Purification and characterization of cytochrome c3, ferredoxin, and rubredoxin isolated from Desulfovibrio desulfuricans Norway

Unusual Reduction Mechanism of Copper in Cysteine-Rich Environment

Copper-cysteine interactions play an important role in Biology and herein we used the copper-substituted rubredoxin (Cu-Rd) from Desulfovibrio gigas to gain further insights into the copper-cysteine redox chemistry. EPR spectroscopy results are consistent with Cu-Rd harboring a Cu^II center in a sulfur-rich coordination, in a distorted tetrahedral structure ( g_∥,⊥ = 2.183 and 2.032 and A_∥,⊥ = 76.4 × 10^-4 and 12 × 10^-4 cm^-1). In Cu-Rd, two oxidation states at Cu-center (Cu^II and Cu^I) are associated with Cys oxidation-reduction, alternating in the redox cycle, as pointed by electrochemical studies that suggest internal geometry rearrangements associated with the electron transfer processes. The midpoint potential of [Cu^I(S-Cys)₂(Cys-S-S-Cys)]/[Cu^II(S-Cys)₄] redox couple was found to be -0.15 V vs NHE showing a large separation of cathodic and anodic peaks potential (Δ E_p = 0.575 V). Interestingly, sulfur-rich Cu^II-Rd is highly stable under argon in dark conditions, which is thermodynamically unfavorable to Cu-thiol autoreduction. The reduction of copper and concomitant oxidation of Cys can both undergo two possible pathways: oxidative as well as photochemical. Under O₂, Cu^II plays the role of the electron carrier from one Cys to O₂ followed by internal geometry rearrangement at the Cu site, which facilitates reduction at Cu-center to yield Cu^I(S-Cys)₂(Cys-S-S-Cys). Photoinduced (irradiated at λ_ex = 280 nm) reduction of the Cu^II center is observed by UV-visible photolysis (above 300 nm all bands disappeared) and tryptophan fluorescence (∼335 nm peak enhanced) experiments. In both pathways, geometry reorganization plays an important role in copper reduction yielding an energetically compatible donor-acceptor system. This model system provides unusual stability and redox chemistry rather than the universal Cu-thiol auto redox chemistry in cysteine-rich copper complexes.

Extracellular electron transfer from cathode to microbes: application for biofuel production

Extracellular electron transfer in microorganisms has been applied for bioelectrochemical synthesis utilizing microbes to catalyze anodic and/or cathodic biochemical reactions. Anodic reactions (electron transfer from microbe to anode) are used for current production and cathodic reactions (electron transfer from cathode to microbe) have recently been applied for current consumption for valuable biochemical production. The extensively studied exoelectrogenic bacteria Shewanella and Geobacter showed that both directions for electron transfer would be possible. It was proposed that gram-positive bacteria, in the absence of cytochrome C, would accept electrons using a cascade of membrane-bound complexes such as membrane-bound Fe-S proteins, oxidoreductase, and periplasmic enzymes. Modification of the cathode with the addition of positive charged species such as chitosan or with an increase of the interfacial area using a porous three-dimensional scaffold electrode led to increased current consumption. The extracellular electron transfer from the cathode to the microbe could catalyze various bioelectrochemical reductions. Electrofermentation used electrons from the cathode as reducing power to produce more reduced compounds such as alcohols than acids, shifting the metabolic pathway. Electrofuel could be generated through artificial photosynthesis using electrical energy instead of solar energy in the process of carbon fixation.

Incorporation of molybdenum in rubredoxin: models for mononuclear molybdenum enzymes

Molybdenum is found in the active site of enzymes usually coordinated by one or two pyranopterin molecules. Here, we mimic an enzyme with a mononuclear molybdenum-bis pyranopterin center by incorporating molybdenum in rubredoxin. In the molybdenum-substituted rubredoxin, the metal ion is coordinated by four sulfurs from conserved cysteine residues of the apo-rubredoxin and two other exogenous ligands, oxygen and thiol, forming a Mo((VI))-(S-Cys)4(O)(X) complex, where X represents -OH or -SR. The rubredoxin molybdenum center is stabilized in a Mo(VI) oxidation state, but can be reduced to Mo(IV) via Mo(V) by dithionite, being a suitable model for the spectroscopic properties of resting and reduced forms of molybdenum-bis pyranopterin-containing enzymes. Preliminary experiments indicate that the molybdenum site built in rubredoxin can promote oxo transfer reactions, as exemplified with the oxidation of arsenite to arsenate.

Rubredoxin as a paramagnetic relaxation-inducing probe

The paramagnetic effect due to the presence of a metal center with unpaired electrons is no longer considered a hindrance in protein NMR spectroscopy. In the present work, the paramagnetic effect due to the presence of a metal center with unpaired electrons was used to map the interface of an electron transfer complex. Desulfovibrio gigas cytochrome c(3) was chosen as target to study the effect of the paramagnetic probe, Fe-rubredoxin, which produced specific line broadening in the heme IV methyl resonances M2(1) and M18(1). The rubredoxin binding surface in the complex with cytochrome c(3) was identified in a heteronuclear 2D NMR titration. The identified heme methyls on cytochrome c(3) are involved in the binding interface of the complex, a result that is in agreement with the predicted complexes obtained by restrained molecular docking, which shows a cluster of possible solutions near heme IV. The use of a paramagnetic probe in (1)HNMR titration and the mapping of the complex interface, in combination with a molecular simulation algorithm proved to be a valuable strategy to study electron transfer complexes involving non-heme iron proteins and cytochromes.

Oxidative phosphorylation linked to the dissimilatory reduction of elemental sulphur by Desulfovibrio

Hydrogenase and cytochrome c3 purified from Desulfovibrio gigas and D. desulfuricans strain Norway form a soluble complex which is capable of transferring electrons from molecular hydrogen to colloidal sulphur (S0). In this reaction, sulphur is reduced to hydrogen sulphide. Since both strains are capable of growth using elemental sulphur as terminal electron acceptor, it was of interest to check for oxidative phosphorylation in this sulphur reduction sytem. Membranes isolated from D. gigas or D. desulfuricans strain Norway contain hydrogenase and c-type cytochromes and catalyse the H2 leads to S0 reaction. With D. gigas, esterification of orthophosphate is coupled to the membrane-mediated transfer of electrons from H2 to S0. A P/2e ratio of 0.1 was observed and this value could be reduced by the addition of colloidal sulphur with c2 may be more than a purely chemical reaction. Since whole cells can use sulphur flower while cell-free extracts react only with colloidal sulphur, it is evident that cells handle sulphur in a way which is not yet fully understood.

Cr(VI) quantification using an amperometric enzyme-based sensor: Interference and physical and chemical factors controlling the biosensor response in ground waters

The development of an amperometric enzyme-based sensor for chromate (CrO(4)(2-)) quantification in ground waters was investigated. Crucial physical and chemical factors characterising ground waters were tested for their influence or interference on chromate quantification: pH (7.6-8.5), temperature (9-25 degrees C), ionic strength (0-0.2M), oxygen, metals, bicarbonate and sulphate. The biosensor's response was dependent on temperature and pH as sensitivity increased with temperature and was higher at pH 7.6 than at pH 8.5. Sensitivity decreased with ionic strength until 0.1M, and was stable for higher values. Dissolved oxygen did not allow chromate quantification when it was present, but O(2) could be eliminated by adding Na(2)SO(3) or bubbling nitrogen gas into the solution. Bicarbonate did not interfere with chromate quantification by the biosensor. Sulphate was detected with a detection threshold 80 times higher than that of chromate and a lower sensitivity. Several metals (V(V), W(VI), Mn(VII), Mo(VI)) similar to chromate due to their oxidative properties and structure (oxyanions) were tested as possible interfering compounds. The sensitivity of the biosensor for these metals was low and the detection level was 30 times higher than that of chromate. These metal concentrations are usually weaker than chromate concentration in polluted ground waters so that dilution of the sample should allow chromate quantification by the biosensor. This study shows that the cytochrome c(3)-based sensor can detect compounds other than chromate but with a lower sensitivity. Although non-specific for the detection of chromate, it can however be adapted and used for the quantification of chromate in ground waters containing low sulphate concentration.

Overexpression and purification of Treponema pallidum rubredoxin; kinetic evidence for a superoxide-mediated electron transfer with the superoxide reductase neelaredoxin

Superoxide reductases are a class of non-haem iron enzymes which catalyse the monovalent reduction of the superoxide anion O2- into hydrogen peroxide and water. Treponema pallidum (Tp), the syphilis spirochete, expresses the gene for a superoxide reductase called neelaredoxin, having the iron protein rubredoxin as the putative electron donor necessary to complete the catalytic cycle. In this work, we present the first cloning, overexpression in Escherichia coli and purification of the Tp rubredoxin. Spectroscopic characterization of this 6 kDa protein allowed us to calculate the molar absorption coefficient of the 490 nm feature of ferric iron, epsilon=6.9+/-0.4 mM(-1) cm(-1). Moreover, the midpoint potential of Tp rubredoxin, determined using a glassy carbon electrode, was -76+/-5 mV. Reduced rubredoxin can be efficiently reoxidized upon addition of Na(2)IrCl(6)-oxidized neelaredoxin, in agreement with a direct electron transfer between the two proteins, with a stoichiometry of the electron transfer reaction of one molecule of oxidized rubredoxin per one molecule of neelaredoxin. In addition, in presence of a steady-state concentration of superoxide anion, the physiological substrate of neelaredoxin, reoxidation of rubredoxin was also observed in presence of catalytic amounts of superoxide reductase, and the rate of rubredoxin reoxidation was shown to be proportional to the concentration of neelaredoxin, in agreement with a bimolecular reaction, with a calculated k(app)=180 min(-1). Interestingly, similar experiments performed with a rubredoxin from the sulfate-reducing bacteria Desulfovibrio vulgaris resulted in a much lower value of k(app)=4.5 min(-1). Altogether, these results demonstrated the existence for a superoxide-mediated electron transfer between rubredoxin and neelaredoxin and confirmed the physiological character of this electron transfer reaction.

Buildup of polyelectrolyte-protein multilayer assemblies on gold electrodes. Role of the hydrophobic effect

The buildup of layer-by-layer assemblies onto gold surfaces from water-soluble charged polyelectrolytes and proteins is examined using quartz crystal microgravimetry (QCM) and electrochemical techniques. Polyelectrolytes such as poly(styrenesulfonate) and poly(ester sulfonic acid) (Eastman AQ-29D polymer) adsorb spontaneously onto gold, contrary to poly(ethyleneimine). From the modification of the gold surface with a thiol and specific adsorption of polymers under polarization conditions, it is concluded that the hydrophobicity of the gold surface seems to be a determining factor in the adsorption process. Alternate adsorption onto gold resonators first coated with AQ-29D polymer gives stable multilayer films in the case of positively charged lysozyme (pI = 11) or polyheme Desulfovibrio vulgaris Hildenborough cytochrome c3 (pI = 10.5). QCM frequency changes with the number of adsorption steps suggest that a linear increase in film mass occurs. Desulfomicrobium norvegicum polyheme cytochrome c3 (pI = 7), which has a null global charge at neutral pH, is shown to give also stable multilayer AQ-29D/cytochrome c3 films, suggesting that several types of interactions, especially the hydrophobic effect, are involved in the buildup process.

Amperometric cytochrome c3-based biosensor for chromate determination

The chromate reductase activity of cytochrome c(3) (Cyt c(3), M(r) 13000), isolated from the sulfate-reducing bacterium Desulfomicrobium norvegicum, was used to develop an amperometric biosensor to measure chromate (CrO(4)(2-)) bioavailability. The performance of various biosensor configurations for qualitative and quantitative determination of Cr(VI) was studied. Biosensor properties depend on the technique used to immobilize the enzyme on the electrode (glassy carbon electrode). Immobilization of Cyt c(3) by entrapment in poly 3,4-ethylenedioxythiophene films denatured the enzyme, while application of an adsorption technique did not affect enzyme activity but the detection range was limited. The best results were obtained with dialysis membranes, which allowed the determination of Cr(VI) from 0.20 to 6.84 mg l(-1) (3.85-132 microM) with a sensitivity of 35 nA mg(-1) l (1.82 nA microM(-1)). No interference was observed with As(V), As(III) and Fe(III). Only a small amount of Cyt c(3) (372 ng of protein) was needed for this biosensor.

The crystal structure of the hexadeca-heme cytochrome Hmc and a structural model of its complex with cytochrome c(3)

Sulfate-reducing bacteria contain a variety of multi-heme c-type cytochromes. The cytochrome of highest molecular weight (Hmc) contains 16 heme groups and is part of a transmembrane complex involved in the sulfate respiration pathway. We present the 2.42 A resolution crystal structure of the Desulfovibrio vulgaris Hildenborough cytochrome Hmc and a structural model of the complex with its physiological electron transfer partner, cytochrome c(3), obtained by NMR restrained soft-docking calculations. The Hmc is composed of three domains, which exist independently in different sulfate-reducing species, namely cytochrome c(3), cytochrome c(7), and Hcc. The complex involves the last heme at the C-terminal region of the V-shaped Hmc and heme 4 of cytochrome c(3), and represents an example for specific cytochrome-cytochrome interaction.

Spectroscopic investigation and determination of reactivity and structure of the tetraheme cytochromec3fromDesulfovibrio desulfuricansEssex 6

Cytochrome c3, a small (14-kDa) soluble tetraheme protein was isolated from the periplasmic fraction of Desulfovibrio desulfuricans strain Essex 6. Its major physiological function appears to be that of an electron carrier for the periplasmic hydrogenase. It has been also shown to interact with the high-molecular-mass cytochrome complex in the cytoplasmic membrane, which eventually feeds electrons into the membraneous quinone pool, as well as with the membrane-associated dissimilatory sulfite reductase. The EPR spectra show features of four different low-spin Fe(III) hemes. Orthorhombic crystals of cytochrome c3 were obtained and X-ray diffraction data were collected to below 2 A resolution. The structure was solved by molecular replacement using cytochrome c3 from D. desulfuricans ATCC 27774 as a search model.

A membrane-bound cytochrome c3: a type II cytochrome c3 from Desulfovibrio vulgaris Hildenborough

A new tetraheme cytochrome c3 was isolated from the membranes of Desulfovibrio vulgaris Hildenborough (DvH). This cytochrome has a molecular mass of 13.4 kDa and a pI of 5.5 and contains four heme c groups with apparent reduction potentials of -170 mV, -235 mV, -260 mV and -325 mV at pH 7.6. The complete sequence of the new cytochrome, retrieved from the preliminary data of the DvH genome, shows that this cytochrome is homologous to the "acidic" cytochrome c3 from Desulfovibrio africanus (Da). A model for the structure of the DvH cytochrome was built based on the structure of the Da cytochrome. Both cytochromes share structural features that distinguish them from other cytochrome c3 proteins, such as a solvent-exposed heme 1 surrounded by an acidic surface area, and a heme 4 which lacks most of the surface lysine patch proposed to be the site of hydrogenase interaction in other cytochrome c3 proteins. Furthermore, in contrast to previously discovered cytochrome c3 proteins, the genes coding for these two cytochromes are adjacent to genes coding for two membrane-associated FeS proteins, which indicates that they may be part of membrane-bound oxidoreductase complexes. Altogether these observations suggest that the DvH and Da cytochromes are a new type of cytochrome c3 proteins (Type II: TpII-c3) with different redox partners and physiological function than the other cytochrome c3 proteins (Type I: TpI-c3). The DvH TpII-c3 is reduced at considerable rates by the two membrane-bound [NiFe] and [NiFeSe] hydrogenases, but catalytic amounts of TpI-c3 increase these rates two- and fourfold, respectively. With the periplasmic [Fe] hydrogenase TpII-c3 is reduced much slower than TpI-c3, and no catalytic effect of TpI-c3 is observed.

Mapping the cytochrome c553 interacting site using 1H and 15N NMR

Cytochrome c553 is the electron transfer partner of formate dehydrogenase and of [Fel-hydrogenase, two metalloenzymes essential in the metabolism of sulfate reducing bacteria. These two enzymes contain a 'ferredoxin-like' domain which presents 30% identity with Desulfovibrio desulfuricans Norway ferredoxin 1. This was chosen as a model for the 'ferredoxin-like' domain involved in the electron transfer reaction with cytochrome c553. ID NMR titration of complex formation gave us the stoichiometry (1:1) and the dissociation constant of the complex (Kd approximately 3x10(-6) M). 2D heteronuclear NMR experiments were performed to analyze the 1H and 15N chemical shift variations that are induced by the protein-protein recognition. This is the first mapping of the interaction site on a c-type cytochrome, using heteronuclear NMR.

The superoxide dismutase activity of desulfoferrodoxin from Desulfovibrio desulfuricans ATCC 27774

Desulfoferrodoxin (Dfx), a small iron protein containing two mononuclear iron centres (designated centre I and II), was shown to complement superoxide dismutase (SOD) deficient mutants of Escherichia coli [Pianzzola, M.J., Soubes M. & Touati, D. (1996) J. Bacteriol. 178, 6736-6742]. Furthermore, neelaredoxin, a protein from Desulfovibrio gigas containing an iron site similar to centre II of Dfx, was recently shown to have a significant SOD activity [Silva, G., Oliveira, S., Gomes, C.M., Pacheco, I., Liu, M.Y., Xavier, A.V., Teixeira, M., Le Gall, J. & Rodrigues-Pousada, C. (1999) Eur. J. Biochem. 259, 235-243]. Thus, the SOD activity of Dfx isolated from the sulphate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 was studied. The protein exhibits a SOD activity of 70 U x mg-1, which increases approximately 2.5-fold upon incubation with cyanide. Cyanide binds specifically to Dfx centre II, yielding a low-spin iron species with g-values at 2.27 (g perpendicular) and 1.96 (g parallel). Upon reaction of fully oxidized Dfx with the superoxide generating system xanthine/xanthine oxidase, Dfx centres I and II become partially reduced, suggesting that Dfx operates by a redox cycling mechanism, similar to those proposed for other SODs. Evidence for another SOD in D. desulfuricans is also presented - this enzyme is inhibited by cyanide, and N-terminal sequence data strongly indicates that it is an analogue to Cu,Zn-SODs isolated from other sources. This is the first indication that a Cu-containing protein may be present in a sulphate-reducing bacterium.

Cross-linking between cytochrome c3 and flavodoxin from Desulfovibrio gigas

Tetraheme cytochrome c3 (13 kDa) and flavodoxin (16 kDa), are small electron transfer proteins that have been used to mimic, in vitro, part of the electron-transfer chain that operates between substract electron donors and respiratory electron acceptors partners in Desulfovibrio species (Palma, N., Moura, I., LeGall, J., Van Beeumen, J., Wampler, J., Moura, J. J. G. (1994) Biochemistry 33, 6394-6407). The electron transfer between these two proteins is believed to occur through the formation of a specific complex where electrostatic interaction is the main driving force (Stewart, D., LeGall, J., Moura, I., Moura, J.J.G., Peck, H.D., Xavier, A.V., Weiner, P.K. and Wampler, J.E. (1988) Biochemistry 27, 2444-2450, Stewart, D., LeGall, J., Moura, I., Moura, J.J.G., Peck, H.D., Xavier, A.V., Weiner, P., Wampler, J. (1989) Eur. J. Biochem. 185, 695-700). In order to obtain structural information of the pre-complex, a covalent complex between the two proteins was prepared. A water-soluble carbodiimide [EDC (1-ethyl-3(3 dimethylaminopropyl) carbodiimide hydrochloride] was used for the cross linking reaction. The reaction was optimized varying a wide number of experimental parameters such as ionic strength, protein and cross linker concentration, and utilization of different cross linkers and reaction time between the crosslinker and proteins.

The structural origin of nonplanar heme distortions in tetraheme ferricytochromes c3

Resonance Raman (RR) spectroscopy, molecular mechanics (MM) calculations, and normal-coordinate structural decomposition (NSD) have been used to investigate the conformational differences in the hemes in ferricytochromes c3. NSD analyses of heme structures obtained from X-ray crystallography and MM calculations of heme-peptide fragments of the cytochromes c3 indicate that the nonplanarity of the hemes is largely controlled by a fingerprint peptide segment consisting of two heme-linked cysteines, the amino acids between the cysteines, and the proximal histidine ligand. Additional interactions between the heme and the distal histidine ligand and between the heme propionates and the protein also influence the heme conformation, but to a lesser extent than the fingerprint peptide segment. In addition, factors that influence the folding pattern of the fingerprint peptide segment may have an effect on the heme conformation. Large heme structural differences between the baculatum cytochromes c3 and the other proteins are uncovered by the NSD procedure [Jentzen, W., Ma, J.-G., and Shelnutt, J. A. (1998) Biophys. J. 74, 753-763]. These heme differences are mainly associated with the deletion of two residues in the covalently linked segment of hemes 4 for the baculatum proteins. Furthermore, some of these structural differences are reflected in the RR spectra. For example, the frequencies of the structure-sensitive lines (nu4, nu3, and nu2) in the high-frequency region of the RR spectra are lower for the Desulfomicrobium baculatum cytochromes c3 (Norway 4 and 9974) than for the Desulfovibrio (D.) gigas, D. vulgaris, and D. desulfuricans strains, consistent with a more ruffled heme. Spectral decompositions of the nu3 and nu10 lines allow the assignment of the sublines to individual hemes and show that ruffling, not saddling, is the dominant factor influencing the frequencies of the structure-sensitive Raman lines. The distinctive spectra of the baculatum strains investigated are a consequence of hemes 2 and 4 being more ruffled than is typical of the other proteins.

The fermenting bacterium Malonomonas rubra is phylogenetically related to sulfur-reducing bacteria and contains a c-type cytochrome similar to those of sulfur and sulfate reducers

Malonomonas rubra is a microaerotolerant fermenting bacterium which can maintain its energy metabolism for growth by decarboxylation of malonate to acetate. 16S rRNA sequence analysis revealed that M. rubra is closely related to the cluster of mesophilic sulfur-reducing bacteria within the delta subclass of the Proteobacteria, with the fermenting bacterium Pelobacter acidigallici and the sulfur reducers Desulfuromusa kysingii, D. bakii and D. succinoxidans as closest relatives. The cells contain high amounts (up to 12% of the total cell protein content) of a c-type cytochrome which is present mainly (> 60%) in the cytoplasm and to minor parts in the periplasm (> 20%) and associated with the membrane fraction (> 10%), independent of the growth substrate. This cytochrome is a tetraheme cytochrome of 13,700 Da molecular mass with a midpoint redox potential of -0.210 V.M. rubra does not reduce sulfur or ferric iron compounds. Since this cytochrome appears not to be involved in the energy metabolism it is concluded that it is a remnant of sulfur-reducing ancestors of this bacterium, without a conceivable physiological function in its present energy metabolism.

A periplasmic and extracellular c-type cytochrome of Geobacter sulfurreducens acts as a ferric iron reductase and as an electron carrier to other acceptors or to partner bacteria

An extracellular electron carrier excreted into the growth medium by cells of Geobacter sulfurreducens was identified as a c-type cytochrome. The cytochrome was found to be distributed in about equal amounts in the membrane fraction, the periplasmic space, and the surrounding medium during all phases of growth with acetate plus fumarate. It was isolated from periplasmic preparations and purified to homogeneity by cation-exchange chromatography, gel filtration, and hydrophobic interaction chromatography. The electrophoretically homogeneous cytochrome had a molecular mass of 9.57 +/- 0.02 kDa and exhibited in its reduced state absorption maxima at wavelengths of 552, 522, and 419 nm. The midpoint redox potential determined by redox titration was -0.167 V. With respect to molecular mass, redox properties, and molecular features, this cytochrome exhibited its highest similarity to the cytochromes c of Desulfovibrio salexigens and Desulfuromonas acetoxidans. The G. sulfurreducens cytochrome c reduced ferrihydrite (Fe(OH)3), Fe(III) nitrilotriacetic acid, Fe(III) citrate, and manganese dioxide at high rates. Elemental sulfur, anthraquinone disulfonate, and humic acids were reduced more slowly. G. sulfurreducens reduced the cytochrome with acetate as an electron donor and oxidized it with fumarate. Wolinella succinogenes was able to reduce externally provided cytochrome c of G. sulfurreducens with molecular hydrogen or formate as an electron donor and oxidized it with fumarate or nitrate as an electron acceptor. A coculture could be established in which G. sulfurreducens reduced the cytochrome with acetate, and the reduced cytochrome was reoxidized by W. succinogenes in the presence of nitrate. We conclude that this cytochrome can act as iron(III) reductase for electron transfer to insoluble iron hydroxides or to sulfur, manganese dioxide, or other oxidized compounds, and it can transfer electrons to partner bacteria.

Studies on the redox centers of the terminal oxidase from Desulfovibrio gigas and evidence for its interaction with rubredoxin

Rubredoxin-oxygen oxidoreductase (ROO) is the final component of a soluble electron transfer chain that couples NADH oxidation to oxygen consumption in the anaerobic sulfate reducer Desulfovibrio gigas. It is an 86-kDa homodimeric flavohemeprotein containing two FAD molecules, one mesoheme IX, and one Fe-uroporphyrin I per monomer, capable of fully reducing oxygen to water. EPR studies on the native enzyme reveal two components with g values at approximately 2.46, 2.29, and 1.89, which are assigned to low spin hemes and are similar to the EPR features of P-450 hemes, suggesting that ROO hemes have a cysteinyl axial ligation. At pH 7.6, the flavin redox transitions occur at 0 +/- 15 mV for the quinone/semiquinone couple and at -130 +/- 15 mV for the semiquinone/hydroquinone couple; the hemes reduction potential is -350 +/- 15 mV. Spectroscopic studies provided unequivocal evidence that the flavins are the electron acceptor centers from rubredoxin, and that their reduction proceed through an anionic semiquinone radical. The reaction with oxygen occurs in the flavin moiety. These data are strongly corroborated by the finding that rubredoxin and ROO are located in the same polycistronic unit of D. gigas genome. For the first time, a clear role for a rubredoxin in a sulfate-reducing bacterium is presented.

Crystal structure of a dimeric octaheme cytochrome c3 (M(r) 26,000) from Desulfovibrio desulfuricans Norway

BACKGROUND

The octaheme cytochrome C3 (M(r) 26,000; cc3) from Desulfovibrio desulfuricans Norway is a dimeric cytochrome made up of two identical subunits, each containing four heme groups. It is involved in the redox transfer chain of sulfate-reducing bacteria, which links the periplasmic oxidation of hydrogen to the cytoplasmic reduction of sulfate. The amino-acid sequence of cc3 shows similarities to that of the tetraheme cytochrome c3 (M(r) 13,000; c3) from the same bacteria. Structural analysis of cc3 forms a basis for understanding the precise roles of the multiheme-containing redox proteins and the reason for the presence of several different multiheme cytochromes in one bacterial strain.

RESULTS

The crystal structure of cytochrome cc3 has been determined at 2.16 A resolution. The subunits display the c3 structural fold with significant amino-acid substitutions, relative to the tetraheme cytochromes c3, in the regions of the dimer interface. The identical subunits are related by a crystallographic twofold axis, with one heme of each subunit in close contact. The overall structure and the environments of the different heme groups are compared with those of the tetraheme cytochromes c3.

CONCLUSIONS

A common scheme for interactions between these types of cytochrome and their redox partners involves the interaction of a heme crevice, surrounded by positively charged lysine residues, with acidic residues surrounding the redox partner's functional group. Despite the relatively acidic character of cytochrome cc3, the crevice of one heme is surrounded by a high number of positively charged residues, in the same manner as has been reported for cytochromes c3. The environment of this heme is formed by four flexible surface loops which are variable in length and orientation in the different c3-type cytochromes although the overall structural folds are very similar. It has been proposed that this region, adapted in topology and charge, is the interaction site for physiological partners and is also most likely to be the interaction site in the dimeric cytochrome cc3.

Biochemical studies of the c-type cytochromes of the sulfate reducer Desulfovibrio africanus. Characterization of two tetraheme cytochromes c3 with different specificity

Three c-type cytochromes were isolated and characterized from the sulfate reducer Desulfovibrio africanus. A basic tetraheme cytochrome c3 of molecular mass 16 kDa was previously described and we have extended its characterization. Two other c3-type cytochromes, not previously observed, have also been characterized. These include an acidic tetraheme cytochrome c3 of molecular mass 15 kDa and an octaheme dimeric cytochrome c3 with a native size of 35 kDa. This is the first report of the presence of two distinct tetraheme cytochromes c3 in a Desulfovibrio species. The physico-chemical properties of the three cytochromes, including optical properties, iron content, cysteine and histidine content, N-terminal amino sequence and redox properties, are characteristic of cytochrome c3 family. The acidic tetraheme cytochrome c3 exhibited similar midpoint potential values for all four hemes (Em1 = -210 mV; Em2 = -240 mV; Em3 = -260 mV; Em4 = -270 mV), whereas in the basic tetraheme cytochrome c3 one heme had a much more positive potential than the others (Em1 = -90 mV; Em2 = -260 mV; Em3 = -280 mV; Em4 = -290 mV). The acidic tetraheme cytochrome c3 exhibited unique properties including amino-acid composition and poor reactivity towards hydrogenase. However, it is readily reduced by this enzyme in the presence of the basic cytochrome c3. The weak reactivity of the acidic tetraheme cytochrome c3 towards hydrogenase has been correlated with its low content of basic residues.

Thermal stability of the polyheme cytochrome c3 superfamily

The cytochrome c3 superfamily includes Desulfovibrio polyheme cytochromes c. We report the characteristic thermal stability parameters of the Desulfovibrio desulfuricans Norway (D.d.N.) cytochromes c3 (M(r) 13,000 and M(r) 26,000) and the Desulfovibrio vulgaris Hildenborough (D.v.H.) cytochrome c3 (M(r) 13,000) and high molecular mass cytochrome c (Hmc), as obtained with the help of electronic spectroscopy, voltammetric techniques and differential scanning calorimetry. The polyheme cytochromes are denatured over a wide range of temperatures: the D.v.H. cytochrome c3 is highly thermostable (Td = 121 degrees C) contrary to the D.d.N. protein (Td = 73 degrees C). The thermostability of the polyheme cytochromes is redox state dependent. The results are discussed in the light of the structural and functional relationships within the cytochrome c3 superfamily.

Control of the redox potential in c-type cytochromes: importance of the entropic contribution

The enthalpic and entropic components of the redox free energy variation of cytochrome c553 from Desulfovibrio vulgaris Hildenborough and its mutant Y64V, flavocytochrome b2 from Saccharomyces cerevisiae, and the different hemes of cytochromes c3 from Desulfovibrio vulgaris Miyazaki and Desulfovibrio desulfuricans Norway have been determined in 0.1 M Tris-HCl pH 7.0 (7.6 for cytochromes c3) at 25 degrees C by using nonisothermal potentiometric titrations. The set of available experimental data demonstrates that the entropic component plays an important role in the control of the redox potential in c-type and b-type cytochromes. The variation of the entropic component within the class of cytochromes characterized by a positive value of E degrees ' is proposed to be mainly determined by the variation of the exposure of the heme propionates to the solvent. In the case of tetraheme cytochromes c3, the thermodynamic characteristics vary largely among the hemes belonging to the same molecule, which reflects the environmental peculiarities of each heme and also the heme-heme redox interactions. This study substantiates the existence of compensatory effects between large and opposite contributions to E degree ' predicted by all the current theoretical models which are based on electrostatic free energy calculations.

NMR studies and redox titration of the tetraheme cytochrome c3 from Desulfomicrobium baculatum. Identification of the low-potential heme

The tetraheme cytochromes c3 isolated from two strains of Desulfomicrobium baculatum were studied by monitoring the spectral changes undergone during redox titrations followed by 1H NMR. The evolution of the three-protein intensity signals at low field allowed the partial identification of the heme methyl resonances in the spectrum of the fully oxidized state. The chemical shift variation shown by the protons of the aromatic sidechains as well as of the substituents of the higher-potential heme HIII [Coutinho, I. B., Turner, D. L., LeGall, J. & Xavier, A. V. (1993) Biochem. J. 294, 899-908] yielded the assignment of the lower midpoint redox potential to heme HII in the three-dimensional structure. This cross-assignment is achieved by comparing the chemical shifts of the resonances in the spectra obtained at intermediate oxidation levels with the pseudocontact shifts predicted to arise from the three lower-potential hemes. The cross-assignment for the cytochromes from these two strains is different from that of the cytochromes from Desulfovibrio vulgaris and Desulfovibrio gigas.

A blue non-heme iron protein from Desulfovibrio gigas

A novel iron-containing blue protein, named neelaredoxin, was isolated from the sulfate-reducing bacterium Desulfovibrio gigas. It is a monomeric protein with a molecular mass of 15 kDa containing two iron atoms/molecule. The N-terminal sequence of neelaredoxin has similarity to the second domain of desulfoferrodoxin, a protein purified from Desulfovibrio vulgaris Hildenborough. This finding supports the hypothesis that the gene coding for desulfoferrodoxin (rbo) might have arisen from a gene fusion [Brumlik, M. J., Leroy, G., Bruschi, M. & Voordouw, G. (1990) J. Bacteriol. 172, 7289-7292]. The visible spectrum exhibits a single band at 666 nm, responsible for the blue color of the protein, which is completely bleached upon reduction with sodium ascorbate. In the oxidized state the EPR spectrum is complex, exhibiting well-resolved features at g = 7.6, 7.0, 5.9, and 5.8 which are assigned to two high-spin (S = 5/2) mononuclear-iron (III) centers with different rhombic distortions (E/D approximately 0.05 and approximately 0.08). The two iron atoms contribute identically to the visible spectrum as judged from visible redox titrations, from which a reduction potential of +190 mV was determined for both iron sites at pH 7.5. At high pH the visible and the EPR spectra become pH-dependent with a pKa above 9: the 666-nm band shifts to 590 nm and the EPR signals are converted into a signal with gmax approximately 4.7. Neelaredoxin is readily reduced both by H2/hydrogenase/cytochrome c3 and by NADH/NADH-rubredoxin oxidoreductase.

Crystal structure of cytochrome c3 from Desulfovibrio desulfuricans Norway at 1.7 A resolution

The crystal structure of cytochrome c3 (M(r) 13,000) from Desulfovibrio desulfuricans (118 residues, four heme groups) has been crystallographically refined to 1.7 A resolution using a simulated annealing method, based on the structure-model at 2.5 A resolution, already published. The final R-factor for 10,549 reflections was 0.198 covering the range from 5.5 to 1.7 A resolution. The individual temperature factors were refined for a total of 1059 protein atoms, together with 126 bound solvent molecules. The structure has been analyzed with respect to its detailed conformational properties, secondary structure features, temperature factor behaviour, bound solvent sites and heme geometry and ligation. The characteristic secondary structures of the polypeptide chain of this molecule are one extended alpha-helix, a short beta-strand and 13 reverse turns. The four heme groups are located in different structural environments, all highly exposed to solvent. The particular structural features of the heme environments are compared to the four hemes of the cytochrome c3 from Desulfovibrio vulgaris Miyazaki.

Amino-acid sequence of the cytochrome c3 (M(r) 26,000) from Desulfovibrio desulfuricans Norway and a comparison with those of the other polyhemic cytochromes from Desulfovibrio

The amino-acid sequence of an octaheme cytochrome c3 isolated from Desulfovibrio desulfuricans Norway is presented. The protein molecule (M(r) 26,000) comprises two identical subunits of 111 amino acids with the characteristics typical of tetrahemic cytochrome c3 class. Comparisons between the amino-acid sequences and physiological properties of cytochrome c3 (M(r) 26,000) and cytochromes c3 (M(r) 13,000) isolated from various species of Desulfovibrio showed the existence of considerable differences. In order to distinguish between the various subclasses in the cytochrome c3 superfamily, the amino-acid sequence of cytochrome c3 (M(r) 26,000) was compared with six known cytochrome c3 (M(r) 13,000) sequences as well as with the sequence of the four c3-like domains of a high molecular weight cytochrome c (Hmc) containing 16 hemes per molecule of 65,500 Da, isolated from Desulfovibrio vulgaris Hildenborough. The evolution and phylogenetic relationships of these various polyhemic cytochromes are discussed.

Localization and specificity of cytochromes and other electron transfer proteins from sulfate-reducing bacteria

Recently data have accumulated concerning the electron transfer chains of sulfate-reducing bacteria in general and of the genus Desulfovibrio in particular. Because of the ever growing number of newly discovered individual redox proteins, it has become essential to try to assign them to physiologically relevant chains. This work presents some new data concerning the localization of these proteins within the bacterial cell and the specificity of electron transfer between the three types of hydrogenases which have been found so far in Desulfovibrio, namely the iron-only, the iron-nickel and the iron-nickel-selenium enzymes. The iron-only hydrogenase reduces cytochromes which have bis-histidinyl heme ligation or histidinyl-methionyl heme ligation. In contrast, the iron-nickel and iron-nickel-selenium hydrogenases cannot reduce cytochromes having a His-Met heme ligation, but are very active toward the cytochromes having a bis-histidinyl ligand. This observation has been used to demonstrate that the tetraheme cytochrome c3 can exchange electrons with the monoheme cytochrome c553. No clear specificity has been established for the reaction of hydrogenases toward the hexadecaheme cytochromes from either D vulgaris or D gigas.

Recent advances in the characterization of the hexadecahemic cytochrome c from Desulfovibrio

The biochemical characterization of the high molecular mass cytochromes c (Hmc) isolated from Desulfovibrio vulgaris has led to some controversy as regards their molecular size and subunit structure as well as their heme content and redox properties. Recently developed genetic techniques have made it possible to reach some definite conclusions about the structural and functional properties of the cytochrome. The hexadecahemic Hmc comprises four domains which resemble the tetrahemic cytochrome c3: the structure-function relationship between these multihemic proteins is examined. An hypothesis is discussed according to which the Hmc might be a peripherally interacting protein associated with the outer face of the cytoplasmic membrane, where it might interact with periplasmic proteins - [Fe] hydrogenase - and membrane-bound components of the hmc operon.

Characterization of the structure and redox behaviour of cytochrome c3 from Desulfovibrio baculatus by 1H-nuclear-magnetic-resonance spectroscopy

Complete assignment of the aromatic and haem proton resonances in the cytochromes c3 isolated from Desulfovibrio baculatus strains (Norway 4, DSM 1741) and (DSM 1743) was achieved using one- and two-dimensional 1H n.m.r. Nuclear Overhauser enhancements observed between haem and aromatic resonances and between resonances due to different haems, together with the ring-current contributions to the chemical shifts of haem resonances, support the argument that the haem core architecture is conserved in the various cytochromes c3, and that the X-ray structure of the D. baculatus cytochrome c3 is erroneous. The relative orientation of the haems for both cytochromes was determined directly from n.m.r. data. The n.m.r. structures have a resolution of approximately 0.25 nm and are found to be in close agreement with the X-ray structure from D. vulgaris cytochrome c3. The proton assignments were used to relate the highest potential to a specific haem in the three-dimensional structure by monitoring the chemical-shift variation of several haem resonances throughout redox titrations followed by 1H n.m.r. The haem with highest redox potential is not the same as that in other cytochromes c3.

Intramolecular electron transfer in ferredoxin II from Desulfovibrio desulfuricans Norway

In order to elucidate the role of the two (4Fe-4S) clusters in ferredoxins and to determine whether an electron-transfer mechanism may occur between the clusters, the in vitro reduction of cytochrome c3 and cytochrome c553 by Desulfovibrio desulfuricans Norway ferredoxin II was studied using spectrophotometric techniques. Ferredoxin II, covalently cross-linked with either cytochrome c3 or c553, is an obligate intermediate in cytochrome reduction by pyruvate dehydrogenase. Both titration of the complex formation under 1H-NMR spectroscopy and cross-linking experiments between ferredoxin II and either cytochrome c3 or cytochrome c553 gave a stoichiometric ratio of 1:1. Modelling the protein yielded differences between the charge distributions around the two (Fe-S) clusters. The fact that Cluster 2 is blocked in the electron-transfer domain facing the cytochrome interacting heme, indicates Cluster 1 receives electron from pyruvate dehydrogenase. Consecutively, cytochrome reduction occurs owing to an intramolecular electron exchange between the two clusters of the ferredoxin. The properties of two (Fe-S) cluster ferredoxins are compared to those of monocluster ferredoxins and discussed in evolutionary terms.