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Applied and Environmental Microbiology, December 2005, p. 8881-8887, Vol. 71, No. 12
0099-2240/05/$08.00+0 doi:10.1128/AEM.71.12.8881-8887.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Wen-Lin Lai,1,
Shuen-Fuh Lin,2
Cheng-Sheng Hsu,3
Shwu-Huey Liaw,4* and
Ying-Chieh Tsai1*
Institute of BiochemistryFaculty of Life Science, National Yang-Ming University, Taipei,1 Department of Life Sciences, National University of Kaohsiung, Kaohsiung,2 Center of General Education, National Taipei College of Nursing, Taipei, Taiwan,3 Faculty of Life Science, National Yang-Ming University, Taipei4
Received 10 May 2005/ Accepted 22 August 2005
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GOOX is a monomeric glycoprotein with a covalently linked flavin adenine dinucleotide (FAD) (16). It catalyzes the oxidization of a variety of carbohydrates with concomitant reduction of molecular oxygen to hydrogen peroxide. Screening of 30 monosaccharides and derivatives of these compounds showed that D-glucose is the only good substrate. In terms of the disaccharides, maltose, cellobiose, and lactose with reducing-end glucosyl residues linked by an
bond or ß-1,4 bonds are good substrates, whereas disaccharides containing other linkage types are not. Moreover, GOOX can react with maltooligosaccharides composed of
-1,4-linked D-glucopyranosyl residues (up to at least seven units); hence, the name of this novel oxidase. The broad substrate specificity of GOOX, particularly with oligosaccharides, suggests that it may have great potential applicability.
GOOX shares some substrate specificity with GOX, CDH, and pyranose oxidase (POX), which exhibit significant structural homology (10, 11, 25). Because of the unique catalytic properties and potential industrial use of A. strictum GOOX, in the present study we isolated the native protein for measurement of the kinetic parameters and identification of internal peptide sequences, cloned and expressed the encoding gene, and analyzed the putative flavinylation residue by site-directed mutagenesis.
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TABLE 1. Substrate specificity of native GOOX
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TABLE 2. N-terminal and internal peptide sequences of native GOOX
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F' cells, and selected on an agar plate containing ampicillin (100 µg/ml) and 5-bromo-4-chloro-3-indolyl-ß-D-galactopyranoside (X-Gal). |
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TABLE 3. Oligonucleotide primers used in this study
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Expression and isolation of the recombinant protein.
Primers GOOX-EX1 and GOOX-EX2 (Table 3) were used to amplify the entire GOOX-encoding gene. The 1.5-kb PCR products were cloned into the pPICZ
A vector with fusion of the
-factor signal peptide at the N terminus for efficient secretion into the medium and c-myc and a His6 tag at the C terminus for protein isolation. The plasmid was confirmed by sequencing and was transformed into Pichia pastoris strain KM71 using electroporation. P. pastoris cells were grown in BMGY medium (Invitrogen) at 30°C to an optical density at 600 nm of 2 to 6. The cells were harvested by centrifugation at 1,500 x g for 5 min, and the cell pellets were resuspended in BMMY medium (Invitrogen) using one-fifth the original culture volume. To induce GOOX expression, the cultures were incubated for 2 to 5 days at 30°C with addition of 0.5% methanol every 24 h. The time course of the level of expression was monitored every 24 h using Western blot analysis and an activity assay. Large-scale high-density fermentation was carried out in a 5-liter BioFlo 3000 fermentor (New Brunswick Scientific).
Pichia cells were removed from the culture broth by centrifugation, and the medium was clarified by passage through a Millipore Opticap prefilter. The filtrate was concentrated to about 200 ml with a Millipore Pellicon filter unit and dialyzed against 10 mM Tris-HCl (pH 8.0). Initial attempts to purify the recombinant protein using an Ni-nitrilotriacetic acid (QIAGEN) column failed because this His6-tagged fusion protein did not bind to the resin. The enzyme was then isolated by using a Toyopearyl Phenyl-650 column with a linear 2.5 to 0 M ammonium sulfate gradient in 10 mM Tris-HCl (pH 8.0). The yellow protein fractions were pooled and concentrated by ultrafiltration using Amicon YM30 membranes. The protein concentrations were determined with a Coomassie protein assay kit (Pierce) and SDS-PAGE analysis with Coomassie blue R-250 staining and bovine serum albumin as the standard.
Site-directed mutagenesis.
The primers used for generation of the H70 mutants are listed in Table 3. Site-directed mutagenesis was carried out using a Quick-Change mutagenesis kit (Stratagene). The mismatching primers with the desired mutations were annealed to the pPICZ
A vector containing the GOOX-encoding gene, and Pfu polymerase was used to replicate the whole plasmid. After PCR, wild-type DNA fragments were selectively digested by DpnI (Roche Molecular Biochemicals). The resultant mixture was used for transformation and amplification.
Nucleotide sequence accession number.
The nucleotide sequence determined in this study has been deposited in the GenBank database under accession number AY573966.
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-1,4 bond). However, severe substrate inhibition by cellobiose and lactose was observed. Third, GOOX may possess an open carbohydrate-binding groove similar to that of CDH, so the non-reducing-end glucose residues can stick out into the solvent and be exposed on the protein surface. The crystal structures of GOX and POX have revealed a "size-exclusion mechanism," in which the shape of the active site cavity is such that the enzyme can accept only monosaccharides (11, 25). On the other hand, CDH has an open carbohydrate-binding groove that allows accommodation of longer-chain oligosaccharides (10).
Catalytic mechanism.
After incubation of the substrate maltose with GOOX, the reaction product was first eluted from a thin-layer plate, purified with a µ-Spherogel column (Beckman),and then identified as maltobionic acid using infrared analysis, 13C and 1H nuclear magnetic resonance, and mass spectrometry. The absorption spectrum of the purified native GOOX had two maxima, at 380 nm and 444 nm, which are spectral characteristics typical of the oxidized FAD cofactor (Fig. 1). Addition of the substrate maltose or sodium hydrosulfite to the enzyme solution eliminated the peak at 444 nm, revealing production of the reduced FAD. Thus, like most of the reactions catalyzed by the FAD-dependent oxidases and dehydrogenases (6), the GOOX-catalyzed reaction may consist of two steps: oxidation of the reducing-end glucosyl residue to glucono-1,5-lactone by FAD and regeneration of the oxidized FAD by dioxygen. The glucono-1,5-lactone is then spontaneously hydrolyzed to gluconic acid. The optimal pH for activity of GOOX (pH 10) implies that a tyrosine residue may serve as a general base (16), whereas CDH and GOX utilize a histidine as a proton shuttle and hence the optimal pH is near pH 6 (10, 25). The similar kcat values of various substrates ranging from glucose to maltoheptaose (Table 1) imply that there is similar stereogeometry between the reactive reducing-end C-1 atom and the flavin N-5 atom. In addition to molecular oxygen, it was found that 2,6-dichlorophenol-indophenol can act as an efficient electron acceptor; this is not true of cytochrome c, phenazine methosulfate, or Fe(CN)63. The apparent Km and kcat for 2,6-dichlorophenol-indophenol using 2 mM cellobiose as the electron donor were 0.85 mM and 6.2 min1, respectively.
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FIG. 1. Flavin absorption spectra. The spectra of the native and wild-type recombinant enzymes and the H70Y mutant are indicated by solid, dashed, and dotted lines, respectively. The protein concentration was 2 mg/ml in 20 mM Tris-HCl (pH 8.0). The native and recombinant enzymes had similar spectra with two maxima, at 380 nm and 444 nm; the maximum wavelength was shifted from 380 nm to 400 nm in the H70 mutant.
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Analysis of the deduced amino acid sequence predicted a processing site at the dibasic Lys-Arg sequence, and this resulted in a 474-residue mature protein, which was consistent with the N-terminal sequencing of the native protein. Several probable transcription elements were observed in the promoter region, including one CAAT element at positions 427 to 421, one TATA box at positions 108 to 102, and a Kozak consensus sequence flanking the start codon. One typical short fungal intron (53 bp) was detected in the genomic gene with consensus 5' and 3' splice sites and lariat sequences (GTPuNGPy, PyAG, and NNCTPuAPy, respectively) (12). The deduced molecular mass, 55,234 Da, is apparently less than the value obtained from size exclusion chromatography (
61 kDa) (16). Based on this, a posttranslational modification, such as glycosylation, may be assumed, since three possible Asn glycosylation sites, N305, N341, and N394, were detected.
Recombinant protein.
Expression of the recombinant GOOX in E. coli was not successful, perhaps due to a need forposttranslational modifications. Instead, the gene was expressed in P. pastoris KM71 at 30°C, and the yield was 300 mg per liter medium in a bioreactor with automatic delivery of methanol. An unusually high absorbance at about 320 nm was observed for the freshly isolated protein, and the value decreased with time. This might have been due to the presence of some reduced FAD molecules and/or contaminants from the Pichia culture medium. The flavin absorption spectrum of the native GOOX, at wavelengths ranging from 350 nm to 500 nm, nearly overlaid the spectruma of the recombinant protein, with maxima at 380 nm and 444 nm (Fig. 1). When maltose was used as the substrate, the native GOOX had a Km of 2.47 mM, which was similar to that of the recombinant protein (2.29 mM) (Tables 1 and 4). However, the kcat for the native protein was 531 min1, while that for the recombinant GOOX was 361 min1. These different kcat values may have been due to different protein processing in distinct organisms (A. strictum versus P. pastoris) or to inaccurate measurements of the protein concentrations by the protein dye-binding assay.
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TABLE 4. Kinetic parameters of recombinant wild-type and mutant GOOXa
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FIG.2. Structure-based sequence alignment. The secondary structure elements for ZmCKX are labeled (SS). The protein accession numbers are indicated at the bottom on the right. The numbers of residues present in gaps are indicated in parentheses. The FAD-interacting residues in the known structures are indicted by magenta shading, while residues in the conservative hydrophobic core are indicated by yellow shading. There are four conserved segments in GOOX and related flavoproteins (motifs A to D), and the conserved residues are indicated by cyan shading. The flavinylation sites, Y384 in PpPCMH, H422 in PsVAO, and the consensus histidine in motif A, such as H105 in ZmCKX and H121 in BsCOX2, are indicated by red type and by asterisks. DNRW, MITR, RUBI, and MCRA are involved in the biosynthesis of antitumor antibiotics in Streptomyces; however, their substrates are still not known. Alignment was performed by manual editing based on the structural information and secondary structure prediction. This alignment suggests that the sugar oxidases, including GOOX, CcHEOX, NlNEC5, and HaCHOX, apparently evolved so that they have similar residues for FAD recognition but dissimilar residues for carbohydrate binding.
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There are four conserved motifs (motifs A to D) in the FAD-binding domain (Fig. 2). Motifs A to C are located in theN-terminal portion, whereas motif D is located in the C-terminal tail. Motif A has features similar to those of the "P-loop," which is highly conserved in nearly all nucleotide-binding proteins and is responsible for binding to the pyrophosphate group of the cofactor nucleotide diphosphate moiety (1). Residues in motif B interact with the isoalloxazine ring, the ribitol, and the pyrophosphate group of the cofactor FAD. On the other hand, the last two motifs are near theFAD-binding pocket and form conserved salt bridges, hydrogen bonds, and hydrophobic contacts for structural stabilization. Thus, it is possible to build a structural model for the FAD-binding domain of GOOX based on the ZmCKX structure.
To date, most of the known sugar oxidases and dehydrogenases catalyze carbohydrate oxidation with FAD assistance. One interesting feature of these flavoenzymes is that enzyme function does not correlate with folding topology. For example, GOOX, NlNEC5, HaCHOX, and CcHEOX belong to the PCMH superfamily, whereas GOX, CDH, and POX belong to the glutathione reductase superfamily. Thus, these sugar oxidases provide elegant examples of convergent evolution, where starting from various ancestral folds, the same FAD-assisted carbohydrate oxidation was obtained at distinct active sites. In addition, it is worth noting that even starting from similar structural folds, these sugar oxidases apparently evolved so that they have dissimilar residues for interaction with the common substrates. For example, although GOOX, CcHEOX (9), and HaCHOX (4) all can catalyze the oxidation of glucose, maltose, lactose, and cellobiose and have similar FAD-binding domains, their substrate-binding domains apparently lack conserved carbohydrate-interacting residues (Fig. 2). Thus, it would be difficult to predict the specific carbohydrate-binding residues unless the three-dimensional structures are available.
Distinct flavinylation.
Five different types of autocatalytic flavinylation have been identified: four types via the 8
-methyl group of the isoalloxazine ring cross-linking to His, Tyr, and Cys and one type via the C-6 atom to Cys (20). The crystal structures of ZmCKX and BsCOX2 provide a structure base for covalent attachment of the 8
-methyl group to the N
1 atom of the consensus histidine in motif A (8
-N1-histidyl FAD) (14, 17). In addition, mutational studies have demonstrated that replacement of this histidine with alanine, threnine, or tyrosine in CsTHCAS (H114A), EcBBE (H104T), and AoHDNO (H71Y) can abolish the flavin incorporation, as well as the enzyme activity (13, 19, 24). Unexpectedly, mutation of the corresponding histidine residue in GOOX, H70, to alanine, serine, cysteine, or tyrosine did not eliminate the covalent FAD linkage and had little effect on the Km (Fig. 3 and Table 4).Instead, the H70 mutants displayed kcat values that were 50- to 600-fold lower. The flavin absorption spectrum of wild-type GOOX has two maxima, at 380 nm and 444 nm. When the spectra of the mutants were compared, the maximum wavelength was shifted from 380 nm to 400 nm in the H70 mutants (Fig. 1). These findings indicate that H70 is crucial for efficient redox catalysis, perhaps through modulation of the oxidative power of the FAD cofactor.
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FIG. 3. SDS-PAGE analysis of purified wild-type (WT) and mutant enzymes. The gel was visualized by transillumination at 312 nm (bottom) and then stained with Coomassie brilliant blue R-250 (top). This analysis demonstrated that the FAD cofactor is covalently bound to the H70 variants.
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-methyl group at nonconserved residues H422 (8
-N3-histidyl FAD) and Y384 (8
-O-tyrosyl FAD), respectively (Fig. 1). Thus, GOOX might have a distinct covalent FAD linkage. Attempts to identify the FAD attachment site using mass spectrometry have not been successful so far.
ADDENDUM
While the manuscript was under review, we solved the crystal structure of the recombinant GOOX, and the results revealed the first known double-attachment flavinylation, 6-S-cysteinyl, 8
-N1-histidyl FAD. The FAD cofactor is cross-linked to the enzyme via the C-6 atom and the 8
-methyl group of the isoalloxazine ring with C130 and H70, respectively.
M.-H.L. and W.-L.L. contributed equally to this work. ![]()
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