Strains, vectors, media and chemicals
The Aspergillus fresenii (JCM 01963) was purchased from RIKEN BioResource Center, Japan Collection of Microorganisms. Escherichia coli TOP 10 and K. phaffii X-33 (Invitrogen, USA) were used as host strains. The bgl T2-opt gene was synthesized according to the codon bias of K. phaffii and constructed into the pPICZαA vector (Invitrogen, USA) with the EcoRI and Xba I restriction enzyme sites. The p-nitrophenyl-β-D-glucopyranoside (pNPG) was purchased from Sigma (USA). Other chemicals that not specifically mentioned were of analytical grade and were available on commercial supplier.
Enzyme assay
The enzyme activity of β-1, 4-glucosidase was assayed according to the description of Parry et al. [25] with some modifications. Using pNPG as the hydrolytic reaction substrate, the release of p-nitrophenol per minute determined stands for the activity of β-1, 4-glucosidase. The reaction mixture contained 100 μL of pNPG (10 mM) in McIlvaine buffer, 100 μL of enzyme solution. After incubating the reaction mixture for 10 min, the reaction was stopped by adding 800 μL of 1.0 M sodium carbonate. The absorbance of the final reaction solution was read at 405 nm, and the reading was calculated to know the amount of p-nitrophenol generated according to the standard graph which prepared under the same conditions.
One β-1, 4-glucosidase enzyme unit (U) was defined as the amount of β-1, 4-glucosidase that released 1 μmol of p-nitrophenol out of pNPG per minute.
Identification of the β-1, 4-glucosidase bgl T2
The A. fresenii (JCM 01963) was cultured on the induction plate (replace the sucrose in Czapek–Dox medium by Avicel PH-101, Sigma) and control plate (replace the sucrose in Czapek–Dox medium by glucose) for 7 days. The mycelium of the A. fresenii on both plates were collected. Their RNA were extracted and broken down into small fragments. Their cDNA were synthesized by reverse transcriptase reactions using random hexamers and double-stranded DNA were synthesized by polymerase chain reaction (PCR). After purification, selection, and amplification of their double-stranded DNA obtained from mRNA, the library for high throughput sequencing was constructed. The library was sequenced by Illumina Hiseq 4000, PE150. Clean reads were obtained at least 6GB for each treatment and assembled by Trinity [26].
The genomic DNA of A. fresenii was extracted as the template to amplify the bgl T2 gene. The primers designed based upon the assembled mRNA result were bgl T2-F (5’-ATGAAGTTTGGTTGGTTCGAGGCGGCG-3’) and bgl T2-R (5’- TTAAACCACCACGGGCAACGAGCCCTG-3’). The PCR mixture contained 5 μl of 5 × HF buffer, 4 μl of 10 mM dNTPs mix, 0.5 μg of genomic DNA of A. fresenii, 0.5 μL of 10 pmol/μL each primers, and 0.5 U of Phusion DNA polymerase (Thermo Scientific) in a total volume of 50 μL. The conditions and procedures of the bgl T2 gene amplifications were set as following: one initialization step at 98 °C for 5 min, 30 times of the amplification cycles (denaturation at 95 °C for 30 s, annealing at 52 °C for 30 s, extension at 72 °C for 2 min), and one final elongation step at 72 °C for 10 min. The DNA sequencing of amplification products were detected by chain-termination methods [27]. The results were compared within National Center for Biotechnology Information (NCBI) databases as well as the assembled mRNA result for similarity analysis and intron detection.
Once the encoding sequence of bgl T2 was confirmed, its amino acids sequence was also compared within NCBI protein BlastX for the similarity study [28].
Construction of the expression plasmid and strain
The bgl T2 coding sequence (CDS) was optimized according to the code bias of (K.phaffii) and synthesized with a 6×His-tag and a restriction sites of EcoRI at 5’ end while a restriction sites of Xba I at 3’ end. Plasmid of pPICZαA and optimized bgl T2 coding sequence were double digested with EcoRI and Xba I. The digested products were purified and ligated as bgl T2 opt-pPICZαA recombinant plasmid. The recombinant plasmid of bgl T2 opt -pPICZαA were transformed into TOP 10 E. coli competent cells by chemical methods [29]. A zeocin-resistant colony was confirmed by sequencing harboring the recombinant plasmid and used to reproduce the recombinant plasmid. 5 μg of the recombinant plasmid was linearized with Sac I, purified and transformed in K.phaffii X-33 strain by electroporation. The positive expression strains were selected by zeocin-resistance (1000 μg/ml). The recombinant transformant that presented highest β-1, 4-glucosidase activity, called bgl T2-7, was used for enzymatic characters study.
Expression bgl T2 by recombinant K.phaffii X-33 and purification
The recombinant K.phaffii X-33 of bgl T2-7 was inoculated into a 250 ml flask containing 25 ml of buffered glycerol-complex medium (BMGY: 1 % yeast extract, 2 % peptone, 1 % glycerol, 0.1 M potassium phosphate at pH 6, 1.34 % Yeast Nitrogen Base with ammonium sulfate without amino acids, and 4 μg biotin) and incubated at 28 °C with 250 rpm shaking. When the culture reached an OD600 of 4, the yeast was harvested by centrifuging at 3,000 g for 5 min at room temperature. Supernatant was decanted. The cell pellet was re-suspended to an OD600 of 1.0 using buffered methanol-complex medium (BMMY: 1 % yeast extract, 2 % peptone, 0.1 M potassium phosphate at pH 6, 1.34 % Yeast Nitrogen Base with ammonium sulfate without amino acids, 4 μg biotin, and 0.5 % methanol) and the culture was incubated in a 500 mL flask with 2 layers of sterile gauze cover at 28 °C with 250 rpm shaking. 100 % methanol was supplied every 24 hours to maintain a final concentration of 0.5 % methanol to induce expression.
bgl T2 was also expressed in a 5 L fermentation vessel to exam its productivity. After culturing 30mL bgl T2-7 in YPD medium (1 % yeast extract, 2 % peptone, and 2 % dextrose) to an OD600 of 1.0, it was transfered into a 500 mL flask with 250 mL YPD medium and incubated it until its OD600 reached to 2.0 with 250 rpm shaking as the start yeast for the fermentation. For the first 48 h biomass enrichment phase, bgl T2-7 was cultivated in pH 5.5 fermentation medium (5 % glucose, 0.5 % monopotassium phosphate, 0.1 % calcium sulphate, 1.8 % potassium sulphate, 0.8 % magnesium sulphate, 5 % ammonium di-hydrogen phosphate, 0.15 % potassium hydroxide, and 4.5 mL/L trace salt solution[1]) with 350 rpm. Glycerol supplementation was applied when the dissolved oxygen reached to 60 %. Before inducement phase, a hunger period of 2 hours was meant to consume all the carbon sources in the vessel. Methanol was added to keep the dissolved oxygen maintaining at 20 % to 60 % during whole 96 hours inducement phase.
The supernatant of bgl T2-7 fermentation was collected by centrifugation. It was purified by Ni-NTA magnetic beads. The purified bgl T2 enzyme activity was tested and its protein concentration was determined by the BAC protein assays kit (ThermoFisher scientific, USA).
Character study of bgl T2
The expression culture was centrifuged at 12,000 rpm (13,105 g, rcf). Its supernatant was diluted and used for the character study of bgl T2. The optimal pH of bgl T2 was performed every 0.5 pH in a range of pH 2.5 to pH 8.0 with McIlvaine buffer. The optimal temperature of bgl T2 was performed every 5 °C from 25 °C to 80 °C. To test the resistance to different pH, ultra-filtrated bgl T2 was treated in McIlvaine buffer from pH 2.5 to pH 8.0 for one hour, and then diluted 100 times by the Mcllvaine buffer at optimal pH 5.5, while the control bgl T2 was mixed with relative McIlvaine buffer and diluted right before the enzymatic activity residue assay. The thermostability of bgl T2 was tested at five time points to calculate the half-life of bgl T2 under different temperature, 50 °C, 55 °C, 60 °C, and 65 °C. bgl T2 mixed with final concentration of 10mM of sodium sulphate, copper sulphate, calcium chloride, ammonium sulphate, potassium chloride, sodium chloride, magnesium chloride, sodium nitrate, manganese sulphate, zinc sulphate, and cobalt sulphate to understand the effects of those chemicals toward bgl T2 activity. Determining the activity of bgl T2 against 2.5 mM, 2 mM, 1.5 mM, and 1.2 mM pNPG under optimal reaction condition, the Km and Vmax were calculated according to Eadie-Hofstee plots [30].
[1] trace salt solution : 6.0 g CuSO4·5H2O, 0.09 g KI, 3.0 g MnSO4·H2O, 0.2 g Na2MoO4·2H2O, 0.02 g boric acid, 0.5 g CoCl2·6H2O, 20 g ZnCl2, 65 g FeSO4·7H2O, 5 mL sulphuric acid, and 0.2 % biotin.