Cyclophilin A Prevents HIV-1 Restriction in Lymphocytes by Blocking Human TRIM5α Binding to the Viral Core

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.

Download Full-text

HIV-1 uncoating occurs via a series of rapid biomechanical changes in the core related to individual stages of reverse transcription

10.1101/2021.01.16.426924 ◽

2021 ◽

Author(s):

Sanela Rankovic ◽

Akshay Deshpande ◽

Shimon Harel ◽

Christopher Aiken ◽

Itay Rousso

Keyword(s):

Reverse Transcription ◽

Viral Genome ◽

Morphological Changes ◽

Viral Capsid ◽

Target Cells ◽

Viral Core ◽

Successful Infection ◽

Capsid Shell ◽

Hiv 1

AbstractThe HIV core consists of the viral genome and associated proteins encased by a cone-shaped protein shell termed the capsid. Successful infection requires reverse transcription of the viral genome and disassembly of the capsid shell within a cell in a process known as uncoating. The integrity of the viral capsid is critical for reverse transcription, yet the viral capsid must be breached to release the nascent viral DNA prior to integration. We employed atomic force microscopy to study the stiffness changes in HIV-1 cores during reverse transcription in vitro in reactions containing the capsid-stabilizing host metabolite IP6. Cores exhibited a series of stiffness spikes, with up to three spikes typically occurring between 10-30, 40-80, and 120-160 minutes after initiation of reverse transcription. Addition of the reverse transcriptase (RT) inhibitor efavirenz eliminated the appearance of these spikes and the subsequent disassembly of the capsid, thus establishing that both result from reverse transcription. Using timed addition of efavirenz, and analysis of an RNAseH-defective RT mutant, we established that the first stiffness spike requires minus-strand strong stop DNA synthesis, with subsequent spikes requiring later stages of reverse transcription. Additional rapid AFM imaging experiments revealed repeated morphological changes in cores that were temporally correlated with the observed stiffness spikes. Our study reveals discrete mechanical changes in the viral core that are likely related to specific stages of reverse transcription. Our results suggest that reverse-transcription-induced changes in the capsid progressively remodel the viral core to prime it for temporally accurate uncoating in target cells.

Download Full-text

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

Download Full-text

Crystal structure of cyclophilin A complexed with a binding site peptide from the HIV-1 capsid protein

Protein Science ◽

10.1002/pro.5560061103 ◽

2008 ◽

Vol 6 (11) ◽

pp. 2297-2307 ◽

Cited By ~ 55

Author(s):

Felix F. Vajdos ◽

Sanghee Yoo ◽

Megan Houseweart ◽

Wesley I. Sundquist ◽

Christopher P. Hill

Keyword(s):

Crystal Structure ◽

Binding Site ◽

Capsid Protein ◽

Cyclophilin A ◽

Hiv 1

Download Full-text

Cell Type-Dependent Escape of Capsid Inhibitors by Simian Immunodeficiency Virus SIVcpz

Journal of Virology ◽

10.1128/jvi.01338-20 ◽

2020 ◽

Vol 94 (23) ◽

Author(s):

Augustin Penda Twizerimana ◽

Rachel Scheck ◽

Daniel Becker ◽

Zeli Zhang ◽

Marianne Wammers ◽

...

Keyword(s):

Antiviral Activity ◽

Simian Immunodeficiency Virus ◽

Pan Troglodytes ◽

Hela Cells ◽

Cyclophilin A ◽

Human Pbmcs ◽

Cell Type ◽

Content Type ◽

Immunodeficiency Virus ◽

Hiv 1

ABSTRACT Pandemic human immunodeficiency virus type 1 (HIV-1) is the result of the zoonotic transmission of simian immunodeficiency virus (SIV) from the chimpanzee subspecies Pan troglodytes troglodytes (SIVcpzPtt). The related subspecies Pan troglodytes schweinfurthii is the host of a similar virus, SIVcpzPts, which did not spread to humans. We tested these viruses with small-molecule capsid inhibitors (PF57, PF74, and GS-CA1) that interact with a binding groove in the capsid that is also used by CPSF6. While HIV-1 was sensitive to capsid inhibitors in cell lines, human macrophages, and peripheral blood mononuclear cells (PBMCs), SIVcpzPtt was resistant in rhesus FRhL-2 cells and human PBMCs but was sensitive to PF74 in human HOS and HeLa cells. SIVcpzPts was insensitive to PF74 in FRhL-2 cells, HeLa cells, PBMCs, and macrophages but was inhibited by PF74 in HOS cells. A truncated version of CPSF6 (CPSF6-358) inhibited SIVcpzPtt and HIV-1, while in contrast, SIVcpzPts was resistant to CPSF6-358. Homology modeling of HIV-1, SIVcpzPtt, and SIVcpzPts capsids and binding energy estimates suggest that these three viruses bind similarly to the host proteins cyclophilin A (CYPA) and CPSF6 as well as the capsid inhibitor PF74. Cyclosporine treatment, mutation of the CYPA-binding loop in the capsid, or CYPA knockout eliminated the resistance of SIVcpzPts to PF74 in HeLa cells. These experiments revealed that the antiviral capacity of PF74 is controlled by CYPA in a virus- and cell type-specific manner. Our data indicate that SIVcpz viruses can use infection pathways that escape the antiviral activity of PF74. We further suggest that the antiviral activity of PF74 capsid inhibitors depends on cellular cofactors. IMPORTANCE HIV-1 originated from SIVcpzPtt but not from the related virus SIVcpzPts, and thus, it is important to describe molecular infection by SIVcpzPts in human cells to understand the zoonosis of SIVs. Pharmacological HIV-1 capsid inhibitors (e.g., PF74) bind a capsid groove that is also a binding site for the cellular protein CPSF6. SIVcpzPts was resistant to PF74 in HeLa cells but sensitive in HOS cells, thus indicating cell line-specific resistance. Both SIVcpz viruses showed resistance to PF74 in human PBMCs. Modulating the presence of cyclophilin A or its binding to capsid in HeLa cells overcame SIVcpzPts resistance to PF74. These results indicate that early cytoplasmic infection events of SIVcpzPts may differ between cell types and affect, in an unknown manner, the antiviral activity of capsid inhibitors. Thus, capsid inhibitors depend on the activity or interaction of currently uncharacterized cellular factors.

Download Full-text

The pH dependence of HIV-1 capsid assembly and its interaction with cyclophilin A

Biophysical Chemistry ◽

10.1016/s0301-4622(03)00063-2 ◽

2003 ◽

Vol 105 (1) ◽

pp. 67-77 ◽

Cited By ~ 7

Author(s):

Marjorie BonHomme ◽

Stanislaus Wong ◽

Carol Carter ◽

Suzanne Scarlata

Keyword(s):

Ph Dependence ◽

Cyclophilin A ◽

Capsid Assembly ◽

Hiv 1

Download Full-text

Molecular recognition in the HIV-1 capsid/cyclophilin A complex 1 1Edited by J. A. Wells

Journal of Molecular Biology ◽

10.1006/jmbi.1997.1051 ◽

1997 ◽

Vol 269 (5) ◽

pp. 780-795 ◽

Cited By ~ 193

Author(s):

Sanghee Yoo ◽

David G Myszka ◽

Chin-yah Yeh ◽

Maureen McMurray ◽

Christopher P Hill ◽

...

Keyword(s):

Molecular Recognition ◽

Cyclophilin A ◽

Hiv 1

Download Full-text

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).

Download Full-text