A highly efficient β-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5
- Hsin-Liang Chen†1,
- Yo-Chia Chen†2,
- Mei-Yeh Jade Lu†1,
- Jui-Jen Chang†1, 3,
- Hiaow-Ting Christine Wang3,
- Huei-Mien Ke1, 7,
- Tzi-Yuan Wang1,
- Sz-Kai Ruan1,
- Tao-Yuan Wang1,
- Kuo-Yen Hung3,
- Hsing-Yi Cho4, 5, 6,
- Wan-Ting Lin6,
- Ming-Che Shih4, 6, 8Email author and
- Wen-Hsiung Li1, 3, 8, 9Email author
© Chen et al; licensee BioMed Central Ltd. 2012
Received: 21 November 2011
Accepted: 19 April 2012
Published: 19 April 2012
Cellulose, which is the most abundant renewable biomass on earth, is a potential bio-resource of alternative energy. The hydrolysis of plant polysaccharides is catalyzed by microbial cellulases, including endo-β-1,4-glucanases, cellobiohydrolases, cellodextrinases, and β-glucosidases. Converting cellobiose by β-glucosidases is the key factor for reducing cellobiose inhibition and enhancing the efficiency of cellulolytic enzymes for cellulosic ethanol production.
In this study, a cDNA encoding β-glucosidase was isolated from the buffalo rumen fungus Neocallimastix patriciarum W5 and is named NpaBGS. It has a length of 2,331 bp with an open reading frame coding for a protein of 776 amino acid residues, corresponding to a theoretical molecular mass of 85.1 kDa and isoelectric point of 4.4. Two GH3 catalytic domains were found at the N and C terminals of NpaBGS by sequence analysis. The cDNA was expressed in Pichia pastoris and after protein purification, the enzyme displayed a specific activity of 34.5 U/mg against cellobiose as the substrate. Enzymatic assays showed that NpaBGS was active on short cello-oligosaccharides from various substrates. A weak activity in carboxymethyl cellulose (CMC) digestion indicated that the enzyme might also have the function of an endoglucanase. The optimal activity was detected at 40°C and pH 5 ~ 6, showing that the enzyme prefers a weak acid condition. Moreover, its activity could be enhanced at 50°C by adding Mg2+ or Mn2+ ions. Interestingly, in simultaneous saccharification and fermentation (SSF) experiments using Saccharomyces cerevisiae BY4741 or Kluyveromyces marxianus KY3 as the fermentation yeast, NpaBGS showed advantages in cell growth, glucose production, and ethanol production over the commercial enzyme Novo 188. Moreover, we showed that the KY3 strain engineered with the NpaNGS gene can utilize 2 % dry napiergrass as the sole carbon source to produce 3.32 mg/ml ethanol when Celluclast 1.5 L was added to the SSF system.
Our characterizations of the novel β-glucosidase NpaBGS revealed that it has a preference of weak acidity for optimal yeast fermentation and an optimal temperature of ~40°C. Since NpaBGS performs better than Novo 188 under the living conditions of fermentation yeasts, it has the potential to be a suitable enzyme for SSF.
KeywordsEndoglucanase β-glucosidase Neocallimastix patriciarum Rumen fungi Simultaneous saccharification and fermentation
Cellulose is the major component in the plant cell wall. It is a linear polymer of polysaccharide consisting of D-glucose units linked by 1,4-β-D-glucosidic bonds. The hydrolysis of plant polysaccharides is catalyzed by microbial cellulases, including endo-β-1,4-glucanases, cellobiohydrolases, cellodextrinases and β-glucosidases . These cellulases are very important in various applications, including saccharification of industrial and agricultural cellulose containing residues, treating cellulose pulp wastes in the paper industry and enhancing the extraction of fermentable substances in the beer brewing and alcohol fermentation industries [2–4]. In the process of cellulose degradation, various endo-β-1,4-glucanases act randomly along the cellulose chains, producing cellulose fragments to generate new sites on which cellodextrinases act to produce cellobiose or oligosaccharides. β-glucosidases then catalyze the hydrolysis of cellobiose and oligosaccharides, which are strong inhibitors of both endo-β-1,4-glucanases and cellodextrinases [5–7]. Thus, converting cellobiose or oligosaccharides to glucose is the key factor for reducing cellobiose inhibition and enhancing the efficient of cellulolytic enzymes [5, 8, 9].
According to the classification by [10, 11], β-glucosidase genes are typically placed into glycosyl hydrolase families 1 and 3 (GH1 and GH3). Generally, the β-glucosidases of bacterial, plant, and mammalian origins that belong to GH1 usually possess a significant level of galactosidase activity in addition to β-glucosidase activity. The other β-glucosidases of fungi, bacteria, and plants are often classified into GH3. The β-glucosidases in both families are known as retaining enzymes because their products retain the same anomeric configuration as the substrate . Their reactions are thought to follow a double-displacement mechanism .
Cellulolytic enzymes from brown- and white-rot fungi have been extensively studied in organisms such as Trichoderma reesei and Phanerochaete chrysosporium[13–16]. It is also known that rumen fungi are able to degrade the most resistant plant cell-wall polymers and therefore are rich sources of fibrolytic enzymes with tremendous potential for industrial and agricultural applications [16–18]. Recently, we reported the transcriptomic and secretomic profiles of the rumen fungus Neocallimastix patriciarum W5 . From the transcriptome, we cloned and expressed a cDNA encoding a β-glucosidase. We call this enzyme NpaBGS and have pursued a detailed characterization in the present study. The protein sequence contains two GH3 domains at the N and C terminals from a domain prediction analysis. In a heterologous expression system, the purified β-glucosidase showed the optimal activity at pH 6 and 40°C and could be significantly enhanced at 50°C by adding Mg2+ or Mn2+ ions. Furthermore, two fermentation yeasts were chosen to assess the potential of NpaBGS for the SSF process.
Results and discussion
Characterization of the β-glucosidase NpaBGS
The cloned NpaBGS cDNA contains 2,331 bp and the deduced amino acid sequence has 776 amino acid residues, with a theoretical molecular mass of 85.1 kDa and isoelectric point of 4.4 (Additional file 1). The cleavage site for the putative signal peptide is located between residues Ala20 and Ile21. Three potential N-glycosylation sites were predicted at residues 51, 223 and 532. Conserved domain prediction suggests that it is a β-glucosidase of the glycosyl hydrolase Family 3 (GH3) carrying a GH3 N-terminal domain (Pfam00933) and a GH3 C-terminal domain (Pfam01915) located at residues 62 ~ 270 and 350 ~ 577, respectively.
Based on amino acid sequences, glucosidases have been classified into several families, with most of the β-glucosidases belonging to either GH1 or GH3[10, 11, 20]. Comparative analyses using BlastX and ExPASy indicated that NpaBGS contains two conserved putative domains of GH3. The aspartic acid residue Asp251 in the conserved domain (GXVMXD) might be the active-site residue of NpaBGS [21–23].
Purification of NpaBGS expressed in Pichia pastoris
Summary of stepwise purification of NpaBGS (β-glucosidase)
Total activity (U)
Total protein (mg)
Specific activity (U/mg)
Recover rate (%)
Ammonium sulfate precipitation
1 st DEAE-Sepharose chromatography
2 nd DEAE-Sepharose chromatography
The evidence from enzymatic assay, bioinformatics and homology modeling studies also strongly suggest that NpaBGS is a member of GH3. In NpaBGS, three putative N-glycosylation sites were found (Additional file 1), but no significant difference was observed between the calculated and the apparent molecular weight on SDS–PAGE using the Pichia expression system (Figure 1). Unlike reported cases of glycosylated β-glycosidases [12, 24], there might be no or little glycosylation on NpaBGS. Furthermore, NpaBGS has also been successfully expressed in Escherichia coli, Bacillus subtilis Kluyveromyces marxianus and K. lactis (data not shown). The enzyme with no or little glycosylation would be easier to express in both eukaryotic and prokaryotic systems, except for species such as S. cerevisiae that have a strong glycosylation mechanism. It will be interesting to do site-directed mutagenesis to study whether any of the three sites are actually glycosylated.
Substrate specificity of NpaBGS
Substrate specificity of purified NpaBGS
Relative activity (%)
Most β-glucosidases can be divided into three groups with respect to their substrate specificity: (a) those that exhibit a high specificity towards aryl β-D-glucosides, (b) those that preferentially hydrolyze cellobiose and cello-oligosaccharides (also known as cellobiases), and (c) those that hydrolyze both types of substrates (i.e., broad-specificity β-glucosidases) . From our experiments, NpaBGS displayed a higher activity on 4-methylumbelliferyl substrates than on cellobiose, demonstrating that NpaBGS has a very high affinity for methylumbelliferyl substrates (Table 2). In addition, NpaBGS hydrolyses CMC (Additional file 2) and MUC (Table 2), suggesting that the enzyme possesses both endo-glucanase and β-glucosidase activities [25–28]. Thus, this enzyme showed a strong β-glucosidase activity and might also possess other cellulase functions.
Effects of different elements on the NpaBGS activity
Effect of metal ions and reducing agents on the activity of purified NpaBGS
control (NpaBGS at 1:100)
According to previous studies, supplementing divalent or trivalent cations is one strategy to increase enzyme reaction efficiency, thermostability or termination reaction. Different levels of inhibitory effect on enzyme activities by metal ions have been reported, especially Cu2+ and Fe2+ for β-glucosidase [24, 29–31]. In a previous study, Ca2+ showed several benefits including protein conformation stabilization, higher affinity for the substrate, and a higher thermostability of an endoglucanase of Clostridium thermocellum. However, Mg2+ and especially Mn2+ showed a stronger enhancement than Ca2+ on the β-glucosidase activity of NpaBGS (Table 3 & Figure 3). In our tests, Al3+, Cu2+ and Fe3+ showed a significant inhibition of NpaBGS activity at 10 mM (Table 3). This indicated that the requirement of free sulfhydryl groups in NpaBGS is similar to those observed in other β-glucosidases . The sequence data also suggested that there are thiol groups presented at the active site that are involved in binding or catalysis, or that such groups are essential for maintaining a proper tertiary structure of the enzyme [34–36]. This is consistent with the suggestion that the cysteine residue is involved in the stability and activity of β-glucosidases . On the other hand, we found the stimulatory effect of ions on NpaBGS (Table 3) as reported in other studies [28, 38]. This stimulation has been regarded as promoting a significant reduction in the binding specificity and/or deactivation of the site .
Performance of NpaBGS in Simultaneous Saccharification and Fermentation
Cellulosic ethanol conversion from napiergrass
For practical applications such as the separate hydrolysis and fermentation (SHF) process, most of the commercial cellulases show a higher efficiency and thermostability at temperatures higher than 40°C . In bio-fuel industry, SSF and simultaneous saccharification and co-fermentation (SSCF) are the two major processes currently used for cellulosic-ethanol production. However, most efficient microbes for ethanol production such as brewer’s yeast live below 40°C. For highly efficient SSF or SSCF, the enzymes should have a large capacity to digest the substrates in order to provide carbon sources for the microbes to grow under the same culture condition. A previously characterized rumen cellulase showed an optimal activity at pH from 4.0 to 7.0 and temperature from 35°C to 50°C . In our experiments, two alcoholic fermentation yeasts were chosen to study the performances of NpaBGS and Novo 188 in SSF at different temperatures. Cell density, glucose concentration and ethanol concentration were used to evaluate the SSF efficiency. Although Novo 188 showed better digestion efficiency and thermostability than NpaBGS at higher temperatures (Figure 2), NpaBGS appeared to be superior to Novo 188 at 40°C. Since 40°C is almost the highest temperature for microbe growth and fermentation, NpaBGS has a potential for a direct application in a bio-reactor system and for CBP.
Although the SSF concept has already been published in many previous studies, most of these studies focused on the enzyme cocktail and the enzyme/substrate blending proportion. Indeed, the related enzyme technology focused on enhancing the thermo-stability or increasing the acid tolerance of the cellulolytic enzymes. In this study, we isolated a new beta-glucosidase and showed that it has advantages over the commercial enzyme Novo 188 in SFF applications and that it can be transformed into a host to replace the use of Novo 188. Since NpaBGS was isolated from one of the best nature SSF system, the buffalo rumen, which undergoes microbial fermentation in 38°C, it may have an advantage for constructing an artificial SSF system for yeast ethanol production. We considered a friendly environment for both host growth and the enzyme reaction. This new concept has the potential to reduce the cost as it requires no external supply of beta-glucosidase and it might improve the efficiency of a bio-process, such as SSF or CBP.
We have successfully cloned and expressed an extracellular β-glucosidase from N. patriciarum W5 and investigated its enzymatic properties. The optimal activity was detected at 40°C and pH 5–6, showing that the enzyme prefers a weak acid condition. Moreover, its activity at 50°C could be enhanced by adding Mg2+ or Mn2+ ions. The enzyme, NpaBGS, showed advantages in cell growth, glucose production, and ethanol production over the commercial enzyme Novo 188 in SSF. In addition, it was also employed with Celluclast 1.5 L to conduct an SSF experiment using dry napiergrass as the sole carbon source. The work presented here is the first study that considers an environment that is friendly for both host growth and the enzyme reaction. This new concept can help to improve the efficiency of bio-process, such as SSF and CBP, and it marks a notion to reassess what has missed in the old industry. Although many different fungal β-glucosidases have been identified and cloned, only a few were derived from rumen fungi. In this study, a novel β-glucosidase, NpaBGS, was isolated from buffalo rumen, which is one of the best natural SSF systems for microorganism fermentation at 38°C, and it is shown to have a good potential for an artificial SSF system for ethanol production. .
Cloning of NpaBGS cDNA
The cDNA of NpaBGS was amplified by PCR using the Platinum Taq DNA Polymerase High Fidelity (Invitrogen, Carlsbad, CA, USA) with the gene-specific primers flanked by restriction site sequences, EcoRI/F1-1 (AATTCATGAAGTTCTCATCTGTTTTATCTACTG), EcoRI/F1-2 (CATGAAGTTCTCATCTGTTTTATCTACTG), XhoI/R1-1 (GTTAGTAAAGTTTGTAAGCTCTCTTC), XhoI/R1-2 (TCGAGTTAGTAAA GTT TGTAAGCTCTCTTC), and PCR products were cloned into the pGEM-T vector (Promega Corp. Madison, WI, USA). The plasmid DNA from a positive clone was digested with Xho I and Eco RI and subcloned in frame with the P. pastoris pPICZ A expression vector. After sequencing confirmation of the NpaBGS cDNA, the recombinant plasmid, pPA-NpaBGS, was used to transform the P. pastoris GS115 (his4) strain (Invitrogen).
Construction of Pichia pastoris recombinant strains expressing NpaBGS
Ten μg of the pPICZA-NpaBGS DNA was linearized with Bgl II and transformed into the yeast P. pastoris GS115 strain by electroporation. A 200 μL aliquot was spread on YPD plates containing 100 μg/mL zeocin and incubated at 30°C. Another aliquot of electroporated cells was spread onto YPD plates containing 1,000 μg/mL zeocin to screen for colonies with high copy insertion. One transformant confirmed for the Mut+ phenotype was scored and grown in 10 mL of BMGY medium. The yeast colony was cultured at 30°C with orbital shaking at 250 rpm for about 20 h until the density reached OD600 of 5.0. The yeast culture was harvested by centrifugation at 2,000 x g for 5 min at room temperature. To induce expression via the AOX1 promoter, the pellet was resuspended in 50 mL of BMMY medium and grown at 30°C with 250 rpm shaking for 5 days, during which methanol was added to the concentration of 0.5 % at 24-hr intervals to maintain induction, and the activity of the culture was examined simultaneously. In order to increase the level of induction, various concentrations of methanol (from 0.5 to 3 %) were also tested.
Purification of recombinant NpaBGS
The yeast broth (4 L) was percolated through filter paper (Toyo Roshi Kaisha, Japan) and concentrated with a stirred ultrafiltration cell (model 8400; Millipore Corp.) equipped with a PM 10 membrane (Millipore Corp., USA) under the nitrogen pressure of 4.0 kg. f/cm2 and dialyzed against 20 mM sodium acetate buffer (pH 5.0). The extracted enzyme was condensated by precipitation at increasing concentrations of ammonium sulfate (0-30 %, 30-50 %, and 50-70 %) at 5°C. The fraction contained better activity and amount of enzyme was found at 50-70 % ammonium sulfate precipitation. The resulting precipitates were collected by cold centrifugation, dissolved in distilled water and dialyzed (0.1 M phosphate buffer, pH 6.0, 48 h, 5°C) to remove excessive salt. The protein (30 mL) was then loaded onto a Toyopearl DEAE-650 S (Tosoh, Japan) column (2.0× 20 cm) and eluted with a step gradient of 0, 200, 300, 400, and 500 mM of NaCl in a volume of 1,000 mL. The fractions showing cellulolytic activity were pooled and concentrated by ultrafiltration, then dialyzed against 50 mM sodium acetate (pH 5.0) containing 0.15 M NaCl. The dialyzed sample (4 mL) was applied to a Sephacryl 300-S HR (GE Healthcare Bio-Sciences AB) column (1.6 × 60 cm) and eluted with the same buffer at a flow rate of 0.5 ml/min. The active fractions were concentrated by ultrafiltration and dialyzed against 20 mM Tris–HCl buffer (pH 8.0) containing 1.5 M (NH4)2SO4. The dialyzed enzyme solution (2.0 mL) was then loaded onto a Resource PHE (Amersham Biosciences, USA) column (1.0 × 1.0 mL) equilibrated with the same buffer containing 1.5 M (NH4)2SO4. The active fractions were eluted with a decreasing linear gradient from 1.5 to 0 M of (NH4)2SO4 in the buffer at a flow rate of 1.0 mL/min. The fractions containing the β-glucosidase activity were further concentrated with an Ultrafree-0.5 centrifugal filter (Millipore Corp., USA), and the purity was checked by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Protein samples were electrophoresed on 12 % (w/v) SDS–PAGE gels and visualized by staining with Coomassie Brilliant Blue R-250 . The molecular weight markers were obtained from Fermentas (USA). Protein concentration was determined using a protein assay kit (Bio-Rad Laboratories Inc., Hercules, California, USA). Native PAGE electrophoresis was carried out similarly by exclusion of SDS from all solutions. Zymogram after native PAGE was performed as described by Feng et al.  and Duan et al. .
Characterization of recombinant NpaBGS enzymatic properties
After optimizing the culture conditions of the P. pastoris recombinant strain for producing NpaBGS, the β-glucosidase activity in the culture medium supernatant was measured. β-glucosidase activity was assayed by adding 10 μl of culture supernatant to 90 μL of 2 % (w ⁄ v) cellobiose (low viscosity), and the amount of glucose assay was carried out according to the manual of Glucose (HK) assay kit (Sigma-Aldrich, USA). One unit (U) of β-glucosidase activity was defined as the amount of 1 μmole glucose released per minute at pH 7.0 under the assay conditions described below. Furthermore, other natural substrates, such as amygdalin, arbutin, larminarin, phenyl-β-D-glucoside, and β-gentiobiose, and substrates, such as 4-methylumbel-liferyl-β-D-cellobioside (MUC), 4-mehtylumbelliferyl-β-D-galactopyronoside (MUG) and 4-methylumbel-liferyl-β-D- glucopyranoside (MUD) were also assayed at in the same condition.
The temperature profile and the optimum temperature of NpaBGS were determined by the activity on cellobiose at 30, 40, 50, and 60°C. The optimum pH was determined using 100 mM buffers: sodium citrate (pH 2.0 and 3.0), sodium acetate (from pH 4.0 to pH 6.0) and Tris–HCl (form pH 6 to pH 9). The thermostability of NpaBGS and the commercial enzyme Novo™ 188 (Novozymes, Bagsvaerd, Denmark) were compared by incubation at 40°C in 100 mM in Tris–HCl buffer (pH 6.0) during a time course and then measured their β-glucosidase activity against cellobiose.
To evaluate the effect on the β-glucosidase activity of metal cations, such as Al3+, Ca2+, Cu2+, Fe3+, Mg2+, Mn2+, and Zn2+, and reducing agents, such as DTT, and β-mercaptoenthanol, these elements were added separately to the standard assay in 100 mM Tris–HCl buffer, pH 6.0, to a final concentration of 1 and 10 mM, respectively.
Efficiency of β-glucosidase in SSF application
S. cerevisiae BY4741 and Kluyveromyces marxianus KY3  were used in SSF experiments to study the effect of different culture temperatures. Both yeasts could grow at 30°C on the solid YPAD medium (1 % yeast extract, 2 % peptone, 24 mg/L adenine hemisulfate, 2 % glucose, and 2 % agar), while separate cultures of K. marxianus KY3 was also examined at 37°C and 40°C for its thermotolerance. First, the two microbes were pre-cultured overnight in YPAD medium and inoculated to initial O.D.600nm 0.1 in 10 ml of fresh YPA medium containing either 2 % glucose or 2 % cellobiose under an aerobic condition. The experimental groups were the YPA medium with 2 % cellobiose and supplemented with an equal unit (2 units) of NpaBGS or Novo™ 188 β-glucosidase in the culture. The growth curve, glucose generation and ethanol production of these cultures were determined at 0, 12, 16, 20, and 24 hrs. The cell density was measured at 600 nm by spectrophotometer (Ultrospec 2100 pro, GE Healthcare Bio-Sciences AB). In a parallel experiment, the SSF experiment was conducted using 2 % dry napiergrass as the sole carbon source, and adding 2 ml of commercial Celluclast 1.5 L in a 50 ml yeast culture at 40°C. In addition, K. marxianus KY3 and KY3-NpaBGS, in which KY3 was transformed with the NpaBGS gene via a commercial expression system (K. lactis Protein Expression Kit, New England Biolabs) , were used in the SSF experiment. Glucose and ethanol assays were performed using Glucose (HK) assay kits and Ethanol Enzymatic BioAnalysis kits (Roche Molecular Biochemicals, Germany) following manufacturer’s procedures.
Simultaneous saccharification and fermentation.
We thank Dr. Huang-Mo Sung and Dr. Andrew H.-J. Wang for advice on experiments and Mr. Shang-Lin Tsai, Mr. Bing-Shi Tsai and Dr. Wen-Yih Jeng for their assistance. This research was supported by funding from National Science Council (NSC 96-3114-P-001-004-Y and NSC 97-3114-P-001-001), Taiwan.
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