Culture and maintenance of Naegleria fowleri
Naegleria fowleri (Carter NF69 strain, ATCC no. 30215) was cultured axenically in Nelsonʼs medium supplemented with 5% fetal bovine serum (FBS; Gibco, Rockville, Maryland, USA) and 1% penicillin/streptomycin at 37 °C [24]. The amoebae were usually sub-cultured every 3 days with the same media and used in this study.
Cloning a gene encoding fowlerstefin
Trophozoites of N. fowleri were collected by centrifugation and rinsed with warm phosphate-buffered saline (PBS, pH 7.4) several times. Total RNAs were isolated by using TRIzol reagent (Invitrogen, Carlsbad, California, USA) according to the manufacturer’s protocols. The purified total RNA was treated with RNase-free DNase (Gibco) to remove any contaminating DNA. The cDNAs were synthesized from the total RNA (2 μg) using a RNA to cDNA EcoDry Premix Kit (Clontech, Mountain View, California, USA) followed by the manufacturer’s instructions. A gene encoding a cysteine protease inhibitor (gene ID: NF0067710) was found by data mining the N. fowleri genomic resource (AmoebaDB, http://amoebadb.org/amoeba/). Fowlerstefin gene was amplified by polymerase chain reaction (PCR) using the primers (5ʹ-ATG AAG AAA ATC ATT CTT GTT GCC TTG-3ʹ and 5ʹ-TTA TCT TCG TTC AGA AAC AGA GAC CAA A-3ʹ) and N. fowleri cDNA. The amplification was carried out with the thermal cycling condition: one cycle of an initial denaturation 95 °C for 5 min, 30 cycles at 95 °C for 1 min, 52 °C for 1 min and 72 °C for 1 min, followed by a final extension step at 72 °C for 10 min. The PCR product was separated by 1.5% agarose gel electrophoresis and the amplified product was purified and ligated into the T&A cloning vector (Real Biotech Corporation, Banqiao City, Taiwan). The ligation mixture was transformed into competent Escherichia coli DH5α cells. Positive clones harboring the appropriate insert were screened by colony PCR. The nucleotide sequence of the insert was determined by automated sequencing. The primary structure of the deduced amino acid sequence was analyzed with DNASTAR (DNASTAR, Madison, WI, USA) and Signal P (http://www.cbs.dtu.dk/services/SignalP/). The phylogenetic tree was constructed using the neighbor-joining method with the MEGA 4 program (http://www.megasoftware.net). The robustness of the nodes were assessed with 1000 bootstrap replications.
Production and purification of recombinant fowlerstefin
To produce recombinant fowlerstefin, a parial gene of fowlerstefin lacking the region encoding signal peptide was amplified by PCR using the following primers: 5ʹ-GGA TCC AGT GTT GTT CCT GGT GGG-3ʹ containing a BamHI site at 5ʹ end and 5ʹ-AAG CTT TTA TCT TCG TTC AGA AAC-3ʹ containing a HindIII site at 5ʹ end. The amplified product was analyzed on 1.5% agarose gel, purified from the gel, ligated into the T&A cloning vector (Real Biotech Corporation) and transformed into E.coli DH5α. The resulting plasmid DNA was digested with BamHI and HindIII, cloned into the corresponding restriction enzyme sites of the pQE-9 expression vector (Qiagen, Hilden, Germany) and transformed into E. coli M15 [pREP4] cells (Qiagen). The E. coli clone was cultured in Luria Bertani broth and the expression of the recombinant protein was induced with 1 mM isopropyl-1-thio-β-D-galactopyranoside (IPTG) at 37 °C for 3 h. The cultured cells were harvested, suspended in native lysis buffer (50 mM NaH2PO4, 300 mM NaCl, 10 mM imidazole, pH 8.0), sonicated on ice and then centrifuged at 4 °C for 30 min at 12,000×g. The recombinant protein was purified by nickel-nitrilotriacetic acid (Ni-NTA) chromatography (Qiagen) according to the protocols provided by the manufacturer. In brief, the recombinant fowlerstefin was eluted with two different elution buffers, buffer 1 (50 mM NaH2PO4, 300 mM NaCl, 100 mM imidazole, pH 8.0) and buffer 2 (50 mM NaH2PO4, 300 mM NaCl, 250 mM imidazole, pH 8.0), to eliminate contamination of non-specific bound proteins. Samples taken at each elution peak were pooled and the purity of the recombinant fowlerstefin was analyzed via 15% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Protein concentration was assayed with PierceTM BCA Protein Assay Kit (Pierce, Rockford, lL, USA). To remove any LPS contamination in the Ni-NTA affinity purified fowlerstefin, the Detoxi-gel endotoxin removing column (Pierce) was used followed by the manufacturer’s protocols. Residual amount of endotoxin was confirmed by Pierce™ LAL Chromogenic Endotoxin Quantitation Kit (Pierce). The residaul amount of endotoxin was less than 0.05 EU when detemined by the chromogenic assay. The LPS-depleted fowlerstefin was filtered with a sterile syringe filter (0.22 μm; Millipore, Billerica, MA, USA) and used for further experiments.
Production of polyclonal antibody for fowlerstefin (anti-fowlerstefin)
Anti-fowlerstefin antibody was produced by immunizing two BALB/c mice intraperitoneally with the purified recombinant fowlerstefin (50 µg) for three times every 2 weeks. The purified recombinant fowlerstefin was mixed with the same volume of Freund’s complete adjuvant (Sigma-Aldrich, St. Louis, MO, USA) for the first immunization and Freund’s incomplete adjuvant (Sigma-Aldrich) for the two booster injections. Two weeks after the final immunization, the mice were sacrificed and their sera were collected. The immunoglobulin G (IgG) fraction was purified with a Protein G-Sepharose (Amersham Biosciences, Piscataway, NJ, USA) according to the manufacturer’s protocols. The specificity of the antibody was confirmed by immunoblot (Additional file 1: Figure S1).
Inhibitory activity of fowlerstefin
The inhibitory activity of fowlerstefin against several cysteine proteases, including human cathepsin B (HCB; Sigma-Aldrich), human cathepsin L (HCL; Sigma-Aldrich), papain (Sigma-Aldrich) and NfCPB-L, was analyzed by assaying the residual enzyme activity after incubation of each enzyme with fowlerstefin. Each enzyme (20 nM) was incubated with different concentrations (0–100 nM) of fowlerstefin in 50 mM sodium phosphate (pH 6.0) for 30 min at 37 °C. The concentration of each enzyme was deretmined by active site titration with transepoxy-succinyl-l-leucylamido(4-guanidino) butane (E-64; Sigma-Aldrich) [25]. Substrate solution was added to the mixture and the residual enzyme activity was assayed by measuring the released fluorescence (excitation at 355 nm; emission at 460 nm) with a Fluoroskan Ascent FL (Thermo Fisher Scientific, Vantaa, Finland). The substrate was benzyloxycarbonyl-L-leucyl-L-arginine 4-methyl-coumaryl-7-amide (Z-LR-MCA; Peptide International, Louisville, KY, USA) and the assay buffers for each enzyme were as follows: HCB and HCL, 50 mM sodium acetate (pH 6.0); papain, 50 mM sodium acetate (pH 5.0); and NfCPB-L, 50 mM sodium acetate (pH 4.5). All assay buffers contained 10 mM dithiothreitol (DTT). Recombinant NfCPB-L was produced using the method described previously [23]. In all assays, E-64 was used as a control inhibitor. All the assays were conducted in triplicate and the mean and standard deviation (SD) were calculated.
pH dependent inhibiton and stability of fowlerstefin
The effect of pH on the inhibitory activity of fowlerstefin was measured by incubating the purified fowlerstefin (20 nM) with the same concentration of HCB, HCL, papain or NfCPB-L in different pH buffers [50 mM sodium acetate (pH 4.0–5.0) or 50 mM sodium phosphate (pH 6.0–7.0)] at 37 °C for 30 min. After incubation, the enzyme activity of each sample was assayed as described above. The thermal stability of fowlerstefin was determined by incubation at different temperatures (37 °C and 95 °C) for 1 to 3 h in 50 mM phosphate buffer (pH 7.0). The samples were cooled on ice for 30 min and the residual inhibitory activity against each enzyme was determined as described above. All the assays were performed in triplicate and the mean and SD values were calculated.
Structural analysis of fowlerstefin
To analyze the native molecular size and structure of fowlerstefin, gel filtration chromatography was performed with a Superdex 200 HR 10/30 column using an Äcta FPLC system (GE Biosciences, Pittsburgh, PA, USA). Purified recombinant fowlerstefin (1 mg) was loaded onto the column and fractions (0.5 ml each) were collected. The collected fractions were separated via SDS-PAGE and their inhibitory activities against NfCPB-L were determined. The column was calibrated with the following molecular weight markers (Sigma-Aldrich): blue dextran (2000 kDa), β-amylase (200 kDa), alcohol dehydrogenase (150 kDa), BSA (66 kDa), carbonic anhydrase (29 kDa), and cytochrome c (12.4 kDa). The Kav value of each protein was calculated based on the equation Kav = (Ve − V0)/(Vt − V0), where Ve is the elution volume of the protein, V0 denotes the elution volume of blue dextran and Vt refers to the total bed volume. The molecular structure of fowlerstefin was further analyzed using electrophoretic methods. Purified recombinant fowlerstefin (20 μg) was electrophoresed in the presence and absence of SDS without heating as described previously [25]. The samples treated as above were analyzed via SDS-PAGE followed by Coomassie blue staining.
Expression profile of fowlerstefin at different developmental stages of N. fowleri
Encystation of N. fowleri trophozoites was induced by incubating the amoebae in encystment medium (120 mM NaCl, 0.03 mM MgCl2, 1 mM NaHPO4, 1 mM KH2PO4, 0.03 mM CaCl2, 0.02 mM FeCl2, pH 6.8) [26]. In brief, N. fowleri trophozoites (approximately 2 × 105 cells) were washed with PBS (pH 7.4) three times and incubated in 6-well plates with 5 ml of encystment medium at 37 °C for 0, 6, 12, 24, 36, 48 or 72 h. The morphological changes of the amoebae at each indicated time were determined using an EVOS® XL Core microscope (Life Technologies, Carlsbad, California, USA). At each time point, amoeba cells were collected, rinsed with PBS several times and the total RNAs were isolated by using TRIzol reagent (Invitrogen) according to the manufacturer’s protocols. The purified total RNA was treated with RNase-free DNase (Gibco) to remove any contaminating DNA. The cDNAs were synthesized from equal amounts of total RNA (1 μg each) using a RNA to cDNA EcoDry Premix Kit (Clontech) according to the manufacturer’s instructions. Reverse transcription PCR (RT-PCR) was performed using specific primers for fowlerstefin, NfCPB and NfCPB-L. Glyceraldehyde 3-phosphate dehydrogenase of N. fowleri (NfGAPDH) was also included as an internal control. The amplified PCR products were analyzed on a 1.5% agarose gel, stained with RedSafe™ Nucleic Acid Staining Solution (Intron Biotechnology, Seongnam, Korea) and visualized under ultraviolet (UV) light. ImageJ (https://imagej.nih.gov/ij/) was used for densitometric analysis. Expression of fowlerstefin was also analyzed by immunoblotting. The lysates of N. foweleri trophozoites and cysts were prepared by repeated freezing-thawing in RIPA Lysis and Extraction buffer (Thermo Fisher Scientific) followed by sonication on ice. The lysate of N. foweleri trophozoites (20 μg) and cysts (20 μg) were separated by 15% SDS-PAGE and transferred electrophoretically onto the nitrocellulose membrane. The membrane was blocked with PBS supplemented with 0.05 Tween 20 (PBST) and 5% skim milk for 1 h and incubated with anti-fowlerstefin (1:1000 dilution in 5% skim milk) at room temperature for 2 h. After several washes with PBST, the membrane was incubated with horseradish peroxidase (HRP)-conjugated anti mouse IgG (Sigma-Aldrich) (1:1000 dilution in 5% skim milk) at room temperature for 2 h. The membrane was washed with PBST several times and immune-reactive bands were detected using the enhanced chemiluminescence (ECL) substrate (Thermo Fisher Scientific).
Localization of fowlerstefin
To analyze the localization of fowlerstefin in the amoebae, immunoblot analysis was performed. The ESP was prepared by incubating N. fowleri trophozoites in PBS for 1 h at 37 °C. After centrifugation at 800×g for 5 min, the supernatant was collected, concentrated and used as the ESP. The N. fowleri lysate was prepared via repeated freezing-thawing of N. fowleri trophozoites. The sample was centrifuged at 20,000×g for 20 min at 4 °C and the supernatant was collected and used as the N. fowleri lysate. The N. fowleri ESP (20 μg) and lysate (20 μg) were separated by SDS-PAGE and transferred electrophoretically onto the nitrocellulose membrane. Immunoblot was carried out with the same protocols described above.
BV-2 cell culture and treatment with recombinant fowlerstefin
The mouse microglia cell line BV-2 was maintained in Dulbecco’s modified Eagle’s medium (DMEM; Welgene, Daegu, Korea) [17]. The experiment was performed by seeding the cells on 6-well dishes (2 × 105 cells/well). Cells were cultured to approximately 70% confluence and a fresh serum-free medium was added for 12 h before lipopolysaccharide (LPS) or fowlerstefin treatment. To determine the non-lethal amounts of fowlerstefin for BV-2 microglial cells, the cell cytotoxicity of different amounts of fowlerstefin was assessed using the CytoTox 96® Non-radioactive cytotoxicity assay kit (Promega, Madison, WI, USA). BV-2 cells (2 × 105 cells/well) cultured in DMEM supplemented with 10% FBS in a 96-well microplate were treated with different concentrations of fowlerstefin (0 to 50 µg/ml) at 37 °C for 24 h. The supernatant was drained from the plate and 50 µl of CytoTox 96® reagent was added to each well. Subsequently, 50 µl of stop solution was added to each well and the reaction was read at 490 nm with a Multiskan FC microplate reader (Thermo Fisher Scientific). No cellular damage was observed when the cells were treated with up to 20 µg/ml of fowlerstefin (Additional file 2: Figure S2) and a final concentration of fowlerstefin (15 µg/ml) was selected for further analysis.
Cytokine array assay
The overall expression profile of diverse cytokines and chemokines in BV-2 cells stimulated with fowlerstefin was analyzed. BV-2 cells were treated with fowlerstefin (15 µg/ml) or PBS for 9 h. The cell culture supernatant was collected by centrifugation at 1000×g for 5 min at 4 °C and analyzed with the Proteome ProfilerTM Mouse Cytokine Array Panel A (R&D systems, Minneapolis, Minnesota, USA) followed by the protocols provided by the manufacturer. The culture supernatant obtained from BV-2 cells treated with PBS was used as a negative control.
RT-PCR for cytokine expressions
To analyze the effect of fowlerstefin on the expression of several major cytokines in BV-2 cell, the cells were stimulated with fowlerstefin (15 µg/ml) for varying time periods (0, 3, 6, 9 and 12 h) and harvested at the indicated time points. The cells were washed with ice-cold PBS and the total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions. The amount of total RNA was quantitated using the DeNovix DS-11 microvolume spectrophotometer (Wilmington, Delaware, USA). Total RNA (1 µg) was reverse-transcribed into cDNA using a RNA to cDNA EcoDry Premix Kit (Clontech) according to the manufacturer’s instructions. The RT reactions were performed for 1 h at 42 °C. Subsequently, PCR was performed using primer sets specific for mouse GAPDH (forward: 5ʹ-ACC ACA GTC CAT GCC ATC AC-3ʹ; reverse: 5ʹ-CAC CAC CCT GTT GCT GTA GCC-3ʹ), mouse TNF (forward: 5ʹ-CAT CTT CTC AAA ATT CGA GTG ACA A-3ʹ; reverse: 5ʹ-TGG GAG TAG ACA AGG TAG AAC CC-3ʹ), mouse IL-6 (forward: 5ʹ-CGG AGA GGA GAC TTC ACA G-3ʹ; reverse: 5ʹ-GGA AAT TGG GGT AGG AAG GA-3ʹ), mouse IL-1α (forward: 5ʹ-ATG GCC AAA GTT CCT GAC TT-3ʹ; reverse: 5ʹ-TGG TCT TCT CCT TGA GCG CT-3ʹ), mouse MIP-2 (forward: 5ʹ-CCA AGG GTT GAC TTC AAG AAC-3ʹ; reverse: 5ʹ-GCG AGG CAC ATC AGG TAC G-3ʹ) and mouse IL-1β (forward: 5ʹ-TGC AGA GTT CCC CAA CTG GTA CAT-3ʹ; reverse: 5ʹ-GTG CTG CCT AAT GTC CCC TTG AAT-3ʹ). The amplified products were separated on a 1.5% agarose gel, stained with RedSafe™ Nucleic Acid Staining Solution (Intron Biotechnology) and were observed under UV light. ImageJ (https://imagej.nih.gov/ij/) was used for densitometric analysis.
Enzyme-linked immunosorbent assay (ELISA)
The production of IL-6 and TNF from BV-2 cells following fowlerstefin stimulation was quantified using the mouse Quantikine IL-6 and TNF ELISA kits (R&D systems). BV-2 cell were treated with fowlerstefin (15 µg/ml) for 0, 3, 6, 9 and 12 h. The culture supernatants were collected at indicated time points and the amount of IL-6 and TNF in the supernatants was measured according to the manufacturer’s protocols. BV-2 cells treated with the PBS and LPS (3 µg/ml) were used as negative and positive controls, respectively.
Mitogen-activated protein kinase (MAPK) signaling pathway analysis
To analyze the proinflammatory signaling pathway induced by fowlerstefin, the effects of MAPK inhibitors on IL-6 and TNF productions in BV-2 cells were analyzed. Inhibitors for p38 (SB203580), c-Jun N-terminal kinase (JNK) (SP600125), extracellular signal-regulated protein kinase (ERK) (U0126), NF-κB (MG132) and AP-1 (SR11302) were used in this study. All inhibitors were purchased from Calbiochem (San Diego, California, USA). BV-2 cells were seeded in 6-well dishes (2 × 105 cells/well) and cultured to approximately 70% confluence. After changing the media with fresh serum-free media, each inhibitor was added to the cells and incubated for 3 h. Fowlerstefin (15 µg/ml) was added to the cells pretreated with each inhibitor followed by incubation for an additional 3 h. BV-2 cells treated with PBS and LPS (3 µg/ml) were used as negative and positive controls, respectively. Cells treated with only fowlerstefin (15 µg/ml) were also included as a control. The cells were washed with ice-cold PBS and the total RNA was isolated using the same protocols described above and reverse-transcribed into cDNA. Changes in IL-6 and TNF expression in the cells were analyzed via PCR as described above. ImageJ (https://imagej.nih.gov/ij/) was used for densitometric analysis. Production of IL-6 and TNF was also comparatively analyzed using the mouse Quantikine IL-6 and TNF ELISA kits (R&D systems).
Statistical analysis
Data were represented as the mean ± SD of three individual assays. Statistical significance was determined by one-way analysis of variance (ANOVA), followed by Dunnett’s post hoc test comparing all the concentrations with the control using GraphPad Prism 7 (GraphPad Software, San Diego, CA). Differences in mean values were considered statistically significant when the P-value was less than 0.05.