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Applied and Environmental Microbiology, June 2008, p. 3426-3433, Vol. 74, No. 11
0099-2240/08/$08.00+0 doi:10.1128/AEM.00377-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Centre for Carbohydrate Bioprocessing (CCB), TNO-University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands, and Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
Received 14 February 2008/ Accepted 5 April 2008
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Inulosucrase enzymes (EC 2.4.1.9) are classified in glycoside hydrolase family GH68, along with other bacterial FS enzymes (http://www.cazy.org). Recently, a few mutagenesis studies focused on determining the structure-function relationship among FS enzymes have been published. For instance, modification of residues located at the –1 sugar-binding subsite of inulosucrase from Lactobacillus reuteri 121 strongly affected the size of the products synthesized (32). Mutagenesis of the Bacillus megaterium levansucrase Arg370 and Asn252 amino acids revealed that these residues are crucial for the polymer-versus-oligosaccharide product ratio of the enzyme (16). However, in spite of the availability of two high-resolution three-dimensional (3D) structures of the levansucrase proteins of Bacillus subtilis (24) and Gluconacetobacter diazotrophicus (23), also with sucrose bound in the active site, little is known about the structure-function relationships in these enzymes responsible for the specificity of the glycosidic linkage in the fructan products.
The type of linkages formed in fructans is most certainly based on differences in the identities and positions of specific amino acid residues present in the active sites of FS enzymes. All lactic acid bacteria FSs have a high level of amino acid sequence similarity (>60%), which does not allow straightforward discrimination between inulosucrase and levansucrase proteins (21, 47) by amino acid sequence alignments, as has been done for the identification of residues determining linkage specificity in glucansucrase enzymes (22). Furthermore, no structural information about inulosucrase enzymes is available and only a limited number of inulosucrase enzymes have been characterized. As reviewed in reference 47, levansucrase genes/enzymes from more than 17 species of gram-positive and gram-negative bacteria have been characterized whereas inulosucrase genes/enzymes have only been found in a few species of lactic acid bacteria, namely, Streptococcus mutans (37), Leuconostoc citreum CW28 (29), and L. reuteri 121 (51). An inulin-producing enzyme from Bacillus sp. has also been characterized, but the gene involved has not been identified (53).
The complete genome sequence (2.0 Mb in size) of the probiotic bacterium Lactobacillus johnsonii strain NCC 533 (formerly Lactobacillus acidophilus La1) has been published (35); it encodes a total of 1,821 proteins (5). L. johnsonii strain NCC 533 is a member of the acidophilus group of intestinal lactobacilli that have been extensively studied for their probiotic activities, pathogen inhibition, epithelial cell attachment, and immunomodulation (7, 12-14, 17, 20, 27). The food company Nestlé, which elucidated the genome sequence of the organism, uses it in a yogurt-like dairy product called LC1. According to the company, LC1 strengthens the body's natural defenses and keeps the bowels healthy (11). The published genome sequence of L. johnsonii NCC 533 contains an open reading frame, AAS08734 (GenBank accession no. AE017198), predicted to encode a levansucrase. Here we report a detailed molecular and biochemical characterization of this novel FS from the probiotic species L. johnsonii. We clearly show that L. johnsonii is capable of synthesizing an inulin polymer in situ. Furthermore, it uses open reading frame AAS08734 (GenBank accession no. AE017198), in fact encoding an inulosucrase, to synthesize this inulin.
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Bacterial strains and culturing conditions.
The L. johnsonii NCC 533 strain was obtained from the Nestlé Research Center, Lausanne, Switzerland. For genomic DNA isolation, the cells were cultivated anaerobically at 37°C in MRS medium containing 200 g liter–1 glucose. MRS with sucrose (200 g liter–1) was used for polysaccharide production by L. johnsonii. Escherichia coli TOP10 (Invitrogen) and BL21 Star (DE3) (Invitrogen) were used as hosts for cloning and expression, respectively. E. coli strains were grown at 37°C at 210 rpm in Luria-Bertani (LB) medium supplemented with 50 µg ml–1 ampicillin in order to maintain plasmid integrity. LB agar plates were made by adding 1.5% agar to the LB medium.
Cloning of the inuJ gene.
Total genomic DNA was extracted from L. johnsonii NCC 533 and purified by the method described in reference 52 and modified as described in reference 26. DNA was amplified on a DNA thermal cycler PTC-200 (MJ Research) with high-fidelity DNA polymerase (Fermentas, Germany). L. johnsonii genomic DNA and primers FTF-Lj-F (5'-TATGTCAACCATGGATGTAAAACAAGTTGAAAAGAAAGAC-3', containing an NcoI site [underlined]) and FTF-Lj-R (5'-TATGTCAAGGATCCTTAATGGTGATGGTGATGGTGTTGGTGTGGCTTCAA-3', containing a BamHI site [underlined], a C-terminal His tag [italics], and stop codon [bold]), were used in a PCR to amplify the 5'- and 3'-truncated L. johnsonii FS (ftf) gene. This truncated ftf gene encodes amino acids 144 to 709 of the InuJ protein with a C-terminal His tag (designated InuJ
144-709His). By using the NcoI and BamHI restriction sites, the inuJ amplicon was cloned into expression vector pET15b (Novagen). The resulting vector (pETInuJ) was transformed into E. coli BL21 Star (DE3) for expression studies. Correct construction of the plasmid was confirmed by nucleotide sequence analysis (GATC, Germany).
InuJ expression and purification.
E. coli BL21 harboring pETInuJ was grown overnight in 600 ml LB medium equally divided among three 1-liter Erlenmeyer flasks. The medium was supplemented with 0.1 mM isopropyl-β-D-thiogalactopyranoside (IPTG) to induce protein expression. The cells were harvested by centrifugation at 3,500 x g for 15 min, and the pellet was resuspended in 20 ml binding buffer (20 mM Na2HPO4-NaH2PO4, pH 8.0) containing 5 mM β-mercaptoethanol and 4 mM imidazole. After sonication, the extract was centrifuged (20,000 x g for 20 min) and the protein present in the supernatant was purified to homogeneity by Ni affinity (Sigma) and anion-exchange chromatography (6-ml ResourceQ column; Amersham Pharmacia, Sweden). The purest enzyme fractions (as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) possessing FS activity after anion-exchange chromatography were pooled, dialyzed overnight against sodium acetate buffer (25 mM, pH 5.4), and stored at 4°C for further studies.
Biochemical characterization of the recombinant inulosucrase.
All assays were performed at 55°C and pH 7.0 in Michaelis' barbital sodium acetate buffer (6) unless described otherwise. Purified enzyme (0.45 µg ml–1) was used for biochemical characterization and kinetic studies. One unit of InuJ enzyme activity is defined as the release of 1 µmol of monosaccharide per min from sucrose. Enzyme concentrations were determined with the Bradford reagent (Bio-Rad, Germany) with bovine serum albumin as the standard.
Effects of pH, temperature, CaCl2, and EDTA.
Michaelis' barbital sodium acetate buffer in a pH range of 4 to 8 was used to study the effect of pH on the activity of recombinant InuJ
144-709His. Enzymatic incubations were performed with reaction mixtures containing 200 mM sodium acetate-sodium barbital buffer supplemented with 500 mM sucrose and 1 mM CaCl2. The activity of the enzyme (0.45 µg ml–1) was measured at 50°C. After preincubation of the assay mixture at the assay temperatures for 10 min, reactions were started by enzyme addition. Samples were taken every 3 min and used to determine the amounts of glucose and fructose released from sucrose (48). The amount of glucose formed reflects the total amount of sucrose utilized during the reaction (VG) (total activity). The amount of fructose (VF) formed is a measurement of hydrolytic activity. The transglycosylation activity was calculated by subtracting the amount of free fructose from glucose (VG – VF). The effect of temperature on the enzyme activity was studied in 200 mM sodium acetate-sodium barbital buffer, pH 7.0, supplemented with 500 mM sucrose and 1 mM CaCl2.
To study the effects of calcium ions on enzyme activity, the experiments were initially conducted with buffer without CaCl2 and all of the solutions used were prepared with MilliQ water. However, no differences in InuJ activity were observed in the presence or absence of Ca2+ ions. Therefore, further studies were conducted in the presence of gradually increasing concentrations of EDTA (from 0 to 800 µM) but without addition of CaCl2. Subsequently, the effect of Ca2+ ions (at concentrations of 0 to 800 µM) was studied in the presence of 600 µM EDTA in the reaction medium.
Kinetic parameters.
For the determination of kinetic parameters, activity assays were performed with 0.45 µg ml–1 protein and sucrose concentrations ranging from 5 to 1,000 mM. The Sigma Plot program (version 10.0) was used for curve fitting of the data by using either the standard Michaelis-Menten formula, y = (a x x)/(c + x), or the three-parameter Hill formula, y = (a x x)b/(cb + xb). In these formulas, y is the specific activity (units per milligram), x is the substrate concentration (millimolar sucrose), a is the maximum rate of metabolism (units per milligram), b is the Hill factor, and c is the Km or K50 (millimolar sucrose; Km in the case of Michaelis-Menten-type kinetics; K50 in the case of Hill-type kinetics).
Polysaccharide production and characterization.
The polysaccharide synthesized by L. johnsonii NCC 533 was produced by growing the strain anaerobically in 20 ml of MRS-sucrose medium for 7 days at 37°C. The culture was centrifuged at 4,000 x g for 10 min, and the supernatant was separated from the cells. The supernatant was run on a thin-layer chromatography (TLC) plate (Silica gel 60 F254; Merck, Darmstadt, Germany) overnight with 1-butanol-ethanol-water (5:5:3) as the mobile phase. The plates were air dried, sprayed with a urea developing solution specific for sugars containing fructose (44), and developed at 80°C. In situ L. johnsonii products were degraded by exo-inulinase of Aspergillus niger (Megazyme, Wicklow, Ireland). For this purpose, the exo-inulinase enzyme (final concentration, 10 U ml–1) was added to a mixture of the sample (the supernatant), 0.3 M phosphate buffer (pH 4.5), and MilliQ water (100 µl each). The reaction mixture was incubated at 40°C for 2 h, and 3 µl of this solution was analyzed with a TLC plate as described above.
To produce fructan oligosaccharides and polymer, the purified recombinant inulosucrase (4.5 µg ml–1) was incubated with sucrose (600 mM) at 55°C in Michaelis' barbital sodium acetate buffer (pH 7.0) containing 1 mM CaCl2 and samples were taken at different time intervals. To characterize the oligosaccharide and polymer products formed, 1-µl aliquots from this reaction mixture (diluted four times) were run on TLC plates overnight as described above. The polymer was precipitated from the rest of the reaction mixture with 2 volumes of 96% cold ethanol and separated by centrifugation at 2,500 x g for 15 min. After being dissolved in MilliQ water, the polymer was precipitated (46). This process was repeated two more times, and the polymer was finally freeze-dried. For nuclear magnetic resonance (NMR) spectroscopy, samples were dissolved in 99.9 atom% D2O (Aldrich). One-dimensional 13C NMR spectra were recorded at 125 MHz on a 500-MHz Varian Inova NMR spectrometer at a probe temperature of 80°C. Chemical shifts are expressed in parts per million relative to the methyl group of internal acetone (
= 31.07). Carbon spectra were recorded in 38K data sets, with a spectral width of 30.166 kHz. Prior to Fourier transformation, the time domain data were apodized with an exponential function corresponding to a 0.5-Hz line broadening.
High-pressure anion-exchange chromatography (HPAEC; Dionex, Sunnyvale, CA) was used to separate oligosaccharides produced by incubation of InuJ with sucrose for 48 h at 37°C as described above. Separation of oligosaccharides was achieved as described previously (32), with the following gradient for eluent A: 0 min, 100%; 10 min, 78%; 25 min, 60%; 80 min, 10%; 83 min, 0%; 91 min, 100%. Eluent A was 0.1 M sodium hydroxide, and eluent B was 0.1 M sodium hydroxide in 0.6 M sodium acetate. As the standard, a 1:1 mixture of Raftiline ST-Gel and Raftiline HP (Orafti, Tienen, Belgium) representing chicory inulin was used.
The molecular weight of the inulin was determined by high-performance size exclusion chromatography coupled on line with multiangle laser light scattering (MALLS) and differential refractive index detection (Schambeck SDF). A Dawn-F-DSP (Wyatt Technology, Santa Barbara, CA) He-Ne laser photometer (
= 690 nm) equipped with a K5 flow cell and 18 detectors at angles ranging from 12.8 to 164.7° was used as a MALLS detector. Samples were filtered through a 0.45-µm filter (MILLEX), and the injection volume was 240 µl. NaNO3 (0.1 M) was used as the eluent at a flow rate of 1.0 ml min–1. Pullulan (pss-pulkitL; Polymer Standards Service) and dextran (T2000; Amersham Pharmacia Biotech, Uppsala, Sweden) samples with molecular masses ranging from 4 x 104 to 2 x 106 Da were used as standards.
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Alignments of the amino acid sequence of InuJ with FTF proteins of other lactic acid bacteria revealed the highest similarities to L. reuteri 121 inulosucrase (60% similarity) and L. gasseri FTF (82% similarity); InuJ clustered most closely with the latter in the phylogenetic tree (Fig. 1). The conserved amino acids reported to be involved in catalysis in FS enzymes were all present in the InuJ sequence. From the 3D structure of the B. subtilis levansucrase, residues D86, D247, and E342 have been identified as the catalytic nucleophile, the transition state stabilizer, and the general acid/base catalyst, respectively (24). In L. reuteri 121 inulosucrase, the importance of equivalent amino acids D272, D424, and E523, which correspond to D272, D425, and E524 in InuJ of L. johnsonii, have been proven by site-directed mutagenesis (34).
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FIG. 1. Unrooted phylogenetic tree of FTF proteins from lactic acid bacteria. Proteins: LEV, levansucrase β(2-6); INU, inulosucrase β(2-1); FTF, unknown linkage specificity. Alignments and dendrogram construction were done (with the complete amino acid sequences) by the neighbor-joining method with MEGA4. Bootstrap values (in percentages) are indicated at the branching points. The scale bar corresponds to a genetic distance of 0.1 substitution per position.
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The truncated inuJ gene of 1,724 bp with a C-terminal His tag was successfully cloned into pET15b after amplification with primers FTF-Lj-F and FTF-Lj-R. This truncated gene encodes a recombinant FTF protein (InuJ
144-709His) of 63 kDa that exhibits very high expression levels in E. coli, yielding about 25 mg of His-tagged, purified protein from a 1-liter culture.
Biochemical characterization of the InuJ enzyme. (i) Effects of pH, temperature, and CaCl2 on enzyme activity.
In order to define the best conditions for subsequent kinetic studies, the pH and temperature optima of InuJ, and the influence of Ca2+ ions on InuJ activity were determined. The effect of pH on enzyme activity was studied at 50°C (data not shown). The highest total inulosucrase activity was observed at pH 7.0, with a rapid decrease in activity at higher pH values. More than 85% of the activity was retained in the pH range of 4.5 to 6.0. The pH optima of several related enzymes have been reported previously, i.e., levansucrase of L. sanfranciscensis (optimum pH of 5.4) (43) and the FS enzymes of L. reuteri 121 (pH optima, 4.5 to 5.5) (49). Levansucrase (LevC) of L. mesenteroides exhibited the highest activity in the pH range of 6.5 to 7 (30). InuJ exhibited its maximum transglycosylation activity in a broad pH range of 4.5 to 7.0 (65 to 71%). Maximum hydrolytic activity was also observed in the same pH range, with a peak (29%) at pH 7.0.
The highest total InuJ enzyme activity was found at 55°C, with a drastic decrease at higher temperatures (data not shown). A large part (84%) of this total activity was coming from the transglycosylation activity. Maximum hydrolytic activity (28% of the total activity) was observed at 40°C. Relatively high optimum temperatures have also been reported for the FS enzymes from L. reuteri 121 (50°C) (50), L. sanfranciscensis (35 to 45°C) (43), and Bacillus sp. (60°C) (3). The increased transglycosylation activity observed at higher temperatures may be due to oligosaccharide formation (see below).
Initially, no differences in InuJ activity were observed in the presence or absence of Ca2+ ions. However, the InuJ enzyme activity decreased with increasing EDTA concentrations, with only 5% of the activity remaining at 700 µM EDTA. The enzyme activity was completely recovered upon the addition of 300 µM Ca2+ ions (Fig. 2). This result is in agreement with the proven essential role of calcium ions in FS activity (31). The latter study used site-directed mutagenesis to demonstrate that Asp520 in the inulosucrase of L. reuteri 121 plays an important role in Ca2+ binding. This residue is highly conserved in family GH68 proteins of gram-positive origin. In the 3D structure of B. subtilis levansucrase, the corresponding Asp339 residue is involved in calcium binding (24). In the case of InuJ, the equivalent amino acid residue is Asp521. The data show that the purified InuJ protein contained bound Ca2+ ions, which were scavenged when EDTA was added, thus decreasing enzyme activity. Calcium ions were also found to have a significant effect on enzyme stability. In the absence of EDTA, the enzyme retained 80% of its total activity after incubation at 55°C for 8 h, whereas it completely lost its activity within 3 h of incubation in the presence of 600 µM EDTA (data not shown).
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FIG. 2. Effects of EDTA ( ) and Ca2+ (at 600 µM EDTA) () on InuJ enzyme activity. The reaction was carried out in Michaelis' barbital sodium acetate buffer (pH 7.0) containing 500 mM sucrose. The reaction was started by the addition of 0.45 µg ml–1 enzyme in a 250-µl reaction mixture. The results are presented with the standard error of the mean indicated by vertical bars (n = 3).
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TABLE 1. FTF activities and comparison of the apparent kinetic constants for FTF activity of InuJ 144-709His inulosucrase protein of L. johnsonii at different temperatures and at sucrose concentrations of 5 to 500 mMa
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FIG. 3. TLC analysis of polysaccharides produced by purified recombinant InuJ and growing cells of L. johnsonii NCC 533 after incubation with MRS-sucrose medium at 37°C for 7 days. Lane 1, in situ production of poly- and oligosaccharides by L. johnsonii cells; lane 2, in situ L. johnsonii products degraded by exo-inulinase of A. niger (TLC analysis of recombinant InuJ [0.45 µg ml–1 purified enzyme] products synthesized from sucrose [600 mM] after incubation at 55°C); lanes 3 to 10, samples taken after 5 min, 10 min, 20 min, 30 min, 40 min, 50 min, 60 min, and 17 h of incubation, respectively. ST, standard; Fru, fructose; Suc, sucrose; Kest, kestose; Nyst, nystose; Pol, polymer.
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TABLE 2. Comparison of 13C NMR chemical shift values of fructans produced by lactic acid bacteria
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FIG. 4. HPAEC analysis of the FOS products synthesized by purified recombinant InuJ 144-709His. Solid line, FOS produced by InuJ; dotted line, inulin standards.
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FIG. 5. 13C NMR spectrum of inulin produced by purified recombinant InuJ 144-709His recorded in D2O at 80°C. Chemical shifts are given in parts per million relative to the signal ( = 31.07) of the acetone internal reference.
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As determined by high-performance size exclusion chromatography-MALLS, the average molecular mass of the inulin produced by recombinant InuJ of L. johnsonii was determined as 4 x 107 Da, which is comparable to the molecular masses, 6 x 107 to 9 x 107 Da and 1 x 107 Da, reported for the inulins produced by S. mutans GS-5 (15) and L. reuteri 121 (51), respectively. The polymer also showed a remarkably small polydispersity index (Mw/Mn; where Mw and Mn denote, in grams per mole, the average molar mass by weight and the average molar mass by number, respectively) of 1.05 to 1.17, indicating that there is not much variation in the Mw of polymer chains and they all contain approximately the same number of monosaccharide units.
Conclusions.
Our results unequivocally show that the putative levansucrase gene present in the genome of L. johnsonii NCC 533 actually encodes an inulosucrase enzyme that is responsible for the synthesis of an inulin-type fructan. With our truncation strategy for improved E. coli protein expression, we were able to obtain high yields of pure inulosucrase protein. The InuJ catalytic properties, Ca2+ dependence, and FOS synthesis largely resemble those of the Inu enzyme of L. reuteri 121.
This is only the second Lactobacillus inulosucrase which has been purified and characterized in detail, the first having been reported in L. reuteri 121 (51). The available FS amino acid sequence information does not yet allow straightforward identification of inulosucrase or levansucrase enzymes. Characterization of more inulosucrase sequences, and/or crystallographic information for an inulosucrase protein, may provide this information in the future. The isolation and characterization of the inulosucrase gene/enzyme that we have reported here may be an important step in this direction.
We thank the Nestlé Research Centre, Lausanne, Switzerland, for providing the L. johnsonii NCC 533 strain and Pieter van der Meulen and Klaas Dijkstra (Department of Biophysical Chemistry, University of Groningen) for their excellent technical support in NMR spectroscopy. We also thank Albert Woortman and Peter Sanders (Netherlands Organization for Applied Scientific Research, TNO) for molecular weight determination and FOS analysis by HPAEC. We are grateful to Rachel van der Kaaij and Sander van Leeuwen for their help in the construction of the phylogenetic tree and the interpretation of NMR spectra, respectively.
Published ahead of print on 11 April 2008. ![]()
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