2.1. DNA Constructs
2.1.1. Wild-Type HsPUM1-HD (wHsPUM1-HD) and Modified HsPUM1-HD (mHsPUM1-HD)
The complete sequence of Homo sapiens pumilio homolog 1 (NM-014676) was obtained from the GenBank. The nucleotides corresponding to the Pumilio-homology domain of this protein (wHsPUM1-HD; nucleotides 2595 - 3641; amino acids 828 - 1176) were selected, and the exact position of amino acids related to eight repeats was identified. In order to change the sequence specificity of wHsPUM1 - HD from consensus UGUAUAUA to UGGAUAAA, the nucleotides (corresponding to amino acids 12, 13, and 16) were modified, based on the recognition code of PUF proteins.
Briefly, to switch the recognition code of repeat 6 from U to G, Glu-1047, Tyr-1044, and Asn-1043 were substituted with glutamic acid, asparagine, and serine, respectively. In addition, to switch the recognition code of repeat 2 from U to A, Glu-903, Tyr-900, and Asn-899 were substituted with glutamine, asparagine, and cysteine, respectively. The UGGAUAAA sequence is located in HCV IRES stem-loop IIIb (nucleotides 199 - 206).
The wHsPUM1-HD (as the negative control) and mHsPUM1-HD fragments, flanked by restriction sites of NheI and NcoI at 5’ and XhoI at 3’, were synthesized and cloned into pBluescript II SK(+) vector by Biomatik Corporation (Ontario, Canada).
2.1.2. Bicistronic Dual Luciferase Reporter (psiCHECK2-IRES)
The bicistronic dual luciferase reporter construct was modified from psiCHECK2 plasmid (Promega Corporation; Madison, WI, USA), as previously described (
18). The psiCHECK2 plasmid contains two luciferase genes, including Renilla and Firefly luciferases. The Renilla luciferase is expressed through SV40 promoter, while the expression of Firefly luciferase is controlled by HSV TK promoter.
The HCV IRES (genotype 1) DNA sequence (341 nucleotides of 5’UTR, along with the first 36 nucleotides of the core gene and the coding sequence for the first 10 amino acids of Firefly luciferase) to retrieve the original sequence of psiCHECK2 plasmid)], flanked by PmeI and ApaI restriction sites, was synthesized and cloned into pBluescript II SK(+) vector by Biomatik Corporation (Ontario, Canada).
In order to implant the DNA sequence of HCV IRES between two luciferase genes, the psiCHECK2 plasmid was cut with the restriction endonucleases,
PmeI and
ApaI (Roche; Basel, Switzerland) (30 bp downstream of the Firefly luciferase gene) and ligated with the HCV IRES-encoding DNA, which had been cut with the same enzymes. Transcription from the resulting construct led to the production of a bicistronic mRNA in which translation of the first Renilla luciferase is cap-dependent, while translation of the second Firefly luciferase is mediated by HCV IRES (
Figure 2).
Dual-Luciferase Reporter Construct. HCV IRES was Inserted Between Renilla and Firefly Luciferase Genes of psiCHECK-2 Plasmid. The Renilla Luciferase in Bicistronic mRNA is Translated in a Cap-Dependent Manner, While the Firefly Luciferase Translation is HCV IRES-Dependent
2.2. Protein Expression in Prokaryotic Cells
In order to express wHsPUM1-HD and mHsPUM1-HD in prokaryotic cells, the two synthesized fragments were digested with NcoI and XhoI and were ligated into the pET-28b expression plasmid (Novagen Inc., Madison, WI, USA), previously digested with NcoI and XhoI. The wHsPUM1-HD-pET-28b plasmid was used as the negative control. Recombinant plasmids were transformed into BL21(DE3) cells, and protein expression was induced as follows: 20 ml of fresh Lysogeny broth medium was inoculated with 1 ml overnight culture of BL21 (DE3) cells, supplemented with ampicillin, and were grown for additional 2 hours at 37°C. To induce protein expression, 1 mM of isopropyl ß-D1-thiogalactopyranoside (IPTG) (Qiagen; Hilden, Germany) was added to the medium, and the cells were grown for 16 hours at 20°C.
Bacterial pellets were resuspended in sonication buffer (20 mM HEPES pH: 7.5, 300 mM NaCl, 100 mM imidazole, 10% (v/v) glycerol, and 2 mM DTT), supplemented with 1 complete protease inhibitor tablet (Roche; Basel, Switzerland), and lysed by sonication. After centrifugation, presence of the protein in the supernatant was examined by both sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis.
2.3. Pull-Down Assay
In order to analyze the sequence-specific binding of mHsPUM1-HD to its cognate sequence, RNA-protein pull-down assay was performed (
Figure 3). To capture potential RNA-binding protein of interest (mHsPUM1-HD) from cell lysate proteins, two biotinylated RNA baits were designed. To include our target (UGGAUAAA) and control (ACAACAUA) sequences in the middle of a loop, let7i backbone was manipulated. The publicly available MFold software was used to predict the optimal secondary structure of the designed RNA stem-loops. The biotinylated RNA sequences were synthesized by Metabion (Planegg, Germany). These RNA baits were supposed to link the RNA-binding protein of interest to the μMACS Streptavidin MicroBeads (MiltenyiBiotek; Bergisch Gladbach, Germany).
RNA-Protein Pull-Down Assay. Biotinylated RNAs, Attached to Streptavidin Magnetic Beads, were Fixed in a Column Held in a Magnetic Field. The mHsPUM1-HD-Expressing Cells were Lysed and the Cell Lysate Passed Through the Column. Unintended Bound Proteins were Washed and the Potential RNA-Binding Protein of Interest was Eluted by the Addition of 1 M Nacl to Binding/Washing Buffer. All Fractions were Analyzed by Both SDS-PAGE and Western Blot
In brief, the cell lysate (900 μL) was incubated with biotinylated RNAs for 1 hour at 4°C on a rocking platform. Streptavidin MicroBeads (100 μL) were added to the mixture and incubated for additional 15 minutes at room temperature. In order to prepare a μColumn (MiltenyiBiotek), two washing steps were performed with 100 μL of equilibration buffer for protein applications, while the column was held by a μMACS Separator (MiltenyiBiotek).
Subsequently, the whole volume of the binding reaction was added to the column. Four washing steps with 200 μL of the binding buffer (10 mM HEPES pH: 7.0, 50 mM KCl, 10% glycerol, 1 mM EDTA, 1 mM DTT, 0.5% Triton X-100, 0.15 µg/ml yeast tRNA, and RNase inhibitor) were performed to clean-up non-specifically bound proteins. In order to elute the potential RNA-binding protein of interest, 200 μL of binding buffer supplemented with 1M NaCl was applied on the column and all fractions were collected. Then, 20 μL of each fraction was analyzed by 10% SDS-PAGE and Western blot method to detect proteins which were retained by the bait RNAs.
2.4. Western Blot
For this purpose, BL21(DE3) cells were transformed with either pET-28b plasmid, containing mHsPUM1-HD or wHsPUM1-HD gene. Then, the cells were induced with IPTG, lysed by sonication, and resolved in SDS-PAGE. Similarly, human embryonic kidney-293 (HEK-293) cells, cotransfected with reporter and mHsPUM1-HD-expressing plasmids, were lysed and resolved using SDS-PAGE. The lysate was then transferred from the gel onto a nitrocellulose membrane and probed, using anti-His primary antibody (Qiagen; Hilden, Germany) and anti-IgG secondary antibody (Southern Biotech; Birmingham, AL, USA). After washing, the bands were visualized by either 0.05% 3,3’-diaminobenzidine tetrahydrochloride hydrate (DAB) (Sigma-Aldrich; St. Louis, MO, USA) and 0.01% H2O2 or enhanced chemiluminescence western blot detection system (Amersham Biosciences; Little Chalfont, UK).
2.5. Expression in Eukaryotic Cells
In order to express wHsPUM1-HD and mHsPUM1-HD in eukaryotic cells, the synthesized fragments were inserted into the pcDNA3.1+ expression plasmid (Invitrogen; Carlsbad, CA, USA), using NheI and XhoI restriction sites. HEK-293 cells were grown in polystyrene flasks (Orange Scientific; Braine-l’Alleud, Belgium) in Minimum Essential Medium (MEM) (Gibco; Paisley, Scotland), supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin at 37°C plus 5% CO2.
When the cells were 80% - 90% confluent, they were harvested with 0.05% trypsin for transfection. For this purpose, HEK-293 cells were seeded into 96-well plates at a density of 2×104 cells per well the day before transfection. For each well, 1 μg of plasmid DNA was diluted in HEPES-buffered saline (HBS) and mixed with 4.5 μL of linear polyethylenimine 25 (LINPEI 25) (10 μM) (Polysciences; Warrington, PA, USA). After 15 minutes of incubation at room temperature, 40 μL of LINPEI 25/DNA complexes were added to the cells and incubated for 6 hours at 37°C. The cells were then rinsed and supplemented with new medium.
2.6. Dual-Luciferase Reporter Assay
For this assay (
Figure 4), HEK-293 cells were seeded into 96-well plates at a density of 2×10
4 cells per well the day before transfection. For each well, 100-ng reporter plasmid (
psiCHECK2-IRES) and 1000-ng mHsPUM1-HD-expressing plasmid were diluted in HBS buffer, mixed with LINPEI 25, and used for transfection. Co-transfection of wHsPUM1-HD-expressing plasmid or empty pcDNA3.1(+), along with the reporter plasmid, was also used as the negative control. After 24, 48, and 72 hours, the luciferase activity of the transfected cells was determined using dual-luciferase reporter assay system (Promega Corporation; Madison, WI, USA), according to the manufacturer’s instructions.
Dual-Luciferase Reporter Assay. The HEK-293 Cells were Cotransfected with pcDNA3.1-mHsPUM1-HD and psiCHECK2-IRES Reporter Plasmids. Upon Translation, mHsPUM1-HD Can Bind to HCV IRES, Inserted Between Renilla and Firefly Luciferase Genes and inhibits IRES-Dependent Translation of Firefly Luciferase Gene
Briefly, passive lysis buffer (PLB) was added to the cells and incubated at room temperature for 20 minutes on a rocking platform. The lysate was then transferred to white plates (Sigma-Aldrich; St. Louis, MO, USA) and 100 μL of luciferase assay reagent II (LAR-II) was added to each well and mixed. The Firefly luciferase activity was quantified and then the Stop & Glo Reagent was added and mixed. The Renilla luciferase activity was also quantified. The luciferase activity was measured by Synergy 2 Multimode Reader (BioTek Company; Bad Friedrichshall, Germany).
The activity of both Firefly and Renilla luciferases was normalized to non-transfected cells. In addition, the level of each Firefly luciferase activity was normalized to the level of Renilla luciferase activity. The mean Firefly luciferase activity from the cells, cotransfected with pcDNA3.1(+) and reporter plasmids, was set at 100% and used to compare with the mean Firefly luciferase activity from mHsPUM1-HD-expressing cells. Assays were performed in triplicate and repeated at least twice; the results were expressed as mean ± SEM.
2.7. Cytotoxicity Assay in HEK-293 Cells
HEK-293 cells were seeded into 96-well plates at a density of 2×104 cells per well and transfected as described above. At 72 hours after transfection, 15 µL of 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) (Promega Corporation; Madison, WI, USA) solution (5 mg/mL) was added to each well and incubated for 4 hours at 37˚C in 5% CO2. The cells were washed with PBS, and then 100 µL of dimethyl sulphoxide was added to dissolve formazan crystals. The plates were finally measured at a wavelength of 570 nm, using the Anthos 2020 microplate reader (Biochrom Ltd; Cambridge, UK).
2.8. Statistical Analysis
All experiments were performed at least twice (in triplicates), and differences between the mean values were compared using analysis of variance (one-way or two-way ANOVA). Statistical analyses were performed, using GraphPad Prism 6 software. P-values less than 0.05 were considered statistically significant.