HIV-1 evasion of restriction factors: cyclophilin A and cell fusion provide a helping hand

AbstractRetroviral restriction factors are important regulators of viral infection, targeting vulnerable steps of the virus lifecycle; steps that are also targeted by antiviral drugs. It has become clear that the route of cellular infection can alter the sensitivity of HIV-1 to these agents. Using CRISPR-Cas9 edited pluripotent stem cell-derived macrophages, we have explored the potential of a modified restriction factor (human TRIMCyp) to inhibit HIV-1 replication in both cell free and cell-cell infection models. We show that the expression of TRIMCyp from the endogenous TRIM5α locus potently restricts infection by cell-free HIV-1. Our results also show the importance of the human cyclophilin A-HIV-1 capsid interaction for viral escape from restriction by native human TRIM5α, highlighting the evolutionary interplay between virus and this host restriction factor. However, when co-cultured with infected T cells, stem cell-derived macrophages are primarily infected by fusion between the cells. We have termed infected cells that result from these fusions heterocytia, and show that their formation overcomes multiple restriction factors and the reverse transcriptase inhibitor AZT.ImportanceAs sentinels of the immune system, macrophages are relatively resistant to infection by pathogens such as HIV-1. However, infected macrophages are found in infected patients and they play key roles in the pathogenesis of the disease as well as being a component of the viral reservoir that must be targeted before treatment can become cure. In this article, we show that some of the mechanisms by which macrophages restrict HIV-1 can be overcome through a recently described cell-cell interaction leading to cell-cell fusion. We also highlight an evolutionary battle between virus and host and show how the virus has co-opted a host protein to protect it from destruction by an antiviral mechanism. These two key findings suggest potential novel treatment strategies that may reduce the viral reservoir and help our natural defences take back control from the virus.

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MxB sensitivity of HIV-1 is determined by a highly variable and dynamic capsid surface

eLife ◽

10.7554/elife.56910 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 1

Author(s):

Richard J Miles ◽

Claire Kerridge ◽

Laura Hilditch ◽

Christopher Monit ◽

David A Jacques ◽

...

Keyword(s):

Nuclear Import ◽

Cytotoxic T Lymphocyte ◽

Cyclophilin A ◽

Conformational Flexibility ◽

Restriction Factors ◽

Nuclear Entry ◽

Linear Forms ◽

Cofactor Binding ◽

Cofactor Recruitment ◽

Hiv 1

The type one interferon induced restriction factor Myxovirus resistance B (MxB) restricts HIV-1 nuclear entry evidenced by inhibition of 2-LTR but not linear forms of viral DNA. The HIV-1 capsid is the key determinant of MxB sensitivity and cofactor binding defective HIV-1 capsid mutants P90A (defective for cyclophilin A and Nup358 recruitment) and N74D (defective for CPSF6 recruitment) have reduced dependency on nuclear transport associated cofactors, altered integration targeting preferences and are not restricted by MxB expression. This has suggested that nuclear import mechanism may determine MxB sensitivity. Here we have use genetics to separate HIV-1 nuclear import cofactor dependence from MxB sensitivity. We provide evidence that MxB sensitivity depends on HIV-1 capsid conformation, rather than cofactor recruitment. We show that depleting CPSF6 to change nuclear import pathway does not impact MxB sensitivity, but mutants that recapitulate the effect of Cyclophilin A binding on capsid conformation and dynamics strongly impact MxB sensitivity. We demonstrate that HIV-1 primary isolates have different MxB sensitivities due to cytotoxic T lymphocyte (CTL) selected differences in Gag sequence but similar cofactor dependencies. Overall our work demonstrates a complex relationship between cyclophilin dependence and MxB sensitivity likely driven by CTL escape. We propose that cyclophilin binding provides conformational flexibility to HIV-1 capsid facilitating simultaneous evasion of capsid-targeting restriction factors including TRIM5 as well as MxB.

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HIV envelope tail truncation confers resistance to SERINC5 restriction

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2101450118 ◽

2021 ◽

Vol 118 (21) ◽

pp. e2101450118

Author(s):

Tafhima Haider ◽

Xenia Snetkov ◽

Clare Jolly

Keyword(s):

T Cells ◽

Envelope Glycoprotein ◽

Cytoplasmic Tail ◽

Restriction Factor ◽

Viral Fusion ◽

Restriction Factors ◽

Complete Resistance ◽

Hiv Envelope ◽

Hiv 1

SERINC5 is a potent lentiviral restriction factor that gets incorporated into nascent virions and inhibits viral fusion and infectivity. The envelope glycoprotein (Env) is a key determinant for SERINC restriction, but many aspects of this relationship remain incompletely understood, and the mechanism of SERINC5 restriction remains unresolved. Here, we have used mutants of HIV-1 and HIV-2 to show that truncation of the Env cytoplasmic tail (ΔCT) confers complete resistance of both viruses to SERINC5 and SERINC3 restriction. Critically, fusion of HIV-1 ΔCT virus was not inhibited by SERINC5 incorporation into virions, providing a mechanism to explain how EnvCT truncation allows escape from restriction. Neutralization and inhibitor assays showed ΔCT viruses have an altered Env conformation and fusion kinetics, suggesting that EnvCT truncation dysregulates the processivity of entry, in turn allowing Env to escape targeting by SERINC5. Furthermore, HIV-1 and HIV-2 ΔCT viruses were also resistant to IFITMs, another entry-targeting family of restriction factors. Notably, while the EnvCT is essential for Env incorporation into HIV-1 virions and spreading infection in T cells, HIV-2 does not require the EnvCT. Here, we reveal a mechanism by which human lentiviruses can evade two potent Env-targeting restriction factors but show key differences in the capacity of HIV-1 and HIV-2 to exploit this. Taken together, this study provides insights into the interplay between HIV and entry-targeting restriction factors, revealing viral plasticity toward mechanisms of escape and a key role for the long lentiviral EnvCT in regulating these processes.

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325. Lentiviral Gene Therapy Against HIV-1 Using a Novel TRIM21-Cyclophilin A Fusion Restriction Factor

Molecular Therapy ◽

10.1016/s1525-0016(16)36129-9 ◽

2012 ◽

Vol 20 ◽

pp. S128

Keyword(s):

Gene Therapy ◽

Cyclophilin A ◽

Restriction Factor ◽

Lentiviral Gene Therapy ◽

Hiv 1

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Cell–cell fusion and internalization of the CNS-based, HIV-1 co-receptor, APJ

Virology ◽

10.1016/s0042-6822(02)00021-1 ◽

2003 ◽

Vol 307 (1) ◽

pp. 22-36 ◽

Cited By ~ 41

Author(s):

Naiming Zhou ◽

Xuejun Fan ◽

Muhammad Mukhtar ◽

Jianhua Fang ◽

Charvi A Patel ◽

...

Keyword(s):

Cell Fusion ◽

Hiv 1 ◽

Cell Cell

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Cell–cell and virus–cell fusion assay–based analyses of alanine insertion mutants in the distal α9 portion of the JRFL gp41 subunit from HIV-1

Journal of Biological Chemistry ◽

10.1074/jbc.ra118.004579 ◽

2019 ◽

Vol 294 (14) ◽

pp. 5677-5687 ◽

Cited By ~ 9

Author(s):

Mizuki Yamamoto ◽

Qingling Du ◽

Jiping Song ◽

Hongyun Wang ◽

Aya Watanabe ◽

...

Keyword(s):

Cell Fusion ◽

Hiv 1 ◽

Insertion Mutants ◽

Cell Cell

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Binding and Susceptibility to Postentry Restriction Factors in Monkey Cells Are Specified by Distinct Regions of the Human Immunodeficiency Virus Type 1 Capsid

Journal of Virology ◽

10.1128/jvi.78.10.5423-5437.2004 ◽

2004 ◽

Vol 78 (10) ◽

pp. 5423-5437 ◽

Cited By ~ 96

Author(s):

Christopher M. Owens ◽

Byeongwoon Song ◽

Michel J. Perron ◽

Peter C. Yang ◽

Matthew Stremlau ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Human Immunodeficiency Virus Type ◽

Virus Type ◽

Cyclophilin A ◽

New World Monkeys ◽

Restriction Factors ◽

Factor Binding ◽

Immunodeficiency Virus ◽

Hiv 1

ABSTRACT In cells of Old World and some New World monkeys, dominant factors restrict human immunodeficiency virus type 1 (HIV-1) infections after virus entry. The simian immunodeficiency virus SIVmac is less susceptible to these restrictions, a property that is determined largely by the viral capsid protein. For this study, we altered exposed amino acid residues on the surface of the HIV-1 capsid, changing them to the corresponding residues found on the SIVmac capsid. We identified two distinct pathways of escape from early, postentry restriction in monkey cells. One set of mutants that were altered near the base of the cyclophilin A-binding loop of the N-terminal capsid domain or in the interdomain linker exhibited a decreased ability to bind the restricting factor(s). Consistent with the location of this putative factor-binding site, cyclophilin A and the restricting factor(s) cooperated to achieve the postentry block. A second set of mutants that were altered in the ridge formed by helices 3 and 6 of the N-terminal capsid domain efficiently bound the restricting factor(s) but were resistant to the consequences of factor binding. These results imply that binding of the simian restricting factor(s) is not sufficient to mediate the postentry block to HIV-1 and that SIVmac capsids escape the block by decreases in both factor binding and susceptibility to the effects of the factor(s).

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Antiviral Activity and Adaptive Evolution of Avian Tetherins

Journal of Virology ◽

10.1128/jvi.00416-20 ◽

2020 ◽

Vol 94 (12) ◽

Author(s):

Veronika Krchlíková ◽

Helena Fábryová ◽

Tomáš Hron ◽

Janet M. Young ◽

Anna Koslová ◽

...

Keyword(s):

Antiviral Activity ◽

Recent Work ◽

Avian Species ◽

Domestic Chicken ◽

Restriction Factor ◽

Restriction Factors ◽

Zoonotic Infections ◽

Avian Viruses ◽

Avian Sarcoma ◽

Hiv 1

ABSTRACT Tetherin/BST-2 is an antiviral protein that blocks the release of enveloped viral particles by linking them to the membrane of producing cells. At first, BST-2 genes were described only in humans and other mammals. Recent work identified BST-2 orthologs in nonmammalian vertebrates, including birds. Here, we identify the BST-2 sequence in domestic chicken (Gallus gallus) for the first time and demonstrate its activity against avian sarcoma and leukosis virus (ASLV). We generated a BST-2 knockout in chicken cells and showed that BST-2 is a major determinant of an interferon-induced block of ASLV release. Ectopic expression of chicken BST-2 blocks the release of ASLV in chicken cells and of human immunodeficiency virus type 1 (HIV-1) in human cells. Using metabolic labeling and pulse-chase analysis of HIV-1 Gag proteins, we verified that chicken BST-2 blocks the virus at the release stage. Furthermore, we describe BST-2 orthologs in multiple avian species from 12 avian orders. Previously, some of these species were reported to lack BST-2, highlighting the difficulty of identifying sequences of this extremely variable gene. We analyzed BST-2 genes in the avian orders Galliformes and Passeriformes and showed that they evolve under positive selection. This indicates that avian BST-2 is involved in host-virus evolutionary arms races and suggests that BST-2 antagonists exist in some avian viruses. In summary, we show that chicken BST-2 has the potential to act as a restriction factor against ASLV. Characterizing the interaction of avian BST-2 with avian viruses is important in understanding innate antiviral defenses in birds. IMPORTANCE Birds are important hosts of viruses that have the potential to cause zoonotic infections in humans. However, only a few antiviral genes (called viral restriction factors) have been described in birds, mostly because birds lack counterparts of highly studied mammalian restriction factors. Tetherin/BST-2 is a restriction factor, originally described in humans, that blocks the release of newly formed virus particles from infected cells. Recent work identified BST-2 in nonmammalian vertebrate species, including birds. Here, we report the BST-2 sequence in domestic chicken and describe its antiviral activity against a prototypical avian retrovirus, avian sarcoma and leukosis virus (ASLV). We also identify BST-2 genes in multiple avian species and show that they evolve rapidly in birds, which is an important indication of their relevance for antiviral defense. Analysis of avian BST-2 genes will shed light on defense mechanisms against avian viral pathogens.

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The Evolutionary Histories of Antiretroviral Proteins SERINC3 and SERINC5 Do Not Support an Evolutionary Arms Race in Primates

Journal of Virology ◽

10.1128/jvi.00972-16 ◽

2016 ◽

Vol 90 (18) ◽

pp. 8085-8089 ◽

Cited By ~ 26

Author(s):

Ben Murrell ◽

Thomas Vollbrecht ◽

John Guatelli ◽

Joel O. Wertheim

Keyword(s):

Viral Infections ◽

Arms Race ◽

Restriction Factor ◽

Restriction Factors ◽

Arms Races ◽

Host Restriction ◽

Host Restriction Factor ◽

Novel Host ◽

Evolutionary Arms Race ◽

Hiv 1

ABSTRACTMolecular evolutionary arms races between viruses and their hosts are important drivers of adaptation. These Red Queen dynamics have been frequently observed in primate retroviruses and their antagonists, host restriction factor genes, such as APOBEC3F/G, TRIM5-α, SAMHD1, and BST-2. Host restriction factors have experienced some of the most intense and pervasive adaptive evolution documented in primates. Recently, two novel host factors, SERINC3 and SERINC5, were identified as the targets of HIV-1 Nef, a protein crucial for the optimal infectivity of virus particles. Here, we compared the evolutionary fingerprints of SERINC3 and SERINC5 to those of other primate restriction factors and to a set of other genes with diverse functions. SERINC genes evolved in a manner distinct from the canonical arms race dynamics seen in the other restriction factors. Despite their antiviral activity against HIV-1 and other retroviruses, SERINC3 and SERINC5 have a relatively uneventful evolutionary history in primates.IMPORTANCERestriction factors are host proteins that block viral infection and replication. Many viruses, like HIV-1 and related retroviruses, evolved accessory proteins to counteract these restriction factors. The importance of these interactions is evidenced by the intense adaptive selection pressures that dominate the evolutionary histories of both the host and viral genes involved in this so-called arms race. The dynamics of these arms races can point to mechanisms by which these viral infections can be prevented. Two human genes, SERINC3 and SERINC5, were recently identified as targets of an HIV-1 accessory protein important for viral infectivity. Unexpectedly, we found that these SERINC genes, unlike other host restriction factor genes, show no evidence of a recent evolutionary arms race with viral pathogens.

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