Background
The influenza A virus, avian influenza H7N9 virus, belongs to the
Orthomyxoviridae family. H7N9 virus emerged in China in 2013 and posed a threat to public health [
1‐
3]. As we all know, the H7N9 influenza viruses have caused over 1500 human infections, with a mortality rate of nearly 40%. A number of previous studies have offered valuable information on the pathogenesis, prevention and control of the H7N9 virus. [
4‐
7]. Most patients infected with H7N9 developed acute respiratory distress syndrome (ARDS) and severe lung pneumonia, which was caused by a fierce increase in the expression levels of cytokines and chemokines [
2,
8]. Wan et al. [
9] found that a ‘cytokine storm’ in the lungs of H7N9-infected patients was associated with activation of gasdermin E (GSDME)-mediated pyroptosis in alveolar epithelial cells. However, the host factors involved in viral replication remains elusive. Thus, a better understanding of the regulatory mechanisms of H7N9 infection would be useful to combat future H7N9 virus outbreaks.
The first line of defense against invading pathogens is the innate immune response. Pattern recognition receptors (PRRs) recognize pathogen-associated molecular patterns, which subsequently activates the downstream innate immune response [
10,
11]. During influenza virus infection, the RIG-I (retinoic acid inducible gene I) receptor senses influenza genomic RNA and recruits the mitochondrial antiviral signaling protein (MAVS) and TANK-binding kinase 1 (TBK1) to induce the phosphorylation, dimerization, and nuclear translocation of interferon regulatory factor 3 (IRF3), which finally induces the production of type I interferons [
12‐
14].
The tripartite motif family (TRIM) of proteins have been intensively studied in virus infection. One member, TRIM46, could regulate cancer cell viability, apoptosis, and the cell cycle [
15‐
17]. However, the function of TRIM46 in H7N9 infection and its underlying mechanism remain to be determined. In this study, we aimed to identify the function of TRIM46 in H7N9 virus infection and the underlying mechanism between TRIM46 and the production of host RLR-dependent type I interferons. The results showed that, during H7N9 virus infection, TRIM46 acts as a negative regulator of the host innate immune response. Upon H7N9 virus infection, TRIM46 expression gradually increased over time. Furthermore, knockdown of TRIM46 resulted in increased production of type I interferons and phosphorylation of IRF3, whereas its overexpression had the opposite effects. Finally, we observed that TRIM46-mediated K48-linked ubiquitination of TBK1 resulted in the inhibition of host innate immunity. Thus, this study revealed novel activities of TRIM46 in innate immunity, which potentiates the study of innate immunity against virus infection.
Methods
Cell culture and virus strain
The American Type Culture Collection (ATCC, Manassas, VA, USA) provided the A549, HEK293T, and Madin-Darby canine kidney (MDCK) cells. The cells were grown in Dulbecco’s modified Eagle medium supplemented with heat-inactivated 10% fetal bovine serum, 1% penicillin (100 U/mL), and streptomycin sulfate (100 mg/mL). All cell lines were cultured in a 37 °C incubator with an atmosphere of 5% CO2. Ten-day-old embryonated specific-pathogen free chicken eggs were used to isolate and propagate Influenza A Virus strain A/Zhejiang/DTID-ZJU01/2013(H7N9). The allantoic fluid from the infected chicken eggs was collected and preserved at − 80 °C. The median tissue culture infectious dose (TCID50) method was used to determine the virus titer, which was calculated using the Reed-Muench method. All the live H7N9 virus experiments were performed in a bio-safety level 3 laboratory at the First Affiliated Hospital, Zhejiang University School of Medicine (Registration No. CNAS BL0022).
For TRIM46 knockdown, two short hairpin interfering (shRNA) sequences were designed against two different regions of TRIM46 (the target sequence of TRIM46#1 was 5’- GCTGCTGACAGAGCTTAACTT -3’, the target sequence of TRIM46#2 was 5’- CTGGCACTATACCGTTGAGTT -3’) and cloned and packed into lentiviruses. A TRIM46 overexpression construct was also created and cloned and packed into lentiviruses. The TRIM46 shRNA and overexpression lentiviruses were transfected separately into A549 cells for 72 h. The transfection efficiency was observed using a fluorescence microscope (Olympus, Tokyo, Japan).
Western blotting analysis
Cells were harvested and lysed for 30 min in radioimmunoprecipitation assay (RIPA) buffer with phenylmethylsulfonyl fluoride (PMSF) and phosphatase inhibitors. The lysed cells were then subjected to centrifugation for 10 min at 12,000 × rpm and 4 °C. We retained the supernatants and determined their protein contents using a bicinchoninic acid protein assay. Equal amounts of proteins were subjected to 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis separation. The separated proteins were electrotransferred onto a polyvinyl difluoride membrane. Non-specific binding was blocked by incubating the membranes in 5% skim milk in Tris-buffered saline-Tween 20 (TBST) at room temperature for 1 h. The membranes were then added with the appropriate primary antibodies and incubated overnight at 4 °C. Next day, three washes with TBST carried out and then the membranes were incubated with the corresponding horseradish peroxidase (HRP)-conjugated secondary antibodies. An enhanced chemiluminescence (ECL) reagent was used to visualize the immune-reactive proteins. Primary antibodies against TRIM46 (ab169044), Influenza A nucleoprotein (NP) (ab128193), Myc tag (ab9106), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (ab8245) were purchased from Abcam (Cambridge, UK). Primary antibodies against phosphorylated (p)-IRF3 (#4947) and IRF3 (#4302) were provided by Cell Signaling Technology, Inc. (Danvers, MA, USA). Sigma-Aldrich (Darmstadt, Germany) provided the anti-FLAG Tag antibody.
Quantitative real-time reverse transcription PCR (qRT-PCR)
The TRIzol reagent (Invitrogen, Waltham, MA, USA) was used to extract total RNA from cells. Reverse transcription was then used to produce cDNA from the total RNA.
For influenza virus replication, NP RNAs were reverse-transcribed with primers as following: NP mRNA using oligo (dT), NP cRNA using 5’- AGTAGAAACAAGG -3’, NP vRNA using 5’- AGCGAAAGCAGG -3’. The cDNA was then quantified using quantitative real-time PCR with gene-specific primers. GAPDH mRNA was quantified as an internal control and the 2−ΔΔCt method was used to analyze the relative quantity of the target genes. The primers used in this study were as follows:
TRIM46
Forward primer: 5ʹ-GATTGCCCGAGCCACTGAA-3ʹ,
Reverse primer: 5ʹ-AGGCACTCGCAGGAAGTTAAG-3ʹ;
NP
Forward primer: 5ʹ-ATCAGACCGAACGAGAATCCAGC-3ʹ,
Reverse primer: 5ʹ-GGAGGCCCTCTGTTGATTAGTGT-3ʹ;
IFNA (encoding interferon alpha)
Forward primer: 5ʹ-GCCTCGCCCTTTGCTTTACT-3ʹ,
Reverse primer: 5ʹ-CTGTGGGTCTCAGGGAGATCA-3ʹ;
IFNB1 (encoding interferon B1)
Forward primer: 5ʹ-AAAGAAGCAGCAATTTTCAGC-3ʹ,
Reverse primer: 5ʹ-CCTTGGCCTTCAGGTAATGCA-3ʹ;
GAPDH
Forward primer: 5ʹ-AGGTGAAGGTCGGAGTCA-3ʹ,
Reverse primer: 5ʹ-GGTCATTGATGGCAACAA-3ʹ.
Co-immunoprecipitation (Co-IP)
The indicated plasmids were transfected into HEK293T cells. The cells were collected and lysed at 4 °C for 30 min in IP lysis buffer (1% NP-40, 0.025 M Tris-HCl, 0.15 M NaCl, 1 mM EDTA, 5% glycerol) supplemented with phosphatase inhibitor/PMSF, followed by centrifugation for 10 min at 12,000 × rpm under 4 °C. We retained the supernatants, one third of which was used for input analysis and the other two thirds were incubated with Anti-Myc Magnetic beads (Pierce #88842, Thermo Fisher Scientific, Waltham, MA, USA), or IgG control, overnight at 4 °C for IP analysis. IP lysis buffer was then used to wash the precipitates three times, followed by boiling the samples in 2 × loading buffer. Western blotting was then used to analyze the precipitates using the indicated primary antibodies, followed by incubation with HRP-conjugated anti-rabbit IgG (conformation specific) (#5127, Cell Signaling Technology) or anti-mouse IgG (Light Chain Specific) (#58,802, Cell Signaling Technology) secondary antibodies. The immune-reactive proteins were visualized using the ECL reagent.
Ubiquitination assay
We transfected HEK293T cells with a TBK1-Flag plasmid (overexpressing FLAG-tagged TBK1) together with the TRIM46-Myc plasmid (overexpressing Myc-tagged TRIM46) or not. The cells were harvested at 24 h after transfection and lysed in 1% SDS buffer (50 mM Tris (pH 8.1), 1% SDS, sodium pyrophosphate, EDTA) supplemented with a protease inhibitor cocktail at 4 °C for 30 min. The cell extracts were then subjected to IP using anti-Flag magnetic beads at 4 °C overnight. The beads were washed three times and then subjected to western blotting using antibodies recognizing wild-type (WT) Ubiquitin (ab134953), K48-linked Ubiquitin (ab140601), and K63-linked Ubiquitin (ab179434) (all from Abcam).
Statistical analysis
Data analysis and processing were carried out using GraphPad Prism software version 7 (GraphPad Inc., La Jolla, CA, USA). The statistical difference between two groups was analyzed using an unpaired Student’s t-test and one-way analysis of variance (ANOVA) was carried out to analyze the differences among multiple groups. Statistical significance was indicated by p < 0.05. In all figures, * indicates p < 0.05, ** indicates p < 0.01, and *** indicates p < 0.001.
Discussion
A number of studies have proposed that influenza virus could use multiple host cellular components to replicate and infect host cells. Besides, influenza has evolved to utilize host factors to inhibit the host innate immune response to evade immune surveillance and eradication [
18‐
22]. For example, the influenza virus NS1 protein, which plays multiple roles between influenza virus and host innate immune responses, inhibits MAVS/IKK-mediated interferon production [
23,
24]. Type I interferons play important roles in defending against virus replication, and virus infection induces a series of cellular antiviral signals to produce type I interferons [
25,
26]. To screen and identify the host protein regulators involved in regulating the innate immune response against viruses would be helpful to identify therapeutic targets that manipulate the cellular antivirus responses. In the present study, we found that H7N9 virus-induced TRIM46 negatively regulated the production of type I IFNs by regulating the phosphorylation of IRF3. Furthermore, we discovered that TRIM46 interacts with TBK1, leading to TBK1 degradation via K48-linked ubiquitination. Our results suggest a novel function of TRIM46 in H7N9 virus infection.
TRIM proteins, belonging to the ubiquitin E3 ligase family, participate in regulating the host innate immune response against virus infection. A number of TRIM family proteins, such as TRIM22, TRIM25, TRIM35, TRIM56, have been found to be involved in the replication or pathogenesis of influenza virus [
27‐
30]. TRIM proteins function as positive or negative regulators in host innate immune signaling pathways by mediating the ubiquitination of signaling protein [
27‐
31]. For example, TRIM21 interacts with MAVS and catalyzes its K27-linked poly-ubiquitination to promote innate immune response against RNA viruses. By contrast, another TRIM family protein, TRIM29, inhibits host innate immunity by inducing K11-linked ubiquitination of MAVS [
32,
33]. Our study demonstrated that TRIM46 promotes H7N9 virus infection by mediating the K48-linked ubiquitination of TBK1, which leads to TBK1 degradation, thus inhibiting innate immunity.
During virus infection, virus RNA is sensed by PRRs, which include RIG-I-like receptors (RLRs), NOD-like receptors (NLRs), and Toll-like receptors (TLRs) [
34‐
37]. After influenza virus infection, influenza viral RNA is recognized by the RIG-I receptor, which activates and recruits the downstream TBK1/IKKγ/IKKε complex to induce IRF3 signaling, resulting in the production of type I interferons [
38,
39]. Notably, viruses have involved multiple strategies to escape host innate immune surveillance and elimination, among which TBK1 is a target for virus-induced degradation. For instance, the SARS-CoV-2 membrane protein inhibits the production of type I interferons through induction of K48-linked ubiquitination of TBK1, which subsequently impairs IRF3 phosphorylation and dimerization [
40]. Ubiquitin-conjugating enzyme 2S could interact with TBK1 and recruit USP15 to remove the K63-linked poly-ubiquitin chains of TBK1 [
41]. Phosphatase PP4 dephosphorylates and deactivates TBK1 to inhibit the production of type I interferons [
42]. The ubiquitin–proteasome pathway plays an important role in protein degradation, and ubiquitination of TBK1 is an important method of modulate the production of type I interferons during virus infection, during which process, viral proteins and host proteins participate [
43‐
45]. In the present study, we found that TRIM46 could promote K48-linked ubiquitination of TBK1, which inhibited the phosphorylation of IRF3 and decreased the production of type I interferons.
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