internal RAB7+ endosomal compartment. Pseudotyping retroviruses with particular glycoproteins, e.g., vesicular stomatitis virus glycoprotein (VSV G), renders the infectivity of particles resistant to inhibition by virion-associated SERINC5. To better understand viral determinants for SERINC5-sensitivity, the effect of SERINC5 was assessed using HIV-1, MLV, and Mason-Pfizer monkey virus (M-PMV) virion cores, pseudotyped with glycoproteins from Arenavirus, Coronavirus, Filovirus, Rhabdovirus, Paramyxovirus, and Orthomyxovirus genera. SERINC5 restricted virions pseudotyped with glycoproteins from several retroviruses, an orthomyxovirus, a rhabdovirus, a paramyxovirus, and an arenavirus. Infectivity of particles pseudotyped with HIV-1, amphotropic-MLV (A-MLV), or influenza A virus (IAV) glycoproteins, was decreased by SERINC5, whether the core was provided by HIV-1, MLV, or M-PMV. In contrast, particles pseudotyped with glycoproteins from M-PMV, parainfluenza virus 5 (PIV5), or rabies virus (RABV) were sensitive to SERINC5, but only with particular retroviral cores. Resistance to SERINC5 did not correlate with reduced SERINC5 incorporation into particles, route of viral entry, or absolute infectivity of the pseudotyped virions. These findings indicate that some non-retroviruses may be sensitive to SERINC5 and that, in addition to the viral glycoprotein, the retroviral core influences sensitivity to SERINC5.
Collapse
|
23
|
Coelacanth SERINC2 Inhibits HIV-1 Infectivity and Is Counteracted by Envelope Glycoprotein from Foamy Virus. J Virol 2021; 95:e0022921. [PMID: 33883219 PMCID: PMC8316019 DOI: 10.1128/jvi.00229-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
SERINC5 restricts nef-defective HIV-1 by affecting early steps of the virus life cycle. Distantly related retroviruses with a wide host range encode virulent factors in response to challenge by SERINC5. However, the evolutionary origins of this antiretroviral activity, its prevalence among the paralogs, and its ability to target retroviruses remain understudied. In agreement with previous studies, we found that four human SERINC paralogs inhibit nef-defective HIV-1, with SERINC2 being an exception. Here, we demonstrate that this lack of activity in human SERINC2 is associated with its post-whole-genome duplication (post-WGD) divergence, as evidenced by the ability of pre-WGD orthologs from Saccharomyces cerevisiae and flies and a post-WGD-proximate SERINC2 from coelacanths to inhibit the virus. Intriguingly, Nef is unable to counter coelacanth SERINC2, indicating that such activity was directed toward other retroviruses found in coelacanths (like foamy viruses). However, foamy virus-derived vectors are intrinsically resistant to the action of SERINC2, and we show that the foamy virus envelope confers this resistance by affecting its steady-state levels. Our study highlights an ancient origin of antiretroviral activity in SERINCs and a hitherto-unknown interaction with a foamy virus. IMPORTANCESERINC5 constitutes a critical barrier to the propagation of retroviruses, as highlighted by parallel emergence of anti-SERINC5 activities among distant retroviral lineages. Therefore, understanding the origin and evolution of these host factors will provide key information about virus-host relationships that can be exploited for future drug development. Here, we show that SERINC5-mediated nef-defective HIV-1 infection inhibition is evolutionarily conserved. SERINC2 from coelacanth restricts HIV-1, and it was functionally adapted to target foamy viruses. Our findings provide insights into the evolutionary origin of antiretroviral activity in the SERINC gene family and uncover the role of SERINCs in shaping the long-term conflicts between retroviruses and their hosts.
Collapse
|
24
|
Downregulation of SERINC5 expression in buffy coats of HIV-1-infected patients with detectable or undetectable viral load. Mol Biol Rep 2021; 48:4247-4252. [PMID: 34097204 DOI: 10.1007/s11033-021-06438-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/26/2021] [Indexed: 10/21/2022]
Abstract
Among the host restriction factors against HIV, SERINC5 has been described in vitro, but the mRNA level of SERINC5 in vivo has been little studied. We compare SERINC5 expression in subjects with HIV-1 (highly active antiretroviral treatment (HAART) and HAART-naïve) with and without suppression of viral load. A cross-sectional study was performed with 107 individuals distributed as follows: 24 with HAART-naïve and detectable viral load (> 50 copies/mL), 13 with HAART and detectable viral load (> 50 copies/mL), 50 with HAART and undetectable viral load (≤ 50 copies/mL), and 20 without HIV-1. SERINC5 expression in buffy coats was determined using RT-qPCR. The viral load was determined using real-time PCR and the amount of CD4 + and CD8 + T-lymphocytes was measured using flow cytometry. The data were normalized with the Shapiro-Wilk test and the Kruskal-Wallis test was subsequently performed. The relative expression was compared with a T-test and the remaining data with the Mann-Whitney U-test. ANCOVA multiple linear regression analysis was performed between characteristics of patients with SERINC5 expression. The mean and SD of the SERINC5 expression in the three groups with HIV-1 was 0.9 ± 0.2 and without HIV-1 was 1.7 ± 0.14 (P < 0.001). Multiple linear regression did not show the participation of CD4 +, CD8 + , viral load, infection time, or treatment time. No differences in the SERINC5 expression were found among the studied groups of patients with HIV-1. When comparing the groups with and without HIV-1 infection, SERINC5 was downregulation in the HIV-1 groups.
Collapse
|
25
|
Alli-Balogun GO, Levine TP. Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses. Proteins 2021; 89:1240-1250. [PMID: 33982326 DOI: 10.1002/prot.26145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/10/2021] [Indexed: 12/13/2022]
Abstract
Ice2p is an integral endoplasmic reticulum (ER) membrane protein in budding yeast S. cerevisiae named ICE because it is required for Inheritance of Cortical ER. Ice2p has also been reported to be involved in an ER metabolic branch-point that regulates the flux of lipid either to be stored in lipid droplets or to be used as membrane components. Alternately, Ice2p has been proposed to act as a tether that physically bridges the ER at contact sites with both lipid droplets and the plasma membrane via a long loop on the protein's cytoplasmic face that contains multiple predicted amphipathic helices. Here we carried out a bioinformatic analysis to increase understanding of Ice2p. First, regarding topology, we found that diverse members of the fungal Ice2 family have 10 transmembrane helices (TMHs), which places the long loop on the exofacial face of Ice2p, where it cannot form inter-organelle bridges. Second, we identified Ice2p as a full-length homolog of SERINC (serine incorporator), a family of proteins with 10 TMHs found universally in eukaryotes. Since SERINCs are potent restriction factors for HIV and other viruses, study of Ice2p may reveal functions or mechanisms that shed light on viral restriction by SERINCs.
Collapse
Affiliation(s)
| | - Tim P Levine
- UCL Institute of Ophthalmology, University College London, London, UK
| |
Collapse
|
26
|
SERINC5 Can Enhance Proinflammatory Cytokine Production by Primary Human Myeloid Cells in Response to Challenge with HIV-1 Particles. J Virol 2021; 95:JVI.02372-20. [PMID: 33597208 DOI: 10.1128/jvi.02372-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/02/2021] [Indexed: 11/20/2022] Open
Abstract
HIV-1 has to overcome physical barriers posed by host cell restriction factors (RFs) for efficient replication. Some RFs, including Trim5α and tetherin, trigger antiviral signaling in addition to directly impairing HIV replication. SERINC5 (S5) is an RF that is incorporated into HIV-1 particles to potently impair their infectivity and is efficiently antagonized by the viral pathogenesis factor Nef. Since effects of S5 on HIV-1 infectivity were mostly studied in reporter cell lines, we analyzed the effects of S5 during infection of primary HIV-1 target cells. In activated CD4+ T lymphocytes, virion incorporation of S5 only moderately impaired virion infectivity and was not associated with altered innate immune recognition. In contrast, in monocyte-derived macrophages, S5 virion incorporation potentiated the production of proinflammatory cytokines with very potent but donor-dependent effects on virion infectivity. Nef counteracted effects of S5 on both cytokine production and virion infectivity. Similar S5-induced cytokine production was observed in immature monocyte-derived dendritic cells. Notably, S5-mediated enhancement of cytokine production was not linked to the efficacy of productive infection and could be overcome by using vesicular stomatitis virus glycoprotein (VSV-G) but not infectivity restriction-insensitive HIV-1 Env for cell entry. Moreover, inhibiting entry of S5-negative HIV-1 ΔNef particles increased proinflammatory cytokine production comparably to virion incorporation of S5. Together, these results describe the sensitization of noninfectious HIV-1 particles to proinflammatory cytokine production by myeloid target cells as an additional and Nef-sensitive activity of S5. Moreover, the study reveals important cell-type and donor-dependent differences in the sensitivity of HIV target cells for antiviral effects of S5.IMPORTANCE SERINC5 (S5) is a host cell restriction factor (RF) that impairs the infectivity of HIV-1 particles in target cell lines. To assess the potential physiological relevance of this restriction, we assessed the effects of S5 on HIV-1 infection of relevant primary human target cells. We found that effects of S5 on infection of CD4+ T lymphocytes were negligible. In myeloid target cells, however, virion incorporation of S5 potently suppressed infectivity and promoted innate immune recognition of HIV-1 particles characterized by proinflammatory cytokine production. Both effects were not observed in cells of all donors analyzed, were exerted independently of one another, and were counteracted by the HIV-1 pathogenesis factor Nef. These results identify the sensitization of HIV-1 particles for innate immune recognition by myeloid target cells as a novel activity of S5 and emphasize the need to study RF function in the context of primary target cells and taking donor variabilities into account.
Collapse
|
27
|
Patient-Derived HIV-1 Nef Alleles Reveal Uncoupling of CD4 Downregulation and SERINC5 Antagonism Functions of the Viral Pathogenesis Factor. J Acquir Immune Defic Syndr 2021; 85:e23-e26. [PMID: 32541384 DOI: 10.1097/qai.0000000000002418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
28
|
Selective Disruption of SERINC5 Antagonism by Nef Impairs SIV Replication in Primary CD4 + T Cells. J Virol 2021; 95:JVI.01911-20. [PMID: 33504599 PMCID: PMC8103682 DOI: 10.1128/jvi.01911-20] [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
The Nef proteins of HIV-1 and SIV enhance viral infectivity by preventing the incorporation of the multipass transmembrane protein serine incorporator 5 (SERINC5), and to a lesser extent SERINC3, into virions. In addition to counteracting SERINCs, SIV Nef also downmodulates several transmembrane proteins from the surface of virus-infected cells, including simian tetherin, CD4 and MHC class I (MHC I) molecules. From a systematic analysis of alanine substitutions throughout the SIVmac239 Nef protein, we identified residues that are required to counteract SERINC5. This information was used to engineer an infectious molecular clone of SIV (SIVmac239nef AV), which differs by two amino acids in the N-terminal domain of Nef that make the virus sensitive to SERINC5 while retaining other activities of Nef. SIVmac239nef AV downmodulates CD3, CD4, MHC I and simian tetherin, but cannot counteract SERINC5. In primary rhesus macaque CD4+ T cells, SIVmac239nef AV exhibits impaired infectivity and replication compared to wild-type SIVmac239. These results demonstrate that SERINC5 antagonism can be separated from other Nef functions and reveal the impact of SERINC5 on lentiviral replication.Importance: SERINC5, a multipass transmembrane protein, is incorporated into retroviral particles during assembly. This leads to a reduction of particle infectivity by inhibiting virus fusion with the target cell membrane. The Nef proteins of HIV-1 and SIV enhance viral infectivity by preventing the incorporation of SERINC5 into virions. However, the relevance of this restriction factor in viral replication has not been elucidated. Here we report a systematic mapping of Nef residues required for SERINC5 antagonism. Counter screens for three other functions of Nef helped identify two residues in the N-terminal domain of Nef, which when mutated make Nef selectively susceptible to SERINC5. Since Nef is multi-functional, genetic separation of SERINC5 antagonism from its other functions affords comparison of the replication of isogenic viruses that are or are not sensitive to SERINC5. Such a strategy revealed the impact of SERINC5 on SIV replication in primary rhesus macaque CD4+ T-cells.
Collapse
|
29
|
Sauter D, Kirchhoff F. Evolutionary conflicts and adverse effects of antiviral factors. eLife 2021; 10:e65243. [PMID: 33450175 PMCID: PMC7811402 DOI: 10.7554/elife.65243] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
Human cells are equipped with a plethora of antiviral proteins protecting them against invading viral pathogens. In contrast to apoptotic or pyroptotic cell death, which serves as ultima ratio to combat viral infections, these cell-intrinsic restriction factors may prevent or at least slow down viral spread while allowing the host cell to survive. Nevertheless, their antiviral activity may also have detrimental effects on the host. While the molecular mechanisms underlying the antiviral activity of restriction factors are frequently well investigated, potential undesired effects of their antiviral functions on the host cell are hardly explored. With a focus on antiretroviral proteins, we summarize in this review how individual restriction factors may exert adverse effects as trade-off for efficient defense against attacking pathogens.
Collapse
Affiliation(s)
- Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical CenterUlmGermany
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital TübingenTübingenGermany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical CenterUlmGermany
| |
Collapse
|
30
|
Ward AE, Kiessling V, Pornillos O, White JM, Ganser-Pornillos BK, Tamm LK. HIV-cell membrane fusion intermediates are restricted by Serincs as revealed by cryo-electron and TIRF microscopy. J Biol Chem 2020; 295:15183-15195. [PMID: 32788212 PMCID: PMC7650252 DOI: 10.1074/jbc.ra120.014466] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/19/2020] [Indexed: 12/13/2022] Open
Abstract
To enter a cell and establish infection, HIV must first fuse its lipid envelope with the host cell plasma membrane. Whereas the process of HIV membrane fusion can be tracked by fluorescence microscopy, the 3D configuration of proteins and lipids at intermediate steps can only be resolved with cryo-electron tomography (cryoET). However, cryoET of whole cells is technically difficult. To overcome this problem, we have adapted giant plasma membrane vesicles (or blebs) from native cell membranes expressing appropriate receptors as targets for fusion with HIV envelope glycoprotein-expressing pseudovirus particles with and without Serinc host restriction factors. The fusion behavior of these particles was probed by TIRF microscopy on bleb-derived supported membranes. Timed snapshots of fusion of the same particles with blebs were examined by cryo-ET. The combination of these methods allowed us to characterize the structures of various intermediates on the fusion pathway and showed that when Serinc3 or Serinc5 (but not Serinc2) were present, later fusion products were more prevalent, suggesting that Serinc3/5 act at multiple steps to prevent progression to full fusion. In addition, the antifungal amphotericin B reversed Serinc restriction, presumably by intercalation into the fusing membranes. Our results provide a highly detailed view of Serinc restriction of HIV-cell membrane fusion and thus extend current structural and functional information on Serinc as a lipid-binding protein.
Collapse
Affiliation(s)
- Amanda E Ward
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Volker Kiessling
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Judith M White
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA.
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA; Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.
| |
Collapse
|
31
|
Tamalet C, Devaux C, Dubourg G, Colson P. Resistance to human immunodeficiency virus infection: a rare but neglected state. Ann N Y Acad Sci 2020; 1485:22-42. [PMID: 33009659 DOI: 10.1111/nyas.14452] [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: 04/15/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 11/29/2022]
Abstract
The natural history of human immunodeficiency virus (HIV) infection is well understood. In most individuals sexually exposed to HIV, the risk of becoming infected depends on the viral load and on sexual practices and gender. However, a low percentage of individuals who practice frequent unprotected sexual intercourse with HIV-infected partners remain uninfected. Although the systematic study of these individuals has made it possible to identify HIV resistance factors including protective genetic patterns, such epidemiological situations remain paradoxical and not fully understood. In vitro experiments have demonstrated that peripheral blood mononuclear cells (PBMCs) from HIV-free, unexposed blood donors are not equally susceptible to HIV infection; in addition, PBMCs from highly exposed seronegative individuals are generally resistant to infection by primary HIV clinical isolates. We review the literature on permissiveness of PBMCs from healthy blood donors and uninfected hyperexposed individuals to sustained infection and replication of HIV-1 in vitro. In addition, we focus on recent evidence indicating that the gut microbiota may either contribute to natural resistance to or delay replication of HIV infected individuals.
Collapse
Affiliation(s)
- Catherine Tamalet
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Gregory Dubourg
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection and Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| |
Collapse
|
32
|
Chen YC, Sood C, Marin M, Aaron J, Gratton E, Salaita K, Melikyan GB. Super-Resolution Fluorescence Imaging Reveals That Serine Incorporator Protein 5 Inhibits Human Immunodeficiency Virus Fusion by Disrupting Envelope Glycoprotein Clusters. ACS NANO 2020; 14:10929-10943. [PMID: 32441921 PMCID: PMC8274448 DOI: 10.1021/acsnano.0c02699] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Serine incorporator protein 5 (SERINC5) is the host antiretroviral factor that reduces HIV-1 infectivity by incorporating into virions and inhibiting the envelope glycoprotein (Env) mediated virus fusion with target cells. We and others have shown that SERINC5 incorporation into virions alters the Env structure and sensitizes the virus to broadly neutralizing antibodies targeting cryptic Env epitopes. We have also found that SERINC5 accelerates the loss of Env function over time compared to control viruses. However, the exact mechanism by which SERINC5 inhibits HIV-1 fusion is not understood. Here, we utilized 2D and 3D super-resolution microscopy to examine the effect of SERINC5 on the distribution of Env glycoproteins on single HIV-1 particles. We find that, in agreement with a previous report, Env glycoproteins form clusters on the surface of mature virions. Importantly, incorporation of SERINC5, but not SERINC2, which lacks antiviral activity, disrupted Env clusters without affecting the overall Env content. We also show that SERINC5 and SERINC2 also form clusters on single virions. Unexpectedly, Env and SERINC molecules exhibited poor codistribution on virions, as evidenced by much greater Env-SERINC pairwise distances compared to Env-Env distances. This observation is inconsistent with the previously reported interaction between Env and SERINC5 and suggests an indirect effect of SERINC5 on Env cluster formation. Collectively, our results reveal a multifaceted mechanism of SERINC5-mediated restriction of HIV-1 fusion that, aside from the effects on individual Env trimers, involves disruption of Env clusters, which likely serve as sites of viral fusion with target cells.
Collapse
Affiliation(s)
- Yen-Cheng Chen
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Chetan Sood
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mariana Marin
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jesse Aaron
- Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, CA 92617, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Gregory B. Melikyan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| |
Collapse
|
33
|
Li W, Zhang Z, Zhang L, Li H, Fan S, Zhu E, Fan J, Li Z, Chen W, Yi L, Ding H, Chen J, Zhao M. Antiviral Role of Serine Incorporator 5 (SERINC5) Proteins in Classical Swine Fever Virus Infection. Front Microbiol 2020; 11:580233. [PMID: 33013817 PMCID: PMC7498654 DOI: 10.3389/fmicb.2020.580233] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 08/17/2020] [Indexed: 12/28/2022] Open
Abstract
Serine incorporator 5 (SERINC5), a multipass transmembrane protein, protects cells from viral infections. The mechanism by which SERINC5 protects against classical swine fever virus (CSFV) infection is unknown. In this study, overexpression of SERINC5 in PK-15 and 3D4/2 cells significantly inhibited the growth of CSFV, whereas SERINC5 silencing enhanced CSFV growth. Additionally, CSFV infection reduced SERINC5 production in cells and tissues. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to identify and analyze protein and peptide molecules that potentially interact with SERINC5. A total of 33 cellular protein candidates were identified. Next, SERINC5 was shown to interact with melanoma differentiation-associated protein 5 (MDA5) by yeast two-hybrid, protein co-localization and co-immunoprecipitation assays. Furthermore, SERINC5 enhanced MDA5-mediated type I interferon (IFN) signaling in a dose-dependent manner. Our results suggest that the anti-CSFV effect of SERINC5 is dependent on the activation of the type I IFN, which may function along with MDA5. The inhibitory effect of SERINC5 on CSFV was disappeared when the endogenous expression of MDA5 was silenced using siRNA, suggesting that SERINC5 exerts an anti-CSFV effect in an MDA5-dependent manner. Our study demonstrated a novel link between SERINC5 and MDA5 in the inhibition of CSFV replication via the type I IFN signaling pathway.
Collapse
Affiliation(s)
- Wenhui Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zilin Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Liangliang Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Hong Li
- Shandong Qianxi Agriculture & Animal Husbandry Development Co., Ltd., Zaozhuang, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Erpeng Zhu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jindai Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhaoyao Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| |
Collapse
|
34
|
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.
Collapse
|
35
|
Abstract
This study examined for the first time the in vivo function of the serine incorporator (SERINC) proteins during retrovirus infection. SERINC3 and SERINC5 (SERINC3/5) restrict a number of retroviruses, including human immunodeficiency virus 1 (HIV-1) and murine leukemia virus (MLV), by blocking their entry into cells. Nevertheless, HIV-1 and MLV encode factors, Nef and glycosylated Gag, respectively, that counteract SERINC3/5 in vitro. We recently developed SERINC3 and SERINC5 knockout mice to examine the in vivo function of these genes. We found that SERINC5 restriction is dependent on the absence of glycosylated Gag and the expression of a specific viral envelope glycoprotein. On the other hand, SERINC3 had no antiviral function. Our findings have implications for the development of therapeutics that target SERINC5 during retrovirus infection. The serine incorporator (SERINC) proteins are multipass transmembrane proteins that affect sphingolipid and phosphatidylserine synthesis. Human SERINC5 and SERINC3 were recently shown to possess antiretroviral activity for a number of retroviruses, including human immunodeficiency virus (HIV), murine leukemia virus (MLV), and equine infectious anemia virus (EIAV). In the case of MLV, the glycosylated Gag (glyco-Gag) protein was shown to counteract SERINC5-mediated restriction in in vitro experiments and the viral envelope was found to determine virion sensitivity or resistance to SERINC5. However, nothing is known about the in vivo function of SERINC5. Antiretroviral function of a host factor in vitro is not always associated with antiretroviral function in vivo. Using SERINC5−/− mice that we had generated, we showed that mouse SERINC5 (mSERINC5) restriction of MLV infection in vivo is influenced not only by glyco-Gag but also by the retroviral envelope. Finally, we also examined the in vivo function of the other SERINC gene with known antiretroviral functions, SERINC3. By using SERINC3−/− mice, we found that the murine homologue, mSERINC3, had no antiretroviral role either in vivo or in vitro. To our knowledge, this report provides the first data showing that SERINC5 restricts retrovirus infection in vivo and that restriction of retrovirus infectivity in vivo is dependent on the presence of both glyco-Gag and the viral envelope.
Collapse
|
36
|
Kriesel F, Schelle L, Baldauf HM. Same same but different - Antiviral factors interfering with the infectivity of HIV particles. Microbes Infect 2020; 22:416-422. [PMID: 32450247 DOI: 10.1016/j.micinf.2020.05.009] [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: 04/05/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus (HIV) is the causative agent of acquired immunodeficiency syndrome (AIDS). Novel strategies to combat this pandemic include the discovery of cellular proteins targeting distinct steps of the HIV replication cycle. Here, we summarize our current knowledge on antiviral proteins interfering with the infectivity of released HIV particles.
Collapse
Affiliation(s)
- Fabian Kriesel
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Luca Schelle
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.
| |
Collapse
|
37
|
Liu Y, Wang H, Zhang J, Yang J, Bai L, Zheng B, Zheng T, Wang Y, Li J, Zhang W. SERINC5 Inhibits the Secretion of Complete and Genome-Free Hepatitis B Virions Through Interfering With the Glycosylation of the HBV Envelope. Front Microbiol 2020; 11:697. [PMID: 32431673 PMCID: PMC7216740 DOI: 10.3389/fmicb.2020.00697] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/25/2020] [Indexed: 12/22/2022] Open
Abstract
Serine incorporator 3 (SERINC3) and SERINC5 were recently identified as host intrinsic factors against human immunodeficiency virus (HIV)-1 and counteracted by HIV-1 Nef. However, whether they inhibit hepatitis B virus (HBV), which is a severe health problem worldwide, is unknown. Here, we demonstrate that SERINC5 potently inhibited HBV virion secretion in the supernatant without affecting intracellular core particle-associated DNA and the total RNA, but SERINC3 and SERINC1 did not. Further investigation discovered that SERINC5 increased the non-glycosylation of LHB, MHB, and SHB proteins of HBV and slightly decreased HBs proteins levels, which led to the decreased HBV secretion. Importantly, SERINC5 co-localized with LHB proteins in the Golgi apparatus, which is important for glycan processing and transport. In addition, we determined the functional domain in SERINC5 required for HBV inhibition, which was completely different from that required for HIV-1 restriction, whereas phosphorylation and glycosylation sites in SERINC5 were dispensable for HBV restriction. Taken together, our results demonstrate that SERINC5 suppresses HBV virion secretion through interfering with the glycosylation of HBV proteins, suggesting that SERINC5 might possess broad-spectrum antiviral activity.
Collapse
Affiliation(s)
- Yue Liu
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China.,Department of Echocardiography, The First Hospital of Jilin University, Changchun, China
| | - Hong Wang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Jun Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Jing Yang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Lu Bai
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Baisong Zheng
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Tianhang Zheng
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| | - Yingchao Wang
- Department of Hepatobiliary Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Jianhua Li
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
| |
Collapse
|
38
|
Stoneham CA, Ramirez PW, Singh R, Suarez M, Debray A, Lim C, Jia X, Xiong Y, Guatelli J. A Conserved Acidic-Cluster Motif in SERINC5 Confers Partial Resistance to Antagonism by HIV-1 Nef. J Virol 2020; 94:e01554-19. [PMID: 31941773 PMCID: PMC7081897 DOI: 10.1128/jvi.01554-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/12/2020] [Indexed: 12/15/2022] Open
Abstract
The cellular protein SERINC5 inhibits the infectivity of diverse retroviruses, and its activity is counteracted by the glycosylated Gag (glycoGag) protein of murine leukemia virus (MLV), the S2 protein of equine infectious anemia virus (EIAV), and the Nef protein of human immunodeficiency virus type 1 (HIV-1). Determining the regions within SERINC5 that provide restrictive activity or Nef sensitivity should inform mechanistic models of the SERINC5/HIV-1 relationship. Here, we report that deletion of the conserved sequence EDTEE, which is located within a cytoplasmic loop of SERINC5 and which is reminiscent of an acidic-cluster membrane trafficking signal, increases the sensitivity of SERINC5 to antagonism by Nef, while it has no effect on the intrinsic activity of the protein as an inhibitor of infectivity. These effects correlated with enhanced removal of the ΔEDTEE mutant relative to that of wild-type SERINC5 from the cell surface and with enhanced exclusion of the mutant protein from virions by Nef. Mutational analysis indicated that the acidic residues, but not the threonine, within the EDTEE motif are important for the relative resistance to Nef. Deletion of the EDTEE sequence did not increase the sensitivity of SERINC5 to antagonism by the glycoGag protein of MLV, suggesting that its virologic role is Nef specific. These results are consistent with the reported mapping of the cytoplasmic loop that contains the EDTEE sequence as a general determinant of Nef responsiveness, but they further indicate that sequences inhibitory to as well as supportive of Nef activity reside in this region. We speculate that the EDTEE motif might have evolved to mediate resistance against retroviruses that use Nef-like proteins to antagonize SERINC5.IMPORTANCE Cellular membrane proteins in the SERINC family, especially SERINC5, inhibit the infectivity of retroviral virions. This inhibition is counteracted by retroviral proteins, specifically, HIV-1 Nef, MLV glycoGag, and EIAV S2. One consequence of such a host-pathogen "arms race" is a compensatory change in the host antiviral protein as it evolves to escape the effects of viral antagonists. This is often reflected in a genetic signature, positive selection, which is conspicuously missing in SERINC5 Here we show that despite this lack of genetic evidence, a sequence in SERINC5 nonetheless provides relative resistance to antagonism by HIV-1 Nef.
Collapse
Affiliation(s)
- Charlotte A Stoneham
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- The VA San Diego Healthcare System, San Diego, California, USA
| | - Peter W Ramirez
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Rajendra Singh
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- The VA San Diego Healthcare System, San Diego, California, USA
| | - Marissa Suarez
- The VA San Diego Healthcare System, San Diego, California, USA
| | - Andrew Debray
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Christopher Lim
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Xiaofei Jia
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - John Guatelli
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- The VA San Diego Healthcare System, San Diego, California, USA
| |
Collapse
|
39
|
Flow Cytometry Analysis of HIV-1 Env Conformations at the Surface of Infected Cells and Virions: Role of Nef, CD4, and SERINC5. J Virol 2020; 94:JVI.01783-19. [PMID: 31852789 DOI: 10.1128/jvi.01783-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022] Open
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.
Collapse
|
40
|
Zutz A, Schölz C, Schneider S, Pierini V, Münchhoff M, Sutter K, Wittmann G, Dittmer U, Draenert R, Bogner JR, Fackler OT, Keppler OT. SERINC5 Is an Unconventional HIV Restriction Factor That Is Upregulated during Myeloid Cell Differentiation. J Innate Immun 2020; 12:399-409. [PMID: 31935717 DOI: 10.1159/000504888] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022] Open
Abstract
Classical antiviral restriction factors promote cellular immunity by their ability to interfere with virus replication and induction of their expression by proinflammatory cytokines such as interferons. The serine incorporator proteins SERINC3 and SERINC5 potently reduce the infectivity of HIV-1 particles when overexpressed, and RNA interference or knockout approaches in T cells have indicated antiviral activity also of the endogenous proteins. Due to lack of reagents for detection of endogenous SERINC proteins, it is still unclear whether SERINC3/5 are expressed to functionally relevant levels in different primary target cells of HIV infection and how the expression levels of these innate immunity factors are regulated. In the current study, analysis of SERINC3/5 mRNA steady-state levels in primary lymphoid and monocyte-derived cells revealed selective induction of their expression upon differentiation of myeloid cells. Contrary to classical antiviral restriction factors, various antiviral α-interferon subtypes and proinflammatory interleukins had no effect on SERINC levels, which were also not dysregulated in CD4+ T cells and monocytes isolated from patients with chronic HIV-1 infection. Notably, HIV-1 particles produced by terminally differentiated monocyte-derived macrophages with high SERINC5 expression, but not by low-expressing monocytes, showed a Nef-dependent infectivity defect. Overall, these findings suggest endogenous expression of SERINC5 to antivirally active levels in macrophages. Our results classify SERINC5 as an unconventional HIV-1 restriction factor whose expression is specifically induced upon differentiation of cells towards the myeloid lineage.
Collapse
Affiliation(s)
- Ariane Zutz
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Christian Schölz
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany,
| | - Stephanie Schneider
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Virginia Pierini
- Center for Infectious Diseases, Integrative Virology, University of Heidelberg, Heidelberg, Germany
| | - Maximilian Münchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,German Center for Infection Research, Site Munich, Munich, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Georg Wittmann
- Department of Transfusion Medicine, Cell Therapeutics, and Hemostaseology, Department of Anesthesiology, University Hospital Munich, Munich, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Rika Draenert
- Division of Infectious Diseases, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany.,German Center for Infection Research, Site Munich, Munich, Germany
| | - Johannes R Bogner
- Division of Infectious Diseases, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany.,German Center for Infection Research, Site Munich, Munich, Germany
| | - Oliver T Fackler
- Center for Infectious Diseases, Integrative Virology, University of Heidelberg, Heidelberg, Germany.,German Center for Infection Research, Site Heidelberg, Heidelberg, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,German Center for Infection Research, Site Munich, Munich, Germany
| |
Collapse
|
41
|
Pye VE, Rosa A, Bertelli C, Struwe WB, Maslen SL, Corey R, Liko I, Hassall M, Mattiuzzo G, Ballandras-Colas A, Nans A, Takeuchi Y, Stansfeld PJ, Skehel JM, Robinson CV, Pizzato M, Cherepanov P. A bipartite structural organization defines the SERINC family of HIV-1 restriction factors. Nat Struct Mol Biol 2020; 27:78-83. [PMID: 31907454 PMCID: PMC6956856 DOI: 10.1038/s41594-019-0357-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022]
Abstract
The human integral membrane protein SERINC5 potently restricts HIV-1 infectivity and sensitizes the virus to antibody-mediated neutralization. Here, using cryo-EM, we determine the structures of human SERINC5 and its orthologue from Drosophila melanogaster at subnanometer and near-atomic resolution, respectively. The structures reveal a novel fold comprised of ten transmembrane helices organized into two subdomains and bisected by a long diagonal helix. A lipid binding groove and clusters of conserved residues highlight potential functional sites. A structure-based mutagenesis scan identified surface-exposed regions and the interface between the subdomains of SERINC5 as critical for HIV-1-restriction activity. The same regions are also important for viral sensitization to neutralizing antibodies, directly linking the antiviral activity of SERINC5 with remodeling of the HIV-1 envelope glycoprotein.
Collapse
Affiliation(s)
- Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London, UK
| | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London, UK
| | - Cinzia Bertelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, Povo, Italy
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, UK
| | - Sarah L Maslen
- Biological Mass Spectrometry and Proteomics Laboratory, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Robin Corey
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Idlir Liko
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, UK
| | - Mark Hassall
- National Institute for Biological Standards and Control, Hertfordshire, UK
| | - Giada Mattiuzzo
- National Institute for Biological Standards and Control, Hertfordshire, UK
| | | | - Andrea Nans
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | - Yasuhiro Takeuchi
- National Institute for Biological Standards and Control, Hertfordshire, UK
- UCL Division of Infection and Immunity, The Rayne Building, London, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Warwick, UK
| | - J Mark Skehel
- Biological Mass Spectrometry and Proteomics Laboratory, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, UK
| | - Massimo Pizzato
- Department of Cellular, Computational and Integrative Biology, University of Trento, Povo, Italy.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London, UK.
- Department of Infectious Disease, Imperial College London, St Mary's Campus, Norfolk Place, London, UK.
| |
Collapse
|
42
|
Characterization of Endogenous SERINC5 Protein as Anti-HIV-1 Factor. J Virol 2019; 93:JVI.01221-19. [PMID: 31597782 PMCID: PMC6880170 DOI: 10.1128/jvi.01221-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/24/2019] [Indexed: 01/07/2023] Open
Abstract
SERINC5 is the long-searched-for antiviral factor that is counteracted by the HIV-1 accessory gene product Nef. Here, we engineered, via CRISPR/Cas9 technology, T-cell lines that express endogenous SERINC5 alleles tagged with a knocked-in HA epitope. This genetic modification enabled us to study basic properties of endogenous SERINC5 and to verify proposed mechanisms of HIV-1 Nef-mediated counteraction of SERINC5. Using this unique resource, we identified the susceptibility of endogenous SERINC5 protein to posttranslational modulation by type I IFNs and suggest uncoupling of Nef-mediated functional antagonism from SERINC5 exclusion from virions. When expressed in virus-producing cells, the cellular multipass transmembrane protein SERINC5 reduces the infectivity of HIV-1 particles and is counteracted by HIV-1 Nef. Due to the unavailability of an antibody of sufficient specificity and sensitivity, investigation of SERINC5 protein expression and subcellular localization has been limited to heterologously expressed SERINC5. We generated, via CRISPR/Cas9-assisted gene editing, Jurkat T-cell clones expressing endogenous SERINC5 bearing an extracellularly exposed hemagglutinin (HA) epitope [Jurkat SERINC5(iHA knock-in) T cells]. This modification enabled quantification of endogenous SERINC5 protein levels and demonstrated a predominant localization in lipid rafts. Interferon alpha (IFN-α) treatment enhanced cell surface levels of SERINC5 in a ruxolitinib-sensitive manner in the absence of modulation of mRNA and protein quantities. Parental and SERINC5(iHA knock-in) T cells shared the ability to produce infectious wild-type HIV-1 but not an HIV-1 Δnef mutant. SERINC5-imposed reduction of infectivity involved a modest reduction of virus fusogenicity. An association of endogenous SERINC5 protein with HIV-1 Δnef virions was consistently detectable as a 35-kDa species, as opposed to heterologous SERINC5, which presented as a 51-kDa species. Nef-mediated functional counteraction did not correlate with virion exclusion of SERINC5, arguing for the existence of additional counteractive mechanisms of Nef that act on virus-associated SERINC5. In HIV-1-infected cells, Nef triggered the internalization of SERINC5 in the absence of detectable changes of steady-state protein levels. These findings establish new properties of endogenous SERINC5 expression and subcellular localization, challenge existing concepts of HIV-1 Nef-mediated antagonism of SERINC5, and uncover an unprecedented role of IFN-α in modulating SERINC5 through accumulation at the cell surface. IMPORTANCE SERINC5 is the long-searched-for antiviral factor that is counteracted by the HIV-1 accessory gene product Nef. Here, we engineered, via CRISPR/Cas9 technology, T-cell lines that express endogenous SERINC5 alleles tagged with a knocked-in HA epitope. This genetic modification enabled us to study basic properties of endogenous SERINC5 and to verify proposed mechanisms of HIV-1 Nef-mediated counteraction of SERINC5. Using this unique resource, we identified the susceptibility of endogenous SERINC5 protein to posttranslational modulation by type I IFNs and suggest uncoupling of Nef-mediated functional antagonism from SERINC5 exclusion from virions.
Collapse
|
43
|
Abstract
The accessory protein Nef of human immunodeficiency virus (HIV) is a primary determinant of viral pathogenesis. Nef is abundantly expressed during infection and reroutes a variety of cell surface proteins to disrupt host immunity and promote the viral replication cycle. Nef counteracts host defenses by sequestering and/or degrading its targets via the endocytic and secretory pathways. Nef does this by physically engaging a number of host trafficking proteins. Substantial progress has been achieved in identifying the targets of Nef, and a structural and mechanistic understanding of Nef's ability to command the protein trafficking machinery has recently started to coalesce. Comparative analysis of HIV and simian immunodeficiency virus (SIV) Nef proteins in the context of recent structural advances sheds further light on both viral evolution and the mechanisms whereby trafficking is hijacked. This review describes how advances in cell and structural biology are uncovering in growing detail how Nef subverts the host immune system, facilitates virus release, and enhances viral infectivity.
Collapse
|
44
|
Evans JP, Liu SL. Multifaceted Roles of TIM-Family Proteins in Virus-Host Interactions. Trends Microbiol 2019; 28:224-235. [PMID: 31732320 DOI: 10.1016/j.tim.2019.10.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/25/2019] [Accepted: 10/10/2019] [Indexed: 01/16/2023]
Abstract
To enhance infection, enveloped viruses exploit adhesion molecules expressed on the surface of host cells. Specifically, phosphatidylserine (PS) receptors - including members of the human T cell immunoglobulin and mucin domain (TIM)-family - have gained attention for their ability to mediate the entry of many enveloped viruses. However, recent evidence that TIM-1 can restrict viral release reveals a new role for these PS receptors. Additionally, viral factors such as the HIV-1 accessory protein Nef can antagonize this antiviral activity of TIM-1 while host restriction factors such as SERINC5 can enhance it. In this review, we examine the various roles of PS receptors, specifically TIM-family proteins, and the intricate relationship between host and viral factors. Elucidating the multifunctional roles of PS receptors in virus-host interaction is important for understanding viral pathogenesis and developing novel antiviral therapeutics.
Collapse
Affiliation(s)
- John P Evans
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA; Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA; Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
45
|
Ramirez PW, Sharma S, Singh R, Stoneham CA, Vollbrecht T, Guatelli J. Plasma Membrane-Associated Restriction Factors and Their Counteraction by HIV-1 Accessory Proteins. Cells 2019; 8:E1020. [PMID: 31480747 PMCID: PMC6770538 DOI: 10.3390/cells8091020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 02/07/2023] Open
Abstract
The plasma membrane is a site of conflict between host defenses and many viruses. One aspect of this conflict is the host's attempt to eliminate infected cells using innate and adaptive cell-mediated immune mechanisms that recognize features of the plasma membrane characteristic of viral infection. Another is the expression of plasma membrane-associated proteins, so-called restriction factors, which inhibit enveloped virions directly. HIV-1 encodes two countermeasures to these host defenses: The membrane-associated accessory proteins Vpu and Nef. In addition to inhibiting cell-mediated immune-surveillance, Vpu and Nef counteract membrane-associated restriction factors. These include BST-2, which traps newly formed virions at the plasma membrane unless counteracted by Vpu, and SERINC5, which decreases the infectivity of virions unless counteracted by Nef. Here we review key features of these two antiviral proteins, and we review Vpu and Nef, which deplete them from the plasma membrane by co-opting specific cellular proteins and pathways of membrane trafficking and protein-degradation. We also discuss other plasma membrane proteins modulated by HIV-1, particularly CD4, which, if not opposed in infected cells by Vpu and Nef, inhibits viral infectivity and increases the sensitivity of the viral envelope glycoprotein to host immunity.
Collapse
Affiliation(s)
- Peter W Ramirez
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Shilpi Sharma
- 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
| | - Charlotte A Stoneham
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Thomas Vollbrecht
- 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.
| |
Collapse
|
46
|
CD4 Expression and Env Conformation Are Critical for HIV-1 Restriction by SERINC5. J Virol 2019; 93:JVI.00544-19. [PMID: 31043528 DOI: 10.1128/jvi.00544-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/25/2019] [Indexed: 12/29/2022] Open
Abstract
Serine incorporator 5 (SERINC5) is a recently identified restriction factor that strongly blocks HIV-1 entry but is counteracted by Nef. Notably, tier 1 HIV-1 Env proteins are sensitive to SERINC5, whereas the majority of tier 2/3 Env proteins are resistant to SERINC5, when viruses are produced from CD4-negative cells and tested by a single-round replication assay. Here, we investigated the Env-dependent SERINC5 antiviral mechanism by comparing tier 1 NL Env with tier 3 AD8 Env proteins. We found that when NL and AD8 viruses were inoculated into CD4+ T cells and human peripheral blood mononuclear cells (PBMCs), the propagation of the two viruses was restricted to a similar level when Nef was not expressed. Using a bimolecular fluorescence complementation (BiFC) assay, we detected Env-Env association and Env-SERINC5 interactions. A much greater level of NL Env-SERINC5 interactions was detected than was AD8 Env-SERINC5 interactions, which was further validated by immunoprecipitation assays. In addition, SERINC5 dissociated the NL Env trimeric complex more effectively than the AD8 Env trimeric complex when CD4 was not expressed. However, when CD4 was expressed, SERINC5 became more capable of interacting with AD8 Env and dissociating its trimeric complex. Moreover, AD8 and several other tier 2/3 viruses produced in the presence of CD4 became sensitive to SERINC5 when measured by the single-round replication assay. Because tier 1 and tier 2/3 Env trimers have open and closed conformations, respectively, and CD4 opens the closed conformation, we conclude that SERINC5 selectively dissociates Env trimers with an open conformation to restrict HIV-1 replication.IMPORTANCE Restriction factors provide the first line of defense against retrovirus infection by posing several blocks to the viral replication cycle. SERINC5 is a novel restriction factor that strongly blocks HIV-1 entry, although it is counteracted by Nef. Currently, it is still unclear how HIV-1 entry is blocked by SERINC5. Notably, this entry block is dependent on viral Env proteins. Laboratory-adapted HIV-1 strains are sensitive, whereas primary isolates are highly resistant to SERINC5. Env proteins mediate virus entry via extensive conformational rearrangements from a closed ground state to a CD4-bound open state. We detected Env-Env associations and Env-SERINC5 interactions in live cells by a novel bimolecular fluorescence assay. We demonstrate that CD4 expression increases the Env sensitivity to SERINC5 and allows SERINC5 to dissociate the Env complex, suggesting that SERINC5 restriction is dependent on Env conformation. Our results provide new insights into the poorly defined Env-dependent SERINC5 antiviral mechanism.
Collapse
|
47
|
Firrito C, Bertelli C, Vanzo T, Chande A, Pizzato M. SERINC5 as a New Restriction Factor for Human Immunodeficiency Virus and Murine Leukemia Virus. Annu Rev Virol 2019; 5:323-340. [PMID: 30265629 DOI: 10.1146/annurev-virology-092917-043308] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
SERINC genes encode for homologous multipass transmembrane proteins with unknown cellular function, despite being highly conserved across eukaryotes. Among the five SERINC genes found in humans, SERINC5 was shown to act as a powerful inhibitor of retroviruses. It is efficiently incorporated into virions and blocks the penetration of the viral core into target cells, by impairing the fusion process with a yet unclear mechanism. SERINC5 was also found to promote human immunodeficiency virus 1 (HIV-1) virion neutralization by antibodies, indicating a pleiotropic activity, which remains mostly unexplored. Counteracting factors have emerged independently in at least three retrovirus lineages, underscoring their fundamental importance during retrovirus evolution. Nef and S2 of primate and equine lentiviruses, and glycoGag of gammaretroviruses, act similarly by targeting SERINC5 to endosomes and excluding it from virions. Here, we discuss the features that distinguish SERINC5 from other known restriction factors, delineating a yet unique class of antiviral inhibitors.
Collapse
Affiliation(s)
- Claudia Firrito
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy ; , , ,
| | - Cinzia Bertelli
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy ; , , ,
| | - Teresa Vanzo
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy ; , , ,
| | - Ajit Chande
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462 066, Madhya Pradesh, India;
| | - Massimo Pizzato
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy ; , , ,
| |
Collapse
|
48
|
Imle A, Kumberger P, Schnellbächer ND, Fehr J, Carrillo-Bustamante P, Ales J, Schmidt P, Ritter C, Godinez WJ, Müller B, Rohr K, Hamprecht FA, Schwarz US, Graw F, Fackler OT. Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures. Nat Commun 2019; 10:2144. [PMID: 31086185 PMCID: PMC6514199 DOI: 10.1038/s41467-019-09879-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/04/2019] [Indexed: 11/09/2022] Open
Abstract
Pathogens face varying microenvironments in vivo, but suitable experimental systems and analysis tools to dissect how three-dimensional (3D) tissue environments impact pathogen spread are lacking. Here we develop an Integrative method to Study Pathogen spread by Experiment and Computation within Tissue-like 3D cultures (INSPECT-3D), combining quantification of pathogen replication with imaging to study single-cell and cell population dynamics. We apply INSPECT-3D to analyze HIV-1 spread between primary human CD4 T-lymphocytes using collagen as tissue-like 3D-scaffold. Measurements of virus replication, infectivity, diffusion, cellular motility and interactions are combined by mathematical analyses into an integrated spatial infection model to estimate parameters governing HIV-1 spread. This reveals that environmental restrictions limit infection by cell-free virions but promote cell-associated HIV-1 transmission. Experimental validation identifies cell motility and density as essential determinants of efficacy and mode of HIV-1 spread in 3D. INSPECT-3D represents an adaptable method for quantitative time-resolved analyses of 3D pathogen spread. Here, using an integrative experimental and computational approach, Imle et al. show how cell motility and density affect HIV cell-associated transmission in a three-dimensional tissue-like culture system of CD4+ T cells and collagen, and how different collagen matrices restrict infection by cell-free virions.
Collapse
Affiliation(s)
- Andrea Imle
- Department of Infectious Diseases, Centre for Integrative Infectious Disease Research (CIID), Integrative Virology, University Hospital Heidelberg, 69120, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Peter Kumberger
- Centre for Modelling and Simulation in the Biosciences, BioQuant, Heidelberg University, 69120, Heidelberg, Germany
| | - Nikolas D Schnellbächer
- Institute for Theoretical Physics and BioQuant, Heidelberg University, 69120, Heidelberg, Germany
| | - Jana Fehr
- Centre for Modelling and Simulation in the Biosciences, BioQuant, Heidelberg University, 69120, Heidelberg, Germany.,Digital Health & Machine Learning, Hasso-Plattner Institute, 14482, Potsdam, Germany
| | - Paola Carrillo-Bustamante
- Centre for Modelling and Simulation in the Biosciences, BioQuant, Heidelberg University, 69120, Heidelberg, Germany.,Vector Biology Unit, Max-Planck Institute for Infection Biology, 10117, Berlin, Germany
| | - Janez Ales
- HCI/IWR, Heidelberg University, 69120, Heidelberg, Germany
| | - Philip Schmidt
- HCI/IWR, Heidelberg University, 69120, Heidelberg, Germany
| | - Christian Ritter
- Biomedical Computer Vision Group, BioQuant, IPMB, and DKFZ, Heidelberg University, 69120, Heidelberg, Germany
| | - William J Godinez
- Biomedical Computer Vision Group, BioQuant, IPMB, and DKFZ, Heidelberg University, 69120, Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Centre for Integrative Infectious Disease Research (CIID), Virology, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, and DKFZ, Heidelberg University, 69120, Heidelberg, Germany
| | | | - Ulrich S Schwarz
- Institute for Theoretical Physics and BioQuant, Heidelberg University, 69120, Heidelberg, Germany
| | - Frederik Graw
- Centre for Modelling and Simulation in the Biosciences, BioQuant, Heidelberg University, 69120, Heidelberg, Germany
| | - Oliver T Fackler
- Department of Infectious Diseases, Centre for Integrative Infectious Disease Research (CIID), Integrative Virology, University Hospital Heidelberg, 69120, Heidelberg, Germany. .,German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.
| |
Collapse
|
49
|
D Urbano V, De Crignis E, Re MC. Host Restriction Factors and Human Immunodeficiency Virus (HIV-1): A Dynamic Interplay Involving All Phases of the Viral Life Cycle. Curr HIV Res 2019; 16:184-207. [PMID: 30117396 DOI: 10.2174/1570162x16666180817115830] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/31/2018] [Accepted: 08/09/2018] [Indexed: 02/08/2023]
Abstract
Mammalian cells have evolved several mechanisms to prevent or block lentiviral infection and spread. Among the innate immune mechanisms, the signaling cascade triggered by type I interferon (IFN) plays a pivotal role in limiting the burden of HIV-1. In the presence of IFN, human cells upregulate the expression of a number of genes, referred to as IFN-stimulated genes (ISGs), many of them acting as antiviral restriction factors (RFs). RFs are dominant proteins that target different essential steps of the viral cycle, thereby providing an early line of defense against the virus. The identification and characterization of RFs have provided unique insights into the molecular biology of HIV-1, further revealing the complex host-pathogen interplay that characterizes the infection. The presence of RFs drove viral evolution, forcing the virus to develop specific proteins to counteract their activity. The knowledge of the mechanisms that prevent viral infection and their viral counterparts may offer new insights to improve current antiviral strategies. This review provides an overview of the RFs targeting HIV-1 replication and the mechanisms that regulate their expression as well as their impact on viral replication and the clinical course of the disease.
Collapse
Affiliation(s)
- Vanessa D Urbano
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Elisa De Crignis
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Maria Carla Re
- Retrovirus Laboratory, Operative Unit of Clinical Microbiology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| |
Collapse
|
50
|
Beitari S, Wang Y, Liu SL, Liang C. HIV-1 Envelope Glycoprotein at the Interface of Host Restriction and Virus Evasion. Viruses 2019; 11:v11040311. [PMID: 30935048 PMCID: PMC6521621 DOI: 10.3390/v11040311] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 12/15/2022] Open
Abstract
Without viral envelope proteins, viruses cannot enter cells to start infection. As the major viral proteins present on the surface of virions, viral envelope proteins are a prominent target of the host immune system in preventing and ultimately eliminating viral infection. In addition to the well-appreciated adaptive immunity that produces envelope protein-specific antibodies and T cell responses, recent studies have begun to unveil a rich layer of host innate immune mechanisms restricting viral entry. This review focuses on the exciting progress that has been made in this new direction of research, by discussing various known examples of host restriction of viral entry, and diverse viral countering strategies, in particular, the emerging role of viral envelope proteins in evading host innate immune suppression. We will also highlight the effective cooperation between innate and adaptive immunity to achieve the synergistic control of viral infection by targeting viral envelope protein and checking viral escape. Given that many of the related findings were made with HIV-1, we will use HIV-1 as the model virus to illustrate the basic principles and molecular mechanisms on host restriction targeting HIV-1 envelope protein.
Collapse
Affiliation(s)
- Saina Beitari
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
- Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.
| | - Yimeng Wang
- Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
| | - Shan-Lu Liu
- Center for Retrovirus Research, Department of Veterinary Biosciences, Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Chen Liang
- Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
- Lady Davis Institute, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada.
| |
Collapse
|