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Applied and Environmental Microbiology, February 2005, p. 621-628, Vol. 71, No. 2
0099-2240/05/$08.00+0 doi:10.1128/AEM.71.2.621-628.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Cheng-Ying Jiang,1,
Qunxin She,2
Shuang-Jiang Liu,1* and
Pei-Jin Zhou1
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China,1 Institute of Molecular Biology, University of Copenhagen, Copenhagen, Denmark2
Received 11 July 2004/ Accepted 15 September 2004
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Studies of the native and recombinant SORs of Acidianus spp. revealed that they are distinctive in several respects. (i) Unlike the SOX enzyme complex with heterologous subunits, the SORs are homoenzymes consisting of identical subunits of
35-kDa peptides (14, 16, 26). (ii) Sulfide, sulfite, and thiosulfate are concomitantly produced during the oxidation of elemental sulfur catalyzed by SORs (5[S] + O2 + 4OH
HSO3 + S2O32 + 2HS + H+); however, thiosulfate is produced only from a spontaneous reaction of sulfite and elemental sulfur. (iii) Cofactors or external electron donors and acceptors for sulfur reduction were not required, and the two enzymatic activities (oxygenase and reductase) could not be separated. As SOR was the only elemental sulfur-oxidizing enzyme found in A. ambivalens, it was assumed that the enzyme catalyzes the initial step of the sulfur-oxidizing pathway in this organism. The structure and function of this type of enzyme, as well as its relationships, are largely unknown.
We have developed a system to actively express the sor gene of A. tengchongensis in Escherichia coli cells and have established a simple procedure to efficiently purify the SOR protein from E. coli cells (10, 26). These developments have allowed us to circumvent the difficulties in the genetic manipulation of, and SOR purification from, an acidothermophilic archaeon like Acidianus. In this study, we conducted site-directed mutagenesis of all cysteine residues of the A. tengchongensis SOR protein and established that all of the cysteine residues are very important to SOR activities. Furthermore, the cooccurrence of SOR activities and the other sulfur-metabolizing enzymes on the cytoplasmic membrane suggests that these enzymatic reactions may be coupled on the membrane.
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Cultivation, growth media, and determination of cell growth.
All E. coli strains (Table 1) were cultivated in Luria-Bertani (LB) broth or on LB agar at 37°C unless otherwise indicated, and ampicillin was added to 100 µg ml1 when applicable. A. tengchongensis was grown at 70°C in Allen's medium (1). The growth of cells was estimated either by monitoring the increase in optical density at 600-nm wavelength or by determining the increase in the protein contents of cultures.
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TABLE 1. Bacterial strains, plasmids, and primers used in this study
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Overexpression and purification of SOR and mutant proteins in Escherichia coli.
E. coli strain HB101 was used as the host for overexpressing the A. tengchongensis sor gene and mutated sor genes. The E. coli strain containing a plasmid carrying the wild-type or a mutated sor gene was cultivated in 500-ml flasks filled with 200 ml of LB medium and supplemented with ampicillin to 100 µg ml1. Cultivation was carried out with shaking at 250 rpm at 30°C. When they had grown to an optical density at 600 nm of 0.6, the cultures were shifted from 30 to 42°C to induce protein synthesis. The cells were harvested by centrifugation after 8 h of induction, and the cell pellets obtained were stored at 70°C until they were used.
At the time of SOR protein purification, a 140-ml Superdex 200 gel filtration column was packed in our laboratory and preequilibrated with buffer B (10 mM KH2PO4-K2HPO4 buffer, pH 7.4). Crude cellular extract was prepared from the stored E. coli cells as described previously (10), and 1.4 ml of the crude cellular extract was incubated at 70°C for 10 min to denature E. coli heat-labile proteins, which were subsequently removed by centrifugation. The resulting supernatant was applied onto the Superdex 200 gel filtration column and fractionated using buffer B at a flow rate of 0.6 ml min1. Fractions were collected at 0.6 ml per tube and assayed for SOR activity. Those that possessed SOR activity were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis for homogeneity. During the purification of the SOR mutant proteins (no SOR activity), the collected fractions were first analyzed by SDS-PAGE to check for the presence of SOR mutant proteins. The mutant SORs were subsequently confirmed by immunoblot analysis with SOR-specific antibody. The purified proteins were concentrated by ultrafiltration with an Amicon Ultra-15 (100 kDa) and stored at 20°C.
SDS-PAGE and Western blotting.
Proteins in fractions from chromatography were separated through SDS-PAGE (15% polyacrylamide) according to the method of Laemmli (18) and were visualized by staining them with Coomassie brilliant blue R-250. Western blotting was performed according to the method of Liu et al. (19). SOR, SOR mutant enzymes, and bovine serum albumin (negative control) were transferred from a gel onto a nitrocellulose membrane. The SOR proteins were then detected by a method described previously, using the antiserum raised against SOR in rabbits (26).
Enzymatic activity assays.
The oxygenase activity of SOR was determined as described by Kletzin (16), except that the assays were conducted at 70°C (26). One unit is defined as the amount of enzyme required for the formation of 1 µmol of sulfite plus thiosulfate per min. Concentrations of SO32 and S2O32 were determined by basic fuchsin and methylene blue through colorimetry, respectively (16). The activities of sulfite:acceptor oxidoreductase (SAOR) and thiosulfate:acceptor oxidoreductase (TAOR) were determined as described previously (13, 28).
Effects of chemicals on SOR activity.
N-Ethylmaleimide (NEM), glutathione (GSH), dithiothreitol (DTT), EDTA, MgCl2, ZnCl2, CuCl2, CoCl2, NiCl2, and MnCl2 were added to the enzyme-buffer assay mixture and incubated for 15 min at room temperature. The enzymatic reaction was then started by raising the temperature to 70°C. The reactions without any chemical added and the reactions without the SOR enzyme added were run in parallel as double controls.
Protein concentration assay.
The protein concentration was determined using a bicinchoninic acid protein assay kit following the instructions of the manufacturer.
Preparation of cellular fractions by centrifugation.
Cells of A. tengchongensis were harvested by centrifugation at 5,000 x g for 15 min at room temperature. The cell pellets were suspended in distilled water with the pH adjusted to 7.5 with 1 M potassium phosphate buffer. Crude cell lysates were generated by sonication, and cell debris was removed by centrifugation at 12,000 x g for 20 min at 4°C. The resulting supernatant was then centrifuged at 120,000 x g for 5 h at 4°C, yielding the cytoplasm fraction (clear supernatant) and the pellet containing the membrane fraction. To avoid any possible contamination by the cytoplasm fraction, the pellet was washed twice with distilled water and finally suspended in 0.1 M potassium phosphate buffer (pH 7.5) to yield the membrane fraction.
Localization of SOR at subcellular level by immunogold electron microscopy.
SOR-specific antibody was raised in rabbits as described previously (26). Colloidal-gold (particle diameter, 10 nm)-cross-linked secondary antibody (goat anti-rabbit serum) was purchased from Sigma. A transmission electron microscope (TEM) and a scanning electron microscope (SEM) were used. The preparation of cells for immunogold TEM and SEM observation was conducted according to a method described previously (6) and the operating instructions for the Critical Point Dryer CPD030 (BAL-TEC Inc., Balzers, Liechtenstein), respectively.
CD measurements and secondary-structure analysis.
The circular-dichroism (CD) spectra of wild and mutant SORs between 190 and 260 nm were acquired at 70°C in a 1-mm-path-length quartz cell with a JASCO model J-715 spectropolarimeter under the following conditions: response time, 2 s; scan speed, 20 nm min1; 0.1-nm data acquisition interval; four accumulations; 2-nm bandwidth; and 100 µg of SOR proteins ml1 in buffer B (see above). The CD spectra were analyzed with the K2D and CDPro software packages, including SELCON3, CONTINLL, CDSSTR, and CLUSTER for determining the secondary-structure and tertiary-structure classes (2, 24, 25).
Determination of fluorescence spectroscopy.
The intrinsic fluorescence spectra of wild and mutated SORs were detected with a HITACHI Model F-2500 fluorescence spectrophotometer. Three hundred micrograms of the proteins/ml dissolved in buffer B was examined at 70°C with the following parameters: exciting wavelength, 295 nm; scanning range, 305 to 400 nm; scanning speed, 60 nm min1; response time, 0.08 s.
Sequence alignment and secondary-structure and hydrophobicity predictions.
The amino acid sequences of SORs from A. tengchongensis, A. ambivalens, Sulfolobus tokodaii, and Aquifex aeolicus were retrieved from public databases. The amino acid sequence of Acidianus brierleyi was obtained directly from the microbial genome project under way at the University of Copenhagen, Copenhagen, Denmark. Sequence alignments were performed with Clustal X software. Secondary-structure prediction based on the amino acid sequence was carried out with a software package including Antheprot version 5.2 and the PredictProtein server (http://cubic.bioc.columbia.edu/pp/). Hydrophobicity prediction was performed by the method of J. Kyte and R. F. Doolittle provided by the BioEdit software.
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FIG. 1. Multiple alignment of SOR sequences showing the conserved cysteine residues (underlined in Aae) and other conserved regions. Ate, A. tengchongensis; Abr, A. brierleyi; Aam, A. ambivalens; Sto, S. tokodaii; Aae, A. aerolicus; Con, consensus.
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-helix and 21 to 23% ß-sheet. A putative extensive
-helix (positions 99 to 129), including a D-H-E-E-M-H box and a C101-X-X-C104 motif, was identified. Hydrophobicity-hydrophilicity analysis revealed that the SOR was generally a hydrophilic molecule with one strongly hydrophilic segment and three moderately hydrophobic segments. The hydrophilic segment overlaps with the putative extensive
-helix, where the two conservative cysteine residues, C101 and C104, are located (positions 99 to 129). The C31 cysteine residue is located in a hydrophobic segment, and this region is largely ß-sheet or coil.
Effects of various reagents on the catalytic properties of SOR.
Different types of chemicals were tested for their effects on SOR activities (Table 2). All tested divalent metal ions strongly inhibited SOR activity, except magnesium, which showed moderate inhibition with a residual activity of 77.2%. The metal ions Cu2+, Co2+, Ni2+, and Mn2+ were strong inhibitors; the treated reaction mixture retained only 0.7 to 34.5% activity. Each of the reducing agents, GSH, DTT, and the nonspecific metal chelator EDTA, on the other hand, increased SOR activity slightly. Strikingly, the thio-binding reagent, NEM, showed very strong inhibition of SOR activity, and almost complete inhibition occurred at a concentration of 0.1 mM. This suggested that an SH group(s) of the enzyme plays an important role in SOR catalysis. The SOR inhibitors NEM and Zn2+ must have interacted with the cysteine residues (C31, C101, and C104) to confer the strong inhibition of SOR activity.
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TABLE 2. Effects of various chemicals on SOR activity
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FIG. 2. Purified wild and mutant SORs stained with Coomassie blue (A and C) and Western blotted (B). Lanes: M, protein molecular markers; 1 and 5, wild-type SOR; 2 and 6, mutant SOR (C31S); 3 and 7, mutant SOR (C101S); 4 and 8, mutant SOR (C104S). Lanes 5 to 8 were without ß-mercaptoethanol. Each lane was loaded with 2 µg of protein.
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TABLE 3. Specific activities of SOR and its mutants
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FIG. 3. Circular dichroism spectra of wild-type and mutated SOR molecules. (A) BME did not exert a noticeable influence (2 mM BME was added to wild-type SOR, and the mixture was incubated at 4°C for 8 h). (B) Wild-type and mutant SOR molecules have identical CD spectra. Protein concentrations were adjusted to 100 µg/ml, and the scanning wavelength range was 260 to 190 nm. mdeg, millidegree.
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FIG. 4. Fluorescence spectroscopy of wild-type and mutant SORs. Intrinsic tryptophan fluorescence emission spectrum analysis of wild-type SOR and its mutants was carried out as described in Materials and Methods. The excitation wavelength was set to 295 nm, and the range of emission wavelengths was set to 305 to 400 nm. Intensity is given in arbitrary units.
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TABLE 4. Distribution of SOR, SAOR, and TAOR activities in cytoplasm and membrane fractions of A. tengchongensis cells
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FIG. 5. Cell morphology (A) and locations of SOR at subcellular level (B, C, and D). (A) SEM of A. tengchongensis. (B and C) TEM of immunogold-labeled A. tengchongensis. (D) TEM of recombinant E. coli that synthesized SOR. The thick and thin arrows indicate the cytoplasmic SOR and the cytoplasmic-membrane SOR, respectively. Preparation of SEM and TEM samples is described in Materials and Methods and reference 6.
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There are several bacterial redox enzymes containing the C-X-X-C motif, and it has been demonstrated that the motif contributes to the redox activities of these enzymes (3, 5, 12, 22). For example, a single substitution of a cysteine residue in the C-X-X-C motif of protein disulfide isomerases resulted in a major loss of activity (4). Although protein disulfide isomerases and SOR are different types of enzymes, our results with SOR are in agreement with those obtained with bacterial redox enzymes.
The possible functions of the SOR cysteines have been studied by structural analysis of the A. tengchongensis SOR. Predictions from secondary structure and hydrophobicity-hydrophilicity analyses indicated that C101 and C104 are located in a hydrophilic region with
-helix structure and that C31 is located in a hydrophobic region with ß-sheet structure. Taking the hydrophobic nature of the substrate (elemental sulfur [S8]) into account, we tentatively proposed that C31 possibly constitutes the substrate binding site and that C101 and C104, together with the previously identified ferric binding motif D-H-E-E-M-H in the same
-helix segment (27), presumably constitute the catalytic site in SOR. Very recently, Urich et al. found that the A. ambivalens SOR resembles bacterial ferritins and proposed that the enzyme represents a new type of nonheme iron enzyme containing a mononuclear iron center coordinated by carboxylate and/or histidine ligands (27). Thus, these putative domains in SORs identified in this and other works (17, 27) provide a basis for continuing investigation of this largely unknown enzyme.
The oxidation of elemental sulfur in A. tengchongensis proceeds in two steps. First, S0 is oxidized to sulfite and thiosulfate by SOR. Second, sulfite and thiosulfate are oxidized to sulfate by SAOR or TAOR. SOR had been purified from the cytoplasm fraction of A. ambivalens, and SAOR and TAOR are membrane-associated enzymes (reference 20 and this study). How the insoluble elemental sulfur crosses the barriers of the cell wall and cytoplasmic membrane is unknown. In this paper, we investigated the subcellular locations of three sulfur-metabolizing enzymes, SOR, TAOR, and SAOR, in the A. tengchongensis cell. Our finding that the activities of TAOR and SAOR and the partial activity of SOR were located together on the cytoplasmic membrane suggested that the functional coupling of the three activities possibly happens on the membrane. Thus, it will be intriguing to investigate whether SOR, TAOR, and SAOR interact physically with each other and whether the membrane-associated and cytoplasmic SOR enzyme has different physiological functions.
Zhi-Wei Chen and Cheng-Ying Jiang contributed equally to this work. ![]()
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