G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology
© The Author(s). 2016
Received: 21 January 2016
Accepted: 6 July 2016
Published: 12 July 2016
The nonstructural protein 1 (NS1) of influenza A viruses can act as a viral replication enhancer by antagonizing type I interferon (IFN) induction and response in infected cells. We previously reported that A/Puerto Rico/8/1934 (H1N1) (PR8) containing the NS1 gene derived from A/swine/IA/15/1930 (H1N1) (IA30) replicated more efficiently than the wild type virus. Here, we identified amino acids in NS1 critical for enhancing viral replication.
To identify a key amino acid in NS1 which can increase the virus replication, growth kinetics of PR8 viruses encoding single mutation in NS1 were compared in A549 cells. NS1 mutant functions were studied using dsRNA-protein pull down, RIG-I mediated IFNβ-promoter activity assays and growth curve analysis in murine lung epithelial type I (Let1) cells.
The G45R mutation in the NS1 of PR8 (G45R/NS1) virus is critical for the enhanced viral replication in A549 cells. G45R/NS1 slightly decreased NS1 binding to dsRNA but did not interfere with its suppression of RIG-I-mediated type I IFN production. Likewise, replication of G45R/NS1 virus was increased in comparison to wild type virus in both wild type and type I interferon receptor null Let1 cells.
The non-conserved amino acid, R45, enhances viral replication which is apparently independent of dsRNA binding and suppression of type I IFN, suggesting a non-characterized function of NS1 for the enhanced viral replication. As G45R/NS1 virus induced the type I IFN induction and response in infected A549 cells, it is also interesting to investigate virus virulence for further studies.
Influenza A virus has evolved a variety of mechanisms to evade host cell defenses to facilitate efficient transmission [1, 2], replication and virulence . Escape from host innate immune responses allows influenza A virus to proficiently replicate in the cells. The most important innate immune response against influenza A virus is the interferon (IFN) system . There are three types of IFN families including type I (−α, − β, −ω and -ɛ), type II (−γ) and type III (−λs or IL28/29) . Type I IFNs, especially -α/β, are essential for host defense against viral infection. It is induced following the recognition of viral components or RNA by pathogen recognition receptors (PRRs) such as retinoic acid-inducible gene I (RIG-I) in the cytoplasm and toll-like receptors (TLR) in the endosome and on the cell surface [6–8].
IFN signaling is mediated via binding between IFN and its receptor, which triggers downstream signaling via Janus Activated Kinase (JAK) and Tyrosine Kinae-2 (TYK2) followed by Signal Transducer and Activators of Transcription (STAT) proteins . After activation, STATs translocate into the nucleus to initiate transcription of IFN-stimulated genes (ISGs), such as 2’-5’oligoadenylate synthetase (OAS1), dsRNA-dependent protein kinase R (PKR) and Mx1, which have antiviral functions [10, 11].
The non-structural protein 1 (NS1) of influenza A virus plays an important role in counteracting the IFNα/β system , thereby preventing the generation of an antiviral state in the cell and facilitating efficient viral replication [13, 14]. This action of NS1 was shown at multiple levels in vitro and is different among influenza A virus strains . NS1 contains two major functional domains, an N-terminal RNA-binding domain (RBD), which binds dsRNA, and a C-terminal effector domain (ED). The RBD has been proposed to sequester dsRNA from RIG-I  and dsRNA-activated antiviral enzymes such as OAS1  and PKR [18, 19] to prevent their antiviral activities.
Previously, we reported that reassortant viruses containing internal gene segments derived from the A/swine/IA/15/30 H1N1 virus (IA30) with the hemagglutinin (HA) and neuraminidase (NA) from the avian influenza virus H5N1 or swine influenza virus H3N2 replicated more efficiently than those with internal gene segments from A/Puerto Pico/8/1934 (H1N1) (PR8) in Madin Darby canine kidney (MDCK) and Vero cells . Among the IA30 genes, IA30 NS has been shown to increase PR8 virus replication more efficiently than wild type PR8 NS1 . In this report, we have identified a non-conserved residue of NS1 that enhanced viral replication independent of its dsRNA-binding ability and the IFN antagonist function.
The RNA-binding domain of IA30 NS1 increased virus replication
We performed multiple alignments of the deduced amino acids of both chimeras. The result shows that few amino acids on NS2 of both chimeras are different. NS2 has a nuclear export signal and interacts with M1 via its C-terminal domain (aa 81–100) to transport the vRNP from nucleus to cytoplasm for viral assembly (Shimizu et al., 2011) and also regulates the accumulation of viral RNA species including viral RNA, cRNA and mRNA, which are important for viral transcription and replication (Robb et al., 2009). According to NS2 functions, we cannot exclude that NS2 translated from chimeric 1 and 2 genes may have an effect on the replication.
A single amino acid substitution, G45R, in PR8 NS1 contributed to enhanced viral replication
To determine amino acids in the RBD of IA30 NS1 that contributed to increased viral replication, amino acid sequences of PR8 and IA30 NS1s were compared. Eight residues in the RBD were different between the two strains. We selected four point mutations at positions 45, 55, 68 and 70, which did not affect NS2 expression, to introduce into the RBD coding region of PR8 NS1 to generate viruses containing PR8 NS1 with G45R, K55E, I68V or K70E mutations via reverse genetics . Growth kinetics of the viruses was assessed in A549 cells at a multiplicity of infection (MOI) of 0.01. Viruses with NS1 mutations at G45R and K55E (G45R and K55E/NS1s) grew to higher titers compared to the wild type (WT), I68V and K70E/NS1s viruses. The G45R/NS1 virus replicated to the highest titer (P ≤ 0.001) at 48 to 96 hpi while the replication rates of I68V and K70E/NS1s mutants were similar to the WT/NS1 virus (Fig. 1b). The increased virus replication with K55E substitution in PR8 NS1 has been addressed previously for cell-based vaccine production . As the G45R/NS1 virus replicated to the highest titer, it was selected for further studies.
G45R/NS1 did not increase binding to dsRNA in vitro
G45R/NS1 did not increase inhibition of RIG-I mediated IFNβ-promoter activation
G45R/NS1 increased virus replication independent of type I IFN induction
The NS1 protein of influenza A virus is multifunctional and associated with increased viral pathogenicity and replication by counteracting host antiviral defense mechanisms . NS1 inhibits IFNα/β induction and the antiviral response through different pathways [4, 15, 29–31], though some functions are strain-specific [32, 33]. It was shown previously that recombinant viruses with different HA and NA subtypes in an IA30 virus background had much higher replication rates compared to viruses in a PR8 virus background . Recently, IA30 NS has been shown to involve in the increased virus replication . Here, we investigated the roles of amino acids in IA30 NS1 in enhancing viral replication. We constructed viruses using reverse genetics that contained the HA and NA genes from X31 in a PR8 background and demonstrated that the single amino acids substitution, G45R, in the RBD of PR8 NS1 accelerated viral replication.
The RBD of NS1 plays a major role in inhibiting host defense mechanisms, in particular type I IFN production. It may sequester dsRNA from PRRs and ISG products that require activation by dsRNA, such as RIG-I, PKR and OAS1 [4, 17, 30]. In addition, NS1 also interacts with these proteins to block their functions [19, 24]. Viruses containing the R38A mutation in NS1 were attenuated, lacked dsRNA binding and were sensitive to IFNβ . However, replication of viruses containing the R38A NS1 mutation was improved in RNaseL knockout cells, suggesting that NS1 was involved in the inhibition of the 2’-5’ OAS/RNaseL pathway, possibly by sequestering dsRNA and preventing activation of OAS1 .
Previously, in silico analysis suggested that the R45 on NS1 of the pandemic virus A/Texas/15/2009 (H1N1) increased the stability of the dsRNA-NS1 complex, which contributed to viral pathogenicity . We investigated whether the enhanced viral replication mediated by G45R/NS1 was due to the increased dsRNA binding in vitro using dsRNA-NS1 pull-down assays. In these assays, G45R/NS1 did not show increased dsRNA-binding compared to WT/NS1. As G45R/NS1 did not act as predicted , we speculated that substitution of G45R on PR8 NS1 may impact dsRNA binding by steric hindrance. Nonetheless, NS1 functions do not depend solely on its dsRNA-binding activity. WSN-NS1 with the triple mutations R38A, K41A and S42G could not bind to dsRNA similar to R38A and K41A, though the virus containing R38A, K41A and S42G decreased activation of the IFNβ promoter and had a higher replication rate compared to the virus containing R38A and K41A .
RIG-I is a crucial cytoplasmic sensor for dsRNA and 5’ppp-ssRNA that triggers downstream signaling to activate type I IFN production during virus infection [24, 25]. It has been reported that NS1 interferes with the RIG-I mediated IFN pathway partly through its RBD, increasing viral replication and pathogenicity [35, 36]. We investigated whether G45R/NS1 increased virus replication by inhibiting RIG-I mediated IFNβ-promoter activation. The reporter assay showed that G45R/NS1 suppressed the activation of IFNβ-promoter comparable to WT/NS1 (Fig. 3). We suggest that the G45R mutation in PR8 NS1 facilitated virus replication independent of dsRNA-binding and RIG-I mediated IFNβ promoter activation.
We confirmed that type I IFNs induction was not relevant to G45R/NS1 virus replication by using IFNARnull Let1 cells. G45R/NS1 replicated to higher titers compared to WT virus while AA/NS1 virus was attenuated in both WT and IFNARnull Let1 cells (Fig. 5) suggesting that G45R/NS1 strongly influenced virus replication in a type I IFN induction-independent manner. In fact, high replication of G45R/NS1 was accompanied by increased type I IFN and STAT1 phosphorylation (Fig. 4 and Additional file 3: Fig. S3), conferring a strong activation of type I IFN signaling. Elevation of type I IFN expression can up-regulate the expression of various cytokines and chemokines to recruit immune cells to the site of infection. In addition, IFNα has been reported to enhance CCL5 and CCL10 expression in influenza virus-infected A549 cells . Rapid virus replication, systemic spread and activation of IFNα/β signaling by influenza virus infection could lead to excessive production of cytokines and chemokines, resulting in increased morbidity and mortality in mice [38, 39]. An adaptation of amino acids on NS1, F103L and M106I, of human influenza A/Hong Kong/1/68(H3N2) has been reported to be associated with the increased virus replication and virulence in mice and human  thereby the occurrence of G45R mutation on NS1 of pandemic human 2009 H1N1 virus might be one of crucial factors to cause severe disease. Even though G45R in NS1 presents in a minor population of the pandemic H1N1 2009 viruses, it has been proposed that G45R mutation might be related to the increased cytokine production observed during infections by these viruses .
We elucidated the function of the non-conserved amino acid, R45, in NS1, which facilitated viral replication by an undefined mechanism. G45R/NS1 does not increase the efficiency of binding to dsRNA or suppress IFNβ induction, which are the established functions of NS1. Thus, increased viral replication of G45R/NS is independent of dsRNA binding and type I IFN induction, suggesting that a non-characterized function of NS1 was responsible for the enhanced viral replication observed in this study. As we have demonstrated that G45R/NS1 virus induced the type I IFN induction and response in infected A549 cells, it is also interesting to investigate virus virulence for further studies.
Human embryonic kidney (293 T), human lung carcinoma (A549) and Mardin-Darby canine kidney (MDCK) cells were cultured in Opti-MEM I reduced serum medium (Gibco, Invitrogen), Kaighn’s Modification of Ham’s F-12 Medium (ATCC) or minimum essential media (Invitrogen), respectively, supplemented with 5 % fetal bovine serum (Invitrogen), L-glutamine (Invitrogen), penicillin and streptomycin (Invitrogen). Murine lung epithelial type I cell line (Let1; wild type or type I IFN receptor null, IFNARnull), kindly provided by Alan Aderem and Alan Diercks , was cultured in Dulbecco’s Modified Eagle Medium (Invitrogen) supplemented with 10 % fetal bovine serum, penicillin and streptomycin. All cells were incubated in a humidified atmosphere of 5 % CO2 at 37 °C.
Construction of plasmids
Two chimeric NS genes—chimera 1 and chimera 2—comprising the 3’UTR and RBD of PR8 NS1 (amino acid 1–73) and the effector domain (ED) (amino acid 74–230) and 5’ UTR derived from IA30 NS1 or vice versa were amplified from plasmids containing full-length NS genes of both strains  using a fusion PCR technique with a pair of specific primers. This strategy was designed to keep the NS2 transcripts intact. To make a single point mutation on NS1 protein of PR8, the NS1 sequences of PR8 and IA30 were compared to determine the different amino acids between the two strains. Four different amino acids on RBD were selected and a single point mutation was introduced into PR8 NS gene using specific primers. Amino acids at position 45, 55, 68 or 70 of PR8 NS1 were replaced with those of IA30. The mutations did not interfere with NS2 expression as they are spliced out to generate the mature mRNA. The dsRNA-binding deficient NS1, R38AK41A (AA) was constructed using similar strategies. The mutated NS genes were digested and inserted into the bidirectional vector pHW2000 .
The RBD (amino acids 1–73) of PR8 NS1 genes were cloned into the pQE80L vector (Qiagen) for protein expression in E. coli strain BL21. The DNA sequences in the positive clones were verified by DNA sequencing (Macrogen, Korea).
Generation of viruses by reverse genetics
The viruses used in this study were generated by transfection using the eight-plasmid reverse genetics system in 293 T and MDCK cells as described previously [20, 42]. The plasmids used were as follows; NS1 from PR8 (WT or mutated PR8 NSs; G45R, K55E, I68V, K70E and AA), HA and NA from X31 or A/Hong Kong/1/1968 (H3N2) and the remaining five genes were from PR8. Briefly, 0.5 μg of each of the eight plasmids were incubated with 12 μl of X-tremeGENE9 transfection reagent (Roche) in 200 μl reaction for 15 min before they were gently overlaid onto a 50:50 293 T-MDCK cell mixture. The transfected cells were cultured in Opti-MEM I reduced serum (Gibco, Invitrogen) containing 1 μg/ml of TPCK-treated trypsin and incubated at 37 °C with 5 % CO2. The reverse genetics viruses were recovered by collecting supernatant at 48–72 hpi, which was then used to inoculate the allantoic cavities of 9-day-old specific pathogen free (SPF) embryonated chicken eggs. The existence of the mutation on each NS1 was confirmed by sequencing.
The rescued viruses with different PR8 NS1 (WT, G45R or AA/NS1s) were used to infect A549 cells grown in 6-well plates in triplicate wells at an MOI of 0.01 or 2. The infected cells were maintained in Kaighn’s Modification of Ham’s F-12 Medium (ATCC) supplemented with 0.3 % BSA (Sigma-Aldrich), penicillin/streptomycin (Invitrogen) plus 1 μg/ml of TPCK-treated trypsin and incubated at 37 °C with 5 % CO2.
The viruses encoding WT, G45R and AA/NS1s were used to infect WT or IFNARnull Let1 cells grown in 6-well plates in triplicate at an MOI of 1 or 1. The numbers of plaque forming units (pfu) in the inoculum were re-examined by plaque assay to confirm the equality of the virus in each inoculum (Additional file 4: Fig. S4). The infected cells were maintained in DMEM (Gibco, Invitrogen) supplemented with 0.3 % BSA (Sigma), penicillin/streptomycin (Gibco, Invitrogen) plus 0.1 μg/ml of TPCK trypsin (Sigma) and incubated at 37 °C with 5 % CO2. The cell supernatants were collected at indicated time points. The viruses collected at each time point were titrated by tissue culture infectious dose (TCID50) assay in MDCK cells and calculated as previously described .
Expression of NS1 RBD
E. coli strain BL21 transformed with pQE plasmids containing the amino acid 1–73 of the RBD of PR8 NS1 including WT or mutants G45R and AA were grown in Luria broth with 100 mg/ml ampicillin (Invitrogen). Protein expression was induced with 0.2 mM IPTG (Invitrogen) at 37 °C for 18 h. The cells were then pelleted by centrifugation at 4000 rpm at 4 °C for 20 min. The cell pellets were mixed well in 30 μl of lysis buffer (1 M Tris, 300 mM NaCl, 1 % Triton X and 1 mM EDTA, pH 8.0). Subsequently, lysozyme and PMSF were added into the mixture at the final concentrations of 0.25 mg/ml and 1 mM, respectively. The mixture was vortex-mixed and incubated on ice for 30 min. The cells suspension was homogenized by sonication followed by centrifugation at 10,000 g at 4 °C for 20 min and the supernatant containing the soluble fraction of RBD NS1 was collected. The proteins were purified using Protino® Ni-TED Resin-gravity-flow column (Macherey-Nagel) under native condition and were then concentrated in a 3 kDa-Centrifugal filter units (Millipore). The presentation of His-RBD NS1 proteins were examined by SDS-PAGE using 15 % acrylamide gels. Western blot analysis was performed using anti-NS1 rabbit hyperimmune serum and goat anti-rabbit IgG-HRP (Millipore) as primary and secondary antibodies, respectively.
dsRNA-protein pull down assay
To generate dsRNA labeled with biotin, the biotinylated sense and antisense single-stranded (ss) RNA were in vitro transcribed. Briefly, the dsDNA template was produced by amplification of a 72 bp DNA fragment using forward and reverse primers containing the promoter sequences for the binding of T7 and T3 RNA polymerases, respectively . The dsDNA fragment was purified using a DNA purification kit (Qiagen) and used as the template to produce biotinylated ssRNA by in vitro transcription using the Biotin RNA Labeling Mix (Roche) plus T7 or T3 RNA polymerase (Promega). The remaining DNA in the in vitro transcription reaction was destroyed by using DNase I (Promega) and the biotinylated ssRNA was purified by using ethanol precipitation method. The purified biotinylated T7- and T3-ssRNA were annealed at room temperature to obtain the biotinylated dsRNA and kept on ice until used in the binding reaction.
To optimize the pull down reaction, various concentrations of biotinylated dsRNA and NS1 RBD were examined in a checker board titration. Additional file 5: Fig. S5 shows an example of the titration results. The optimal condition was selected. In the pull down assay, 0.4 mg of each purified NS1 was incubated with 0.6 μM biotinylated dsRNA in 20 μl of binding buffer containing 50 mM Tris–HCl, pH 8.3, 75 mM KCl, 3 mM MgCl2, 8 % (v/v) glycerol, 0.1 % (v/v) Triton® X-100 (Amresco), 1 mM DTT (Invitrogen), 5 μg yeast tRNA (Roche) and 40 Unit RNase OUT (Invitrogen). The reaction mixtures were incubated at room temperature without agitation for 30 min. After incubation, the dsRNA-NS1 complex was pulled down with NeutraAvidinAgarose Resin (Pierce, Thermo Scientific) by incubation at room temperature for 45 min. The resin was boiled in Lamelli sample buffer (Bio-Rad). The pulled-down protein was separated by using SDS-PAGE in 15 % gel. Western blot was performed by using anti-NS1 rabbit serum and goat-anti rabbit IgG-HRP (Millipore) as primary and secondary antibodies, respectively. The membrane was incubated in Clarity® western ECL substrate (Bio-Rad) for 5 min. The chemiluminescent signal was detected by Fusion® FX imaging analyzer (VilberLourmat).
RIG-I mediated IFNβ-promoter activity assay
The plasmids expressing IFNβ-promoter (−125) firefly luciferase, Renilla Luciferase vector (pRL-TK; Promega), RIG-I and each PR8 NS1 (WT, G45R and AA) were co-transfected into 293 T cells grown in 24-well plate as previously described  with some modifications. Briefly, the indicated plasmids were transfected to the cells using XtremeGene HP transfection reagent (Roche). At 24 h post transfection (pt), the cells were lysed in passive lysis buffer (Invitrogen) and subjected for luciferase activity measurement using dual-luciferase kit following the manufacturer’s instruction (Promega). The firefly luciferase activity signals were normalized to the Renilla luciferase activity. The experiments were done in triplicate. NS1 expression levels in transfected cells were shown by western blot analysis (Additional file 2: Fig. S2).
Quantitative real-time PCR (qRT-PCR)
Total RNA was isolated from A549 cells infected with the rX31 viruses encoding PR8 NS1 (WT and G45R) using Trizol® reagent (Invitrogen) following the manufacturer’s instruction. Total RNA was isolated by using Direct-zol™ RNA MiniPrep (Zymo research). One microgram of total RNA was reverse transcribed using a high-capacity cDNA reverse transcription kit (Applied Biosystem). Realtime PCR was performed by using a 7500 Fast real-time PCR system (Applied Biosystem). In 15 μl reaction, 0.4 mM of forward and reverse primers and equal amount of cDNA were mixed with the SYBR® Select master mix (Applied Biosystem) according to the manufacturer’s protocol. The qRT- PCR cycle were conducted under the following conditions: enzyme activation at 95 °C for 2 min followed by 40 cycles of denaturation at 95 °C for 3 s, annealing and extension at 60 °C for 30 s. Three biological replicates and two technical repeats were performed for each sample. The housekeeping gene, β-actin, was used as a reference control. The data of each sample and negative control (mock infected cells) were normalized to the reference using the threshold cycle (2-∆∆CT ) method .
Mean titers of the viruses at each time point, luciferase activity and relative mRNA expression level were compared and statistically calculated using analysis of variance (ANOVA) and student t-test method. Mean titers of the viruses as TCID50/ml was converted into base-10 logarithms and plotted against time points and a bar corresponding to SEM was demonstrated. A difference was considered significant if the p-value was < 0.05.
This work was supported by Thailand Research Fund (TRF) through the Royal Golden Jubilee Ph.D. Program and Kasetsart University (Grant No. PHD/0153/2552), National Research Council of Thailand (NRCT) (Grant No. Po Ko/2554-36) and the American Lebanese Syrian Associated Charities (ALSAC).
CK designed and performed the experiments and drafted the manuscript. MZ carried out the plaque assay and drafted the manuscript. HH and RW participated in the study design and revised the manuscript. PL supervised the project and revised the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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