scholarly journals Residues T48 and A49 in HIV-1 NL4-3 Nef are responsible for the counteraction of autophagy initiation, which prevents the ubiquitin-dependent degradation of Gag through autophagosomes

Retrovirology ◽  
2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Sergio Castro-Gonzalez ◽  
Yuexuan Chen ◽  
Jared Benjamin ◽  
Yuhang Shi ◽  
Ruth Serra-Moreno
Keyword(s):  
Defense Mechanism ◽  
Virus Protein ◽  
Primary Role ◽  
Mhc I ◽  
Mucosal Transmission ◽  
Post Translational Modifications ◽  
Virion Assembly ◽  
Mutual Antagonism ◽  
Viral Components ◽  
Hiv 1

Abstract Background Autophagy plays an important role as a cellular defense mechanism against intracellular pathogens, like viruses. Specifically, autophagy orchestrates the recruitment of specialized cargo, including viral components needed for replication, for lysosomal degradation. In addition to this primary role, the cleavage of viral structures facilitates their association with pattern recognition receptors and MHC-I/II complexes, which assists in the modulation of innate and adaptive immune responses against these pathogens. Importantly, whereas autophagy restricts the replicative capacity of human immunodeficiency virus type 1 (HIV-1), this virus has evolved the gene nef to circumvent this process through the inhibition of early and late stages of the autophagy cascade. Despite recent advances, many details of the mutual antagonism between HIV-1 and autophagy still remain unknown. Here, we uncover the genetic determinants that drive the autophagy-mediated restriction of HIV-1 as well as the counteraction imposed by Nef. Additionally, we also examine the implications of autophagy antagonism in HIV-1 infectivity. Results We found that sustained activation of autophagy potently inhibits HIV-1 replication through the degradation of HIV-1 Gag, and that this effect is more prominent for nef-deficient viruses. Gag re-localizes to autophagosomes where it interacts with the autophagosome markers LC3 and SQSTM1. Importantly, autophagy-mediated recognition and recruitment of Gag requires the myristoylation and ubiquitination of this virus protein, two post-translational modifications that are essential for Gag’s central role in virion assembly and budding. We also identified residues T48 and A49 in HIV-1 NL4-3 Nef as responsible for impairing the early stages of autophagy. Finally, a survey of pandemic HIV-1 transmitted/founder viruses revealed that these isolates are highly resistant to autophagy restriction. Conclusions This study provides evidence that autophagy antagonism is important for virus replication and suggests that the ability of Nef to counteract autophagy may have played an important role in mucosal transmission. Hence, disabling Nef in combination with the pharmacological manipulation of autophagy represents a promising strategy to prevent HIV spread.

scholarly journals Structural study of the transmembrane and membrane proximal domains of HIV-1 gp41

2014 ◽  
Vol 70 (a1) ◽  
pp. C122-C122
Author(s):  
Zhen Gong ◽  
Raimund Fromme ◽  
Felicia Craciunescu ◽  
Tsafrir Mor ◽  
Petra Fromme ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Proximal Region ◽  
Target Cells ◽  
Primary Role ◽  
Biological Functions ◽  
Broadly Neutralizing Antibodies ◽  
Mucosal Transmission ◽  
C Terminus ◽  
Tm Domain ◽  
Hiv 1

The transmembrane subunit (gp41) of the envelope glycoprotein (Env) of HIV-1 associates non-covalently with the surface subunit (gp120) and together they play essential roles in viral mucosal transmission and infection of target cells. The membrane proximal region (MPR) of gp41 is highly conserved and contains epitopes of broadly neutralizing antibodies. The transmembrane (TM) domain of gp41 is involved in many essential biological functions and its primary role is to anchor the Env in both viral and cellular membranes. Despite having many important biological functions, the atomic structure of gp41 TM domain remains unknown. While high-resolution X-ray structures of some segments of the MPR were solved in the past, they represent the prefusion or post-fusion conformations, which could not be recognized by the broadly neutralizing antibodies 2F5 and 4E10. Here we describe the expression, purification, biophysical characterization and crystallization of a chimera construct including maltose binding protein (MBP) and MPR-TM of gp41. The purified MBP-MPR-TM protein reacts with the broadly neutralizing antibodies 2F5 and 4E10 with nanomolar affinities and thereby may represent an immunologically relevant conformation mimicking a pre-hairpin intermediate of gp41. Crystals could not be obtained initially when MPR-TM was fused to the C terminus of MBP with linker 1 (MBP-linker1-MPR-TM) but could be obtained after changing the linker (MBP-linker2-MPR-TM). The crystal belongs to space group P32 with unit cell constants of a=172 Å, b=172 Å, c= 70 Å and alpha=beta=90 and gamma=120. The 2.5 Å crystal structure reveals the conformation of MBP and part of the linker region of this chimera, but the MPR-TM segment is unstructured.

scholarly journals HIV-1 Nef sequesters MHC-I intracellularly by targeting early stages of endocytosis and recycling

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Brennan S. Dirk ◽  
Emily N. Pawlak ◽  
Aaron L. Johnson ◽  
Logan R. Van Nynatten ◽  
Rajesh A. Jacob ◽  
...  
Keyword(s):  
Mhc I ◽  
Early Stages ◽  
Hiv 1

scholarly journals 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 ◽  
2017 ◽  
Vol 8 (6) ◽  
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.

scholarly journals Inhibitors of Deubiquitinating Enzymes Block HIV-1 Replication and Augment the Presentation of Gag-Derived MHC-I Epitopes

Viruses ◽  
2017 ◽  
Vol 9 (8) ◽  
pp. 222 ◽  
Author(s):  
Christian Setz ◽  
Melanie Friedrich ◽  
Pia Rauch ◽  
Kirsten Fraedrich ◽  
Alina Matthaei ◽  
...  
Keyword(s):  
Deubiquitinating Enzymes ◽  
Mhc I ◽  
Hiv 1

scholarly journals Mathematical model of the Tat-Rev regulation of HIV-1 replication in an activated cell predicts the existence of oscillatory dynamics in the synthesis of viral components

BMC Genomics ◽  
2014 ◽  
Vol 15 (Suppl 12) ◽  
pp. S1 ◽  
Author(s):  
Vitaly A Likhoshvai ◽  
Tamara M Khlebodarova ◽  
Sergei I Bazhan ◽  
Irina A Gainova ◽  
Valery A Chereshnev ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Oscillatory Dynamics ◽  
Viral Components ◽  
Hiv 1

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

2019 ◽  
Author(s):  
Kengo Hirao ◽  
Sophie Andrews ◽  
Kimiko Kuroki ◽  
Hiroki Kusaka ◽  
Takashi Tadokoro ◽  
...  
Keyword(s):  
Immune Evasion ◽  
Immune Regulation ◽  
Titration Calorimetry ◽  
Viral Control ◽  
Mhc I ◽  
Infected People ◽  
Sorting Motif ◽  
Α Helix ◽  
Hiv 1

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.

Inhibitors of HIV-1 Nef-Mediated Activation of the Myeloid Src-Family Kinase Hck Block HIV-1 Replication in Macrophages and Disrupt MHC-I Downregulation

2022 ◽  
Author(s):  
Lori A. Emert-Sedlak ◽  
Omar Moukha-Chafiq ◽  
Haibin Shi ◽  
Shoucheng Du ◽  
John J. Alvarado ◽  
...  
Keyword(s):  
Src Family Kinase ◽  
Mhc I ◽  
Hiv 1

Cellular Cysteine Network and Neurodegeneration

2020 ◽  
pp. 303-325
Author(s):  
Shubhangi H. Pawar ◽  
Vishal S. Gulecha ◽  
Manoj S. Mahajan ◽  
Aman B Upaganiawar ◽  
Chandrashekhar D. Upasani
Keyword(s):  
Oxidative Stress ◽  
Defense Mechanism ◽  
Free Radical Scavenger ◽  
Cellular Damage ◽  
Radical Scavenger ◽  
Post Translational Modifications ◽  
Cellular Defense ◽  
Brain Antioxidants ◽  
The Brain ◽  
Oxidative Species

Oxidative stress is strongly linked to neurodegeneration and oxidative species can modify many amino acids and proteins in the brain. Cysteine amino acid is most susceptible to oxidative post-translational modifications (PTMs). Reversible or irreversible cysteine PTMs can cause dyshomeostasis, which further continued to cellular damage. Many cysteine dependent proteins and many non-proteins using cysteine as their structural components are affected by oxidative stress. Several cysteine dependent enzymes are acting as antioxidants. Cysteine is a major contributor to glutathione (GSH) and superoxide dismutase (SOD) synthesis. Cysteine precursor N-acetylcysteine (NAC) supplementation is proven as a potent free radical scavenger and increase brain antioxidants and subsequently potentiates the natural antioxidant cellular defense mechanism. Thus, in this chapter, the authors explore the linkage of cellular cysteine networks and neurodegenerative disorders.

scholarly journals Expression of Nef Downregulates CXCR4, the Major Coreceptor of Human Immunodeficiency Virus, from the Surfaces of Target Cells and Thereby Enhances Resistance to Superinfection

2006 ◽  
Vol 80 (22) ◽  
pp. 11141-11152 ◽  
Author(s):  
Stephanie Venzke ◽  
Nico Michel ◽  
Ina Allespach ◽  
Oliver T. Fackler ◽  
Oliver T. Keppler
Keyword(s):  
Human Immunodeficiency Virus ◽  
T Lymphocytes ◽  
Maximum Level ◽  
Target Cells ◽  
Class I Mhc ◽  
Mhc I ◽  
Immunodeficiency Virus ◽  
Infected Cells ◽  
Stromal Cell Derived Factor ◽  
Hiv 1

ABSTRACT Lentiviral Nef proteins are key factors for pathogenesis and are known to downregulate functionally important molecules, including CD4 and major histocompatibility complex class I (MHC-I), from the surfaces of infected cells. Recently, we demonstrated that Nef reduces cell surface levels of the human immunodeficiency virus type 1 (HIV-1) entry coreceptor CCR5 (N. Michel, I. Allespach, S. Venzke, O. T. Fackler, and O. T. Keppler, Curr. Biol. 15:714-723, 2005). Here, we report that Nef downregulates the second major HIV-1 coreceptor, CXCR4, from the surfaces of HIV-infected primary CD4 T lymphocytes with efficiencies comparable to those of the natural CXCR4 ligand, stromal cell-derived factor-1 alpha. Analysis of a panel of mutants of HIV-1SF2 Nef revealed that the viral protein utilized the same signature motifs for downmodulation of CXCR4 and MHC-I, including the proline-rich motif P73P76P79P82 and the acidic cluster motif E66E67E68E69. Expression of wild-type Nef, but not of specific Nef mutants, resulted in a perinuclear accumulation of the coreceptor. Remarkably, the carboxy terminus of CXCR4, which harbors the classical motifs critical for basal and ligand-induced receptor endocytosis, was dispensable for the Nef-mediated reduction of surface exposure. Functionally, the ability of Nef to simultaneously downmodulate CXCR4 and CD4 correlated with maximum-level protection of Nef-expressing target cells from fusion with cells exposing X4 HIV-1 envelopes. Furthermore, the Nef-mediated downregulation of CXCR4 alone on target T lymphocytes was sufficient to diminish cells' susceptibility to X4 HIV-1 virions at the entry step. The downregulation of chemokine coreceptors is a conserved activity of Nef to modulate infected cells, an important functional consequence of which is an enhanced resistance to HIV superinfection.

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