Cells and viruses.
MDBK cells were stored in our laboratory and cultured in RPMI-1640 containing 10% fetal bovine serum (cell-box, AUS-01S-02-S). The AV303 strain (NCP type) was purchased from the China Veterinary Culture Collection Center and preserved by our laboratory.
Proteomic sequencing and analysis.
The protein was extracted using the SDT lysis method (4% (w/v) SDS, 100 mM Tris/HCl pH 7.6, 0.1 M DTT) and then quantified using the BCA method. An appropriate amount of protein was extracted from each sample, and the filter-aided protein preparation (FASP) method was used for trypsin hydrolysis. 18 cartridges were used to desalinate the peptide segments. After freeze-drying, 40 µL of 0.1% formic acid solution was added for reconstitution, and the peptide segments (OD280) were quantified. Peptide segments (100 µg) from each sample were labeled according to the instructions of the Thermo TMT labeling kit. Each group contained 3 biological replicates, for a total of 6 samples. The labeled peptides were fractionated with a high-pH reversed-phase peptide fractionation kit (Thermo Scientific). The dried peptide mixture was reconstituted and acidified with 0.1% TFA solution and loaded onto an equilibrated, high-pH, reversed-phase fractionation spin column. Peptides are bound to the hydrophobic resin under aqueous conditions and desalted by washing the column with water via low-speed centrifugation. A step gradient of increasing acetonitrile concentrations in a volatile high-pH elution solution is then applied to the columns to elute bound peptides into 10 different fractions collected by centrifugation. The collected fractions were desalted on C18 cartridges (EmporeTM SPE cartridges C18 (standard density), bed I.D. 7 mm, Volume 3 ml, Sigma) and concentrated by vacuum centrifugation. Each sample was separated via an easy nLC HPLC system with a nanoliter flow rate. The chromatographic column was equilibrated with 95% A solution, and the sample was loaded onto a loading column (Thermo Scientific Acclaim PepMap100, 100 µm * 2 cm, nanoViper C18) via an automatic sampler. The sample was then separated on an analytical column (Thermo Scientific EASY column, 10 cm, ID 75 µm, 3 µm, C18-A2) at a flow rate of 300 nL/min. After chromatographic separation, the sample was analyzed via mass spectrometry using a Q Exactive mass spectrometer. The detection method was positive ion mode, with a scanning range of 300–1800 m/z for parent ions, a primary mass spectrometry resolution of 70000 at 200 m/z, an automatic gain control (AGC) target of 1e6, a maximum internal time (IT) of 50 ms, and a dynamic exclusion time of 60.0 s. The mass-charge ratios of the peptides and peptide fragments were determined using the following method: 20 fragment spectra (MS2 scan) were collected after each full scan, with an MS2 activation type HCD isolation window of 2 m/z, a secondary mass spectrometry resolution of 17500 at 200 m/z, a normalized collision energy of 30 eV, and an underwater energy of 0.1%. The raw data used for mass spectrometry analysis were RAW files, and the software programs Mascot 2.2 and Proteome Discoverer 1.4 were used for inventory identification and quantitative analysis, including principal component analysis (PCA), partial least square discriminant analysis (PLS-DA), univariate analysis, and pathway analysis. For metabolomics analysis, multivariate statistical analyses such as PCA and PLS-DA and univariate statistical analyses (Student’s t test, Mann–Whitney-Wilcoxon U test, analysis of variance [ANOVA], and correlation analysis) were performed.
Cell proliferation assay.
Adherent cells and cell suspensions after virus infection were treated using the BeyoClick™ EdU Cell Proliferation Kit with Alexa Fluor 594 and observed using a confocal fluorescence microscope (Ningbo Sunny RX50RFL) and flow cytometry (Thermo CytoFLEX).
Total RNA was extracted, and real-time quantitative reverse transcription PCR (RT‒qPCR) was performed.
The cells were lysed using RNAiso Plus (Takara, Kyoto, Japan). Cell RNA was extracted using reagents, including chloroform, isopropanol, and absolute ethanol, with shaking and centrifugation according to the manufacturer's protocol. One percent gel electrophoresis was used to verify the integrity of the RNA, after which the RNA was reverse transcribed to cDNA using EasyScript® One-Step gDNA Removal and cDNA Synthesis SuperMix. The quantitative detection of mRNA was performed using a real-time PCR instrument (qTOWER3G, Analytik Jena) with a program set at 94°C/5 min, 94°C/30 s→ 60°C/30 s × 35 cycles. The following primers (Table 1A) were designed in NCBI (National Center for Biotechnology Information) and Primer3 Input 4.0 and synthesized by Sango, and detection was performed using MCE (MedChemExpress) qPCR Master Mix and YBR Green qPCR Master Mix (Universal).
Assessment of autophagy flux.
The cells were seeded onto slides and transfected at a density of 50–70% using the lentiviral vector Mchery EGFP-LC, purchased from HanBio Technology (Shanghai, China). The principle is based on the stability of two fluorescent environments with different pH values. When autophagosomes are formed both green and red fluorescence can be detected, and autophagosomes can be observed as yellow fluorescence. However, when autophagosomes are formed and the pH is acidic, and GFP fluorescence is quenched, only red fluorescence can be observed. Therefore, when both red dot fluorescence (mCherry) and green dot fluorescence (GFP) increase, this indicates an increase in autophagy flux.
Western blotting.
Adherent cells were lysed with RIPA protein lysis buffer (Solarbio), and their concentrations were determined and normalized using a BCA protein quantification kit (Shanghai Yaenzyme Biotechnology). The extracted protein was added to the sample buffer in equal proportions, and the SDS‒PAGE mixture was prepared for electrophoresis with a Bio-Rad electrophoresis-transfer device and a PVDF membrane for transfer. The membrane was subsequently placed in commercial rapid blocking solution (Shanghai Yazyme) for 15 min, after which the primary antibodies were incubated at 4°C overnight. The following primary antibodies were used: BVDV E2 mAb (rabbit, VMRD P130715), ATG5 (rabbit, Abcam Cat#ab228668), LC3B (rabbit, Abcam Cat#ab48394), nucleoprin p62 (rabbit, Abcam Cat#ab96134), Akt (rabbit, Abcam Cat#ab8805), Akt (S473) (rabbit, Abcam Cat#ab81283), mTOR (rabbit, Abcam Cat#ab32028), mTOR (phospho S2448) (rabbit, Abcam Cat#ab109268), MyD88 (rabbit, Proteintech Cat#23230-1-AP), TLR7 (rabbit, cst Cat#5632), IRF3 (rabbit, HUABIO Cat#ET1612-14), IRF7 (rabbit, ABclonal Cat#A0159), and ERK1/2 (rabbit, ABclonal, The samples were subsequently rinsed with TBST 3‒5 times for 10 min and incubated with the secondary antibody at room temperature for 1‒2 h after aspiration. The secondary antibodies used were goat anti-rabbit IgG H&L (Bioss, bs-80295G-HRP) and goat anti-mouse IgG H&L (Bioss, bs-0296G-HRP).
Immunofluorescence.
After cells are infected by viruses, the cells were fixed with 4% paraformaldehyde, permeabilized with 0.2% Triton X-100 and PBST (PBS + 0.1% Twenn20) supplemented with 1% BSA, and incubated with the Alexa Fluor-conjugated primary antibody in a wet cassette for 1 h, followed by incubation with the secondary antibody for 1 h at room temperature in the dark, and incubation for 5–10 min with the nuclear dye Hoechst. Mounting medium was used to mount and observe the samples under a fluorescence microscope.
Transfection by Electroporation.
RNA oligonucleotides were synthesized by GenePharma. The sequences for the Si MyD88 oligonucleotides are as follows (5' to 3'): Sense: CUUGACGAAUACCUGCAATT; Antisense: UUGCAGGUAUUCGUCAGAGTT. The sequences for the NC (negative control) oligonucleotides were as follows: sense: UUCUCCGAACGUCACGUTT; antisense: ACGUGACACGUUCGGAGAATT. Cells that had been passaged normally were cultivated to 80% confluence. Next, the cells were trypsinized, centrifuged, and washed three times with serum-free medium. The cells were then resuspended in electrophoresis buffer. For electroporation, 10 µL of NC or Si MyD88 plasmids were added to each 200 µL of cell suspension, which was then transferred into an electrode cup. The electroporation instrument was set to deliver a 900 V square wave. After electroporation, the cell suspensions were transferred to a six-well cell culture plate and stabilized by the addition of 5% fetal bovine serum. The cells were then incubated for 6 hours.
Transmission electron microscopy.
Discard the culture medium from the cell culture well plate (cell density not greater than 80%) then trypsin and medium were added to obtain a cell suspension, which was aspirated into a centrifuge tube and centrifuged at low speed (no more than 3000 rpm) for approximately 3–5 min. The supernatant was discarded, electron microscope fixative solution was added (the fixative solution needed to be restored to room temperature in advance), and the cell mass was removed and resuspended. The mixture was fixed at room temperature in the dark for 30 min, transferred to 4°C for storage, and transferred to Wuhan Saiwei Biotechnology Co., Ltd., for imaging.
Statistical analysis.
GraphPad Prism version 8.0 (GraphPad software) was used for statistical analysis. All data are presented as means ± SDs, and p < 0.05 was considered to indicate a statistically significant difference. All the samples were analyzed in triplicate. Proteomics uses Fisher's exact test to compare the distribution of various GO classifications (or KEGG pathways or domains) in the target protein set and overall protein set and performs GO annotation or KEGG pathway enrichment analysis on the target protein set.