Human Three Prime Repair Exonuclease 1 Promotes HIV-1 Integration by Preferentially Degrading Unprocessed Viral DNA

Three Prime Repair Exonuclease 1 (TREX1) is the most abundant 3′→5′ exonuclease in mammalian cells. It has been suggested that TREX1 degrades HIV-1 DNA to enable the virus evade the innate immune system. However, the exact role of TREX1 during early steps of HIV-1 infection is not clearly understood. In this study, we report that HIV-1 infection is associated with upregulation, perinuclear accumulation, and nuclear localization of TREX1. However, TREX1 overexpression did not affect reverse transcription or nuclear entry of the virus. Surprisingly, HIV-1 DNA integration was increased in TREX1-overexpressing cells, suggesting a role of the exonuclease in post-nuclear entry step of infection. Accordingly, preintegration complexes (PICs) extracted from TREX1-overexpressing cells retained higher levels of DNA integration activity. TREX1 depletion resulted in reduced levels of proviral integration and PICs formed in TREX1-depleted cells retained lower DNA integration activity. Addition of purified TREX1 to PICs also enhanced DNA integration activity suggesting that TREX1 promotes HIV-1 integration by stimulating PIC activity. To understand the mechanism, we measured TREX1 exonuclease activity on substrates containing viral DNA ends. These studies revealed that TREX1 preferentially degrades the unprocessed viral DNA but the integration competent 3’-processed viral DNA remains resistant to degradation. Finally, we observed that TREX1 addition stimulates the activity of HIV-1 intasomes assembled with the unprocessed viral DNA but not of intasomes containing the 3’-processed viral DNA. These biochemical analyses provide a mechanism by which TREX1 directly promotes HIV-1 integration. Collectively, our study demonstrates that HIV-1 infection upregulates TREX1 to facilitate viral DNA integration. Importance Productive HIV-1 infection is dependent on a number of cellular factors. Therefore, a clear understanding of how the virus exploits the cellular machinery will identify new targets for inhibiting HIV-1 infection. The three prime repair exonuclease 1 (TREX1) is the most active cellular exonuclease in mammalian cells. It has been reported that TREX1 prevents accumulation of HIV-1 DNA and enables the virus to evade the host innate immune response. Here, we show that HIV-1 infection results in the upregulation, perinuclear accumulation, and nuclear localization of TREX1. We also provide evidence that TREX1 promotes HIV-1 integration by preferentially degrading viral DNAs that are incompatible to chromosomal insertion. These observations identify a novel role of TREX1 in a post-nuclear entry step of HIV-1 infection.

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PF74 Inhibits HIV-1 Integration by Altering the Composition of the Preintegration Complex

Journal of Virology ◽

10.1128/jvi.01741-18 ◽

2018 ◽

Vol 93 (6) ◽

Cited By ~ 11

Author(s):

Muthukumar Balasubramaniam ◽

Jing Zhou ◽

Amma Addai ◽

Phillip Martinez ◽

Jui Pandhare ◽

...

Keyword(s):

Reverse Transcription ◽

Integrase Inhibitor ◽

Antiviral Effect ◽

Inhibitory Effect ◽

Clear Understanding ◽

Nuclear Entry ◽

Preintegration Complex ◽

Gradient Based ◽

Hiv 1

ABSTRACTThe HIV-1 capsid protein (CA) facilitates reverse transcription and nuclear entry of the virus. However, CA’s role in post-nuclear entry steps remains speculative. We describe a direct link between CA and integration by employing the capsid inhibitor PF74 as a probe coupled with the biochemical analysis of HIV-1 preintegration complexes (PICs) isolated from acutely infected cells. At a low micromolar concentration, PF74 potently inhibited HIV-1 infection without affecting reverse transcription. Surprisingly, PF74 markedly reduced proviral integration owing to inhibition of nuclear entry and/or integration. However, a 2-fold reduction in nuclear entry by PF74 did not quantitatively correlate with the level of antiviral activity. Titration of PF74 against the integrase inhibitor raltegravir showed an additive antiviral effect that is dependent on a block at the post-nuclear entry step. PF74’s inhibitory effect was not due to the formation of defective viral DNA ends or a delay in integration, suggesting that the compound inhibits PIC-associated integration activity. Unexpectedly, PICs recovered from cells infected in the presence of PF74 exhibited elevated integration activity. PF74’s effect on PIC activity is CA specific since the compound did not increase the integration activity of PICs of a PF74-resistant HIV-1 CA mutant. Sucrose gradient-based fractionation studies revealed that PICs assembled in the presence of PF74 contained lower levels of CA, suggesting a negative association between CA and PIC-associated integration activity. Finally, the addition of a CA-specific antibody or PF74 inhibited PIC-associated integration activity. Collectively, our results demonstrate that PF74’s targeting of PIC-associated CA results in impaired HIV-1 integration.IMPORTANCEAntiretroviral therapy (ART) that uses various combinations of small molecule inhibitors has been highly effective in controlling HIV. However, the drugs used in the ART regimen are expensive, cause side effects, and face viral resistance. The HIV-1 CA plays critical roles in the virus life cycle and is an attractive therapeutic target. While currently there is no CA-based therapy, highly potent CA-specific inhibitors are being developed as a new class of antivirals. Efforts to develop a CA-targeted therapy can be aided through a clear understanding of the role of CA in HIV-1 infection. CA is well established to coordinate reverse transcription and nuclear entry of the virus. However, the role of CA in post-nuclear entry steps of HIV-1 infection is poorly understood. We show that a CA-specific drug PF74 inhibits HIV-1 integration revealing a novel role of this multifunctional viral protein in a post-nuclear entry step of HIV-1 infection.

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The Role of Capsid in HIV-1 Nuclear Entry

Viruses ◽

10.3390/v13081425 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1425

Author(s):

Anabel Guedán ◽

Eve R. Caroe ◽

Genevieve C. R. Barr ◽

Kate N. Bishop

Keyword(s):

Nuclear Pore ◽

Outer Face ◽

Nuclear Entry ◽

Nuclear Compartment ◽

Critical Step ◽

Technological Advances ◽

Dividing Cells ◽

Hiv 1 ◽

Gain Access

HIV-1 can infect non-dividing cells. The nuclear envelope therefore represents a barrier that HIV-1 must traverse in order to gain access to the host cell chromatin for integration. Hence, nuclear entry is a critical step in the early stages of HIV-1 replication. Following membrane fusion, the viral capsid (CA) lattice, which forms the outer face of the retroviral core, makes numerous interactions with cellular proteins that orchestrate the progress of HIV-1 through the replication cycle. The ability of CA to interact with nuclear pore proteins and other host factors around the nuclear pore determines whether nuclear entry occurs. Uncoating, the process by which the CA lattice opens and/or disassembles, is another critical step that must occur prior to integration. Both early and delayed uncoating have detrimental effects on viral infectivity. How uncoating relates to nuclear entry is currently hotly debated. Recent technological advances have led to intense discussions about the timing, location, and requirements for uncoating and have prompted the field to consider alternative uncoating scenarios that presently focus on uncoating at the nuclear pore and within the nuclear compartment. This review describes recent advances in the study of HIV-1 nuclear entry, outlines the interactions of the retroviral CA protein, and discusses the challenges of investigating HIV-1 uncoating.

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From Capsids to Complexes: Expanding the Role of TRIM5α in the Restriction of Divergent RNA Viruses and Elements

Viruses ◽

10.3390/v13030446 ◽

2021 ◽

Vol 13 (3) ◽

pp. 446

Author(s):

Kevin M. Rose ◽

Stephanie J. Spada ◽

Rebecca Broeckel ◽

Kristin L. McNally ◽

Vanessa M. Hirsch ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Molecular Basis ◽

Human Population ◽

Rna Viruses ◽

Arms Race ◽

Innate Immune ◽

Immunodeficiency Virus ◽

Underlying Mechanisms ◽

Hiv 1

An evolutionary arms race has been ongoing between retroviruses and their primate hosts for millions of years. Within the last century, a zoonotic transmission introduced the Human Immunodeficiency Virus (HIV-1), a retrovirus, to the human population that has claimed the lives of millions of individuals and is still infecting over a million people every year. To counteract retroviruses such as this, primates including humans have evolved an innate immune sensor for the retroviral capsid lattice known as TRIM5α. Although the molecular basis for its ability to restrict retroviruses is debated, it is currently accepted that TRIM5α forms higher-order assemblies around the incoming retroviral capsid that are not only disruptive for the virus lifecycle, but also trigger the activation of an antiviral state. More recently, it was discovered that TRIM5α restriction is broader than previously thought because it restricts not only the human retroelement LINE-1, but also the tick-borne flaviviruses, an emergent group of RNA viruses that have vastly different strategies for replication compared to retroviruses. This review focuses on the underlying mechanisms of TRIM5α-mediated restriction of retroelements and flaviviruses and how they differ from the more widely known ability of TRIM5α to restrict retroviruses.

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Adenoviruses — Model for DNA Replication in Mammalian Cells — Role of Viral Proteins in Viral DNA Replication

DNA Synthesis ◽

10.1007/978-1-4684-0844-7_59 ◽

1978 ◽

pp. 839-867

Author(s):

M. Green ◽

W. S. M. Wold

Keyword(s):

Dna Replication ◽

Mammalian Cells ◽

Viral Proteins ◽

Viral Dna ◽

Viral Dna Replication

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Mitochondrial Iron in Human Health and Disease

Annual Review of Physiology ◽

10.1146/annurev-physiol-020518-114742 ◽

2019 ◽

Vol 81 (1) ◽

pp. 453-482 ◽

Cited By ~ 14

Author(s):

Diane M. Ward ◽

Suzanne M. Cloonan

Keyword(s):

Human Health ◽

Mammalian Cells ◽

Molecular Mechanisms ◽

Innate Immune ◽

Biological Functions ◽

Mitochondrial Homeostasis ◽

Innate Immune Signaling ◽

Mitochondrial Iron ◽

Health And Disease

Mitochondria are an iconic distinguishing feature of eukaryotic cells. Mitochondria encompass an active organellar network that fuses, divides, and directs a myriad of vital biological functions, including energy metabolism, cell death regulation, and innate immune signaling in different tissues. Another crucial and often underappreciated function of these dynamic organelles is their central role in the metabolism of the most abundant and biologically versatile transition metals in mammalian cells, iron. In recent years, cellular and animal models of mitochondrial iron dysfunction have provided vital information in identifying new proteins that have elucidated the pathways involved in mitochondrial homeostasis and iron metabolism. Specific signatures of mitochondrial iron dysregulation that are associated with disease pathogenesis and/or progression are becoming increasingly important. Understanding the molecular mechanisms regulating mitochondrial iron pathways will help better define the role of this important metal in mitochondrial function and in human health and disease.

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Role of miRNA-146a in the regulation of the innate immune response and cancer

Biochemical Society Transactions ◽

10.1042/bst0361211 ◽

2008 ◽

Vol 36 (6) ◽

pp. 1211-1215 ◽

Cited By ~ 135

Author(s):

Andrew E. Williams ◽

Mark M. Perry ◽

Sterghios A. Moschos ◽

Hanna M. Larner-Svensson ◽

Mark A. Lindsay

Keyword(s):

Immune Response ◽

Innate Immune Response ◽

Mammalian Cells ◽

Mrna Translation ◽

Nuclear Factor Κb ◽

Causal Link ◽

Innate Immune ◽

Major Function ◽

Biological Responses

In mammalian cells, miRNAs (microRNAs) are the most abundant family of small non-coding RNAs that regulate mRNA translation through the RNA interference pathway. In general, it appears that the major function of miRNAs is in development, differentiation and homoeostasis, which is indicated by studies showing aberrant miRNA expression during the development of cancer. Interestingly, changes in the expression of miR-146a have been implicated in both the development of multiple cancers and in the negative regulation of inflammation induced via the innate immune response. Furthermore, miR-146a expression is driven by the transcription factor NF-κB (nuclear factor κB), which has been implicated as an important causal link between inflammation and carcinogenesis. In the present article, we review the evidence for a role of miR-146a in innate immunity and cancer and assess whether changes in miR-146a might link these two biological responses.

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SJP-L-5, a novel small-molecule compound, inhibits HIV-1 infection by blocking viral DNA nuclear entry

BMC Microbiology ◽

10.1186/s12866-015-0605-3 ◽

2015 ◽

Vol 15 (1) ◽

Cited By ~ 5

Author(s):

Ru Bai ◽

Xing-Jie Zhang ◽

Yan-Li Li ◽

Jing-Ping Liu ◽

Hong-Bin Zhang ◽

...

Keyword(s):

Small Molecule ◽

Nuclear Entry ◽

Viral Dna ◽

Small Molecule Compound ◽

Hiv 1

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Polymorphisms in Human APOBEC3H Differentially Regulate Ubiquitination and Antiviral Activity

Viruses ◽

10.3390/v12040378 ◽

2020 ◽

Vol 12 (4) ◽

pp. 378 ◽

Cited By ~ 3

Author(s):

Nicholas M. Chesarino ◽

Michael Emerman

Keyword(s):

Antiviral Activity ◽

Nuclear Localization ◽

Immune Defense ◽

Innate Immune ◽

Cytidine Deaminases ◽

Innate Immune Defense ◽

Immunodeficiency Virus ◽

Apobec3 Family ◽

Active Variant ◽

Hiv 1

The APOBEC3 family of cytidine deaminases are an important part of the host innate immune defense against endogenous retroelements and retroviruses like Human Immunodeficiency Virus (HIV). APOBEC3H (A3H) is the most polymorphic of the human APOBEC3 genes, with four major haplotypes circulating in the population. Haplotype II is the only antivirally-active variant of A3H, while the majority of the population possess independently destabilizing polymorphisms present in haplotype I (R105G) and haplotypes III and IV (N15del). In this paper, we show that instability introduced by either polymorphism is positively correlated with degradative ubiquitination, while haplotype II is protected from this modification. Inhibiting ubiquitination by mutating all of the A3H lysines increased the expression of haplotypes III and IV, but these stabilized forms of haplotype III and IV had a strict nuclear localization, and did not incorporate into virions, nor exhibit antiviral activity. Fusion chimeras with haplotype II allowed for stabilization, cytoplasmic retention, and packaging of the N15del-containing haplotype III, but the haplotype III component of these chimeras was unable to restrict HIV-1 on its own. Thus, the evolutionary loss of A3H activity in many humans involves functional deficiencies independent of protein stability.

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The Role of Toll-Like Receptors in Skin Host Defense, Psoriasis, and Atopic Dermatitis

Journal of Immunology Research ◽

10.1155/2019/1824624 ◽

2019 ◽

Vol 2019 ◽

pp. 1-13 ◽

Cited By ~ 2

Author(s):

Lixiang Sun ◽

Wenjie Liu ◽

Ling-juan Zhang

Keyword(s):

Atopic Dermatitis ◽

Human Body ◽

Lupus Erythematosus ◽

Mammalian Cells ◽

Skin Diseases ◽

Inflammatory Responses ◽

Innate Immune ◽

Host Responses ◽

Molecular Patterns

As the key defense molecules originally identified in Drosophila, Toll-like receptor (TLR) superfamily members play a fundamental role in detecting invading pathogens or damage and initiating the innate immune system of mammalian cells. The skin, the largest organ of the human body, protects the human body by providing a critical physical and immunological active multilayered barrier against invading pathogens and environmental factors. At the first line of defense, the skin is constantly exposed to pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs), and TLRs, expressed in a cell type-specific manner by various skin cells, serve as key molecules to recognize PAMPs and DAMPs and to initiate downstream innate immune host responses. While TLR-initiated inflammatory responses are necessary for pathogen clearance and tissue repair, aberrant activation of TLRs will exaggerate T cell-mediated autoimmune activation, leading to unwanted inflammation, and the development of several skin diseases, including psoriasis, atopic dermatitis, systemic lupus erythematosus, diabetic foot ulcers, fibrotic skin diseases, and skin cancers. Together, TLRs are at the interface between innate immunity and adaptive immunity. In this review, we will describe current understanding of the role of TLRs in skin defense and in the pathogenesis of psoriasis and atopic dermatitis, and we will also discuss the development and therapeutic effect of TLR-targeted therapies.

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