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Applied and Environmental Microbiology, August 2006, p. 5173-5180, Vol. 72, No. 8
0099-2240/06/$08.00+0 doi:10.1128/AEM.00568-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom,1 School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom2
Received 9 March 2006/ Accepted 15 May 2006
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and ß subunits of 140 kDa and 58 kDa, respectively. It is expressed predominantly under anaerobic conditions in the presence of nitrate, and while it readily reduces chlorate, it displays no selenate reductase activity in vitro. The selenate reductase is expressed under aerobic conditions and expressed poorly during anaerobic growth on nitrate. The enzyme is a heterotrimeric (
ß
) complex with an apparent molecular mass of
600 kDa. The individual subunit sizes are
100 kDa (
),
55 kDa (ß), and
36 kDa (
), with a predicted overall subunit composition of
3ß3
3. The selenate reductase contains molybdenum, heme, and nonheme iron as prosthetic constituents. Electronic absorption spectroscopy reveals the presence of a b-type cytochrome in the active complex. The apparent Km for selenate was determined to be
2 mM, with an observed Vmax of 500 nmol SeO42 min1 mg1 (kcat,
5.0 s1). The enzyme also displays activity towards chlorate and bromate but has no nitrate reductase activity. These studies report the first purification and characterization of a membrane-bound selenate reductase. |
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One of the most successful methods for selenate detoxification is via biotic reduction of selenate to selenite (SeO32) catalyzed by a microbial reductase, followed by either biotic or abiotic reduction of selenite to insoluble, less toxic elemental selenium (Se0) (16, 28). Microbes that can reduce the selenium oxyanions selenate (SeO42) and selenite (SeO32) are not restricted to any particular group/subgroup of prokaryotes, and examples are found throughout the bacterial and archaeal domains (18, 22, 23, 28). It has been suggested that selenate reduction may be catalyzed in many cases by a secondary reaction of the bacterial nitrate reductases, and a selenate reductase activity of both the membrane-bound (NAR) and periplasmic (NAP) nitrate reductases from Ralstonia eutropha, Paracoccus denitrificans, and Paracoccus pantotrophus has been reported (5, 25). Similarly, both NarG and NarZ in membrane fractions from Escherichia coli have been reported to show selenate reductase activity, but only when assayed in the presence of excess (160 mM) sodium selenate (1). Clearly, it is evident that membrane-bound nitrate reductases are poor reducers of selenate (1, 31) and may not contribute significantly to global selenate reduction, particularly in areas enriched with both selenate and nitrate. Consequently, novel enzyme systems that selectively catalyze the reduction of selenate have been sought (2, 26, 32), and to date, detailed biochemical studies have been limited mainly to a single species, Thauera selenatis (7, 17, 19, 26). Under anaerobic conditions, T. selenatis can respire with selenate as the sole terminal electron acceptor. The selenate reductase (SER) from T. selenatis is a periplasmic trimeric enzyme with an apparent molecular mass of
180 kDa (26). The three subunits consist of SerA (96 kDa), SerB (40 kDa), and SerC (23 kDa). The SerA subunit has an N-terminal cysteine-rich motif, probably coordinating a [4Fe-4S] cluster, and also contains the molybdenum (Mo) active site in the form of the molybdopterin guanine dinucleotide (bis-MGD) cofactor (20, 26). The SerB subunit also has a number of cysteine-rich motifs, which again suggest the presence of iron-sulfur clusters. The SerC subunit contains a b-type cytochrome, as shown by visible absorption spectroscopy (26). DNA sequence analysis of T. selenatis has identified the presence of a fourth component (SerD) that may function as a specific chaperone assembly protein involved in MGD cofactor insertion into SerA (17). A membrane-bound component analogous to NapC or NarI in the nitrate reductase systems has not yet been identified, so the process by which SerABC receives electrons from the quinol pool remains to be established. The selenate reductase shows surprising substrate selectivity and does not reduce nitrate or sulfate (26). Amino acid sequence alignment of SerA with the periplasmic (NapA) and membrane-bound (NarG) nitrate reductases from all available sequences has shown that SerA is more closely related to NarG than NapA, despite its periplasmic location. The highly conserved Asp222 residue (E. coli NarG numbering), shown to coordinate the Mo in recent NAR X-ray structures (4, 14), is also present in SerA, placing SerA as a member of a distinct subgroup of the D-group (type II) molybdo-enzymes, which also include chlorate reductase (ClrA) from Ideonella dechloratans (30), dimethyl sulfide dehydrogenase (DdhA) from Rhodovulum sulfidophilum (21), perchlorate reductase (PcrA) from Dechloromonas sp. (3), and ethylbenzene dehydrogenase (EbdA) from Azoarcus sp.-like strain EbN1 (13).
Enterobacter cloacae SLD1a-1 (ATCC 700258), a bacterium isolated from Se-contaminated drainage water in the San Joaquin Valley, California, can also reduce Se oxyanions to elemental selenium (9, 18, 31, 32) but cannot utilize selenate as the sole electron acceptor when grown anaerobically on nonfermentable carbon sources (32). However, it is the ability of this organism to readily catalyze the reduction of selenate to selenium under aerobic conditions that has interested those developing bioremediation strategies. The observation that elemental selenium accumulates near the cytoplasmic membrane prior to expulsion has led to the suggestion that the reduction of selenate to selenite by E. cloacae SLD1a-1 may occur via a membrane-bound selenate reductase expressed under aerobic conditions (18). We have suggested previously that E. cloacae SLD1a-1 expresses two distinct membrane-bound reductases for the reduction of nitrate and selenate and presented evidence that the selenate reductase is a molybdo-enzyme associated with the cytoplasmic membrane and orientated such that its active site faces the periplasmic compartment (32). For the present study, we have purified and characterized both the respiratory membrane-bound nitrate reductase and the membrane-bound selenate reductase from E. cloacae SLD1a-1. The subunit composition, cofactor analysis, and substrate selectivity of each enzyme are presented.
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Purification of nitrate and selenate reductases from E. cloacae SLD1a-1 membranes.
The nitrate reductase was purified from solubilized membranes extracted from anaerobically grown cells by a two-step anion-exchange chromatography protocol. A Source 30Q column was equilibrated with 50 mM Tris-HCl, 2% (wt/vol) OGP, pH 8.6 (buffer A), on an AKTA Prime (Amersham Biosciences) purification system using a constant flow rate of 1 ml/min. The solubilized membrane fraction (10 ml) was filtered through a 0.2-µm filter and loaded onto the column at 1 ml/min, and the flowthrough was collected. The column was washed with 100% buffer A at 1 ml/min until all unbound proteins were removed. The bound proteins were eluted using a step gradient of 20% 50 mM Tris-HCl, 1 M NaCl, 2% (wt/vol) OGP, pH 8.6 (buffer B), and the proteins were collected in 0.5-ml fractions. A large protein peak was eluted at 200 mM NaCl, with the nitrate reductase activity located to the right of the peak. The active fractions were pooled and desalted using two 5-ml desalting columns (Amersham Biosciences) in series on an AKTA Prime system. The pooled fractions were concentrated, loaded onto a Resource 15Q column, equilibrated with buffer A, and eluted using a 0 to 100% gradient of buffer B. The maximum peak with nitrate reductase activity was eluted at 290 mM NaCl. Active fractions were pooled, spin concentrated, and frozen at 20°C prior to use.
The selenate reductase was purified from solubilized membranes extracted from aerobically grown cells by a combination of anion-exchange and size-exclusion chromatography. Both OGP and Thesit (when used at a protein-to-detergent ratio of
1:1) were successful for solubilization and purification of the selenate reductase, but it was found that the enzyme purified using OGP was less stable and degraded rapidly over several hours. The effects of both temperature and oxygen sensitivity were also assessed prior to purification. A Source 30Q column was equilibrated with 50 mM Tris-HCl, 2% (wt/vol) Thesit, pH 8.6, using a constant flow rate of 1 ml/min. Thesit-solubilized membrane fractions (10 ml) were filtered through a 0.2-µm filter and loaded onto the column at 1 ml/min, and the flowthrough was collected. The column was washed with 100% buffer A at 1 ml/min until all unbound proteins were removed. The bound proteins were eluted using a step gradient of 20% 50 mM Tris-HCl, 1 M NaCl, 2% (wt/vol) Thesit, pH 8.6, and the proteins were collected in 0.5-ml fractions. Again, a large protein peak was eluted at 200 mM NaCl, with the selenate reductase activity located to the right of the major peak. The fractions with the highest activities were pooled and loaded onto a Superdex 200 prep-grade column (60 ml; Amersham Biosciences) pre-equilibrated with 50 mM Tris-HCl, 100 mM NaCl, 2% (wt/vol) Thesit, pH 8.6, at 1 ml/min. The sample was injected at 1 ml/min, and the eluted protein was collected as 1-ml fractions. These fractions were analyzed for selenate, nitrate, and chlorate reductase activities and were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). In order to determine the molecular weights of the active peaks, a molecular weight calibration kit (Amersham Biosciences) was utilized according to the manufacturer's instructions.
Spectrophotometric enzyme activity assays.
Reductase activities of purified proteins and cell fractions were measured in a cuvette (3 ml) at 20°C by following the oxidation of reduced methyl viologen spectrophotometrically at 600 nm (6), coupled to the reduction of substrates or potential substrates. These included sodium selenate, sodium selenite, potassium nitrate, potassium nitrite, potassium chlorate, potassium chlorite, sodium perchlorate, potassium bromate, potassium arsenate, potassium sulfate, potassium thiosulfate, dimethyl sulfoxide (DMSO), and trimethylamine-N-oxide (TMAO). Substrates were assayed at a range of concentrations. Activities, where detected, were calculated from the initial rates by using an extinction coefficient of 13,700 M1 cm1 for the methyl viologen radical. Values for Km and Vmax cited in the text and tables are the mean values (n = 3) calculated using nonlinear regression analysis in Grafit v3.0 (Erithacus Software).
In order to assay multiple fractions eluted from the anion-exchange and size-exclusion columns, a microtiter plate assay was developed. Incubation buffer (50 mM potassium phosphate, pH 7.2, 1 mM methyl viologen) was placed in a rubber septum-sealed bottle, purged with O2-free nitrogen gas for 20 min, and equilibrated to 30°C. Sodium dithionite (0.5 M) was prepared, purged with nitrogen, and equilibrated to 30°C. Stock substrate solutions of sodium selenate (1 M), potassium nitrate (1 M), potassium chlorate (0.5 M), potassium bromate (0.5 M), sodium thiosulfate (1 M), and sodium perchlorate (0.5 M) were prepared in sterile water in septum-sealed bottles and purged with nitrogen for 20 min. Fractions eluted from the size-exclusion column (50 µl) and incubation buffer (141 µl) were added to the wells of a 96-well flat-bottomed microtiter plate. Blank wells contained incubation buffer (191 µl) only. Sodium dithionite (3 µl) was added to each well and mixed. To initiate the reaction, substrates were added at the following final concentrations: selenate, 30 mM; thiosulfate, 30 mM; perchlorate, 30 mM; TMAO, 30 mM; DMSO, 30 mM; nitrate, 15 mM; chlorate, 15 mM; and bromate, 30 mM. Immediately following the addition of substrate, the absorbance at 600 nm was measured using a UV/Vis plate reader and monitored until no further absorbance changes were detected.
Polyacrylamide gel electrophoresis and activity/heme staining.
SDS-PAGE was done using gels with a 12% linear gradient of acrylamide and a discontinuous buffer system. Proteins were also separated using nondenaturing PAGE (6% Tris-glycine gels), and gels were stained with dithionite-reduced methyl viologen (5 mM) under anaerobic conditions, using a small anaerobic chamber built in-house and purged with O2-free nitrogen for 30 min. Protein bands with selenate or nitrate reductase activity were identified by the addition of either selenate or nitrate for 15 min and observed as clear bands due to the substrate-dependent reoxidation of reduced methyl viologen, changing the color from dark blue to colorless. Staining for heme-linked peroxidase activity was performed as described previously (29).
Protein sequencing.
Protein subunits identified for N-terminal sequencing analysis were blotted from SDS-PAGE gels onto polyvinylidene difluoride membranes. N-terminal amino acid sequence determination was attempted by the molecular biology facility at the University of Newcastle.
Spectroscopy.
The oxidized and dithionite-reduced electron absorption spectra of the purified selenate reductase were recorded using a Varian Cary 4E UV/visible spectrophotometer. The electron paramagnetic resonance (EPR) spectrum of the Mo(V) species of nitrate reductase (NarG) was measured at 70 K by using a Bruker EMX spectrometer (X-band at 9.38 GHz) equipped with an ER4112HV liquid-helium-flow cryostat system. Iron and molybdenum contents were determined by using a Thermo electron solar atomic absorption spectrophotometer and comparing the results to standard calibration curves prepared from Fe and Mo standards (Fisher Scientific).
DNA sequencing.
An internal portion of the narG homolog was amplified by PCR from the E. cloacae SLD1a-1 genome. Conditions were maintained as described by Gregory et al. (11) by use of Thermostart master mix (ABgene) and degenerate primers designed from a composite of nitrate reductase sequences (T37 and T39) (11). The PCR fragment (
1.3 kb) was ligated to the pGEMT vector (Promega), transformed into competent E. coli JM109 cells, and cultivated. The plasmid was extracted using the Fastplasmid method (Eppendorf), and then a lyophilized sample was supplied to MWG-Biotech for sequencing using primers for the T7 and SP6 promoter regions.
Nucleotide sequence accession number.
The E. cloacae SLD1a-1 narG DNA sequence has been deposited with GenBank under accession number DQ355973.
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140 kDa and
58 kDa (Fig. 1A), and by analogy to membrane-bound nitrate reductases from other organisms, these have been designated the
and ß subunits, respectively. The third,
subunit that is present in other prototype NAR enzymes (NarI component) was not detectable by SDS-PAGE and may have been lost during the purification procedure. Furthermore, attempts to detect the b-type cytochrome moiety by electronic absorption spectroscopy were unsuccessful. The sizes of the
and ß subunits are comparable to those of the NarG and NarH subunits in other enteric bacteria, for example, E. coli NarG is
140 kDa and NarH is
58 kDa (4, 14). Using degenerate primers (T37 and T39) derived from multiple alignments of NarG sequences (11), a 1,393-bp fragment of the E. cloacae SLD1a-1 NarG gene was PCR amplified and sequenced. The translated amino acid sequence showed
93% identity to NarG from E. coli, with all redox cofactor ligands being conserved. The purified
/ß complex displayed nitrate reductase activity, with the following catalytic constants: Km(NO3), 0.24 mM; and Vmax, 1.0 µmol NO3 min1 mg1. It also displayed chlorate reductase activity, with the following catalytic constants: Km(ClO3), 0.52 mM; and Vmax, 1.5 µmol ClO3 min1 mg1. Metal analysis of the
/ß complex gave total metal contents of 18 ± 0.8 mol Fe per mol of enzyme and 0.8 ± 0.06 mol Mo per mol of enzyme, consistent with the
and ß subunits coordinating the five iron-sulfur clusters and the Mo cofactor that are present in the E. coli homologue (4, 14). Further analysis of the Mo center by EPR spectroscopy gave Mo(V) signals typical of those observed for the low-pH form of NarG from E. coli (data not shown). The purified
/ß complex was resolved as a single band on native PAGE gels and produced a strong clear band when stained for nitrate reductase activity (Fig. 1B). Attempts to detect any selenate reductase activity were unsuccessful. Cuvette-based spectrophotometric assays in the presence of increasing selenate concentrations of up to 200 mM did not detect any enzyme-dependent reoxidation of either methyl or benzyl viologen. Furthermore, native PAGE gels stained with reduced methyl viologen and submerged in selenate (100 mM) failed to reveal clear bands indicative of selenate reductase activity (Fig. 1B). In order to determine whether selenate was actually binding to the active site of the enzyme, nitrate reductase rates were measured in the presence of increasing selenate concentrations (0 to 200 mM). With the nitrate concentration fixed at 1 mM, the rate of nitrate reduction remained constant with increasing selenate concentrations. No selenate-dependent inhibition was observed. Similarly, with the nitrate concentration fixed well below the Km for nitrate, at 0.1 mM, again there was no observed inhibition of the nitrate reductase activity. These data strongly suggest that the selenate reduction observed in whole cells is not catalyzed by the respiratory nitrate reductase and that another membrane-bound enzyme must be utilized instead.
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FIG. 1. Purified membrane-bound nitrate reductase. (A) SDS-PAGE gel stained with Simply Blue Safestain (Invitrogen). Lane 1, molecular size marker; lane 2, purified nitrate reductase resolved into and ß subunits. (B) Native PAGE gel with purified nitrate reductase stained for activity using reduced methyl viologen (5 mM) as the electron donor and developed by the addition of nitrate (10 mM) or selenate (50 mM). Nitrate reductase activity is indicated.
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2.2 µmol SeO42 min1 ml1) was extracted successfully from membranes by using either OGP or Thesit (2.0 to 2.5% [wt/vol]) detergent. The enzyme extracted using OGP, however, was labile, and its activity was readily lost after it was stored for a few hours at either 4 or 20°C. The enzyme extracted with Thesit remained active for 24 h when stored at 4°C and retained >50% activity after being frozen at 20°C for prolonged periods. Given the inherent instability of the selenate reductase complex once extracted from the membrane, the present purification protocol and characterization have been developed with over 50 batches of solubilized membranes, and the purification process is now routinely completed within a 16-h time frame.
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FIG. 2. Growth curve and selenate reductase activity profile for E. cloacae SLD1a-1. Cells were cultured aerobically in the presence of 1 mM sodium molybdate, and growth was monitored by the optical density at 600 nm (OD600) ( ). Selenate reductase activity ( ) was measured using methyl viologen as the electron donor. The data presented are typical of the results obtained for three independent experiments.
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200 mM NaCl (Fig. 3A, inset). No nitrate reductase activity was detected in this fraction, but activity was detected with chlorate as a substrate, resolving into two distinct activity peaks. Fractions displaying selenate reductase activities of >2.5 µmol SeO42 min1 ml1 were pooled and loaded onto a Superdex 200 size-exclusion column. In order to track eluted active fractions, a microtiter plate, methyl viologen-based assay was developed. This allowed for the rapid identification of active fractions and permitted a range of substrates to be tested simultaneously. The elution profile from the size-exclusion column is shown in Fig. 3A. Fractions F46-96 were assayed for both selenate- and nitrate-dependent reoxidation of reduced methyl viologen in the microtiter plate assay. Two peak fractions were detected, with maximum selenate reductase activities of 75 nmol SeO42 min1 ml1 and 40 nmol SeO42 min1 ml1. These active fractions corresponded to complexes with molecular masses of
600 and
100 kDa, respectively. No reductase activity was detected in either peak when nitrate, sulfate, perchlorate, or thiosulfate was used as the substrate. Selenate reductase and nitrate reductase activities, when measurable in the same sample, did not coelute from any of the columns. Analysis of the
600-kDa peak fraction (F53) by SDS-PAGE resolved the presence of three distinct peptides, migrating to positions corresponding to molecular masses of
100,
55, and
36 kDa (Fig. 3B). SDS-PAGE analysis of the fraction corresponding to the
100-kDa activity peak (F73-76) revealed the presence of a number of smaller peptides of between 40 and 60 kDa and a distinct band at
100 kDa (not shown). It is considered unlikely that the
100-kDa protein is a distinct second selenate reductase since only one activity band was observed in solubilized membrane fractions resolved by nondenaturing PAGE (Fig. 4A, lane 2). We speculate that the
100-kDa protein represents the active subunit dissociated from the holocomplex. In order to confirm the overall enzyme subunit composition, membranes displaying high selenate reductase activities were solubilized (2% [wt/vol] Thesit) and analyzed by nondenaturing PAGE, and activity was stained to reveal the location of the selenate reductase (Fig. 4A). The active band was extracted from the gel, and the protein was electroeluted and subsequently analyzed by SDS-PAGE. Peptides with molecular masses of
100 kDa,
55 kDa, and
36 kDa were again resolved (data not shown). The combined data from these studies strongly suggest that the selenate reductase complex comprises only three subunits. Given that the holocomplex has an observed molecular mass of
600 kDa, we suggest that when the complex is solubilized in Thesit detergent, the overall subunit arrangement forms a trimer of heterotrimers (
3ß3
3), giving a calculated mass of 573 kDa. This subunit arrangement resembles that of formate dehydrogenase N from E. coli, whose crystal structure also displays an
3ß3
3 subunit composition, with an overall molecular mass of 510 kDa (15). |
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TABLE 1. Purification summary for the membrane-bound selenate reductase from E. cloacae SLD1a-1
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FIG. 3. Purification of membrane-bound selenate reductase. (A) Reductase activities in fractions eluted from a Superdex 200 column, assayed with selenate ( ) and nitrate ( ) as substrates by the microtiter plate method. The column was calibrated using thyroglobin (655 kDa), ferritin (398 kDa), catalase (226 kDa), and cytochrome c (12 kDa) as molecular size markers (dotted line). Fraction numbers represent the elution volume in milliliters. Peaks with selenate reductase activity, labeled 1 and 2, were resolved at molecular masses of 600 kDa and 100 kDa, respectively, as indicated by the arrows. The data presented are typical of the results obtained from five independent batches of protein. The inset shows the activity profile for fractions eluted during Source 30Q anion-exchange chromatography. (B) SDS-PAGE analysis of pure selenate reductase (lane 1). Lane 2, molecular size marker.
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FIG. 4. Subunit composition and heme analysis of the membrane-bound selenate reductase. (A) Native PAGE gel with solubilized membranes stained for the following: lane 1, total protein; lane 2, selenate reductase activity; and lane 3, heme Fe. (B) Electronic absorption spectra of membrane-bound selenate reductase from E. cloacae SLD1a-1. The purified enzyme was used at a protein concentration of 86 µg/ml. Spectra for the air-oxidized enzyme (dotted line) and sodium dithionite-reduced enzyme (solid line) are shown.
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600-kDa complex gave total metal contents of 18.4 ± 0.8 mol Fe per mol of enzyme and 0.6 ± 0.2 mol Mo per mol of enzyme, consistent with the coordination of a Mo cofactor and a number of iron-containing centers. Evidence for the presence of a heme-containing subunit in the selenate reductase complex was demonstrated by heme stain analysis of nondenatured membrane fractions (Fig. 4A). The heme-stained gel (lane 3) clearly show a protein at the corresponding position to that detected for selenate reductase activity. The presence of covalently attached c-type cytochromes was not detected for the denatured protein in SDS gels. The purified oxidized selenate reductase complex exhibited an electronic absorbance spectrum with a Soret maximum at 411 nm. Broad absorption bands are also visible from 420 to 500 nm and 600 to 650 nm, possibly arising from oxidized [Fe-S] clusters and Mo(VI), respectively. Upon reduction with sodium dithionite, these features are lost and replaced with absorbance maxima at 428 nm,
528 nm, and
556 nm, which are characteristic of reduced b-type cytochromes (Fig. 4B), and a broad feature at 575 to 625 nm, possibly from Mo(IV). The cytochrome content was determined to be 0.9 ± 0.14 mol of heme per mol of enzyme based upon the extinction coefficient of cytochrome b (
556-540 nm = 24 mM1 cm1) and the predicted molecular mass (600 kDa) of the selenate reductase complex. The involvement of cytochromes in selenate reduction was demonstrated by monitoring the selenate-dependent reoxidation of the reduced cytochromes at 556 nm. Additional analysis of the metal centers of selenate reductase by EPR spectroscopy at this stage was not possible due to the low concentration of pure sample. These data suggest that the selenate reductase complex comprises three subunits with an overall molecular mass of
600 kDa and includes an
100-kDa molybdenum-binding active
subunit that readily dissociates from the iron-sulfur- and heme-containing holocomplex during purification. The functional involvement of cytochromes and the presence of nonheme iron suggest that the
and ß subunits form a conventional electron transfer chain, mediating the transfer of electrons from the Q pool to the selenate reductase active site, and as such, the selenate reductase resembles other well-characterized membrane-bound molybdo-enzymes.
Specificity for selenate and nitrate.
Kinetic analysis (Table 2) of the purified selenate reductase holocomplex (
600 kDa), using reduced methyl viologen as the electron donor, revealed that in addition to reducing selenate [Km(SeO42), 2.1 mM; Vmax, 0.5 µmol SeO42 min1 mg1], the complex also used chlorate [Km(ClO3), 3.0 mM; Vmax, 0.035 µmol ClO3 min1 mg1] as a substrate. Based upon the native molecular mass of 600 kDa, the membrane-bound selenate reductase reduces selenate at a calculated turnover rate (kcat) of 5.0 s1 (kcat/Km =
2.4 x 103 s1 M1) and chlorate at a turnover rate (kcat) of 0.35 s1 (kcat/Km =
117 s1 M1). A low level of activity was also detected with bromate as a substrate (catalytic constants were not determined). The purified enzyme displayed no reductase activity when nitrate, sulfate, perchlorate, DMSO, TMAO, or thiosulfate was tested as the substrate. The selenate reductase activity of the
100-kDa fraction was also examined, and the observed kinetic constants were as follows: Km(SeO42), 5.5 mM; and Vmax, 0.34 µmol SeO42 min1 mg1 (Table 2).
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TABLE 2. Kinetic properties of membrane-bound nitrate and selenate reductases
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FIG. 5. Resolution of selenate and nitrate reductases in membrane fractions of E. cloacae SLD1a-1, using nitrate, selenate, and chlorate as substrates. (A) Native PAGE gels with solubilized membranes. Gel 1, solubilized membranes from cells grown anaerobically using nitrate as the sole electron acceptor and stained for nitrate reductase activity; gel 2, solubilized membranes from cells grown aerobically and stained for selenate reductase activity; gel 3, solubilized membranes from cells grown aerobically and stained for chlorate reductase activity. The distinct reductases are indicated. (B) Model showing subunit composition of the membrane-bound nitrate and selenate reductases from E. cloacae SLD1a-1.
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The membrane-bound selenate reductase is the first of its type to be purified to homogeneity. The molybdo-enzyme complex comprises three subunits, with molecular masses of
100 kDa,
55 kDa, and
36 kDa (Fig. 5B). The enzyme displays no apparent nitrate reductase activity but readily reduces the substrates chlorate and bromate, although with lower affinities than that for selenate. The enzyme shows a number of features similar to those of the well-characterized periplasmic SER from T. selenatis (17, 26). Notably, both are molybdo-enzymes, their catalytic
subunits are of similar sizes (SerA is
96 kDa), both are unable to reduce nitrate, both contain b-type cytochromes, and both have active sites located in the periplasm. Furthermore, although it was previously not reported, both SER and the membrane-bound selenate reductase from E. cloacae SLD1a-1 readily reduce chlorate. The obvious difference between SER and the membrane-bound enzyme reported in this study is that SER is freely soluble in the periplasm and not anchored to the cytoplasmic membrane. The affinities for selenate of the two enzymes are also markedly different. The observed Km for selenate of SER is
16 µM, in contrast to the low affinity (Km,
2 mM) of the membrane-bound enzyme. However, the observed Km for the membrane-bound selenate reductase may be misleadingly high owing to the use of a nonphysiological electron donor. It has been reported that the Km for nitrate of NAR from P. denitrificans is
20-fold lower when determined using duroquinol rather than methyl viologen (6).
The membrane-bound selenate reductase from E. cloacae SLD1a-1, unlike other similar molybdo-enzymes, including SerABC from T. selenatis, cannot support anaerobic growth on nonfermentable carbon substrates and seems to have a role only in selenate detoxification. The combination of low substrate affinity and the fact that QH2-selenate electron transfer is not electrogenic may well suit its detoxification role, since the process will only function at elevated/toxic selenate concentrations and will not be subjected to negative thermodynamic feedback via the proton motive force generated through aerobic respiration. The observation that the membrane-bound selenate reductase is not up regulated under anaerobic growth conditions or induced by the presence of a substrate in the growth medium further supports its function in detoxification rather than respiration and highlights that it has a very different mechanism of transcriptional control than both NAR and SER.
Finally, factors that control the substrate selectivity of the oxyanion reductases remain to be established. Modeling the SerA component from the periplasmic selenate reductase on the crystal structure of the respiratory nitrate reductase from E. coli identified a number of highly conserved residues within NarG, surrounding the active site and the proposed substrate entry channel, that may enhance selectivity towards trigonal planar (NO3) rather than tetrahedral (SeO42) substrates (8). Furthermore, the difference in charge between selenate and nitrate may also be a means by which the oxyanions are discriminated. Attempts to locate and sequence the genes encoding the individual subunits of the membrane-bound selenate reductase are currently in progress and should provide further insight into the regulation, mechanism of substrate selection, and molecular structure of this novel enzyme.
We thank Joe Gray (Molecular Biology Facility, University of Newcastle) for help with peptide sequencing and Duncan Harvey (University of Newcastle) for help with the metal analysis. We also thank James Allen (University of Oxford) and Joanne Santini (University College London) for useful discussions.
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