The redox properties and activation of the F420)-non-reactive hydrogenase of Methanobacterium formicicum

Effects of trace element addition on volatile fatty acid conversions in anaerobic granular sludge reactors

The effect of the addition of trace elements on the conversion of a mixture of volatile fatty adds (Acetate, Propionate, Butyrate, in a ratio 3:1:1) by anaerobic granular sludge was investiated. Two Upflow Anaerobic Sludge Bed reactors (pH 7, ranging 30 degrees C) were operated for 140 days at an organic loading rate from 2 g COD l(-1) d(-1) up to 10 g COD l(-1) d(-1) and a hydraulic retention time of 12 hours. One reactor (R1) was supplied with a trace metal cocktail in the basal medium, whereas trace metals were omitted from the influent of the second reactor (R2). As a result, the trace metal concentration in the granules from R2 steadily decreased at a rate of 48 microg metal g(-1) TS d(-1) down to 35% of their initial value. In contrast, trace metals accumulated in granules present in R1. At the end of the experiment, the COD removal efficiencies were 99 and 77% for, respectively, the control (R1) and deprived (R2) reactors. This difference was due to lack of propionate conversion by sludge from R2. No difference in the acetate and butyrate conversion capacity of both reactors was observed. The conversion of acetate, propionate and methanol were stimulated by the continuous addition of metals to the influent, a sludge of R1 had higher maximum specific activity values compared to sludge of R2. However, both sludges had a similar maximum specific activity with butyrate. Surprisingly, maximum specific activity tests using individual trace metals showed that the addition of a particular trace element in the activity test medium did not affect the degradation rates of aspecific substrate, i.e. acetate, propionate, butyrate and methanol.

Influence of Sulfur Metalation on the Accessibility of the Ni(II/I) Couple in [N,N'-Bis(2-mercaptoethyl)-1,5-diazacyclooctanato]nickel(II): Insight into the Redox Properties of [NiFe]-Hydrogenase

A redox model study of [NiFe] hydrogenase has examined a series of five polymetallics based on the metalation of the dithiolate complex [1,5-bis(mercaptoethyl)-1,5-diazacyclooctane]Ni(II), Ni-1. Crystal structures of three polymetallics of the series have been reported earlier: [(Ni-1)(2)()Ni]Cl(2)(), [(Ni-1)(2)()FeCl(2)()](2)(), and [(Ni-1)(3)()(ZnCl)(2)()]Cl(2)(). Two are described here: [(Ni-1)(2)()Pd]Cl(2)().2H(2)()Ocrystallizes in the monoclinic system, space group P2(1)/c with cell constants a = 12.212(4) Å, b = 7.642(2) Å, c = 16.625(3) Å, beta = 107.69(2) degrees, V = 1443.230(0) Å(3), Z = 2, R = 0.051, and R(w) = 0.056. [(Ni-1)(2)()CoCl]PF(6)() crystallizes in the triclinic system, space group P&onemacr;, with cell constants a = 8.14(2) Å, b = 13.85(2) Å, c = 15.67(2) Å, alpha = 113.59(10) degrees, beta = 101.84(14) degrees, gamma = 94.0(2) degrees, V = 1561.620(0)Å(3), Z = 2, R = 0.072, and R(w) = 0.077. In all Ni-1 serves as a bidentate metallothiolate ligand with a "hinge" angle in the range 105-118 degrees and Ni-M distances of 2.7- 3.7 Å. The most accessible redox event is shown by EPR and electrochemistry to reside in the N(2)S(2)Ni unit and is the Ni(II/I) couple. Charge neutralization of the thiolate sulfurs by metalation can (dependent on the interacting metal) stabilize the Ni(I) state as efficiently as methylation forming a thioether. The implication of these results for the heterometallic active site of [NiFe]-hydrogenase as structured from Desulfovibrio gigas (Volbeda, A., et al. Nature, 1995, 373, 580), the generality of the Ni(&mgr;-SR)(2)M hinge structure, and a possible explanation for the unusual redox potentials are discussed.

Biochemical characterization of the 8-hydroxy-5-deazaflavin-reactive hydrogenase from Methanosarcina barkeri Fusaro

The membrane-associated coenzyme F420-reactive hydrogenase of the anaerobic methanogenic archaeon Methanosarcina barkeri Fusaro has been purified 95-fold to apparent homogeneity. A new purification procedure and altered storage conditions gave substantially higher yield (13.4% versus 4.3%) and specific coenzyme F420-reducing activity (82.8 mumol.min-1.mg protein-1 versus 11.5 mumol.min-1.mg protein-1) than reported previously [Fiebig, K. & Friedrich, B. (1989) Eur. J. Biochem. 184, 79-88]. The predominant coenzyme F420-reactive form of the hydrogenase has an apparent molecular mass of 198 kDa and is composed of three non-identical subunits with apparent molecular masses of 48 (alpha), 33 (beta), and 30 kDa (gamma), apparently in a stoichiometry of alpha 2 beta 2 gamma 1. This minimal coenzyme F420-reducing hydrogenase formed aggregates with apparent molecular masses of approximately 845 kDa. 1 mol of the 198-kDa form of hydrogenase contained 2 mol FAD, 2 mol nickel, 28-32 mol non-heme iron, and 34 mol acid-labile sulfur; in addition, 0.2 mol selenium was detected. The isoelectric point was 5.30. The amino acid sequence PXXRXEGH, where X is any amino acid, was found to be conserved in the N-termini of the putative nickel-binding subunits of most [NiFe]- and [NiFeSe]hydrogenases of methanogenic Archaea and Bacteria. However, this motif was not detected in the protein sequences of [Fe]hydrogenases. Maximal coenzyme F420-reducing activity was obtained with reductively reactivated enzyme at 55 degrees C in the pH range 6.5-7.25. The Km values of the purified enzyme for H2 with coenzyme F420 or methylviologen as electron acceptor were extremely low, namely 3 microM and 4 microM. The catalytic efficiency coefficients (kcat/Km) for H2 with both reducible cosubstrates were high: 2.5 x 10(7) M-1.s-1 with coenzyme F420 and 6.9 x 10(7) M-1.s-1 with methylviologen.

Expression of the bile acid-inducible NADH:flavin oxidoreductase gene of Eubacterium sp. VPI 12708 in Escherichia coli

The intestinal microorganism Eubacterium sp. VPI 12708 synthesizes a bile acid-inducible NADH:flavin oxidoreductase (NADH:FOR) which presumably functions in the 7 alpha-dehydroxylation of cholic acid to deoxycholic acid. The baiH gene encoding NADH:FOR was subcloned into an IPTG-inducible expression vector, pBaiH2.2. Escherichia coli DH5 alpha cells transformed with pBaiH2.2 expressed 10-fold higher levels of NADH:FOR upon induction with IPTG than did Eubacterium sp. VPI 12708 cells induced with cholic acid. The NADH:FOR produced by E. coli DH5 alpha(pBaiH2.2) was purified to > 95% electrophoretic homogeneity in three steps. The purified NADH:FOR was similar to that of Eubacterium sp. VPI 12708 in subunit and native M(r) (ca. 72,000 and 210,000, respectively), pH optimum, sensitivity to inhibitors, and electron acceptor specificity. It contained 1 mol of FAD, up to 2 mol of iron, and 1 mol of copper per mol of subunit. The enzyme reduced synthetic quinones, dyes, flavins, and O2 with NADH as the electron donor, but did not reduce disulfide compounds, various unsaturated bile acids, cytochrome c, physiological quinones, or cell fractions from Eubacterium sp. VPI 12708. Addition of purified NADH:FOR to Eubacterium sp. VPI 12708 cell extracts altered the balance of oxidized and reduced bile acid intermediates produced during cholic acid 7 alpha-dehydroxylation, suggesting that the enzyme may regulate the cellular ratio of NAD to NADH.

Distinct redox behaviour of prosthetic groups in ready and unready hydrogenase from Chromatium vinosum

The redox behaviour of the Ni(III)/Ni(II) transition in hydrogenase from Chromatium vinosum is described and compared with the redox behaviour of the nickel ion in the F420-nonreducing hydrogenase from Methanobacterium thermoautotrophicum. Analogous to the situation in the oxidised hydrogenase of Desulfovibrio gigas (Fernandez, V.M., Hatchikian, E.C., Patil, D.S. and Cammack, R. (1986) Biochim. Biophys. Acta 883, 145-154), the C. vinosum enzyme can also exist in two forms: the 'unready' form (EPR characteristics of Ni(III): gx,y,z = 2.32, 2.24, 2.01) and the 'ready' form (EPR characteristics Ni(III): gx,y,z = 2.34, 2.16, 2.01). Like in the oxidised enzyme of M. thermoautotrophicum the Ni(III)/Ni(II) transition for the unready form titrated completely reversible (both at pH 6.0 and pH 8.0). In contrast, the reversibility of the Ni(III)/Ni(II) transition in the ready enzyme was strongly dependent on pH and temperature. At pH 6.0 and 2 degrees C reduction of Ni(III) in ready enzyme was completely irreversible, whereas at pH 8.0 and 30 degrees C Ni(III) in both ready and unready enzyme titrated with E0' = -115 mV (n = 1). Hampered redox equilibration between the ready enzyme and the mediating dyes is interpreted in terms of an obstruction of the electron transfer from nickel at the active site to the artificial electron acceptors in solution. The origin of this obstruction might be related to possible changes in the protein structure induced by the activation process. The E0'-value of the Ni(III)/Ni(II) equilibrium was pH sensitive (-60 mV/delta pH) indicating that reduction of nickel is coupled to a protonation. A similar pH-dependence was observed for the titration of the spin-spin interaction of Ni(III) and a special form of the [3Fe-4S]+ cluster (E0' = +150 mV, pH 8.0, 30 degrees C). Redox equilibration of this coupling was extremely sensitive to pH and temperature. The uncoupled [3Fe-4S]+ cluster titrated pH-independently with E0' = -10 mV (pH 8.0, 30 degrees C).

The structure and mechanism of iron-hydrogenases

Hydrogenases devoid of nickel and containing only Fe-S clusters have been found so far only in some strictly anaerobic bacteria. Four Fe-hydrogenases have been characterized: from Megasphaera elsdenii, Desulfovibrio vulgaris (strain Hildenborough), and two from Clostridium pasteurianum. All contain two or more [4Fe-4S]1+,2+ or F clusters and a unique type of Fe-S center termed the H cluster. The H cluster appears to be remarkably similar in all the hydrogenases, and is proposed as the site of H2 oxidation and H2 production. The F clusters serve to transfer electrons between the H cluster and the external electron carrier. In all of the hydrogenases the H cluster is comprised of at least three Fe atoms, and possibly six. In the oxidized state it contains two types of magnetically distinct Fe atoms, has an S = 1/2 spin state, and exhibits a novel rhombic EPR signal. The reduced cluster is diamagnetic (S = 0). The oxidized H cluster appears to undergo a conformation change upon reduction with H2 with an increase in Fe-Fe distances of about 0.5 A. Studies using resonance Raman, magnetic circular dichroism and electron spin echo spectroscopies suggest that the H cluster has significant non-sulfur coordination. The H cluster has two binding sites for CO, at least one of which can also bind O2. Binding to one site changes the EPR properties of the cluster and gives a photosensitive adduct, but does not affect catalytic activity. Binding to the other site, which only becomes exposed during the catalytic cycle, leads to loss of catalytic activity. Mechanisms of H2 activation and electron transfer are proposed to explain the effects of CO binding and the ability of one of the hydrogenases to preferentially catalyze H2 oxidation.

Soluble hydrogenase of Anabaena cylindrica. Cloning and sequencing of a potential gene encoding the tritium exchange subunit

A gene potentially encoding a subunit of the soluble hydrogenase of Anabaena cylindrica was isolated from a genomic library by screening with a set of redundant oligonucleotides, the sequence of which was deduced from the amino acid sequence of the purified hydrogenase subunit that catalyses tritium exchange. The nucleotide sequence of the potential gene was determined from two overlapping DNA fragments spanning 7237 bp of the A. cylindrica genome. The region sequenced contained an open reading frame encoding a protein of 383 amino acids with a predicted molecular mass of 41,108 Da. The NH2-terminal amino acid sequence of the purified enzyme, determined by Edman degradation, corresponds exactly with that deduced from the nucleic acid sequence. No significant amino acid or nucleotide similarity is evident between this gene and the periplasmic hydrogenases from three species of Desulfovibrio (D. vulgaris, D. baculatus and D. gigas), or with the membrane-bound 'uptake' hydrogenases of Bradyrhizobium japonicum and Rhodobacter capsulatus. This suggests that the soluble enzyme from cyanobacteria represents a discrete class of hydrogenase. The gene encoding the second subunit (m = 50 kDa) of the soluble hydrogenase, which is required for the catalysis of hydrogen production from dithionite-reduced methyl viologen [Ewart, G. D. & Smith, G. D. (1989) Arch. Biochem. Biophys. 268, 327-337], apparently comprises a separate transcription unit since it appears not to be located adjacent to that for the 42-kDa subunit.

Inhibition of Desulfovibrio gigas hydrogenase with copper salts and other metal ions

The effect of several transition metals on the activity of Desulfovibrio gigas hydrogenase has been studied. Co(II) and Ni(II) at a concentration of 1 mM did not modify the activity of the enzyme; nor did they affect the pattern of activation/deactivation. Cu(II) inhibited the active hydrogenase, prepared by treatment with hydrogen, but had little effect on the 'unready' enzyme unless a reductant such as ascorbate was present, in which case inactivation took place either in air or under argon. Hg(II) also inactivated the enzyme irreversible in the 'unready' state without the requirement for reductants. The reaction of H2 uptake with methyl viologen was much more sensitive to inhibition than the H2/tritium exchange activity. EPR spectra of this preparation showed that the rates of decline were [3Fe-4S] signal greater than H2-uptake activity greater than Ni-A signal. Similar results were obtained when the protein was treated with Hg(II). The results demonstrate that the [3Fe-4S] cluster is not essential for H2-uptake activity with methyl viologen, but the integrity of [4Fe-4S] clusters is probably necessary to catalyze the reduction of methyl viologen with hydrogen. D. gigas hydrogenase was found to be highly resistant to digestion by proteases.

Purification and properties of the membrane-associated coenzyme F420-reducing hydrogenase from Methanobacterium formicicum

The membrane-associated coenzyme F420-reducing hydrogenase of Methanobacterium formicicum was purified 87-fold to electrophoretic homogeneity. The enzyme contained alpha, beta, and gamma subunits (molecular weights of 43,000, 36,700, and 28,800, respectively) and formed aggregates (molecular weight, 1,020,000) of a coenzyme F420-active alpha 1 beta 1 gamma 1 trimer (molecular weight, 109,000). The hydrogenase contained 1 mol of flavin adenine dinucleotide (FAD), 1 mol of nickel, 12 to 14 mol of iron, and 11 mol of acid-labile sulfide per mol of the 109,000-molecular-weight species, but no selenium. The isoelectric point was 5.6. The amino acid sequence I-N3-P-N2-R-N1-EGH-N6-V (where N is any amino acid) was conserved in the N-termini of the alpha subunits of the F420-hydrogenases from M. formicicum and Methanobacterium thermoautotrophicum and of the largest subunits of nickel-containing hydrogenases from Desulfovibrio baculatus, Desulfovibrio gigas, and Rhodobacter capsulatus. The purified F420-hydrogenase required reductive reactivation before assay. FAD dissociated from the enzyme during reactivation unless potassium salts were present, yielding deflavoenzyme that was unable to reduce coenzyme F420. Maximal coenzyme F420-reducing activity was obtained at 55 degrees C and pH 7.0 to 7.5, and with 0.2 to 0.8 M KCl in the reaction mixture. The enzyme catalyzed H2 production at a rate threefold lower than that for H2 uptake and reduced coenzyme F420, methyl viologen, flavins, and 7,8-didemethyl-8-hydroxy-5-deazariboflavin. Specific antiserum inhibited the coenzyme F420-dependent but not the methyl viologen-dependent activity of the purified enzyme.

Redox-dependent inactivation of the NAD-dependent hydrogenase from Alcaligenes eutrophus Z1

A novel inactivation mechanism of the NAD-dependent hydrogenase from Alcaligenes eutrophus Z1 comprising redox-dependent steps is described. The model of the hydrogenase inactivation process is proposed which implies that the enzyme may exist in several forms which differ in their stability and spectral properties. One of these forms, existing within a limited (approximately -200 +/- 30 mV) potential range, undergoes a rapid and irreversible inactivation. The dissociation of the FMN prosthetic group from the apohydrogenase appears to be the main reason for the enzyme inactivation. The rationale for the enzyme stabilization under real operational conditions based on the chemical modification of the hydrogenase molecule is suggested.

Effect of redox potential on the activation of the NAD-dependent hydrogenase from Alcaligenes eutrophus Z1

A formal kinetic treatment of the autocatalytic activation cycle of the NAD-dependent hydrogenase from Alcaligenes eutrophus Z1 is presented. The value for the enzyme first-order activation rate constant is estimated to be (2.0 +/- 0.6) s-1 (pH 7.8, 25 degrees C). The effect of the redox potential on the activation properties of the NAD-dependent hydrogenase is studied. Hydrogenase activation is controlled by a midpoint redox potential of approximately -100 mV (pH 7.8). Once activated the enzyme is not immediately transformed back into an inactive state on rapid reoxidation and is able to preserve its catalytic properties for at least 3-4 h of intense oxigenation. Several lines of evidence show that the reductive activation of the NAD-dependent hydrogenase is accompanied by a structural reorganization of the protein. A possible origin of the -100 mV transition is discussed. A model for the activation process of the NAD-dependent hydrogenase is suggested.

Nickel-[iron-sulfur]-selenium-containing hydrogenases from Desulfovibrio baculatus (DSM 1743). Redox centers and catalytic properties

The hydrogenase from Desulfovibrio baculatus (DSM 1743) was purified from each of three different fractions: soluble periplasmic (wash), soluble cytoplasmic (cell disruption) and membrane-bound (detergent solubilization). Plasma-emission metal analysis detected in all three fractions the presence of iron plus nickel and selenium in equimolecular amounts. These hydrogenases were shown to be composed of two non-identical subunits and were distinct with respect to their spectroscopic properties. The EPR spectra of the native (as isolated) enzymes showed very weak isotropic signals centered around g approximately 2.0 when observed at low temperature (below 20 K). The periplasmic and membrane-bound enzymes also presented additional EPR signals, observable up to 77 K, with g greater than 2.0 and assigned to nickel(III). The periplasmic hydrogenase exhibited EPR features at 2.20, 2.06 and 2.0. The signals observed in the membrane-bound preparations could be decomposed into two sets with g at 2.34, 2.16 and approximately 2.0 (component I) and at 2.33, 2.24, and approximately 2.0 (component II). In the reduced state, after exposure to an H2 atmosphere, all the hydrogenase fractions gave identical EPR spectra. EPR studies, performed at different temperatures and microwave powers, and in samples partially and fully reduced (under hydrogen or dithionite), allowed the identification of two different iron-sulfur centers: center I (2.03, 1.89 and 1.86) detectable below 10 K, and center II (2.06, 1.95 and 1.88) which was easily saturated at low temperatures. Additional EPR signals due to transient nickel species were detected with g greater than 2.0, and a rhombic EPR signal at 77 K developed at g 2.20, 2.16 and 2.0. This EPR signal is reminiscent of the Ni-signal C (g at 2.19, 2.14 and 2.02) observed in intermediate redox states of the well characterized Desulfovibrio gigas hydrogenase (Teixeira et al. (1985) J. Biol. Chem. 260, 8942]. During the course of a redox titration at pH 7.6 using H2 gas as reductant, this signal attained a maximal intensity around -320 mV. Low-temperature studies of samples at redox states where this rhombic signal develops (10 K or lower) revealed the presence of a fast-relaxing complex EPR signal with g at 2.25, 2.22, 2.15, 2.12, 2.10 and broad components at higher field. The soluble hydrogenase fractions did not show a time-dependent activation but the membrane-bound form required such a step in order to express full activity.(ABSTRACT TRUNCATED AT 400 WORDS)