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Journal of Bacteriology, October 2005, p. 7056-7061, Vol. 187, No. 20
0021-9193/05/$08.00+0 doi:10.1128/JB.187.20.7056-7061.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
Received 27 April 2005/ Accepted 27 July 2005
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Three of the four AOR family enzymes have been purified and characterized in some detail: aldehyde ferredoxin oxidoreductase (AOR) (11), glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR) (12) and formaldehyde ferredoxin oxidoreductase (FOR) (17). AOR has a broad substrate specificity but appears to be most active on aldehydes derived from amino acids (11). FOR has the highest activity on to aldehydes with one to three carbons (17), and both AOR and FOR are thought to play a role in peptide fermentation. In contrast, GAPOR is only known to convert the substrate glyceraldehyde-3-phosphate. It functions in glycolysis where it converts glyceraldehyde-3-phosphate to 3-phosphoglycerate, replacing glyceraldehyde-3 phosphate dehydrogenase and phosphoglycerate kinase in an unusual Emden-Meyerhof glycolysis (12).
A fourth tungsten-containing enzyme, WOR4, was more recently purified from P. furiosus grown in the presence of S0 (16). No activity has been identified yet, but the protein may play a role in S0 reduction because it could not be purified in the absence of S0 in the growth medium. From microarray analysis it is known that the expression of WOR4 at the mRNA level is upregulated in cold-adapted cells that were grown for many generations at 72°C. Cells that were incubated for shorter periods at 72°C (1 to 5 h) showed a fivefold increase in the expression of the putative fifth tungsten-containing enzyme, WOR5 (19). Also, the adjacent open reading frame (ORF) PF1479, coding for a 19-kDa protein with 16 cysteine residues that could bind multiple iron sulfur clusters, is upregulated to the same order of magnitude. This suggests coregulation of both proteins. The presence of four possible iron sulfur clusters in this protein associated with WOR5 indicates a role in electron transfer for the 19-kDa protein similar to the role of ferredoxin in the reactions catalyzed by the other enzymes from the AOR family.
In the present study we describe the purification and characterization of WOR5. This enzyme was discovered in a side fraction during a standard FOR purification. During this purification all fractions were examined for formaldehyde and crotonaldehyde oxidation activity, to discriminate between fractions that contain FOR and those that contain AOR. Some fractions showed an unexpected ratio for these two activities. Further examination has led us to the identification of WOR5 as a fifth aldehyde oxidoreductase with very broad substrate specificity.
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WOR5 eluted from the column between 175 and 270 mM NaCl with a gradient (1,400 ml) from 0 to 500 mM NaCl. Fractions with WOR5 activity were combined and loaded onto a hydroxyapatite (HAP) column (Vc = 120 ml) equilibrated with 5 mM potassium phosphate buffer, pH 7.5. WOR5 eluted from the column as 110 to 270 mM potassium phosphate was applied, using a gradient from 5 to 300 mM potassium phosphate in 500 ml. Fractions containing WOR5 activity were pooled and concentrated by ultrafiltration using an Amicon PM-30 membrane. The concentrated sample of WOR5 was applied to a Superdex-200 column (Vc = 320 ml), equilibrated with 20 mM Tris-HCl, pH 8, and 150 mM NaCl. Fractions containing WOR5 were combined, concentrated, and washed to a maximal salt concentration of 50 mM NaCl before application to a Mono-Q column (Vc = 1 ml) equilibrated with 20 mM PIPES (piperazine-diethanesulfonic acid, pH 6.8). WOR5 eluted from the column at 72 to 85 mM NaCl using a gradient (60 ml) from 70 to 200 mM NaCl.
Enzyme assays. WOR5 activity was routinely assayed at 60°C, under anaerobic conditions, with 5 mM hexanal as the substrate and 1 mM methyl viologen as the electron acceptor in 50 mM EPPS [4-(2-hydroxyethyl)-1-piperazinepropanesulfonic acid] buffer, pH 8.4. Hexanal and other aldehydes tested were added to the assay mixture as a solution in 100% ethanol. The activities of AOR, GAPOR, and FOR were determined as previously described (11, 12, 17). The specific activities are on the basis of protein concentration.
Other assays. Protein concentration was determined using the bicinchoninic acid assay method with bovine serum albumin as the standard. The tungsten content of the purified WOR5 protein was determined by catalytic adsorptive stripping voltammetry (6). Subunit molecular weight and degree of purity were determined with sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis on a Phast System (GE Healthcare) in 8 to 25% SDS. Iron and acid-labile sulfur were determined colorimetrically (3, 14). Metal analysis was carried out by diluting the protein sample up to a volume of 1.5 ml (0.2% HNO3) and introducing it in an inductively coupled plasma optical emission spectrometer Optima 4300 DV (Perkin Elmer, Norwalk, Conn.). Total element content was determined at 280.271 nm (Mg) and 393.366 nm (Ca). Standard calibration curves between 0 and 1 mg/liter were measured immediately after the sample and were used for final calculations.
Cyclic voltammetry. Cyclic voltammograms of P. furiosus ferredoxin and WOR5 were recorded with an Autolab PSTAT10 potentiostat. The electrochemical experiments were performed with a three electrode microcell using the method previously described (7). The working electrode was a nitric acid activated glassy carbon disk. A micro platinum electrode was used as counter electrode and the potential was measured with reference to an Ag/AgCl electrode. A droplet with a volume of 25 µl containing 50 µM of ferredoxin in 25 mM morpholinepropanesulfonic acid (MOPS) buffer, pH 7.2, and 7 mM of neomycin was placed on the working electrode. WOR5 was added to a final concentration of 5 µM and hexanal was added to a final concentration of 50 mM. The voltammograms were recorded at a scan rate of 10 mV/s at 60°C.
Spectroscopy. X-band electron paramagnetic resonance spectra were recorded on a Bruker ER 200D spectrometer, using facilities and data handling as detailed elsewhere (13). For the reduction of enzyme with substrate, a sample of WOR5 (120 µM) was incubated with hexanal (10 mM) for up to 1 hour at 60°C. The UV-visible spectrum was recorded with a Hewlett Packard 8452A diode array spectrophotometer.
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TABLE 1. Purification of WOR5 from P. furiosus
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TABLE 2. Specific activity of AOR, FOR, and WOR5 for the oxidation of aldehydes, determined at 80°C and with methyl viologen as electron acceptor unless indicated otherwise
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Molecular properties of WOR5. Purified WOR5 gave a single band in SDS-polyacrylamide gel electrophoresis that corresponded to a size of 67 ± 2 kDa (Fig. 1). The apparent size as determined by native PAGE was 135 ± 5 kDa, suggesting that the enzyme is a homodimer (data not shown). The presence of a single subunit was confirmed by N-terminal sequence analysis, which resulted in a single sequence (MYAYNGKLLDVDLTREKVKEV) that matched 100% with the N terminus of the ORF (PF1480, wor5) in the genome sequence of P. furiosus. ORF wor5 encodes a 64.9-kDa protein based on the deduced amino acid sequence, which is in good agreement with experimental data (67 kDa). WOR5 has a high sequence identity with the four other members of the family: AOR (30%), FOR (34%), GAPOR (27%), and WOR4 (31%).
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FIG. 1. SDS-PAGE of purified WOR 5, lane 1: Low molecular weight markers from top: 94, 67, 43, 30, 20,14 kDa, lane 2: purified WOR 5.
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Spectroscopy. The as-isolated WOR5 enzyme was electron paramagnetic resonance silent. Incubation with 10 mM hexanal substrate for 1 hour at 60°C resulted in partial reduction of the prosthetic groups showing up as W(V) and [4Fe-4S]1+ in the electron paramagnetic resonance, as shown in Fig. 2. At low temperature, 15 K, the spectrum was dominated by the iron-sulfur cluster; weak features of the partially saturated and overmodulated tungsten signal were also detected. The iron-sulfur signal had approximate g values of 2.08, 1.93, and 1.87, however, the spectral shape was rather broad and exhibited small extra peaks, perhaps as the result of magnetic interaction. Possible origins of dipolar interaction are coupling between two cubanes of a protein dimer or coupling between a cubane and high-spin W(IV) within a subunit. No high-spin signals were detected, suggesting that the cluster was purely S = 1/2. In GAPOR (5) and FOR (our unpublished observation), the [4Fe-4S]1+ cluster exists as a mixture of an S = 1/2 and an S = 3/2 ground state, and the cubane in AOR has been found to occur essentially only in the high spin state (10). In oxidized WOR4 an unusual signal was assigned to a high-potential iron protein type of [4Fe-4S]3+ cluster (16).
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FIG. 2. Electron paramagnetic resonance spectra of the tungsten center and the iron-sulfur cluster in substrate-reduced WOR5. The enzyme, 8 mg/ml, was incubated with 10 mM hexanal for 1 h at 60°C. Trace A is a low-temperature spectrum (15 K) dominated by the signal from the [4Fe-4S]1+ cluster; trace B is a high-temperature spectrum (50 K) from W(V) in tungstobispterin. Electron paramagnetic resonance conditions: microwave frequency, 9,533 MHz; microwave power, 50 mW (A) and 200 mW (B); modulation frequency, 100 kHz; modulation amplitude, 6.3 Gauss (A) and 3.2 Gauss (B).
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40 G in all directions is just detectable as shoulders in Fig. 2B. Spin quantitation gave 0.45 spins per monomer of WOR5 for the cubane and 0.07 spins for W(V). The g values of the tungsten signal are comparable to the g values found for a tungsten signal at low redox potential in AOR (1.989, 1.901, and 1.863) (10). These comparable g values indicate that the tungsten ion is present in a similar coordination in the bispterin cofactor. The tungsten signal at low redox potential in GAPOR has significantly lower g values (1.948, 1.887, and 1.831) (5). In the electron paramagnetic resonance spectrum of WOR4 no tungsten signal could be detected (16).
The optical spectrum of WOR5 as isolated (Fig. 3) shows a protein peak at 280 nm and a broad feature with a maximum at circa 390 nm, characteristic for iron-sulfur clusters of higher nuclearity such as cubanes. A shoulder is observed at approximately 320 nm. Extinction coefficients of
390 = 1.15 mM1 cm1 and
280 = 6.44 mM1 cm1 were determined from the UV-visible spectrum of WOR5 defining a purity index of A390/A280 = 0.18.
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FIG. 3. UV-visible absorption spectrum of P. furiosus WOR5. The protein concentration was 8 mg/ml in 20 mM Tris, pH 8.
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TABLE 3. Oxidation of aldehydes by WOR5 at 60°C and methyl viologen as the electron acceptora
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The temperature dependence of the specific activity of WOR5 for the oxidation of hexanal was determined from 30°C to 100°C (Fig. 4). Up to 80°C the activities were fitted with an Arrhenius equation that describes reaction rate as a function of temperature. The maximum specific activity was measured at 80°C. At temperatures higher than 80°C the specific activity rapidly decreased in time, probably due to instability of the protein.
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FIG. 4. Temperature dependence of the hexanal-oxidizing activity of WOR5. Activities have been fitted to the Arrhenius equation with an activation energy Ea of 70 ± 7 kJ/mol.
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FIG. 5. Cyclic voltammogram of P. furiosus ferredoxin in the presence of WOR5 without hexanal (A) and with hexanal at 60°C (B). The droplet volume was 25 µl and contained 25 mM MOPS buffer, pH 7.2, 7 mM neomycin, 50 µM ferredoxin, 5 µM WOR5, and 50 mM hexanal. The potential scan rate was 10 mV/s.
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' dimer and can therefore be considered as one protein. In Table 4, these fifth aldehyde oxidoreductases are compared with WOR5 to visualize the low homology between these enzymes and WOR5. In fact this fifth putative aldehyde oxidoreductase in both P. horikoshii and P. abyssi has more homology with P. furiosus AOR (approximately 40% sequence identity). From this genome comparison we can conclude that WOR5 is the only P. furiosus oxidoreductase that has no true homolog in one of the other Pyrococcus species. There are also no true homologues (identity greater than 40%) identified when the sequence of WOR5 is blasted against all the genomes collected in the Expasy database (http://www.expasy.org/tools/BLAST/). |
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TABLE 4. Genes homologous to the five oxidoreductases from P. furiosus present in the genome sequences of P. horikoshii (9) and P. abyssi (http://www.genoscope.cns.fr/pab/) expressed as the sequence identity between the deduced amino acid sequences
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Concluding remarks. With the purification of the fifth and presumably last member of the tungsten-containing family of oxidoreductases from P. furiosus, a next challenge will be to elucidate their functions and mutual relations. It is an intriguing question why the cell needs at least four aldehyde oxidoreductase enzymes with relatively broad substrate specificities expressed under similar conditions.
This research was supported by a grant from the Council for Chemical Sciences of the Netherlands Organization for Scientific Research (700.51.301).
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