Structure of HIV-2 Nef reveals unique features distinct from HIV-1 involved in immune regulation

SummaryThe HIV accessory protein Nef plays a major role in establishing and maintaining infection, particularly through immune evasion. Many HIV-2 infected people experience long-term viral control and survival, resembling HIV-1 elite control. HIV-2 Nef has overlapping but also distinct functions from HIV-1 Nef. Here we report the crystal structure of HIV-2 Nef core. The dileucine sorting motif forms a helix bound to neighboring molecules, and moreover, isothermal titration calorimetry demonstrated that the CD3 endocytosis motif can directly bind to HIV-2 Nef, ensuring AP-2 mediated endocytosis for CD3. The highly-conserved C-terminal region forms a α-helix, absent from HIV-1. We further determined the structure of SIV Nef harboring this region, demonstrating similar C-terminal α-helix, which may contribute to AP-1 binding for MHC-I downregulation. These results provide new insights into the distinct pathogenesis of HIV-2 infection.

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Effects of Mutations on Replicative Fitness and Major Histocompatibility Complex Class I Binding Affinity Are Among the Determinants Underlying Cytotoxic-T-Lymphocyte Escape of HIV-1 Gag Epitopes

mBio ◽

10.1128/mbio.01050-17 ◽

2017 ◽

Vol 8 (6) ◽

Cited By ~ 7

Author(s):

Yushen Du ◽

Tian-Hao Zhang ◽

Lei Dai ◽

Xiaojuan Zheng ◽

Aleksandr M. Gorin ◽

...

Keyword(s):

Binding Affinity ◽

High Throughput ◽

Peptide Binding ◽

Virus Evolution ◽

Mhc I ◽

Hla Alleles ◽

Ctl Escape ◽

Peptide Binding Affinity ◽

Hiv 1

ABSTRACT Certain “protective” major histocompatibility complex class I (MHC-I) alleles, such as B*57 and B*27, are associated with long-term control of HIV-1 in vivo mediated by the CD8+ cytotoxic-T-lymphocyte (CTL) response. However, the mechanism of such superior protection is not fully understood. Here we combined high-throughput fitness profiling of mutations in HIV-1 Gag, in silico prediction of MHC-peptide binding affinity, and analysis of intraperson virus evolution to systematically compare differences with respect to CTL escape mutations between epitopes targeted by protective MHC-I alleles and those targeted by nonprotective MHC-I alleles. We observed that the effects of mutations on both viral replication and MHC-I binding affinity are among the determinants of CTL escape. Mutations in Gag epitopes presented by protective MHC-I alleles are associated with significantly higher fitness cost and lower reductions in binding affinity with respect to MHC-I. A linear regression model accounting for the effect of mutations on both viral replicative capacity and MHC-I binding can explain the protective efficacy of MHC-I alleles. Finally, we found a consistent pattern in the evolution of Gag epitopes in long-term nonprogressors versus progressors. Overall, our results suggest that certain protective MHC-I alleles allow superior control of HIV-1 by targeting epitopes where mutations typically incur high fitness costs and small reductions in MHC-I binding affinity. IMPORTANCE Understanding the mechanism of viral control achieved in long-term nonprogressors with protective HLA alleles provides insights for developing functional cure of HIV infection. Through the characterization of CTL escape mutations in infected persons, previous researchers hypothesized that protective alleles target epitopes where escape mutations significantly reduce viral replicative capacity. However, these studies were usually limited to a few mutations observed in vivo. Here we utilized our recently developed high-throughput fitness profiling method to quantitatively measure the fitness of mutations across the entirety of HIV-1 Gag. The data enabled us to integrate the results with in silico prediction of MHC-peptide binding affinity and analysis of intraperson virus evolution to systematically determine the differences in CTL escape mutations between epitopes targeted by protective HLA alleles and those targeted by nonprotective HLA alleles. We observed that the effects of Gag epitope mutations on HIV replicative fitness and MHC-I binding affinity are among the major determinants of CTL escape. IMPORTANCE Understanding the mechanism of viral control achieved in long-term nonprogressors with protective HLA alleles provides insights for developing functional cure of HIV infection. Through the characterization of CTL escape mutations in infected persons, previous researchers hypothesized that protective alleles target epitopes where escape mutations significantly reduce viral replicative capacity. However, these studies were usually limited to a few mutations observed in vivo. Here we utilized our recently developed high-throughput fitness profiling method to quantitatively measure the fitness of mutations across the entirety of HIV-1 Gag. The data enabled us to integrate the results with in silico prediction of MHC-peptide binding affinity and analysis of intraperson virus evolution to systematically determine the differences in CTL escape mutations between epitopes targeted by protective HLA alleles and those targeted by nonprotective HLA alleles. We observed that the effects of Gag epitope mutations on HIV replicative fitness and MHC-I binding affinity are among the major determinants of CTL escape.

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Long-Term Control of Simian Immunodeficiency Virus (SIV) in Cynomolgus Macaques Not Associated with Efficient SIV-Specific CD8+T-Cell Responses

Journal of Virology ◽

10.1128/jvi.03723-14 ◽

2015 ◽

Vol 89 (7) ◽

pp. 3542-3556 ◽

Cited By ~ 16

Author(s):

Timothée Bruel ◽

Chiraz Hamimi ◽

Nathalie Dereuddre-Bosquet ◽

Antonio Cosma ◽

So Youn Shin ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

T Cell Activation ◽

T Cell Responses ◽

Cell Depletion ◽

Viral Control ◽

Cell Responses ◽

Cynomolgus Macaques ◽

Hiv 1

ABSTRACTThe spontaneous control of human and simian immunodeficiency viruses (HIV/SIV) is typically associated with specific major histocompatibility complex (MHC) class I alleles and efficient CD8+T-cell responses, but many controllers maintain viral control despite a nonprotective MHC background and weak CD8+T-cell responses. Therefore, the contribution of this response to maintaining long-term viral control remains unclear. To address this question, we transiently depleted CD8+T cells from five SIV-infected cynomolgus macaques with long-term viral control and weak CD8+T-cell responses. Among them, only one carried the protective MHC allele H6. After depletion, four of five controllers experienced a transient rebound of viremia. The return to undetectable viremia was accompanied by only modest expansion of SIV-specific CD8+T cells that lacked efficient SIV suppression capacityex vivo. In contrast, the depletion was associated with homeostatic activation/expansion of CD4+T cells that correlated with viral rebound. In one macaque, viremia remained undetectable despite efficient CD8+cell depletion and inducible SIV replication from its CD4+T cellsin vitro. Altogether, our results suggest that CD8+T cells are not unique contributors to the long-term maintenance of low viremia in this SIV controller model and that other mechanisms, such as weak viral reservoirs or control of activation, may be important players in control.IMPORTANCESpontaneous control of HIV-1 to undetectable levels is associated with efficient anti-HIV CD8+T-cell responses. However, in some cases, this response fades over time, although viral control is maintained, and many HIV controllers (weak responders) have very low frequencies of HIV-specific CD8+T cells. In these cases, the importance of CD8 T cells in the maintenance of HIV-1 control is questionable. We developed a nonhuman primate model of durable SIV control with an immune profile resembling that of weak responders. Transient depletion of CD8+cells induced a rise in the viral load. However, viremia was correlated with CD4+T-cell activation subsequent to CD8+cell depletion. Regain of viral control to predepletion levels was not associated with restoration of the anti-SIV capacities of CD8+T cells. Our results suggest that CD8+T cells may not be involved in maintenance of viral control in weak responders and highlight the fact that additional mechanisms should not be underestimated.

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Preferential CTL targeting of Gag is associated with relative viral control in long-term surviving HIV-1 infected former plasma donors from China

Cell Research ◽

10.1038/cr.2012.19 ◽

2012 ◽

Vol 22 (5) ◽

pp. 903-914 ◽

Cited By ~ 13

Author(s):

Mingming Jia ◽

Kunxue Hong ◽

Jianping Chen ◽

Yuhua Ruan ◽

Zhe Wang ◽

...

Keyword(s):

Viral Control ◽

Hiv 1

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Impact of the time to achieve viral control on the dynamics of circulating HIV-1 reservoir in vertically infected children with long-term sustained virological suppression: A longitudinal study

PLoS ONE ◽

10.1371/journal.pone.0205579 ◽

2018 ◽

Vol 13 (10) ◽

pp. e0205579 ◽

Cited By ~ 1

Author(s):

Matías Moragas ◽

Maximiliano Distefano ◽

Debora Mecikovsky ◽

Solange Arazi Caillaud ◽

Carolina Cernadas ◽

...

Keyword(s):

Longitudinal Study ◽

Virological Suppression ◽

Viral Control ◽

Hiv 1

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HIV-1 Nef interacts with LMP7 to attenuate immunoproteasome formation and MHC-I antigen presentation

10.1101/697946 ◽

2019 ◽

Author(s):

Yang Yang ◽

Weiyong Liu ◽

Dan Hu ◽

Rui Su ◽

Man Ji ◽

...

Keyword(s):

Immune Responses ◽

Viral Replication ◽

Protein Degradation ◽

Antigen Presentation ◽

Immune Evasion ◽

Mhc I ◽

Specific Ctls ◽

Distinct Mechanism ◽

Hiv 1 ◽

Presentation Activity

AbstractProteasome is major protein degradation machinery and plays essential roles in diverse biological functions. Upon cytokine inductions, proteasome subunits β1, β2, and β5 are replaced by β1i/LMP2, β2i/MECL-1, and β5i/LMP7, leading to the formation of immunoproteasome. Immunoproteasome-degraded products are loaded onto the major histocompatibility complex class I (MHC-I) to regulate immune responses and induce cytotoxic-T-lymphocytes (CTLs). Human immunodeficiency virus type 1 (HIV-1) is the causal agent of acquired immunodeficiency syndrome (AIDS). HIV-1-specific CTLs represent critical immune responses to limit viral replication. HIV-1 negative regulatory factor (Nef) counteracts host immunity, especially the MHC-I/CTL. This study reveals a distinct mechanism by which Nef facilitates immune evasion through attenuating the functions of immunoproteasome and MHC-I. Nef interacts with LMP7 on the endoplasmic reticulum (ER) to down-regulate the incorporation of LMP7 into immunoproteasome, and thereby attenuating immunoproteasome formation. Moreover, Nef represses immunoproteasome protein degradation function, MHC-I trafficking, and antigen presentation activity.ImportanceUbiquitin-proteasome system (UPS) is essential for degradation of damaged proteins, which takes place in proteasome. Upon cytokine inductions, proteasome catalytic activities are replaced by distinct isoforms resulting in formation of immunoproteasome. Immunoproteasome generates peptides for MHC-I antigen presentation and plays important roles in immune responses. HIV-1 is the agent of AIDS, and HIV-1-specific CTLs represent immune responses to limit viral replication. This study reveals a distinct mechanism by which HIV-1 promotes immune evasion. Viral protein Nef interacts with immunoproteasome component LMP7 to attenuate immunoproteasome formation and protein degradation function, and repress MHC-I antigen presentation activity. Therefore, HIV-1 targets LMP7 to inhibit immunoproteasome activation and LMP7 may be used as a target for the development of anti-HIV-1/AIDS therapy.

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The Role of the Nef Protein in MHC-I Downregulation and Viral Immune Evasion by HIV-1

Journal of Clinical & Cellular Immunology ◽

10.4172/2155-9899.1000375 ◽

2015 ◽

Vol 06 (06) ◽

Author(s):

Hannah Elliott ◽

Gerard F Hoyne

Keyword(s):

Immune Evasion ◽

Mhc I ◽

Viral Immune Evasion ◽

Hiv 1

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Contribution of the clathrin adaptor AP-1 subunit µ1 to acidic cluster protein sorting

The Journal of Cell Biology ◽

10.1083/jcb.201602058 ◽

2017 ◽

Vol 216 (9) ◽

pp. 2927-2943 ◽

Cited By ~ 20

Author(s):

Paloma Navarro Negredo ◽

James R. Edgar ◽

Antoni G. Wrobel ◽

Nathan R. Zaccai ◽

Robin Antrobus ◽

...

Keyword(s):

Mhc Class I ◽

Binding Pocket ◽

Down Regulation ◽

Mhc I ◽

Mutant Proteins ◽

Sorting Signals ◽

Clathrin Adaptor ◽

Hiv 1

Acidic clusters act as sorting signals for packaging cargo into clathrin-coated vesicles (CCVs), and also facilitate down-regulation of MHC-I by HIV-1 Nef. To find acidic cluster sorting machinery, we performed a gene-trap screen and identified the medium subunit (µ1) of the clathrin adaptor AP-1 as a top hit. In µ1 knockout cells, intracellular CCVs still form, but acidic cluster proteins are depleted, although several other CCV components were either unaffected or increased, indicating that cells can compensate for long-term loss of AP-1. In vitro experiments showed that the basic patch on µ1 that interacts with the Nef acidic cluster also contributes to the binding of endogenous acidic cluster proteins. Surprisingly, µ1 mutant proteins lacking the basic patch and/or the tyrosine-based motif binding pocket could rescue the µ1 knockout phenotype completely. In contrast, these mutants failed to rescue Nef-induced down-regulation of MHC class I, suggesting a possible mechanism for attacking the virus while sparing the host cell.

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The Neurology of AIDS

10.1093/med/9780195399349.001.0001 ◽

2012 ◽

Cited By ~ 5

Keyword(s):

Viral Disease ◽

Neurological Complications ◽

Psychiatric Disease ◽

Viral Reservoirs ◽

Large Measure ◽

Infected People ◽

Cellular Factors ◽

Muscle Nerve ◽

Hiv 1

This resource discusses how neurological complications of progressive HIV-1 infection remain a common cause of morbidity even during widespread use of antiretroviral therapy (ART). It addresses how long-term resistance to ART, drug compliance, untoward drug side effects, a myriad of opportunistic infection, depression and other psychiatric disease manifestations, concomitant drug abuse, neuropathies, and an inability to clear viral reservoirs, explain, in large measure, disease progression and immune deterioration. It then covers the association with a number of psychiatric, muscle, nerve, infectious, as well as cognitive, behavioral, and motor disturbances seen in infected people, with a focus on the neurological complications, molecular and viral disease processes, cellular factors influencing viral replication therapeutic challenges, and the changing epidemiological patterns of disease.

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