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Applied and Environmental Microbiology, December 2005, p. 7955-7960, Vol. 71, No. 12
0099-2240/05/$08.00+0 doi:10.1128/AEM.71.12.7955-7960.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
College of Natural Resources and Life Science, Dong-A University, Busan 604-714,1 Department of Biochemistry and Molecular Biology, College of Oriental Medicine, Dongguk University, Kyung-Pook 780-350, South Korea2
Received 26 March 2005/ Accepted 26 August 2005
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We recently isolated a new bacterium, Citrobacter sp. strain KCTC 18061P, that has a higher decolorization capability than any microorganism reported to date, even at high concentrations of triphenylmethane dyes (1). We have biochemically purified from Citrobacter sp. strain KCTC 18061P and characterized an enzyme that decolorizes triphenylmethane dyes. This enzyme is designated triphenylmethane reductase (TMR) in this paper. We also report the cloning of the gene encoding this enzyme and its heterologous expression in Escherichia coli.
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Purification of TMR.
All purification procedures were carried out at 4°C in 20 mM sodium phosphate buffer (pH 7.0). Frozen cells were suspended in 20 mM sodium phosphate buffer (pH 7.0), disrupted by sonication on ice, and centrifuged at 15,000 x g for 20 min. The supernatant was used as the crude enzyme source for purification and was applied at 1 ml/min to a HiPrep 16/10 Q XL column (Amersham Bioscience, NJ) equilibrated with buffer. After the column was washed with buffer at 1 ml/min, proteins were eluted with a linear gradient of 0 to 0.5 M NaCl in buffer at a flow rate of 1 ml/min. The most enzymatically active fractions were pooled and dialyzed against the same buffer. After solid ammonium sulfate was added to a final concentration of 1 M, the pooled fraction was applied at 1 ml/min to a HiTrap phenyl Sepharose column (Amersham Bioscience) equilibrated with buffer containing 1 M ammonium sulfate. After the column was washed with the same buffer at 1 ml/min, proteins were eluted from the column at a flow rate of 0.5 ml/min with a decreasing linear gradient of 1.0 to 0 M ammonium sulfate. The most active fractions were pooled and dialyzed against the buffer, and the pooled fraction was applied at 1 ml/min to a fast protein liquid chromatography Mono Q HR 5/5 column (Amersham Bioscience) equilibrated with buffer. After the column was washed with buffer at 1 ml/min, proteins were eluted with a linear gradient of 0 to 0.5 M NaCl in buffer at a flow rate of 0.5 ml/min. Active enzyme fractions with a single protein peak were pooled and concentrated by ultrafiltration with a Centricon-YM10 filter (Millipore, MA). The purified enzyme was stored at 20°C until use.
Protein concentrations were determined using the Bio-Rad (Hercules, CA) protein assay kit according to the manufacturer's instructions. Bovine serum albumin was used as the protein standard for the calibration curve.
Enzyme assays.
The standard assay system for TMR comprised 20 mM sodium phosphate buffer (pH 7.0), 20 µM crystal violet, 0.1 mM NADH, and a suitable amount of the enzyme in a total volume of 1 ml. Each reaction was initiated by the addition of the enzyme, and the initial reaction rate was determined by monitoring the decrease in absorbance at 590 nm in the first 2 min in a temperature-controlled cuvette in a 1.0-cm light path at 40°C. Enzyme activity was a linear function of both incubation time and protein concentration. One unit of enzyme activity was defined as the amount that catalyzed the reduction of 1 µmol of crystal violet per min by using a molar absorption coefficient of 110,916 M1 cm1. The corresponding wavelengths and molar absorption coefficients were used when other triphenylmethane or azo dyes were tested in place of crystal violet (see Table 2). To determine the kinetic parameters of the triphenylmethanedyes, their concentrations were varied from 4 to 20 µM, while the concentration of NADH was kept constant at 100 µM. For kinetic studies of NADH and NADPH, their concentrations were varied from 40 to 240 µM. The concentration of basic fuchsin was set at 40 µM. Km and Vmax values were determined by fitting the data to Lineweaver-Burk plots using SWIFT II Applications software (Amersham Bioscience).
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TABLE 2. Substrate specificity and kinetic analysis of the purified TMRa
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Analysis of reaction products.
The presumed product formed from crystal violet or malachite green by purified TMR was analyzed using an Ultrospec 2100 pro spectrophotometer (Amersham Bioscience). An assay mixture containing 20 mM sodium phosphate buffer (pH 7.0), 50 µM crystal violet or malachite green, 0.1 mM NADH, and 0.5 µg of the purified enzyme was incubated at 40°C for various periods. It was extracted with an equal volume of dichloromethane, and the reaction products in the dichloromethane extract were analyzed spectrophotometrically. Product formation was detected by measuring the change in absorbance at the visible wavelength maximum for each dye. The UV-visible spectra of the reaction products were compared with those of authentic leuco crystal violet or leucomalachite green dissolved in dichloromethane and used as standards. Reaction products were also analyzed by thin-layer chromatography (TLC) with Kieselgel 60 F254 (Merck, Darmstadt, Germany), to which 40 µl of dichloromethane extract was applied in a line 2 cm from the bottom of the TLC plate and developed with n-hexane-ethyl acetate (4:6, vol/vol) or propanol-water-glacial acetic acid (90:9:1, vol/vol/vol).
Other methods.
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was performed using 12% polyacrylamide gels according to the method of Laemmli (13). Native PAGE was performed using the same method as for SDS-PAGE, but without SDS. Low-range protein standards and Precision Plus protein standards (Bio-Rad) were used as molecular mass markers for SDS-PAGE and native PAGE, respectively. Activity staining was performed using a crystal violet solution containing NADH. After native PAGE, the gel was placed in a substrate solution containing 73.5 µM crystal violet and 0.1 mM NADH, and this mixture was incubated at 37°C until a clear band developed in the background of the dye-stained gel.
The native molecular mass of the purified enzyme was determined by size exclusion chromatography on a Superdex 200 HR 10/30 column (Amersham Bioscience) that had been equilibrated with 20 mM sodium phosphate buffer (pH 7.0) containing 0.15 M NaCl. The column was calibrated with the following proteins as standards: alcohol dehydrogenase (150 kDa), bovine serum albumin (67 kDa), ovalbumin (43 kDa), carbonic anhydrase (29 kDa), and cytochrome c (12.4 kDa).
Digestion of the purified enzyme by trypsin (Promega, Madison, WI) and the subsequent separation of tryptic fragments by reversed-phase high-performance liquid chromatography (RP-HPLC) were performed as described previously (21). N-terminal and internal amino acid sequences of the purified enzyme were determined with an Applied Biosystems model 492 Procise protein-sequencing system at the Korea Basic Science Institute (Daejon, Korea).
Cloning and DNA sequencing of the TMR gene.
Chromosomal DNA, isolated from Citrobacter sp. strain KCTC 18061P as described previously (15), was used as the template for PCR. PCR conditions were five cycles at 94°C for 40 s, 37°C for 40 s, and 72°C for 1 min. This was followed by 30 cycles at 94°C for 40 s, 55°C for 40 s, and 72°C for 1 min. PCR products were subcloned into the pGEM-T Easy vector (Promega), and their nucleotide sequences were determined. Hybridization and detection were performed using the DIG DNA Labeling and Detection kit (Roche Applied Science, IN) according to the manufacturer's instructions. Clones showing a significant reaction to the probe were selected. Plasmid DNA prepared from these clones was subcloned into the corresponding sites of the pUC119 or pBluescript SK(+) vector and then sequenced. Analysis of sequence data and sequence similarity searches were performed using the BLAST(N) program of the National Center for Biotechnology Information (NCBI).
Expression of the TMR gene in E. coli.
The entire open reading frame (ORF) of TMR was amplified by PCR using Pyrobest DNA polymerase (Takara Biomedicals, Tokyo, Japan). PCR was undertaken with a sense P1 primer that contained a unique NdeI restriction site (underlined) and an ATG initiation codon (boldfaced) (5'-CTCATATGTCAATTGCGGTTACAGGTGCTAC-3') and an antisense P3 primer that contained a unique XhoI restriction site (underlined) (5'-CACTCGAGTTACATTTTCAGGGCTTGTTTTACGG-3'). The amplified gene fragment (0.9 kb) was inserted into the SmaI site of the pUC119 vector, yielding pUTMR. The nucleotide sequence of the inserted fragment was then confirmed by DNA sequencing. The NdeI/XhoI fragment of pUTMR was introduced into the corresponding sites of the pET-29a(+) plasmid, resulting in pET-TMR. Escherichia coli BL21(DE3) cells transformed with pET-TMR were grown in LB medium containing kanamycin (50 µg/ml) at 37°C with shaking. Protein production was induced by addition of 0.5 mM isopropyl-1-thio-ß-D-galactopyranoside (IPTG) when the culture turbidity at 660 nm was 0.8.
Chemicals.
Crystal violet, malachite green, basic fuchsin, brilliant green, bromophenol blue, methyl violet, Congo red, methyl red, leuco crystal violet, leucomalachite green, FAD, NAD, and NADPH were purchased from Sigma (St. Louis, MO). All other chemicals were of reagent grade and were also purchased from Sigma.
Nucleotide sequence accession number.
The nucleotide sequence reported in this paper was deposited in the GenBank database under accession number AY756172.
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TABLE 1. Purification of TMR from Citrobacter sp. strain KCTC 18061P and recombinant E. coli TMR
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FIG. 1. Nondenaturing PAGE (A) and SDS-PAGE (B) of the protein obtained after purification of TMR from Citrobacter sp. strain KCTC 18061P. (A) The sample after the final Superdex 200 HR column chromatography analyzed by native PAGE (lane 1) and activity staining with crystal violet (lane 2). (B) Protein obtained from each purification step was analyzed by SDS-PAGE. Lane 1, 38 µg of protein from crude extract; lane 2, 16 µg of protein from the HiPrep Q XL column step; lane 3, 0.8 µg of protein from the HiTrap phenyl Sepharose column step; lane 4, 0.6 µg of protein from the Mono Q HR column step. Lanes M, marker proteins.
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Identification of the reaction products.
Triphenylmethane dyes such as malachite green and crystal violet are converted to their colorless leuco derivatives by intestinal microflora and several anaerobic bacteria (12, 16). UV-visible spectral analysis showed the disappearance of crystal violet, which has an absorbance maximum at 590 nm, and the concomitant appearance of a product with an absorbance maximum at 260 nm, which is characteristic of authentic leuco crystal violet (Fig. 2). TLC analysis of the reaction products showed that during incubation, the amount of crystal violet in the extract decreased whereas the amount of product increased (Fig. 3). This product comigrated with authentic leuco crystal violet. These results indicate that TMR catalyzes the reduction of crystal violet to leuco crystal violet in the presence of NADH as the electron donor. The reduction of malachite green to its leuco form by TMR was also detected by UV-visible spectral and TLC analyses (data not shown).
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FIG. 2. (Upper panel) Spectral changes observed during conversion of crystal violet to leuco crystal violet by the purified TMR. Spectral changes were recorded after enzymatic reactions for the indicated times (see the key). (Lower panel) The spectrum of authentic leuco crystal violet (20 µM) dissolved in dichloromethane is shown as the standard.
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FIG. 3. Thin-layer chromatogram of the reaction product of crystal violet with TMR. Crystal violet was incubated with the purified enzyme, and the reaction products were sampled at various time points and analyzed by TLC using n-hexane-ethyl acetate (4:6, vol/vol) (A) and propanol-water-glacial acetic acid (90:9:1, vol/vol/vol) (B) as solvents. Lanes L, authentic leuco crystal violet (the standard); lane M, methyl violet dissolved in methanol. Numbers on the right of panel B are as follows (7): 1, N,N',N"-trimethylpararosaniline; 2, N,N,N',N"-tetramethylpararosaniline; 3, N,N,N',N',N"-pentamethylpararosaniline; 4, N,N,N',N',N",N"-hexamethylpararosaniline (crystal violet).
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TABLE 3. Sequences of the N terminus, tryptic peptides, and deduced primers
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Comparative sequence analyses using the BLAST program showed that TMR has 99% identity with the conserved hypothetical protein encoded in the genome sequence of Listeria monocytogenes strain 4b H7858 deposited in the NCBI database (GenBank accession no. ZP_00230411), even though it has no overall sequence similarity to any known protein, including other bacterial reductases. However, the amino acid sequence of the N-terminal region of TMR shows significant similarity to those of pyridine nucleotide-dependent enzymes in that it contains the characteristic motif of three conserved glycines and six conserved hydrophobic residues. The TMR sequence fulfils the 11 criteria for a nucleotide-binding sequence established by Wierenga et al. (25). An exception is the additional residue between the first and second glycines in the fingerprint sequence (GXXGXXG). This additional residue is also present in malate dehydrogenase, UDP-galactose 4-epimerase, and dihydrodipicolinate reductase, the tertiary structures of which are known to contain the classic NADP-binding ß
ß-fold (3, 4, 19). This motif (GXXGXXG) is also found near the N termini of NADPH-dependent enzymes such as azoreductase (5), flavin reductase (18), and phenylcoumaran benzylic ether reductase (9). Moreover, a search of the NCBI conserved-domain database showed that this motif, which corresponds to amino acid residues 7 to 13 in TMR, is fully conserved in the isoflavone reductase family (pfam02716), the predicted nucleotide diphosphate-sugar epimerase family (COG0702), and the putative NADH-flavin reductase family (COG2910). These findings suggest that this motif of TMR is involved in NADP binding to facilitate enzyme activity.
Expression and characterization of TMR in E. coli.
When E. coli BL21(DE3) cells carrying pET-TMR were induced for 3 h with 0.5 mM IPTG at 37°C, TMR activity was detected in the soluble fraction. However, it was not detected in the extracellular or insoluble fractions. Furthermore, a predominant band corresponding to the expected size (31 kDa) of the recombinant enzyme was also observed in the soluble fraction of induced cells (data not shown). The expressed enzyme constituted about 30% of the total soluble proteins in the intracellular fraction. These results indicate that the recombinant enzyme was efficiently overexpressed in a soluble and active form in the cytoplasm of E. coli. The recombinant enzyme was purified from the intracellular fraction of E. coli by using a protocol similar to that used for the native enzyme and was characterized biochemically. The process resulted in 2.7-fold purification over the sonicated extract with 2.7% recovery of total activity; the final specific activity of the purified enzyme was 77 U/mg (Table 1). The recombinant enzyme displayed physical characteristics and kinetic parameters similar to those observed for the native enzyme.
In conclusion, we have described both the first TMR to be characterized from any organism and the first biochemical characterization of an enzyme responsible for the decolorization of triphenylmethane dyes in bacteria. We also report for the first time the molecular cloning and heterogeneous expression of the TMR gene. Moreover, we have succeeded in inducing the overexpression of recombinant TMR with enzymatic properties similar to those of the native enzyme. The availability of abundant quantities of recombinant TMR should permit more-detailed studies of the structure and function of this enzyme. X-ray crystallographic analysis of this enzyme is now in progress using the purified recombinant protein.
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ß-fold in proteins, using an amino acid sequence fingerprint. J. Mol. Biol. 187:101-107.[CrossRef][Medline]
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