Human immunodeficiency virus type 1 (HIV-1) causes profound immune deregulation that results in immune hyperactivation, CD4
+ T-cell depletion, and progression to AIDS (reviewed in reference
5). HIV-1 has also evolved numerous mechanisms to evade various aspects of the innate and adaptive immune response (reviewed in reference
36), including the ability to subvert several host innate immune factors that limit retroviral replication (reviewed in reference
14). Since the immune system fails to eradicate HIV-1 in infected cells, further studies are required to evaluate the strategies utilized by HIV-1 to counteract the innate immune response.
The recognition of viral RNA differs between TLRs and RLRs due to their subcellular localizations and capacities to recognize specific nucleic acid sequences and structures. TLRs sense incoming viral nucleic acids present in the extracellular environment or in endosomes (reviewed in reference
48). Several studies have highlighted a critical role for TLRs in the regulation of HIV-1 replication. Indeed, uridine-rich oligonucleotides derived from HIV-1 RNA have been shown to induce the production of IFN-α and proinflammatory cytokines via TLR7 and TLR8 in dendritic cells and macrophages (
20,
43). Furthermore, in human plasmacytoid dendritic cells (pDCs), TLR7 is crucial for the detection of HIV-1 infection (
3). Recently, TLR8 and DC-SIGN have been shown to promote HIV-1 replication by enhancing the transcription of full-length viral transcripts (
19). Although TLR7 and TLR8 play a major role in HIV-1 recognition, the persistent activation of TLRs by HIV-1 can often lead to chronic immune activation that enhances CD4
+ T-cell loss (
1,
7,
43).
In contrast to the TLR-dependent sensing of HIV-1 RNA, the RLRs RIG-I and melanoma differentiation-associated gene 5 (MDA5) are DExD/H box RNA helicases that detect viral RNA in the cytoplasm of infected cells. RLRs are pivotal for the recognition of viral infection in almost all cell types, including epithelial, fibroblastic, and conventional dendritic cells (cDCs), as well as macrophages (
31,
74). Upon RNA binding through the helicase domain, RIG-I interacts with the downstream CARD-containing adapter molecule MAVS (mitochondrial antiviral signaling protein [also called IPS-1, VISA, or CARDIF]) (
35,
45,
64,
78). MAVS in turn activates the IKK-related kinases TBK1 and IKKε, which results in the phosphorylation and activation of interferon regulatory factor 3 (IRF-3) and IRF-7. The coordinated activation of these factors as well as NF-κB and AP-1 results in the induction of the IFN response (
24,
41,
56).
Retroviral genomic RNAs (gRNAs) are capped and polyadenylated, as are host mRNAs, yet they contain complex secondary structures in their 5′- and 3′-untranslated regions, which may be recognized by the cellular innate immune system. Mature HIV-1 viral particles contain two copies of the full-length positive-sense viral genomic RNA that are found tightly associated as a compact dimer. The conformation of the stable dimeric RNA structure appears to be important for the production of infectious HIV-1 particles (
8,
9; reviewed in reference
47). Indeed, RNA from infectious mature virions is mainly dimeric, while RNA isolated from immature, noninfectious viral particles obtained from protease-defective (PR
−) mutant viruses is predominantly monomeric (
18). Although the significance of HIV-1 genomic RNA dimerization is still not fully understood, it appears that HIV-1 protease plays a key role in this event.
MATERIALS AND METHODS
Cell culture, transfections, and luciferase assays.
Peripheral blood mononuclear cells (PBMCs) were obtained from healthy donors at the Royal Victoria Hospital, Montreal, Quebec, Canada, with informed consent, in agreement with Royal Victoria Hospital, Jewish General Hospital, and McGill University Research Ethics Committees. PBMCs were isolated by density centrifugation on Ficoll-Paque Plus (Amersham Biosciences, Uppsala, Sweden) from fresh apheresis specimens obtained with informed consent from healthy donors. Monocytes were isolated from PBMCs by magnetic cell sorting using anti-CD14-conjugated microbeads and an Automacs instrument (Miltenyi Biotec, Auburn, CA) and cultured in Iscove medium (Wisent Technologies, Rocklin, CA) supplemented with 2% human serum A/B (Wisent Technologies), 700 U/ml granulocyte-macrophage colony-stimulating factor (GM-CSF) (a generous gift from Cangene Corporation, Mississauga, Canada), 100 U/ml penicillin G, and 100 μg/ml streptomycin in gas-permeable thermoplastic nonadherent culture bags (Origen Biomedical). On day 7, monocyte-derived macrophages (MDMs) were harvested and resuspended in complete McCoy's 5A medium (supplemented with 10% fetal bovine serum [FBS] and antibiotics) (Wisent Technologies). Monocyte-derived macrophage differentiation and purity were analyzed by flow cytometry as described previously (
59).
Human hepatoma Huh7.0 cells, HEK293 cells, HeLa cells, and RIG-I knockout (RIG-I
−/−) and MDA5
−/− mouse embryonic fibroblasts (MEFs) as well as the corresponding wild-type (WT) MEFs were used for transient transfections and were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum and antibiotics. Both RIG-I
−/− and MDA5
−/− MEFs were obtained from Robert H. Silverman, Lerner Research Institute, Cleveland Clinic, with the permission of Shizuo Akira, Osaka University, who generated the original RIG-I and MDA5 knockout mice (
31,
33). For luciferase assays, subconfluent HeLa cells and WT and MDA5
−/− MEFs were transfected by using TransIT-LT1 transfection reagent (Mirus) with 100 ng of the pRL-TK reporter (
Renilla luciferase [Luc] for an internal control) and 100 ng of the respective Luc or pGL3 reporter (firefly luciferase, experimental reporter). RNA transfection was performed 24 h later with 2 μg of HIV-1 RNA dimers and RNA monomers, respectively, and 500 ng of RNA bearing 5′-triphosphate by using Transmessenger transfection reagent (Qiagen). At 24 h post-RNA transfection, reporter gene activity was measured by a dual-luciferase reporter assay, according to the manufacturer's instructions (Promega). Luciferase activity was measured as the fold activation (relative to the basal level of the reporter gene of the nontransfected sample after normalization with the cotransfected
Renilla luciferase activity). In RIG-I
−/− and RIG-I WT MEFs, HIV-1 gRNA transfections were performed as described above. For dose-response experiments, subconfluent HEK293 cells were transfected by the calcium phosphate coprecipitation method with 100 ng of the pRL-TK reporter (
Renilla luciferase for an internal control); 100 ng of the
IFNB pGL3 reporter (firefly luciferase, experimental reporter); 200 ng of the ΔRIG-I, TBK1, and pEGFP-C1 expression plasmids; and 50 to 500 ng of the green fluorescent protein (GFP)-protease expression plasmid as indicated.
IFNB promoter activity was measured at 24 h posttransfection by use of the dual-luciferase reporter assay as described above. Single-cycle infections were performed with subconfluent HEK293 cells, where cells were transfected by the calcium phosphate coprecipitation method with 1 μg of Myc-RIG-I expression plasmid and 1 μg of either WT BH10 or the BH10-PR
− proviral clone.
Plasmid constructs.
HIV-1 protease cDNA was amplified from the pNL4.3 HIV-1 expression plasmid and cloned into the pEGFP C1 expression plasmid at the EcoRV and BamHI cloning sites using the following set of primers: 5′-CCGCGAATTCGATGCCTCAGATCACTCTTTGG-3′ (forward) and 5′-CCGCTCTAGACTAAAAATTTAAAGTGCAGCCAATCTG-3′ (reverse). Plasmids encoding ΔRIG-I, RIG-I, RIG-IC, TBK1, IFN-β-pGL3, interferon-stimulated response element (ISRE)-Luc, NF-κB-pGL3, and pRL-TK were previously described (
35,
38,
65,
80).
Isolation of HIV-1 viral RNA.
HIV-1 genomic RNA dimers and monomers were produced by the transfection of HeLa cells with BH10 WT, BH10-PR
− (protease defective), and FL proviral clones for 48 h (
29). In the BH10 FL transfection, HeLa cells were incubated with the protease inhibitor saquinavir (1 μM) (
28). Virus-containing supernatants were collected and centrifuged at 40,000 rpm for 1 h onto a 20% (wt/vol) sucrose cushion in phosphate-buffered saline (PBS) by using a Beckman SW40 rotor. The virus pellet was dissolved in sterile lysis buffer (50 mM Tris [pH 7.4], 50 mM NaCl, 10 mM EDTA, 1% [wt/vol] SDS, 50 μg of tRNA/ml, and 100 μg proteinase K/ml) and extracted twice at 4°C with an equal volume of buffer-saturated phenol-chloroform-isoamyl alcohol (25:24:1) (Invitrogen). The aqueous phase containing the viral RNA was precipitated overnight at −80°C with 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2.5 volumes of 95% (vol/vol) ethanol and centrifuged at 4°C for 30 min. The gRNA pellet was rinsed in 70% (vol/vol) ethanol and dissolved in 20 μl of buffer S (10 mM Tris [pH 7.5], 100 mM NaCl, 10 mM EDTA, 1% SDS). The genomic viral RNA concentration was determined by absorption at 260 nm using a Nanodrop ND-1000 spectrophotometer, while the purity of RNA dimers and monomers was verified by electrophoresis on a nondenaturing 1% (wt/vol) agarose gel and subsequently analyzed by Northern blotting as described previously (
29,
68). Densitometric analysis was performed by using NIH 1.6.3 software to evaluate the amount of dimers and monomers in each RNA preparation prior to RNA transfection (further described in reference
28). The percentage of monomeric RNA in the FL mutant was approximately 93% ± 8%. A total of 2 μg of HIV-1 RNA dimers and RNA monomers was used for transfections.
Viral stocks and infections.
The R5-tropic HIV-1 B primary isolate was provided by the McGill AIDS Center at the Lady Davis Institute (Montreal, Canada) and was isolated from a treatment-naïve HIV-1-infected patient from Montreal. MDMs and THP-1 cells were infected in a pellet for 2 h at a multiplicity of infection (MOI) of 1 and washed twice with PBS to remove unbound viral particles. Cells were then plated onto RPMI 1640 medium supplemented as described above. Cells were harvested at 6, 24, and 72 h after infection for RNA extraction. MDMs and THP-1 cells were infected with SeV at 40 hemagglutinating units (HAU) per 10E6 cells in serum-free medium for the first 2 h, and cells were harvested for RNA or protein extraction at 6 h. SeV strain Cantell was obtained from Charles River Laboratories (North Franklin, CT). The HIV-1 proviral clones WT BH10, BH10-PR− (protease defective), and pNL4.3 were generously provided by Mark Wainberg (McGill AIDS Center, Montreal, Canada).
Reagents.
Cells were treated with 5 μM MG132 (Boston Biochem), 50 μM Z-VAD-fmk (R&D systems), 10 μM E64 (Roche Applied Science), 5 μM saquinavir (NIH AIDS Research and Reference Reagent Program), and 10 μg/ml of TLR7 ligand ssRNA40/LyoVec (Invivogen). 5′-PPP RNA was synthesized by using the T7 Megascript kit (Ambion).
Immunoblot analysis.
Whole-cell extracts (WCEs) were prepared in Nonidet P-40 (NP-40) lysis buffer (50 mM HEPES [pH 7.4], 150 mM NaCl, 1% NP-40, 2 mM EDTA, 10% glycerol, 5 mM NaF, 0.1 mM Na
3VO
4, 10 mM β-glycerophosphate [pH 7.4], 10 mM
p-nitrophenyl phosphate disodium salt hexahydrate [PNPP], 0.1 mM phenylmethylsulfonyl fluoride [PMSF], and 5 μg/ml each of leupeptin, pepstatin, and aprotinin). Cell debris was removed by centrifugation at 15,000 rpm for 30 min. For subcellular fractionation, cell pellets were washed with PBS and further lysed in a solution containing 1% NP-40, 1% SDS, and 0.5% deoxycholate (DOC), followed by sonication. WCEs (50 μg) were subjected to electrophoresis on 7.5 to 12% acrylamide gels by SDS-PAGE and were transferred onto nitrocellulose membranes (Bio-Rad Laboratories, Mississauga, Canada). The membranes were blocked in 5% dried milk in PBS plus 0.1% Tween 20 and then probed with primary antibodies. Anti-Flag (M2) and anti-Myc (9E10), each used at a concentration of 1 μg/ml, were purchased from Sigma-Aldrich (Oakville, Canada), and anti-GFP (Roche) was prepared in blocking solution. Anti-IRF-3 (1:1,000; IBL, Japan) and the phospho-specific antibodies directed against IRF-3 Ser-396 (1:1,000) (
63), anti-p24 (1:1,000; in-house) (
10), anti-RIG-I (1:1,000; in-house) (
42), and β-actin (MAb1501; Chemicon) were prepared in 5% bovine serum albumin (BSA)-PBS-Tween. After washing in PBS-0.1% Tween 20, the membranes were incubated for 1 h with horseradish peroxidase-conjugated goat anti-rabbit or anti-mouse IgG (1:8,000). Immunoreactive bands were visualized with an enhanced chemiluminescence detection system (ECL, Amersham Biosciences).
Real-time PCR.
DNase-treated total RNA was prepared by using the RNeasy kit (Qiagen Inc.). Total RNA was reverse transcribed with 100 U of Superscript II Plus RNase H− reverse transcriptase (RT) using oligonucleotide AnCT primers (Gibco BRL Life Technologies). Quantitative PCR (Q-PCR) assays were performed in triplicates using FastStart Universal SYBR green master mix (Rox) (Roche) on the AB 7500 Fast real-time PCR system (Applied Biosystems, Foster City, CA). The human primer pairs used were as follows: 5′-TTGTGCTTCTCCACTACAGC-3′ (forward) and 5′-CTGTAAGTCTGTTAATGAAG-3′ (reverse) for IFN-β, 5′-CCTGATGAAGGAGGACTCCATT-3′ (forward) and 5′-AAAAAGGTGAGCTGGCATACG-3′ (reverse) for IFN-α2, 5′-ACCCGCAGATGTCCATGAG-3′ (forward) and 5′-GTGGCATCATGTAGTTGTGAACCT-3′ (reverse) for IRF-7, 5′-AGCTCCATGTCGGTGTCAG-3′ (forward) and 5′-GAAGGTCAGCCAGAACAGGT-3′ (reverse) for ISG15, 5′-CAACCAAGCAAATGTGAGGA-3′ (forward) and 5′-AGGGGAAGCAAAGAAAATGG-3′ (reverse) for ISG56, 5′-TTCCTGCAAGCCAATTTTGTC-3′ (forward) and 5′-TCTTCTCACCCTTCTTTTTCATTGT-3′ (reverse) for CXCL10, 5′-ATGCTCCAGAAGGCCAGACA-3′ (forward) and 5′-CCTCCACTGTGCTGGTTTTATCT-3′ (reverse) for interleukin-12α (IL-12α), 5′-GGAGACTTGCCTGGTGAAAA-3′ (forward) and 5′-ATCTGAGGTGCCCATGCTAC-3′ (reverse) for IL-6, 5′-GGTCAGAGGACGGCATGAGA-3′ (forward) and 5′-GCAGGACCCAGGTGTCATTG-3′ (reverse) for APOBEC3G, and 5′-CCTTCCTGGGCATGGAGTCCT-3′ (forward) and 5′-AATCTCATCATCTTGTTTTCTGCG-3′ (reverse) for β-actin. The HIV-1 Gag primer set was 5′-GGAGCTAGAACGATTCGCAGTTA-3′ (forward) and 5′-GGTTGTAGCTGTCCCAGTATTTGTC-3′ (reverse). The mouse primers set used were as follows: 5′-CACAGCCCTCTCCATCAACT-3′(forward) and 5′-TCCCACGTCAATCTTTCCTC-3′ (reverse) for mouse IFN-β (mIFN-β), 5′-GAAGGACAGGAAGGATTTTGGA-3′ (forward) and 5′-TGAGCCTTCTGGATCTGTTGGT-3′ (reverse) for mIFN-α4, 5′-GGGCCACAGCAACATCTATGA-3′ (forward) and 5′-CCGCTGGGACACCTTCTTC-3′ (reverse) for mISG15, 5′-CAACCAAGCAAATGTGAGGA-3′ (forward) and 5′-AGGGGAAGCAAAGAAAATGG-3′ (reverse) for mISG56, and 5′-CACCAGTTCGCCATGGAT-3′ (forward) and 5′-CCTCGTCACCCACATAGGAG-3′ (reverse) for mβ-actin. All data are presented as relative quantification (RQ) using the comparative threshold cycle (CT) method as the expression of the target gene versus the reference gene β-actin. The absence of genomic DNA contamination was demonstrated routinely by analyses of PCRs performed with total RNA using each of the primer sets.
RT-PCR.
DNase-treated total RNA was prepared by using the RNeasy kit (Qiagen Inc.). Total RNA was reverse transcribed with 100 U of Superscript II Plus RNase H− reverse transcriptase using oligonucleotide AnCT primers (Gibco BRL Life Technologies). The cDNAs were amplified in 50 μl of PCR buffer containing deoxynucleoside triphosphate (dNTP), MgCl2, and Taq polymerase (Amersham Biosciences, England). A total of 20, 25, 30, and 35 cycles were carried out, and PCR products were analyzed by electrophoresis on a 2% agarose gel. Pictures show ethidium bromide fluorescence of PCR products obtained at a given number of PCR cycles, i.e., before reaching saturation levels. The primer pairs used were 5′-TGCAAGCTGTGTGCCTCT-3′ (forward) and 5-CATCTTTGTCTGGCATCTGG-3′ (reverse) for RIG-I and 5′-CCTTCCTGGGCATGGAGTCCT-3′ (forward) and 5′-AATCTCATCATCTTGTTTTCTGCG-3′ (reverse) for β-actin.
Confocal microscopy.
A549 cells were seeded onto Ibidi (München, Germany) μ-Slides VI
0.4 and grown overnight to 50% confluence. A549 cells were transfected by using Lipofectamine LTX and Plus reagent (Invitrogen) with GFP or GFP-protease with or without saquinavir (5 μM), respectively. Cells were maintained in F-12K nutrient mixture (Kaighn's modified) supplemented with 10% heat-inactivated fetal bovine serum, antibiotics, and 25 mM HEPES to help maintain cell viability during the experiment (
17). At 15 h posttransfection, A549 cells were set up for live imaging at 37°C in a humidified 5% CO
2 chamber using a Chamlide environmental control system (LCI, Seoul, South Korea) installed on a Leica DM16000B microscope. The microscope was equipped with a WaveFX spinning disk confocal head (Quorum Technologies, Ontario, Canada), and images were acquired with a Hamamatsu ImageEM EM-charge-coupled-device (CCD) camera. After confirming the expression of GFP-positive live cells, samples were fixed with 4% paraformaldehyde for 15 min and washed in PBS. Cells were permeabilized and blocked in 3% BSA and 0.25% Triton X-100 in PBS. Primary anti-LAMP-1 antibody (DSHB) and anti-RIG-I (1:1,000; in-house) (
42) were incubated for 1 h at room temperature. Secondary antibodies, anti-rabbit IgG(H+L)-Alexa Fluor546 (1:1,000) (catalog number A11071; Molecular Probes) and anti-rat IgG(H+L)-Alexa Fluor647 (1:200) (catalog number A21472; Molecular Probes) conjugates, were applied for 1 h at room temperature. Controls were prepared by immunostaining without the primary antibody. Images were acquired by using a 63×/1.4-plan-apochromat oil immersion objective. The images were acquired by using Volocity Imaging software (version 4.3.2; Improvision, Perkin-Elmer, Waltham, MA) and then processed by using the Fiji package of ImageJA (version 1.44f).
Statistical analysis.
Data were analyzed as means ± standard errors of the means (SEM). Statistical significance was assessed by a paired Student's t test. Analyses were performed by using Prism 5 software (GraphPad). Statistical significance was evaluated by using the following P values: a P values of <0.05, a P value of <0.01, or a P value of <0.001.
DISCUSSION
Recent studies highlighted the importance of the RIG-I sensor in the recognition of incoming virus RNA structures (
76); an understanding of the evasion strategies used by viruses to circumvent this crucial antiviral response is an important step in the development of novel therapies. To date, there has been no evidence to suggest that RIG-I signaling is triggered by retroviral infection. The present study provides new insights concerning the involvement of RIG-I in HIV-1 infection: (i) the sensing of HIV-1 RNA occurs through a RIG-I-dependent but not MDA5-dependent pathway (in addition to a TLR7-dependent pathway), (ii) HIV-1 gRNA monomers induce a stronger activation of RIG-I than do HIV-1 gRNA dimers, and (iii) despite RIG-I triggering by viral RNA, downstream antiviral gene expression is inhibited by the HIV-1 protease, which causes a depletion of the cytoplasmic fraction of endogenous RIG-I and redistribution to the membranous lysosomal compartment. In support of these conclusions, the intracellular amount of RIG-I was decreased during
de novo single-cycle infection by BH10 provirus, but not by the protease-deficient provirus (BH10-PR
−) (Fig.
5), and by the ectopic expression of the PR (Fig.
6B). RIG-I downregulation was not mediated by proteasomal degradation or caspase-dependent cleavage (Fig.
7) and was not dependent on protease activity
per se, since the protease inhibitor saquinavir did not block RIG-I relocalization (Fig.
7C and
8C). Moreover, RIG-I protein levels were restored by the lysosomal protease inhibitor E64 (Fig.
8D), suggesting that HIV-1 PR relocalized cytoplasmic RIG-I to the lysosomal compartment for degradation. Interestingly, the RIG-I cytoplasmic fraction was relocalized in the insoluble fraction following viral entry in
de novo HIV-1-infected MDMs (Fig.
8B). By virtue of removing RIG-I from the cytosol, PR may impede RIG-I interaction with the mitochondrial adaptor MAVS and thus disconnect early innate antiviral signaling.
The detection of incoming viral RNA by RIG-I is dependent on numerous structural RNA modifications as well as specific secondary or tertiary RNA conformations. Indeed, the base-paired, panhandle structure at the 5′ end of RNA, together with a 5′-PPP moiety, appears to be important for RIG-I activation (
61,
62); furthermore, the 5′-PPP-bearing viral RNAs from influenza A and rabies viruses effectively activate RIG-I (
2,
26,
54,
57,
58). Other structural features of RNA may also be important for RIG-I recognition, since RNAs lacking 5′-PPP, such as short strands of synthetic poly(I:C), also activate RIG-I (
32,
69). In addition, an A-U-rich motif in the 3′-untranslated region of the HCV genome was shown previously to induce RIG-I (
60), thus indicating that distinct RNA species can trigger RIG-I in virally infected cells. Interestingly, small self-RNAs generated by the action of the antiviral endoribonuclease RNase L were also shown previously to be recognized by RIG-I (
40).
HIV-1 genomic RNA is transcribed via a Tat/RNA polymerase II-dependent mechanism and harbors primarily 5′-capped transcripts. However, the presence of some uncapped (5′-triphosphorylated) RNAs at the 5′ end of HIV-1 RNA cannot be formally excluded; in fact, a mixture of capped and 5′-triphosphorylated RNAs was previously detected in producer cells and virions at early stages after virus entry (
44). Several stem-loop structures composed of A-U-rich sequences in the 5′-untranslated region (5′-UTR) of HIV-1 RNA may stimulate RIG-I, due to their propensity to form complex secondary structures. This idea is supported by the observation that RIG-I was activated to a greater extent by HIV-1 monomers than by RNA dimers (Fig.
1B). RNA monomers might allow the stimulatory region to be further exposed, whereas the more condensed form of RNA found in dimers restricts the accessibility of the 5′-UTR for RNA sensors such as RIG-I and TLR7. Another IFN signaling pathway involved in viral RNA degradation, the 2′,5′-oligoadenylate synthetase (OAS)/RNase L pathway, is activated by the 5′ transactivation responsive element (TAR) region present in HIV-1 mRNA (
39). Because much of the HIV-1 genomic structure remains uncharacterized (>85%) (
75), further structural analysis of the 5′-UTR and the viral genome is required to identify the precise structural determinants recognized by RIG-I.
Despite clear evidence that purified genomic RNA can be recognized by RIG-I, an activation of RIG-I following
de novo HIV-1 infection in human macrophages was not observed. The production of IFN was also not detected after infection, suggesting that HIV-1 had developed a strategy to counteract the early innate IFN response. An inhibition of RIG-I signaling occurred through an HIV-1 protease-dependent mechanism, since the coexpression of an active form of RIG-I along with increasing amounts of the PR led to a decrease in
IFNB promoter activity in a concentration-dependent manner as well as an inhibition of IRF-3 phosphorylation (Fig.
6).
A major function of HIV-1 protease in the virus life cycle is to process the Gag and Gag-Pol precursors to yield mature virion proteins. The protease is initially synthesized in an inactive form as part of the Gag-Pol precursor and is activated within the virion during the final stages of virus assembly and virus maturation. PR is required for virion maturation, and its inhibition gives rise to immature virions that are unable to reinfect cells (reviewed in reference
11). The active protease present in incoming virions is thus poised to target host antiviral responses. The cleavage of cellular proteins by PR has been well documented; for example, the antiapoptotic protein Bcl-2 is cleaved by HIV-1 protease, leading to apoptosis (
4). The death of HIV-1-infected T cells is linked to the cleavage of procaspase 8 to Casp8p41 by protease, which, once cleaved, induces apoptosis (
50).
Protease expression resulted in a reduction in the expression levels of IFN and ISGs; the inability of HIV-1-infected cells to induce IFN-stimulated host restriction factors may indirectly contribute to increased viral replication. For example, the cellular deaminase APOBEC3G incorporates into HIV-1 virions and inhibits viral replication by inducing cytidine-to-uracil deamination in the newly transcribed single-stranded proviral DNA (
66). The HIV-1 viral accessory protein Vif counteracts the antiretroviral effects of APOBEC3G by triggering the ubiquitinylation of APOBEC3G, leading to its proteasomal degradation (reviewed in references
12,
16, and
66). Thus, HIV-1 may act on APOBEC3G at two levels: at the transcriptional level, by ablating APOBEC3G induction via the PR-mediated inhibition of RIG-I and the IFN response, and at the protein level, via the Vif-mediated degradation of APOBEC3G. Furthermore, data from studies performed by two different groups have suggested that HIV-1 disrupts IFN signaling at the level of IRF-3 in CD4
+ T-cell lines (
13,
51). HIV-1 targets IRF-3 for protein depletion through the action of the HIV-1 accessory proteins Vif and Vpr, allowing HIV-1 to evade the host immune response. Similarly, the viral protein Vpu antagonizes the IFN-inducible viral restriction factor tetherin (also called BST-2, HM1.24, or CD317) by reducing its cell surface expression through Vpu-tetherin interactions, resulting in the relocalization and degradation of the restriction factor in perinuclear compartments (
15,
71). The trafficking of tetherin from its functional location on the cell surface promotes increased HIV-1 virion release (
49). The present study provides an additional example of how HIV-1 may disrupt the host innate response, by relocalizing a crucial RNA-sensing protein away from its functional microenvironment.
The ectopic expression of RIG-I or the helicase domain of RIG-I alone had an inhibitory effect on HIV-1 replication (Fig.
3). Interestingly, RNA helicases are known to participate in different steps of HIV-1 replication, and the DDX30 helicase in particular was previously reported to influence HIV-1 replication by decreasing the infectivity of nascent viral particles (
81). As yet, it is not clear whether RIG-I helicase activity inhibits HIV-1 at the level of gRNA recognition or during reverse transcription. In contrast to the reduction in IFN and ISG expression levels, proinflammatory cytokine production was induced by HIV-1 replication early after infection, in part by NF-κB-dependent signaling (reviewed in reference
21). However, a rapid decrease in the expression levels of these proinflammatory cytokines was observed after infection, perhaps related to the expression of viral proteins such as Tat and Vpr (
27,
46). This study provides for the first time a mechanism by which HIV-1 evades the activation of RNA sensors. Interestingly, a recent study by Yan et al. demonstrated that the cystolic exonuclease TREX1 suppresses IFN activation following HIV-1 infection. TREX1 binds and digests cytoplasmic HIV-1 DNA that would normally be detected by an unidentified DNA sensor that converges on the adaptor STING and the kinase TBK1 (
79). Overall, these recent studies demonstrate the multifaceted strategies used by HIV-1 to suppress viral RNA- and DNA-sensing pathways.
In conclusion, this study demonstrates that HIV-1 genomic RNA is recognized by RIG-I, yet RIG-I signaling is inactivated via a unique PR-dependent mechanism that circumvents the host innate immune response. HIV-1 protease interferes with cytoplasmic RIG-I, leading to a trapped pool of perinuclear RIG-I. The inability to coimmunoprecipitate RIG-I and PR directly suggests that the PR-mediated relocalization of RIG-I may occur via an indirect interaction (data not shown). Since protease inhibitors are used extensively for HIV-1 therapy, and the PR-dependent ablation of RIG-I signaling is independent of protease activity, improved strategies to generate antiprotease drugs will be required to combat this specific mode of host immune response evasion.