1 Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße, D-35043 Marburg, Germany
2 Biochemisches Institut, Fachbereich Humanmedizin, Justus-Liebig-Universität Giessen, Germany
Correspondence
Reiner Hedderich
hedderic{at}staff.uni-marburg.de
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ABSTRACT |
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This work is dedicated to Professor Dr Rudolf K. Thauer on the occasion of his 65th birthday.
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INTRODUCTION |
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The saccharolytic clostridia are well-studied members of the obligate fermenting bacteria (Gottschalk, 1986). H2 metabolism has in particular been studied in Clostridium pasteurianum. The organism ferments glucose via the Embden-Meyerhof pathway. Pyruvate is oxidized to acetyl-CoA and CO2 by pyruvate : ferredoxin oxidoreductase (POR). Reduced ferredoxin functions as electron donor for two soluble monomeric Fe-only hydrogenases (Adams, 1990
). A portion of the NADH generated in the glyceraldehyde-3-phosphate dehydrogenase reaction serves to reduce ferredoxin, and thus electrons derived from NADH can also be used for H2 production (Jungermann et al., 1973
). The reaction is catalysed by an NADH : ferredoxin oxidoreductase. Since the reduction of ferredoxin (E0' 420 mV) by NADH (E0' 320 mV) is energetically unfavourable, the NADH : ferredoxin oxidoreductase reaction is thought to be driven by reverse electron transport at high external hydrogen partial pressure [p(H2)]. A membrane-bound NADH : ferredoxin oxidoreductase has recently been purified from Clostridium tetanomorphum (W. Buckel, personal communication).
Another example of a micro-organism involved in fermentative H2 production is Thermotoga maritima, a thermophilic, strictly anaerobic bacterium (Schröder et al., 1994). H2 evolution in Tt. maritima is catalysed by a heterotrimeric cytoplasmic Fe-only hydrogenase (Verhagen et al., 1999
). The purified enzyme accepts neither reduced ferredoxin nor NAD(P)H as electron donor. However, sequence analysis predicts that the enzyme is a flavoprotein containing a multiple ironsulfur cluster that uses NAD(P)H as the electron donor (Verhagen et al., 1999
). Another type of hydrogenase is responsible for fermentative H2 production in the hyperthermophilic archaeon Pyrococcus furiosus. The genome of P. furiosus contains the putative mbhAN operon encoding a 14-subunit membrane-bound [NiFe] hydrogenase complex (Sapra et al., 2000
; Silva et al., 2000
). This enzyme complex is now thought to be responsible for fermentative H2 production in P. furiosus. An intact Mbh complex has not yet been purified. However, washed membranes of P. furiosus and partially purified Mbh preparations catalyse H2 production with reduced P. furiosus ferredoxin as electron donor (Silva et al., 2000
). With inverted membrane vesicles of P. furiosus, it was shown that H2 evolution from reduced ferredoxin results in the generation of both a
pH and a
, which could be coupled to ATP synthesis. Hence, in addition to substrate-level phosphorylation, the organism gains energy by respiration. This also explains why P. furiosus has an unusual glycolytic pathway that uses ferredoxin in place of the expected NAD+ as electron acceptor for glyceraldehyde 3-phosphate oxidation (Sapra et al., 2003
).
A classical example of fermentative H2 production in a facultative fermenting organism is the mixed acid fermentation of Escherichia coli (reviewed by Sawers, 1994). In this organism, pyruvate is converted to acetyl-CoA and formate by the pyruvate : formate lyase. Formate is subsequently converted to CO2 and H2. This latter reaction is catalysed by the formate : hydrogen lyase complex, which consists of a formate dehydrogenase, a polyferredoxin and a membrane-bound multisubunit [NiFe] hydrogenase (Böhm et al., 1990
; Sauter et al., 1992
).
In this study, the H2 metabolism in Ta. tengcongensis, a thermophilic Gram-positive bacterium recently isolated from a hot spring in China, was investigated. Batch cultures of this organism were previously shown to ferment starch or glucose via the EmbdenMeyerhof pathway to acetate, ethanol, CO2 and H2 (Xue et al., 2001). We show here that the organism forms two distinct hydrogenases involved in H2 production during fermentation: a heterotetrameric NAD(H)-dependent Fe-only hydrogenase and a ferredoxin-dependent multisubunit membrane-bound [NiFe] hydrogenase.
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METHODS |
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Growth of the organism.
Ta. tengcongensis strain MB4T was from the Japan Collection of Microorganisms (JCM11007). The organism was cultivated at 75 °C and pH 7·5 in the medium described previously (Xue et al., 2001), with a few modifications. The medium was supplemented with tryptone (2 g l1) and yeast extract (2 g l1), and either soluble starch (10 g l1) or glucose (25 mM) as energy substrate. The medium did not contain sodium thiosulfate or other external electron acceptors. Media were made anoxic by flushing with N2. Resazurin was used as redox indicator. The organism was cultivated either in 2 litre bottles (containing 1 litre of medium) tightly closed with rubber stoppers or in 12 litre fermenters (10 l medium), which were continuously flushed with N2 (
200 ml min1) and stirred at 5000 r.p.m. Cultures at an OD578 of
2 (fermenter cultures) were harvested under N2. Cells were stored at 20 °C.
Preparation of cell extracts and anaerobic procedures.
Cell extracts were routinely prepared from 40 g (wet wt) cells suspended in 120 ml 50 mM MOPS/KOH (pH 7·0) containing 2 mM dithiothreitol (DTT) (buffer A). Cells were disrupted by sonication at 4 °C with four bursts at 7 min intervals using an energy output of 200 W (Bandelin sonicator). Undisrupted cells and cell debris were removed by centrifugation at 10 000 g for 20 min. Cell extracts had to be kept strictly anoxic because hydrogenases were highly oxygen sensitive. All procedures for the preparation of cell fractions and enzyme purifications were carried out anoxically under an N2/H2 (95/5, v/v) atmosphere. All buffers were boiled, flushed with N2, supplied with 2 mM DTT, and maintained under a slight overpressure of N2.
Purification of the membrane-bound [NiFe] hydrogenase.
Crude membranes were isolated from cell extracts by ultracentrifugation at 160 000 g for 2 h. The 160 000 g supernatant was stored for the isolation of the soluble NADH-dependent hydrogenase. Crude membranes were resuspended in 130 ml buffer A using a Teflon Potter homogenizer. After a second ultracentrifugation at 160 000 g for 2 h, washed membranes were homogenized in 300 ml buffer A (1·8 mg protein ml1). Dodecyl
-D-maltoside was added to a concentration of 16 mM [4·5 mg (mg protein)1]. The suspension was incubated for 12 h at 4 °C with slight swirling. After centrifugation at 160 000 g for 40 min, the solubilized membrane proteins present in the supernatant were loaded onto a Q-Sepharose HiLoad column (2·6x15 cm) equilibrated with buffer A containing 2 mM dodecyl
-D-maltoside (buffer A+detergent). The column was washed with 80 ml buffer A+detergent. Protein was eluted in a stepwise NaCl gradient at a flow rate of 5 ml min1 (0·1, 0·2, 0·3, 0·4 and 0·5 M; 80 ml each in buffer A+detergent). The membrane-bound hydrogenase was recovered in the fractions eluting with 0·3 M NaCl. Hydrogenase-containing fractions were loaded on a ceramic hydroxyapatite column (1·6x20 cm) equilibrated with 0·03 M potassium phosphate buffer (pH 7·0) containing 2 mM DTT and 2 mM dodecyl
-D-maltoside. Protein was eluted using a linear gradient from 0·03 to 1 M potassium phosphate (400 ml). The membrane-bound [NiFe] hydrogenase was recovered in the fractions eluting with 1 M potassium phosphate. Fractions containing hydrogenase activity were concentrated by ultrafiltration (YM100 ultrafiltration membranes, 100 kDa cut-off, Millipore) and applied to a Superdex 200 gel filtration column (2·6x60 cm) equilibrated with buffer A+detergent+0·1 M NaCl. The enzyme eluted after 225 ml (peak maximum). Protein was concentrated by ultrafiltration and stored in buffer A+detergent at a concentration of 3 mg protein ml1 at 4 °C.
Purification of an NAD(H)-dependent Fe-only hydrogenase.
All buffers used throughout the purification contained 2 mM FMN. The 160 000 g supernatant (see above) was loaded onto a Q-Sepharose HiLoad column (2·6x15 cm) equilibrated with buffer A. The column was washed with 80 ml buffer A. Protein was eluted in a stepwise NaCl gradient at a flow rate of 5 ml min1 (0·1, 0·2, 0·3, 0·4 and 0·5 M; 80 ml each in buffer A). The NAD+-reducing hydrogenase activity was recovered in the fractions eluting with 0·3 M NaCl. These fractions were brought to 0·6 M ammonium sulfate and loaded onto a hydrophobic interaction chromatography column (Phenyl-Sepharose HiLoad; 2·6x10 cm) equilibrated with 0·8 M ammonium sulfate in buffer A. Protein was eluted in a stepwise ammonium sulfate gradient at a flow rate of 5 ml min1 (0·8, 0·6, 0·4, 0·2 and 0 M; 60 ml each in buffer A). NAD+-reducing hydrogenase activity was recovered in the fractions eluting with buffer A (0 M ammonium sulfate). These fractions were subjected to anion-exchange chromatography on Source 30 Q (5x10 cm). The column was washed with 100 ml buffer A. Protein was eluted in a stepwise NaCl gradient at a flow rate of 5 ml min1 (0·1, 0·12, 0·14, 0·16, 0·18 and 0·2 M; 100 ml each in buffer A). The NAD+-reducing hydrogenase was recovered in the fractions eluting with 0·2 M NaCl. Fractions containing hydrogenase activity were concentrated and desalted by ultrafiltration and applied to a Superdex 200 gel filtration column (2·6x60 cm) equilibrated with buffer A+0·1 M NaCl. The enzyme eluted after 220 ml (peak maximum). The protein was concentrated by ultrafiltration and stored at a concentration of 8 mg protein ml1 in buffer A at 4 °C.
Purification of ferredoxin.
Ta. tengcongensis ferredoxin was purified under anoxic conditions from the 160 000 g supernatant by chromatography on Q-Sepharose HiLoad (elution at 0·5 M NaCl), Phenyl Sepharose (elution at 0·4 M ammonium sulfate), and Superdex 75 (elution after 275 ml, peak maximum). The as-isolated oxidized ferredoxin showed absorption maxima at 280 and 390 nm, and an A390/A280 of 0·75. An 390 of 12·8 mM1 cm1 was used for the determination of ferredoxin concentrations. MALDI-TOF analysis resulted in a single peak corresponding to a molecular mass of 5724 Da.
Determination of enzyme activities.
Enzymes were routinely assayed at 70 °C either in 8 ml serum bottles or in 1·5 ml cuvettes (sealed with rubber stoppers) under anoxic conditions. In hydrogenase assays, 1 U enzyme activity corresponds to 1 µmol H2 formed or consumed min1. Hydrogen-uptake activity with dyes as electron acceptors was determined by following the reduction of methylviologen (MV) or benzylviologen (BV) at 578 nm. The 0·8 ml assays contained buffer A and 4 mM BV or MV. Cuvettes were allowed to equilibrate with a 100 % H2 headspace (1·2x105 Pa). H2-formation activity with reduced MV as electron donor was measured by following the oxidation of reduced MV at 578 nm. The standard assay contained buffer A and 4 mM MV, which was reduced with sodium dithionite to a A578 of 2. N2 (1·2x105 Pa) was the gas phase. The reaction was started by addition of enzyme (6 mU). Ferredoxin-dependent reduction of metronidazole by H2 was measured by following the decrease in A320 (
metronidazole=9·3 mM1 cm1, corresponding to a six-electron reduction). The 0·8 ml assay contained buffer A, 2 mM dodecyl
-D-maltoside, 0·2 mM metronidazole, 20 µM ferredoxin, enzyme (0·5 mU) and 100 % H2 (1·2x105) Pa as the gas phase. To ensure completely anoxic conditions, 0·1 mM sodium dithionite was added. Ferredoxin-dependent H2 formation with sodium dithionite as electron donor was followed by determining the H2 concentration in the gas phase. The 1 ml assay in 8 ml serum bottles contained buffer A, 15 mM sodium dithionite, 20 µM ferredoxin (or as indicated) and enzyme (1·5 mU) under N2 as gas phase (1·2x105 Pa). The solution was stirred vigorously with a magnetic bar. At time intervals of 0·5 min, samples from the gas phase were withdrawn and H2 was quantified after separation by gas chromatography (see below). NAD(P)+-reducing hydrogenase activity was assayed by measuring the formation of NAD(P)H at 340 nm. The assay contained buffer A in a total volume of 0·8 ml. Cuvettes were allowed to equilibrate with 100 % H2 in the headspace (1·2x105 Pa). The reaction was initiated by the addition of NAD(P)+ (1·5 mM) or enzyme (0·1 U). NADH-dependent H2 formation was followed by determining the H2 concentration in the gas phase by gas chromatography (see below). The 1 ml assay in 24 ml serum bottles contained buffer A, 2 mM FMN, 1 mM Ti(III)citrate and 0·25 U enzyme. After a 2 min preincubation the reaction was initiated by the addition of NADH (50 mM). The solution was stirred vigorously with a magnetic bar. At 0·5 min intervals, samples from the gas phase were withdrawn and H2 was quantified after separation by gas chromatography. NADH : BV oxidoreductase activity was determined by following the NADH-dependent reduction of BV at 578 nm. The standard assay contained buffer A and 4 mM BV, which was reduced with sodium dithionite to an
A578 of 0·1. N2 (1·2x105 Pa) was the gas phase. The reaction was started by addition of NADH (0·2 mM) or enzyme (0·1 mU). Alcohol dehydrogenase (ADH) activity was assayed in both the forward and the reverse direction by measuring the oxidation or formation of NAD(P)H at 340 nm at 70 °C under a N2 gas phase. One unit of activity was defined as the amount of enzyme that forms or oxidizes 1 µmol NAD(P)H min1. The reaction mixture (total volume, 1 ml) contained 50 mM Tris/HCl (pH 7·5 at 70 °C), 1·5 mM NAD(P)+, and 1·2 mM ethanol or 2-propanol (reverse direction); or 50 mM Tris/HCl (pH 7·5 at 70 °C), 0·2 mM NADH or NADPH, 1·2 mM acetaldehyde and enzyme (3 mU) (forward direction). Aldehyde dehydrogenase (ALDH) activity was determined by the acetaldehyde- and CoA-dependent reduction of NAD(P)+. One unit of ALDH activity was defined as the amount of enzyme that reduces 1 µmol NAD(P)+ min1 at 70 °C under anoxic conditions. The reaction mixture (total volume: 1 ml) contained 50 mM Tris/HCl (pH 7·5), 1·5 mM NAD+ or NADP+, 1·2 mM acetaldehyde, 1·5 mM CoA and enzyme (1 mU).
Amino acid sequence analysis.
Sequence data of the Ta. tengcongensis genome were obtained from The Institute for Genomic Research website (http://www.tigr.org). For the prediction of transmembrane helices in proteins, programs at non-commercial servers were used (http://www.cbs.dtu.dk/services/TMHMM-2.0/). Multiple sequence alignments were made using the program at http://www.ebi.ac.uk/fasta3/.
Determination of amino acid sequences.
For determination of amino-terminal amino acid sequences, polypeptides were separated by SDS-PAGE and blotted on to PVDF membranes (Applied Biosystems) as described previously (Künkel et al., 1998). Sequences were determined using an Applied Biosystems 4774 protein/peptide sequencer and the protocol given by the manufacturer.
Analytical methods.
Protein concentration was routinely measured by the method of Bradford (1976) (Rotinanoquant; Roth) using BSA as a standard. Nickel was determined by atomic absorption spectroscopy on a 3030 Perkin Elmer atomic absorption spectrometer fitted with an HGA-600 graphite furnace assembly and an AS-60 autosampler. For identification of flavin and determination of the flavin content of the NADH-dependent hydrogenase, the enzyme was extensively washed by ultrafiltration with FMN-free buffer A. Protein (100 µl, 15 mg ml1) was denatured by exposure to 10 % (w/v) trichloroacetic acid. Denatured protein was removed by centrifugation; the resulting supernatant was adjusted to pH 6 with 2 M K2HPO4 and analysed by chromatography using a reversed-phase HPLC column (LiChrospher 60 RP 18, 5 µm, 125x4 mm, Merck) equilibrated in 50 mM ammonium formate containing 25 % methanol. Flavins were eluted isocratically with the equilibration buffer. FAD and FMN standards were used to identify and quantify the flavin. H2 was determined by gas chromatography. The gas chromatograph (Carlo Erba GC Series 6000) was equipped with a thermal conductivity detector. Gases were separated by a molecular sieve (0·5 nm). The oven and injection port were at 110 °C; the detector was at 150 °C. The carrier gas was N2 at a flow rate of 30 ml min1. Glucose was determined enzymically with glucose oxidase, peroxidase and 2,2-azino-di-(3-ethylbenzthiazoline)-6-sulfonate (ABTS) as chromogen (Kunst et al., 1981
). Ethanol was determined enzymically with ADH and NAD+. Acetate was determined enzymically with acetyl-CoA synthetase, myokinase, pyruvate kinase and lactate dehydrogenase following the oxidation of NADH (Dorn et al., 1978
). For the determination of ethanol in fermenter cultures, the outlet gas was led through 5 litres of cooled water (4 °C) to trap the ethanol.
EPR spectroscopy measurements.
EPR spectra at X-band (9·45 GHz) were obtained with a Bruker EMX spectrometer. All spectra were recorded with a field modulation frequency of 100 kHz and a modulation amplitude of 0·6 mT. The sample was cooled by an Oxford Instrument ESR 900 flow cryostat with an ITC4 temperature controller. EPR signals were simulated using non-commercial programs supplied by Dr S. P. J. Albracht Swammerdam Institute for Life Sciences, University of Amsterdam, Netherlands, and were based on formulas described previously (Beinert & Albracht, 1982).
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RESULTS |
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A ferredoxin-dependent [NiFe] hydrogenase in the membrane fraction of Ta. tengcongensis
The membrane fraction of Ta. tengcongensis exhibited ferredoxin-dependent hydrogenase activity using Methanosarcina barkeri ferredoxin as substrate. This assay was used to identify and purify a ferredoxin from Ta. tengcongensis (see Methods), which was used in the studies described here. For routine activity measurements the H2-dependent-reduction of MV and the ferredoxin- and H2-dependent reduction of metronidazole were followed (Table 1). The enzyme could be solubilized by dodecyl
-D-maltoside without loss of activity. Using the chromatographic steps summarized in Table 1
, the enzyme was purified 200-fold to apparent homogeneity with a yield of 12 %. An analysis of the purified enzyme by SDS-PAGE revealed the presence of five polypeptides with apparent molecular masses of 69, 40, 32, 17 and 14 kDa (Fig. 1
A). The enzyme exhibited an oxidized minus reduced UV/visible spectrum characteristic for ironsulfur proteins (not shown). The enzyme contained 4·8 nmol Ni per mg protein, corresponding to 0·9 mol Ni per mol enzyme (187·7 kDa, see below).
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Purified Ech hydrogenase from Ta. tengcongensis catalysed H2 evolution with reduced ferredoxin as electron donor at a Vmax of 200 U (mg protein)1 at 70 °C. The apparent Km for the reduced ferredoxin was 3 µM. The catalytic efficiency coefficient (kcat/Km) of 2x108 M1 s1 was calculated based on a molecular mass for Ech hydrogenase of 187·7 kDa. To determine the rate of ferredoxin reduction by H2, the metronidazole assay was used (Chen & Blanchard, 1979). Ech hydrogenase catalysed the reduction of metronidazole by H2 only in the presence of ferredoxin, which indicates that the ferredoxin is a direct electron acceptor of the enzyme. Reduced ferredoxin is oxidized in a fast chemical reaction by metronidazole. Ech hydrogenase catalysed the reduction of metronidazole and thus the reduction of the ferredoxin at a Vmax of 70 U (mg protein)1. The enzyme exhibited an apparent Km for the oxidized ferredoxin of 15 µM. A catalytic efficiency coefficient (kcat/Km) of 1·5x107 M1 s1 was calculated. The enzyme was also assayed with MV as artificial electron donor or acceptor. The enzyme catalysed the reduction of MV by H2 at an apparent rate of 380 U (mg protein)1 and H2 evolution from reduced MV at an apparent rate of 1260 U (mg protein)1.
An NAD(H)-dependent Fe-only hydrogenase in the soluble fraction of Ta. tengcongensis
An NAD(H)-dependent Fe-only hydrogenase was purified from the soluble fraction of Ta. tengcongensis. The enzyme was enriched 20-fold with a yield of 27 %. For routine activity measurements, both the H2-dependent reduction of MV and the H2-dependent reduction of NAD+ were determined (Table 3). Activities with NAD(H) as substrate were significantly higher when FMN was added to all buffers used throughout the purification. SDS-PAGE of the purified enzyme revealed four polypeptides with apparent molecular masses of 65, 64, 20 and 14 kDa (Fig. 1B
). The purified enzyme contained less than 0·06 mol Ni per mol enzyme. Upon autooxidation of the enzyme (for 20 min at 70 °C under N2), the EPR spectrum shown in Fig. 3
was obtained at 30 K. A rhombic signal with gxyz=2·106, 2·046 and 1·996 was identified in the spectrum. This signal could be simulated (Fig. 3
, upper spectrum) and is characteristic for the oxidized H-cluster of Fe-only hydrogenases (Adams, 1990
). The remaining features of the spectrum most probably resulted from the [4Fe4S] clusters or [2Fe2S] clusters of the enzyme (see below), which were not fully oxidized under the conditions employed. In addition the enzyme contained 6·6 nmol FMN per mg protein, which corresponded to 1 mol FMN per mol enzyme.
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The determination of the amino-terminal sequences allowed the identification of the encoding genes in the completely sequenced genome of Ta. tengcongensis (Bao et al., 2002; Table 4
). The genes are clustered and form a putative transcription unit (Fig. 4
). The sequence of the 64 kDa subunit (HydA) (581 amino acids) could be perfectly aligned (42 % sequence identity) with the single-subunit hydrogenase from Cl. pasteurianum, for which the crystal structure is known (Fig. 5
) (Peters et al., 1998
). In addition to the H-cluster present in the catalytic centre, the Cl. pasteurianum hydrogenase harbours three [4Fe4S] clusters and one [2Fe2S] cluster. The cysteine residues coordinating these clusters are also conserved in the Ta. tengcongensis 64 kDa subunit, which identifies this subunit as the hydrogenase catalytic subunit.
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As shown in Fig. 4, an additional ORF (TTE0891) is located between hydD and hydC in the Ta. tengcongensis genome. It encodes a 20·7 kDa protein, which was not part of the purified enzyme. The protein showed high sequence similarity to the ATP-binding domain of histidine kinases.
Fermentation products and enzymic activities in Ta. tengcongenis cultures grown at different p(H2)
It has previously been shown that Ta. tengcongensis, when grown in batch cultures, produces 1 mmol acetate, 0·7 mmol ethanol, 1·5 mmol CO2 and 0·3 mmol H2 per mmol glucose consumed. In that study, thiosulfate was added as external electron acceptor (Xue et al., 2001). In the present study, the fermentation balance was determined with cultures grown in the absence of any external electron acceptors. Since growth on glucose in a closed system in the absence of thiosulfate was extremely poor (growth rate, µ=0·1 h1), starch was used as carbon and energy source. This resulted in a µ of 0·27 h1. Acetate, ethanol and H2 were formed in a 1·4±0·2 : 0·6±0·2 : 2·8±0·2 ratio. The maximal p(H2) attained in batch cultures was 101 atm. Growth of Ta. tengcongensis was most probably inhibited at higher p(H2), as has previously been described for other fermenting organisms (Schröder et al., 1994
; van Niel et al., 2003
).
Growth of Ta. tengcongensis in a fermenter continuously flushed with N2 to keep the p(H2) low resulted in higher growth rates (µ=0·24 h1 with glucose as substrate). Glucose or starch could be used as substrate. Per mmol glucose consumed, 2±0·2 mmol acetate was formed. Only trace amounts of ethanol were detected (0·02 mmol per mmol glucose consumed). H2 could not be quantified accurately in these experiments owing to the high N2 flushing rates; however, since glucose was almost quantitatively converted to acetate and since no external electron acceptors were added, reduction of H+ to H2 is the only way to release the reducing equivalents generated during glucose oxidation to acetate. Thus, 4 mmol H2 must have been formed per mmol glucose consumed, to account for an even [H] balance.
To study if the enzymes involved in H2 and ethanol formation are regulated in response to p(H2), activities of the key enzymes in cell extracts were measured. For these experiments starch was used as substrate for the closed-bottle cultures and glucose was used as substrate for the fermenter cultures; under these conditions, the two cultures exhibited similar growth rates (µ=0·24 h1 or 0·27 h1). Cell extracts of fermenter-grown cells catalysed H2 production from NADH with specific activities of 0·6 U (mg protein)1 and from reduced ferredoxin with specific activities of 1·8 U (mg protein)1. While the specific activity of the ferredoxin-dependent hydrogenase activity was not influenced by the growth conditions, the NAD(H)-dependent hydrogenase activity was about fourfold lower in cell extracts from closed-bottle cultures. Also the activities of the two key enzymes involved in ethanol formation, alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH), were determined (Table 5). As will be described in more detail in the Discussion, ethanol formation has been extensively studied in Thermoanaerobacter ethanolicus. In this organism the ADH responsible for fermentative ethanol formation was NADP(H) specific and, in addition to ethanol, used secondary alcohols as substrate. Cell extracts of closed-bottle cultures catalysed the NADPH-dependent reduction of acetaldehyde to ethanol with specific activities of 15 U (mg protein)1. Cell extracts of fermenter cultures catalysed this reaction at fivefold lower rates [3 U (mg protein)1]. When NADPH as electron donor was replaced by NADH, the rates of acetaldehyde reduction were approximately 15-fold lower. The reverse reaction, the NADP+- or NAD+-dependent oxidation of ethanol, was catalysed at significantly lower rates (Table 5
). 2-Propanol was also tested as substrate of T. tengcongensis. Cell extracts from closed-bottle cultures catalysed the NADP+-dependent oxidation of 2-propanol at a rate of 11 U (mg protein)1; cell extracts from fermenter cultures catalysed the oxidation at a rate of 1·5 U (mg protein)1. ALDH activity was determined by following the acetaldehyde-dependent reduction of NADP+. Cell extracts from closed-bottle cultures catalysed this reaction with a specific activity of 1·8 U (mg protein)1 and those from fermenter cultures with a specific activity of 0·2 U (mg protein)1. The reaction was strictly CoA-dependent, which indicated the formation of acetyl-CoA. No activity was observed when NADP+ was replaced by NAD+ as substrate.
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DISCUSSION |
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The [NiFe] hydrogenase of Ta. tengcongensis belongs to a small family of multisubunit membrane-bound enzymes that have been identified in a few bacteria and archaea in recent years. These enzymes form a distinct group within the large family of [NiFe] hydrogenases (Vignais et al., 2001). This list of enzymes includes hydrogenases, three from Escherichia coli (Böhm et al., 1990
; Sauter et al., 1992
), CO-induced hydrogenase from Rhodospirillum rubrum and Carboxydothermus hydrogenoformans (Fox et al., 1996b
; Soboh et al., 2002
) and Ech hydrogenase from Ms. barkeri (Künkel et al., 1998
; Meuer et al., 1999
). The large and small subunits of these hydrogenases show surprisingly little sequence similarity to other (standard) [NiFe] hydrogenases, except for the conserved residues coordinating the active site and the proximal [FeS] cluster (Albracht & Hedderich, 2000
). In addition to the hydrogenase large and small subunits, these enzymes contain four other subunits: two hydrophilic proteins and two integral membrane proteins. These six subunits are conserved and form the basic module of these hydrogenases. To date, only two members of this hydrogenase family have been purified: Ech hydrogenase from Ms. barkeri (Meuer et al., 1999
) and the hydrogenase from C. hydrogenoformans. The latter enzyme forms a tight complex with a CO dehydrogenase and a polyferredoxin (Soboh et al., 2002
). This enzyme complex catalyses the conversion of CO to CO2 and H2. Ech from Ms. barkeri can use a ferredoxin isolated from Ms. barkeri as substrate. Kinetic studies have revealed that ferredoxin reduction by H2 is slightly favoured over H2 evolution using reduced ferredoxin as electron donor (Meuer et al., 1999
). Genetic studies have shown that both reactions are of physiological importance (Meuer et al., 2002
). A few other members of this hydrogenase family having a much more complex subunit architecture, with up to 20 predicted subunits, have been identified. These include the Mbh hydrogenase from Pyrococcus furiosus (Sapra et al., 2000
; Silva et al., 2000
) and the Eha and Ehb hydrogenases from Methanothermobacter species (Tersteegen & Hedderich, 1999
); these enzymes have not yet been purified. The subunits conserved in Ech-type hydrogenases show a striking amino acid sequence similarity to six subunits of the energy-conserving NADH : quinone oxidoreductase, also known as complex I (Albracht & Hedderich, 2000
; Friedrich & Scheide, 2000
; Friedrich & Weiss, 1997
; Hedderich, 2004
; Yano & Ohnishi, 2001
). From growth experiments with R. rubrum and C. hydrogenoformans (Kerby et al., 1995
; Svetlichny et al., 1991
), from cell-suspension experiments and genetic studies with Ms. barkeri (Bott & Thauer, 1989
; Meuer et al., 2002
), and from experiments with inverted membrane vesicles of P. furiosus (Sapra et al., 2003
), it can be inferred that the [NiFe] hydrogenases in these organisms probably pump protons or sodium ions. These enzymes have therefore been designated energy-converting [NiFe] hydrogenases (Ech) (Vignais et al., 2001
).
Here we report the first purification of a member of this hydrogenase family from a fermentative organism. The kinetic data obtained strongly indicate that Ta. tengcongensis ferredoxin is the physiological substrate. Ech from Ta. tengcongensis favours hydrogen evolution over H2 uptake, which is in agreement with its role in H2 production during fermentative growth. The same function has recently been proposed for the Mbh hydrogenase from P. furiosus. The membrane fraction of P. furiosus catalyses H2 production from reduced ferredoxin at high rates (Silva et al., 2000). Addition of reduced ferredoxin to inverted membrane vesicles of P. furiosus results in the generation of both a
pH and a
, which can be coupled to ATP synthesis (Sapra et al., 2003
). This proton respiration is proposed to also operate in Ta. tengcongensis.
The multimeric NADH-dependent Fe-only hydrogenase from Ta. tengcongensis is most closely related to the HndABCD hydrogenase from Dv. fructosovorans and to the HydABC hydrogenase from Tt. maritima (Malki et al., 1995; Verhagen et al., 1999
). The subunit architecture is conserved in the three enzymes, with only a few differences (Fig. 5
). The Ta. tengcongensis enzyme and the Dv. fructosovorans enzyme contain a fourth subunit (HydD and HndB) not present in the Tt. maritima hydrogenase. The function of this subunit, which contains three conserved cysteine residues, is unknown. Subunit HydB of the Tt. maritima and the Ta. tengcongensis enzyme contains an amino-terminal extension of 106 amino acids, which is lacking in the corresponding subunit (HndC) of the Dv. fructosovorans enzyme. This extension of HydB is predicted to ligate a [2Fe2S] cluster. The Tt. maritima HydA subunit contains a carboxy-terminal extension of 65 amino acids with one [2Fe2S] binding motif. This extension is lacking in subunit HydA of the Ta. tengcongensis enzyme and in subunit HndA of the Dv. fructosovorans enzyme.
The low amount of the enzyme from Dv. fructosovorans relative to the other cell proteins has prevented its purification. However, the characterization of an hndC deletion mutant has shown that the enzyme is responsible for the reduction of NADP+ by H2 (Malki et al., 1995). H2-dependent NADP+-reductase activity is 10-fold higher in H2-grown cells. NAD+ is not reduced by cell extracts of Dv. fructosovorans. Therefore, the enzyme from Dv. fructosovorans is thought to function as an NADP+-reducing H2-uptake hydrogenase (Malki et al., 1995
). The HydABC hydrogenase from Tt. maritima has been purified as a heterotrimeric enzyme. Sequence analysis predicts a flavoprotein containing multiple ironsulfur clusters that uses NADH or NADPH as the electron donor. However, the purified enzyme neither contains a flavin nor does it catalyse NAD(P)H-dependent H2 evolution or reduction of NAD(P)+ by H2 (Verhagen et al., 1999
).
In contrast, the enzyme from Ta. tengcongensis contained equimolar amounts of FMN and could utilize NAD(H) as substrate. Analysis of the deduced amino acid sequence of the enzyme predicts the presence of two active sites: the hydrogenase active site containing the H-cluster and the NAD(H) oxidation/reduction active site containing the flavin cofactor. Both active sites are interconnected by a large number of ironsulfur clusters. The activities of the two active sites could be determined individually using viologen dyes as one redox partner. The enzyme catalysed the NADH-dependent reduction of BV and H2 evolution from reduced MV at very high rates. Compared to these activities, the total activity, the NADH-dependent H2 evolution and the reduction of NAD+ by H2 were approximately 130- to 170-fold lower. Hence, the electron transfer between the two catalytic centres must be the rate-limiting step. One possible reason for the low electron transfer rate could be that one of the electron-transferring metal centres became damaged during enzyme purification. However, even in cell extracts, the rate of NADH-dependent H2 evolution was approximately 140-fold lower than the individual activities determined with viologen dyes (not shown). Hence, the low electron transfer rate might be an intrinsic property of the enzyme. On the other hand, the rates of NADH-dependent H2 evolution [0·5 U (mg protein)1] determined in cell extracts should be sufficient to account for the growth of the organism since the rates of glucose consumption in growing cultures were in the same range [0·3 µmol min1 (mg protein)1; data not shown].
In Ta. tengcongensis the Fe-only hydrogenase gene-cluster contains an additional ORF(TTE0891), which does not encode a hydrogenase subunit (Fig. 4). TTE0891 encodes a 21 kDa protein. Closely related proteins (40 % sequence identity) with a similar molecular mass are encoded by the genomes of Tt. maritima (TM1665) and Clostridium thermocellum. While in Tt. maritima the encoding gene is not linked to a hydrogenase gene cluster, in Cl. thermocellum, this gene is part of a gene cluster encoding a putative NAD(H)-dependent Fe-only hydrogenase. This was deduced from the preliminary genome sequence of Cl. thermocellum (http://genome.jgi-psf.org/draft_microbes/cloth/cloth.home.html). A sequence analysis revealed a high level of sequence identity between the amino-terminal domain of the protein from these three organisms (first 90 amino acids) and the ATP-binding kinase domain of histidine kinases (West & Stock, 2001
). The proteins, however, lack the dimerization domain of histidine kinases with the conserved histidine residue. The carboxy-terminal sequence of the protein (90 amino acids) does not show significant sequence similarity to known proteins. Since the ATP-binding domain of histidine kinases is also conserved in the ATPase domain of gyrase B and the chaperone Hsp90, the function of the protein encoded by TTE0891 remains elusive. This gene product could also be involved in hydrogenase assembly. Thus far, accessory genes possibly required for Fe-hydrogenase assembly have not been identified. In addition to the Ta. tengcongensis hydrogenase, the Fe-only hydrogenase from Tt. maritima is the only example studied where non-structural genes (TM1420, TM1421, TM1422, TM1423 and TM1427) are part of the hydrogenase gene-cluster. Three of the five accessory genes associated with the hydrogenase genes in Tt. maritima encode ironsulfur proteins but their function is not yet known (Pan et al., 2003
). In the Ta. tengcongensis genome these genes are also conserved but are not in the proximity of the hydrogenase genes.
Interestingly, both hydrogenases of Ta. tengcongensis are related to complex I. The Fe-only hydrogenase is related to the NADH-dehydrogenase fragment of complex I. The subunits of the enzyme were incorrectly annotated as complex I subunits NuoG (75 kDa subunit), NuoE (24 kDa subunit) and NuoF (51 kDa subunit) (Bao et al., 2002). The results presented here show that these subunits form an Fe-only hydrogenase and are not part of complex I. The [NiFe] hydrogenase is related to the central energy-conserving module of complex I as described above.
Ta. tengcongensis uses the enzymes of the EmbdenMeyerhof pathway to convert glucose to pyruvate. The pathway generates 2 ATP and 2 NADH. Subsequently, pyruvate is oxidized to acetyl-CoA and CO2 via pyruvate : ferredoxin oxidoreductase (POR), thus generating reduced ferredoxin. Acetyl-CoA is converted to acetate via phosphate transacetylase and acetate kinase. The reaction results in the formation of 1 mol ATP per mol acetate. The formation of the enzymes catalysing the different steps has recently been shown in proteomic studies (Wang et al., 2004). Formation of POR was also shown in this study via activity measurements (data not shown). When the p(H2) in the culture was kept low (approx. 104 atm), glucose was completely converted to acetate, CO2 and H2. Thus, both the oxidation of NADH and the oxidation of reduced ferredoxin are coupled to H2 formation. At a p(H2) of 104 atm and glucose, acetate and
, each at a concentration of
10 mM, the
G' for the conversion of glucose to 2 acetate, 2 CO2 and 4 H2 is 329 kJ (mol glucose)1 at 25 °C (Tewes & Thauer, 1980
). At 70 °C, the
G' increases to approximately 352 kJ mol1 (Amend & Plyasunov, 2001
; Amend & Shock, 2001
). This would allow the formation of 5 mol ATP, assuming that +70 kJ are required to drive the synthesis of ATP from ADP and Pi at physiological concentrations and under irreversible conditions (Thauer et al., 1977
). This is significantly more than the 4 mol ATP generated by substrate-level phosphorylation. Hence, the thermodynamic data would allow the conservation of extra energy in the Ech hydrogenase reaction as has been proposed above. In cultures grown in closed bottles, where a p(H2) of up to 101 atm was obtained, the reaction becomes less exergonic (
G'=284 kJ mol1 at 70 °C). Therefore, the metabolism is shifted towards ethanol formation, which results in the formation of less ATP. Under these conditions reduced ferredoxin is the major source for H2 production; more than 50 % of the NADH is oxidized via the reduction of acetyl-CoA to ethanol.
The metabolic shift by Ta. tengcongensis in response to the p(H2) is consistent with the observation that in cells grown in closed bottles, the NADH-dependent hydrogenase activity was lower than in cells grown in the fermenter, whereas ALDH and ADH activities were higher in cells grown in closed bottles. The activity of the ferredoxin-dependent hydrogenase was almost identical under the two culture conditions (Table 5). The changes in the activities of NADH-dependent hydrogenase, ADH and ALDH indicate that either the formation of these enzymes at the transcriptional or translational level is regulated, or these enzymes are directly (in)activated at the protein level.
In this study, the enzymes involved in ethanol production by Ta. tengcongensis were investigated only in cell extracts. In earlier studies, ethanol fermentation has been studied in detail in Ta. ethanolicus, which produces ethanol as the major fermentation product. From this organism, a primary and a so-called secondary ADH have been purified and characterized (Burdette et al., 1996; Burdette & Zeikus, 1994
). Both enzymes utilize a broad range of alcohols as substrates, but the enzymes can be clearly distinguished by their cofactor and substrate preferences. The secondary ADH is specific for NADP(H), while the primary ADH uses both pyridine nucleotides. The secondary ADH also reduces 2-propanol or butan-2-ol, which are not substrates of the primary ADH. The secondary ADH is a bifunctional ADH-acetyl-CoA thioesterase that catalyses the reduction of acetyl-CoA to ethanol. It has been proposed that this is the physiological reaction catalysed by the enzyme in vivo. A Tt. ethanolicus mutant strain that lacks the primary ADH is still able to carry out ethanol fermentation, which indicates that the secondary ADH is responsible for fermentative ethanol production (Burdette et al., 2002
). The Ta. tengcongensis genome contains an ORF (TTE0695) encoding a protein with 96 % sequence identity to the secondary ADH from Tt. ethanolicus. It also contains an ORF (TTE0696) encoding a protein with 91 % sequence identity to the primary ADH of Tt. ethanolicus. The activity profile determined in cell extracts of Ta. tengcongensis (Table 5
) indicated that both ADHs are formed also in Ta. tengcongensis. Although cell extracts of Ta. tengcongensis exhibited high ALDH activity, the genome does not encode an ALDH related to one of the characterized ALDHs. The secondary ADH of Ta. tengcongensis has high sequence identity to the corresponding enzyme from Tt. ethanolicus and therefore is proposed to be bifunctional as well, exhibiting both ADH and ALDH activities. A point to be clarified in a future study is how the NADH generated in the glyceraldehyde-3-phosphate dehydrogenase reaction is converted to NADPH, which is the substrate of the bifunctional ALDH/ADH. Glyceraldehyde-3-phosphate dehydrogenase of Ta. tengcongensis was found to be NAD+-specific (data not shown).
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ACKNOWLEDGEMENTS |
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Received 11 March 2004;
revised 14 April 2004;
accepted 16 April 2004.
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