Membrane-bound oxygen reductases of the anaerobic sulfate-reducing Desulfovibrio vulgaris Hildenborough: roles in oxygen defence and electron link with periplasmic hydrogen oxidation

Cytoplasmic membranes of the strictly anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough contain two terminal oxygen reductases, a bd quinol oxidase and a cc(b/o)o3 cytochrome oxidase (Cox). Viability assays pointed out that single Δbd, Δcox and double ΔbdΔcox deletion mutant strains were more sensitive to oxygen exposure than the WT strain, showing the involvement of these oxygen reductases in the detoxification of oxygen. The Δcox strain was slightly more sensitive than the Δbd strain, pointing to the importance of the cc(b/o)o3 cytochrome oxidase in oxygen protection. Decreased O2 reduction rates were measured in mutant cells and membranes using lactate, NADH, ubiquinol and menadiol as substrates. The affinity for oxygen measured with the bd quinol oxidase (Km, 300 nM) was higher than that of the cc(b/o)o3 cytochrome oxidase (Km, 620 nM). The total membrane activity of the bd quinol oxidase was higher than that of the cytochrome oxidase activity in line with the higher expression of the bd oxidase genes. In addition, analysis of the ΔbdΔcox mutant strain indicated the presence of at least one O2-scavenging membrane-bound system able to reduce O2 with menaquinol as electron donor with an O2 affinity that was two orders of magnitude lower than that of the bd quinol oxidase. The lower O2 reductase activity in mutant cells with hydrogen as electron donor and the use of specific inhibitors indicated an electron transfer link between periplasmic H2 oxidation and membrane-bound oxygen reduction via the menaquinol pool. This linkage is crucial in defence of the strictly anaerobic bacterium Desulfovibrio against oxygen stress.

Bioremediation of chromate: thermodynamic analysis of the effects of Cr(VI) on sulfate-reducing bacteria

Developing new bioremediation processes for soils and effluents polluted by Cr(VI) requires the selection of the most efficient and the most heavy-metal-resistant bacteria. The effects of Cr(VI) on bioenergetic metabolism in two sulfate-reducing bacteria (SRB), Desulfovibrio vulgaris Hildenborough and Desulfomicrobium norvegicum, were monitored using isothermal microcalorimetry. The complete reduction of Cr(VI) to Cr(III) was studied by spectrophotometry and by speciation using a combination of high-performance liquid chromatography and inductively coupled plasma-mass spectrometry. Results revealed that Cr(VI) induces an inhibition of growth with concomitant production of energy, which can be compared to the reaction of the bacteria to a stress such as oxidative stress. Moreover, the sensitivity of bacteria towards this metal is as a characteristic of the strain, which leads to differences in the kinetics of Cr(VI) reduction. The study by microcalorimetry of heavy metal effects on SRB bioenergetic metabolism thus appears an appropriate tool to identify better strains to be used for industrial bioremediation process development.

Deletion of the hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough hampers hydrogen metabolism and low-redox-potential niche establishment

The hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough encodes a transmembrane redox protein complex (the Hmc complex) that has been proposed to catalyze electron transport linking periplasmic hydrogen oxidation to cytoplasmic sulfate reduction. We have replaced a 5-kb DNA fragment containing most of the hmc operon by the cat gene. The resulting chloramphenicol-resistant mutant D. vulgaris H801 grows normally when lactate or pyruvate serve as electron donors for sulfate reduction. Growth with hydrogen as electron donor for sulfate reduction (acetate and CO2 as the carbon source) is impaired. These results confirm the importance of the Hmc complex in electron transport from hydrogen to sulfate. Mutant H801 is also deficient in low-redox-potential niche establishment. On plates, colony development takes 14 days longer than colony development of the wild-type strain, when the cells use hydrogen as the electron donor. This result suggests that, in addition to transmembrane electron transport from hydrogen to sulfate, the redox reactions catalyzed by the Hmc complex are crucial in establishment of the required low-redox-potential niche that allows single cells to grow into colonies.

Escherichia coli is able to produce heterologous tetraheme cytochrome c(3) when the ccm genes are co-expressed

The production of Desulfovibrio vulgaris Hildenborough cytochrome c(3) (M(r) 13000), which is a tetraheme cytochrome, in Escherichia coli was examined. This cytochrome was successfully produced in an E. coli strain co-expressing the ccmABCDEFGH genes involved in the cytochrome c maturation process. The apocytochrome c(3) was matured in either anaerobic or aerobic conditions, but aerobic growth in the presence of delta-aminolevulinic acid was found to be best for cytochrome c(3) production. Site-directed mutagenesis was performed to investigate the effect of the presence of four amino acids in between the two cysteines of the heme binding sites 2 and 4 on the maturation of holocytochrome c(3) in E. coli.

Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex

The combination of docking algorithms with NMR data has been developed extensively for the studies of protein-ligand interactions. However, to extend this development for the studies of protein-protein interactions, the intermolecular NOE constraints, which are needed, are more difficult to access. In the present work, we describe a new approach that combines an ab initio docking calculation and the mapping of an interaction site using chemical shift variation analysis. The cytochrome c553-ferredoxin complex is used as a model of numerous electron-transfer complexes. The 15N-labeling of both molecules has been obtained, and the mapping of the interacting site on each partner, respectively, has been done using HSQC experiments. 1H and 15N chemical shift analysis defines the area of both molecules involved in the recognition interface. Models of the complex were generated by an ab initio docking software, the BiGGER program (bimolecular complex generation with global evaluation and ranking). This program generates a population of protein-protein docked geometries ranked by a scoring function, combining relevant stabilization parameters such as geometric complementarity surfaces, electrostatic interactions, desolvation energy, and pairwise affinities of amino acid side chains. We have implemented a new module that includes experimental input (here, NMR mapping of the interacting site) as a filter to select the accurate models. Final structures were energy minimized using the X-PLOR software and then analyzed. The best solution has an interface area (1037.4 A2) falling close to the range of generally observed recognition interfaces, with a distance of 10.0 A between the redox centers.

Cytochrome c(3) mutants of Desulfovibrio desulfuricans

To explore the physiological role of tetraheme cytochrome c(3) in the sulfate-reducing bacterium Desulfovibrio desulfuricans G20, the gene encoding the preapoprotein was cloned, sequenced, and mutated by plasmid insertion. The physical analysis of the DNA from the strain carrying the integrated plasmid showed that the insertion was successful. The growth rate of the mutant on lactate with sulfate was comparable to that of the wild type; however, mutant cultures did not achieve the same cell densities. Pyruvate, the oxidation product of lactate, served as a poor electron source for the mutant. Unexpectedly, the mutant was able to grow on hydrogen-sulfate medium. These data support a role for tetraheme cytochrome c(3) in the electron transport pathway from pyruvate to sulfate or sulfite in D. desulfuricans G20.

A sequential electron transfer from hydrogenases to cytochromes in sulfate-reducing bacteria

A central step in the energy metabolism of sulfate-reducing bacteria is the oxidation of molecular hydrogen, catalyzed by a periplasmic hydrogenase. The resulting electrons are then transferred to various electron transport chains and used for cytoplasmic sulfate reduction. The complex formation between [NiFeSe] hydrogenase and the soluble periplasmic polyheme cytochromes from Desulfomicrobium norvegicum was characterized by cross-linking experiments, BIAcore and kinetics analysis. Analysis of electron transfer between [NiFeSe] hydrogenase and octaheme cytochrome c(3) (M(r) 26¿ omitted¿000) pointed out that this cytochrome is reduced faster in the presence of catalytic amounts of tetraheme cytochrome c(3) (M(r) 13¿ omitted¿000) isolated from the same organism. The activation of the hydrogenase-dependent reduction of polyheme cytochromes by cytochrome c(3) (M(r) 13¿ omitted¿000), which is now described in both Desulfovibrio and Desulfomicrobium, is proposed as a general mechanism. During this process, cytochrome c(3) (M(r) 13¿ omitted¿000) would act as an electron shuttle in between hydrogenase and the polyheme cytochromes and its conductivity appears to be an important factor.

15N-labelling and preliminary heteronuclear NMR study of Desulfovibrio vulgaris Hildenborough cytochrome c553

When using heteronuclear NMR, 15N-labelling is necessary for structural analysis, dynamic studies and determination of complex formation. The problems that arise with isotopic labelling of metalloproteins are due to their complex maturation process, which involves a large number of factors. Cytochromes c are poorly expressed in Escherichia coli and the overexpression that is necessary for 15N-labelling, requires an investigation of the expression host and special attention to growth conditions. We have succeeded in the heterologous expression and the complete and uniform isotopic 15N-labelling of the cytochrome c553 from Desulfovibrio vulgaris Hildenborough, in a sulphate-reducing bacterium, D. desulfuricans G200, by using a growth medium combining 15N-ammonium chloride and 15N-Celtone. These conditions allowed us to obtain approximately 0.8 mg x L-1 of pure labelled cytochrome c553. 1H and 15N-assignments for both the oxidized and the reduced states of cytochrome c553 were obtained from two-dimensional heteronuclear experiments. Pseudocontact effects due to the haem Fe3+ have been analysed for the first time through 15N and 1H chemical shifts in a c-type cytochrome.

Key role of phenylalanine 20 in cytochrome c3: structure, stability, and function studies

Aromatic residues in c-type cytochromes might have an important function in the folding and/or electron transferring properties of the molecule. In the tetraheme cytochrome c3 (Mr 13 000) from Desulfovibrio vulgaris Hildenborough, Phe20, is located between heme 1 and heme 3 with its aromatic ring close and almost parallel to the ring plane of heme 1. We replaced this residue by a nonaromatic hydrophobe residue, leucine, and analyzed the effects in terms of functional, structural, and physicochemical properties. While the F20L replacement did not have any strong effects on the heme region stability, a decrease of the thermostability of the whole molecule was observed. In the same way, the four macroscopic redox potentials were affected by the mutation as well as the flexibility of the surface loop around heme 4. The F20L replacement itself and/or this structural modification might be responsible for the loss of the intermolecular cooperativity between F20L cytochrome c3 molecules.

Tyrosine 64 of cytochrome c553 is required for electron exchange with formate dehydrogenase in Desulfovibrio vulgaris Hildenborough

Replacement of tyrosine 64 by alanine in cytochrome c553 from Desulfovibrio vulgarisHildenborough prevents electron transfer with the formate dehydrogenase. Biophysical and biochemical studies show that the protein is correctly folded and that the oxidoreduction potential is not modified. The solution structure of the mutant cytochrome determined by two-dimensional (2D) NMR clearly establishes that the overall fold of the molecule is nearly identical to that of the wild-type cytochrome. The electrostatic surface charge distributions for the wild-type and mutant cytochrome are similar, suggesting that the interaction site of the physiological partners is not modified by the mutation. The lack of the aromatic ring induces slight destabilization of the hydrophobic core of the molecule and modifications of the hydrogen bond at position 64, as well as conformational disorder of the side chain of K63. The loss of the hydrogen bond from tyrosine 64 and the increase of the solvent exposure of the heme are probably responsible of the loss of electron transfer between formate dehydrogenase and cytochrome c553.

The formate dehydrogenase-cytochrome c553 complex from Desulfovibrio vulgaris Hildenborough

The electron transfer between formate dehydrogenase and cytochrome c553 from the anaerobic bacteria Desulfovibrio vulgaris Hildenborough has been investigated. Parameters of the electron transfer kinetics are reported. The ionic strength dependence of the complex formation has been evidenced. Two mutants of cytochrome c553 have been obtained using site-directed mutagenesis with the substitutions K62E and K62E,K63E. According to one-dimensional and two-dimensional NMR analysis, the two variants were found to have the same folding pattern as that of the wild-type cytochrome. The replacements of the lysine residues by acidic groups have important effects on the affinity between the two oxidoreduction partners. K62 and K63 are essential for recognition between the formate dehydrogenase and the cytochrome c553. Previous structural studies of cytochrome c553 have demonstrated the involvement of the polypeptide chain in the modulation of the particular low oxidoreduction potential of this cytochrome. The present study provides evidence that, during the evolution of cytochromes from the anaerobic metabolism to aerobic respiration and photosynthesis, the electrostatic distribution at the recognised encounter surface around the heme is highly conserved in all cytochromes.

The Desulfuromonas acetoxidans triheme cytochrome c7 produced in Desulfovibrio desulfuricans retains its metal reductase activity

Multiheme cytochrome c proteins that belong to class III have been recently shown to exhibit a metal reductase activity, which could be of great environmental interest, especially in metal bioremediation. To get a better understanding of these activities, the gene encoding cytochrome c7 from the sulfur-reducing bacterium Desulfuromonas acetoxidans was cloned from genomic DNA by PCR and expressed in Desulfovibrio desulfuricans G201. The expression system was based on the cyc transcription unit from Desulfovibrio vulgaris Hildenborough and led to the synthesis of holocytochrome c7 when transferred by electrotransformation into the sulfate reducer Desulfovibrio desulfuricans G201. The produced cytochrome was indistinguishable from the protein purified from Desulfuromonas acetoxidans cells with respect to several biochemical and biophysical criteria and exhibited the same metal reductase activities as determined from electrochemical experiments. This suggests that the molecule was correctly folded in the host organism. Desulfovibrio desulfuricans produces functional multiheme c-type cytochromes from bacteria belonging to a different genus and may be considered a suitable host for the heterologous biogenesis of multiheme c-type cytochromes for either structural or engineering studies. This report, which presents the first example of the transformation of a Desulfovibrio desulfuricans strain by electrotransformation, describes work that is the first necessary step of a protein engineering program that aims to specify the structural features that are responsible for the metal reductase activities of multiheme cytochrome c7.

Structural and kinetic studies of the Y73E mutant of octaheme cytochrome c3 (Mr = 26 000) from Desulfovibrio desulfuricans Norway

A combination of structural, kinetic, and interaction experiments has been used to study the role of a highly conserved aromatic residue, Tyr73, parallel to the sixth heme axial ligand of heme 4 in multiheme cytochrome c3 (Mr = 26 000), also called cytochrome cc3 or octaheme cytochrome, from Desulfovibrio desulfuricans Norway. This residue is expected to be involved in intermolecular electron transfer and protein-protein interaction, since heme 4 is described to be the interaction site between physiological partners. The kinetic experiments show that the Y73E replacement provokes no significant change in the electron-transfer reaction with the physiological partner, the [NiFeSe] hydrogenase, but that the protein-protein interaction between cytochrome c3 (Mr = 26 000) and hydrogenase is strongly affected by the mutation. The aromatic residue does not play a role in maintaining the axial heme ligand in a particular orientation, since the mutation did not affect the orientation of histidine 77, the sixth axial ligand of heme 4. The structural analysis by X-ray crystallography clearly shows that a rearrangement of the charged residues in the vicinity of the mutation site is responsible for the change in protein-protein interaction, which is of an electrostatic nature. Lys22 and Arg66, residues which are located at the interacting surface, are twisted toward the mutated position Glu73 in order to compensate for the negative charge and therefore are no longer accessible for the docking with a physiological partner. Tyr73 has instead a structural function and probably a role in maintaining the hydrophobic environment of the heme 4 cavity rather than a function in the intermolecular electron transfer with the physiological partners.

1H-NMR study of the structural influence of Y64 substitution in Desulfovibrio vulgaris Hildenborough cytochrome c553

Y64 has been replaced in cytochrome c553 from Desulfovibrio vulgaris Hildenborough by phenylalanine, leucine, valine, serine and alanine residues. An NMR study of structural variation induced in both oxidoreduction states of the molecule has been carried out by analysing observed chemical-shift variations. Dynamic changes were evidenced using NH exchange. We have observed that the substitution has a drastic effect on the stability of the molecule in the reduced state, although there is no effect on the reduction potential of the cytochrome. Y64-->F substitution induces particular effects on the NH exchange at the N-terminal, C-terminal and central alpha-helices and increases the stability of the oxidized molecule.

Characterization of the cytochromes C from Desulfovibrio desulfuricans G201

A monoheme cytochrome c553 and a hexadecaheme high molecular weight cytochrome (Hmc) have been isolated and characterized from the sulfate-reducing bacteria Desulfovibrio desulfuricans G201, in addition to the tetraheme cytochrome c3 (Mr 13000) that has been previously described. Both cytochromes are homologous with respect to several biochemical properties to the corresponding cytochromes found in other Desulfovibrio species. However, they are acidic proteins while the corresponding molecules, isolated from other Desulfovibrio species, are relatively more basic. The D. desulfuricans cytochrome content appears identical to that of D. vulgaris Hildenborough. Isolation of these cytochromes from a Desulfovibrio desulfuricans strain is of great interest in order to get more insight on the physiological function of these molecules.

A single mutation in the heme 4 environment of Desulfovibrio desulfuricans Norway cytochrome c3 (Mr 26,000) greatly affects the molecule reactivity

The gene encoding Desulfovibrio desulfuricans Norway cytochrome c3 (Mr 26,000), a dimeric octaheme cytochrome belonging to the polyheme cytochrome c3 superfamily, has been cloned and successfully expressed in another sulfate reducing bacteria, D. desulfuricans G201. The gene, named cycD, is monocistronic and encodes a cytochrome precursor of 135 amino acids with an extension at the NH2 terminus of 24 amino acids. This extension acts as a signal sequence which allows export across the cytoplasmic membrane into the periplasmic space. Tyrosine 73, which is in a close contact with the histidine sixth axial ligand to the heme 4 iron atom, has been replaced by a glutamate residue using site-directed mutagenesis. The cytochrome mutant when expressed in D. desulfuricans G201, is correctly folded and matured. A global increase of the oxidoreduction potentials of about 50 mV is measured for the Y73E cytochrome. The mutation also has a strong influence on the interaction of the cytochrome with its redox partner, the hydrogenase. This suggests, like the tetraheme cytochrome c3 (Mr 13, 000), heme 4 is the interactive heme in the cytochrome-hydrogenase complex and that alteration of the heme 4 environment can greatly affect the electron transfer reaction with its redox partner.

The cytochrome c3 superfamily: amino acid sequence of a dimeric octahaem cytochrome c3 (M(r) 26,000) isolated from Desulfovibrio gigas

Cytochrome c3 (M(r) 26000) isolated from Desulfovibrio gigas is a dimeric cytochrome consisting of two identical subunits of 109 amino acids, each of which contains four haem groups. On the basis of its amino acid sequence, this cytochrome clearly belongs to the cytochrome c3 superfamily, and will be classified in class III of the c-type cytochromes as defined by Ambler [(1980) in From Cyclotrons to Cytochromes (Robinson, A. B. and Kaplan, N. O., eds.), pp. 263-279, Academic Press, London]. It contains ten cysteine and nine histidine residues in each subunit, and eight cysteines and eight histidines linked to the four haem groups were found to be invariant on alignment of all known cytochrome c3 sequences. Two intermolecular disulphide bridges have been determined between cysteine residues 5 and 46 of the two monomers. Cytochrome c3 (M(r) 26,000) from D gigas is clearly different from cytochrome c3 (M(r) 13,000) from the same strain, with which it shows only 27% sequence identity. Compared with cytochrome c3 (M(r) 26,000) from D. desulfuricans Norway, the three-dimensional structure of which has been determined, 26.95% of the residues have been conserved. In the enzyme from D. desulfuricans Norway, hydrophobic interactions have been described across the dimer interface. Residues involved in similar interactions seem to be well conserved in the equivalent D. gigas cytochrome. This sequence provides structural data to allow specification of this new subclass of polyhaem cytochromes. Furthermore, D. gigas cytochrome c3 (M(r) 26,000) is the first polyhaem cytochrome shown to contain two disulphide bridges linking two identical subunits, which could induce more rigid folding. The folding and the evolution of this family of polyhaem cytochromes are discussed.

New conformational properties induced by the replacement of Tyr-64 in Desulfovibrio vulgaris Hildenborough ferricytochrome c553 using isotopic exchanges monitored by mass spectrometry

In order to study the conformational stability induced by the replacement of Tyr-64 in Desulfovibrio vulgaris Hildenborough (DvH) cytochrome c553, fast peptic digestion of deuterated protein followed by separation and measurement of related peptides using liquid chromatography coupled to electrospray ionization mass spectrometry was performed. We show that the H-bonding and/or solvent accessibility properties were modified by the single-site mutation. The mutant proteins can be classified into two groups: the Y64F and Y64L mutants with nearly unchanged deuterium incorporation compared to the wild-type protein and the Y64S, Y64V and Y64A mutants with increased deuterium incorporation. The 70-74 peptide was the most affected by mutation of Tyr-64, the phenylalanine mutant inducing slight stabilization whereas the serine mutant was significantly destabilized. In addition, from the analysis of the overlapping 37-57 and 38-57 peptides we can conclude that the amide proton of Tyr-38 has been replaced by deuterium in all proteins.

Study of the new stability properties induced by amino acid replacement of tyrosine 64 in cytochrome C553 from Desulfovibrio vulgaris Hildenborough using electrospray ionization mass spectrometry

Hydrogen/deuterium exchange as well as charge state distribution monitored by electrospray ionization mass spectrometry were demonstrated to be a powerful and effective new tool for probing conformational properties of proteins in solution. In this paper, the influence of single amino acid replacements on the global conformation of cytochrome C553 from Desulfovibrio vulgaris Hildenborough using isotopic exchange monitored by electrospray ionization mass spectrometry is reported. Based on their respective charge state distributions and isotopic exchanges, we have differentiated relative stability of mutants and a ladder classification with the order being wild-type > Y64F = Y64L > Y64V > Y64A, under specific conditions of pH, is proposed.

Interfacial properties of the polyheme cytochrome c3 superfamily from Desulfovibrio

In order to compare the interfacial behavior of the polyheme cytochromes c which belong to the cytochrome c3 superfamily, the monomolecular film technique was used to determine whether and how these metalloproteins interact with (phospho)lipids). Measurements of the variations of surface pressure and surface potential versus time have shown differences in their penetration capacity into phosphatidylcholine, dicaprin, and phosphatidylglycerol films. The Desulfovibrio vulgaris Hildenborough cytochrome with 16 hemes (Hmc) and Desulfovibrio desulfuricans Norway tetra- and octaheme cytochromes c3, which have been assumed to be soluble periplasmic molecules, may be considered as extrinsic membrane proteins, unlike the D. vulgaris Hildenborough cytochrome c3 (Mr 13 000). The interfacial properties are discussed in terms of the available three-dimensional structural data, the electrostatic potential calculation, and the results obtained by hydrophobic cluster analysis of the cytochrome sequences. The very different behavior of the two cytochromes c3 (Mr 13 000) enlightens the role of a particular surface loop in the interaction with a model membrane. A functional interpretation is proposed assuming that the D. vulgaris Hildenborough Hmc and both cytochromes c3 (Mr 13 000) and (Mr 26 000) from the Norway strain might provide the link between periplasmic hydrogen oxidation and cytoplasmic sulfate reduction.

Drastic influence of a single heme axial ligand replacement on the thermostability of cytochrome c3

The thermostability of wild type Desulfovibrio vulgaris Hildenborough tetraheme cytochrome c3 and its H22M, H25M, H35M and H70M mutants was studied by circular dichroism technique in the far UV and Soret regions. It was shown that wild type cytochrome is extremely thermostable and retains structural and functional properties up to 110 degrees C. Mutations do not change overall secondary structure and local structure of the hemes vicinity. All mutants are much more unstable to heat denaturation than the wild type cytochrome. Point mutation (His/Met replacement) results in extraordinary 30-45 degrees C decrease in the protein thermostability depending on the mutation. We may conclude therefore that the heme region is important not only for the functional properties of the cytochrome but also for the overall protein thermostability.

Effects of the Tyr64 substitution on the stability of cytochrome c553, a low oxidoreduction-potential cytochrome from Desulfovibrio vulgaris Hildenborough

Cytochrome c553 from sulfate-reducing bacteria is a low-oxidoreduction-potential cytochrome. The primary and tertiary structures show notable differences when compared to mitochondrial cytochromes. Tyr64 replacement in cytochrome c553 provides evidence that this residue is not directly involved in the potential modulation but is mostly implicated in the hydrogen-bond network around the heme. While the different variants obtained did not induce drastic structural modifications, they did affect the stability of the protein. This decrease of stability in acidic and alkaline environments was observed by variations in the optical spectra and by mass spectrometry. In addition, the mobility of aromatic side-chain was found to be increased in the mutant proteins as monitored by two-dimensional NMR spectroscopy.

Characterization and oxidoreduction properties of cytochrome c3 after heme axial ligand replacements

Cytochrome c3 (M(r) 13,000) is a tetrahemic cytochrome in which the four heme iron atoms are coordinated by 2 histidine residues at the axial positions. The presence of several oxidoreduction centers in the same molecule raises the question of their coupling. To investigate this mechanism, four single mutations were introduced in cytochrome c3 by site-directed mutagenesis, leading to the replacement of each histidine, the sixth axial ligand of the heme iron atom, by a methionine residue. Characterization of the new set of molecules using biochemical and biophysical techniques was carried out. The novel methionine was correctly coordinated to the iron atom of hemes 3 and 4 in H25M and H70M cytochromes c3, respectively, and this coordination induced a large increase in the oxidoreduction potential of the mutated heme. In contrast, in the case of H22M and H35M cytochromes c3, in which the corresponding methionine is in an oxidized form, only slight changes in redox potential values were observed. In H22M, H25M, and H35M cytochromes c3, two conformations of the molecule were possible, in which the methionine is either free or coordinated to the iron atom. The rate constants for the electron exchange reactions between the cytochrome mutants and the hydrogenase were measured using electrochemical techniques. Distinct behaviors were revealed depending on the mutation. The values of the rate constants for the electron exchange reactions are interpreted in terms of intramolecular electron exchange among the four hemes of the cytochrome.

The protein moiety modulates the redox potential in cytochromes c

Cytochrome c is one of the most thoroughly documented oxidoreduction proteins. Its electron transfer activity, which involves an association between the heme group and the polypeptidic chain, is correlated with the redox potential value of the heme group. The redox potential covers a wide range up to 0.8 V, an extreme case being observed in the low-potential cytochromes c from sulfate reducing bacteria. On of the main roles of the polypeptidic moiety consists of modulating the redox potential value of the heme group. In this paper, some structural factors that seem likely to be involved in maintaining the redox potential value are described.

Involvement of electrostatic interactions in cytochrome c complex formations

Structural studies on various electron transfer complexes involving the tetrahemic cytochrome c3 provided evidence that one of the hemes (heme 4) is the interacting site on the molecule. The reactivity of this particular heme is allocated to the positive charges found around the heme group which are strongly involved in the electrostatic interaction processes. Electrostatic and hydrophobic effects in complex formation are considered on the basis of two electron transfer complex examples: the soluble cytochrome c-cytochrome c peroxidase and the membrane bound photosynthetic reaction center.

Site-directed mutagenesis of tetraheme cytochrome c3. Modification of oxidoreduction potentials after heme axial ligand replacement

The nature of the axial ligands of a heme group is an important factor in maintaining the oxidation-reduction potential of a c-type cytochrome. Cytochrome c3 from Desulfovibrio vulgaris Hildenborough contains four bis-histidinyl coordinated hemes with low oxidation-reduction potentials. Site-directed mutagenesis was used to generate a mutant in which histidine 70, the sixth axial ligand of heme 4, has been replaced by a methionine. The mutant protein was expressed in Desulfovibrio desulfuricans G200 at a level similar to the wild type cytochrome. A model for the three-dimensional structure of D. vulgaris Hildenborough cytochrome c3 was generated on the basis of the crystal structure of D. vulgaris Miyazaki cytochrome c3 in order to investigate the effects of the H70M mutation. The model, together with NMR data, suggested that methionine 70 has effectively replaced histidine 70 as the sixth axial ligand of heme 4 without significant alteration of the structure. A large increase of at least 200 mV of one of the four oxidation-reduction potentials was observed by electrochemistry and is interpreted in terms of structure/potential relationships.

Nucleotide sequence of dcrA, a Desulfovibrio vulgaris Hildenborough chemoreceptor gene, and its expression in Escherichia coli

The amino acid sequence of DcrA (Mr = 73,000), deduced from the nucleotide sequence of the dcrA gene from the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, indicates a structure similar to the methyl-accepting chemotaxis proteins from Escherichia coli, including a periplasmic NH2-terminal domain (Mr = 20,700) separated from the cytoplasmic COOH-terminal domain (Mr = 50,300) by a hydrophobic, membrane-spanning sequence of 20 amino acid residues. The sequence homology of DcrA and these methyl-accepting chemotaxis proteins is limited to the COOH-terminal domain. Analysis of dcrA-lacZ fusions in E. coli by Western blotting (immunoblotting) and activity measurements indicated a low-level synthesis of a membrane-bound fusion protein of the expected size (Mr = approximately 137,000). Expression of the dcrA gene under the control of the Desulfovibrio cytochrome c3 gene promoter and ribosome binding site allowed the identification of both full-length DcrA and its NH2-terminal domain in E. coli maxicells.

Identification of the site of interaction between cytochrome c3 and ferredoxin using peptide mapping of the cross-linked complex

Structural studies carried out on a cross-linked complex between cytochrome c3 and ferredoxin I, both isolated from Desulfovibrio desulfuricans Norway, allowed the identification of the site of interaction between the two redox proteins. Staphylococcus aureus proteinase and chymotrypsin digestions led to characterization of peptides containing both cytochrome c3 and ferredoxin sequences. The cytochrome c3 sequences involved in the three isolated cross-linked peptides contained several lysine residues localized around the heme 4 crevice. This analysis stressed the peculiar role of lysines 100, 101, 103, 104 and 113, which could be considered as major cross-link sites, as opposed to the lysines 75, 79 and 82, which could be considered as minor cross-link sites. One cross-linked peptide, containing two ferredoxin sequences joined to one cytochrome c3 sequence, had been isolated, suggesting the possibility of more than one cross-link per covalent complex. All these results led to the identification of heme 4 of cytochrome c3 as the site of interaction for the ferredoxin I. This study confirms the proposal that could be deduced from the hypothetical structure of the complex built by computer graphics modelling (Cambillau, C., Frey, M., Mosse, J., Guerlesquin, F. and Bruschi, M. (1988) Proteins: struct., funct. genet. 4, 63-70).

Ferredoxin electron transfer site on cytochrome c3. Structural hypothesis of an intramolecular electron transfer pathway within a tetra-heme cytochrome

To specify electron exchanges involving Desulfovibrio desulfuricans Norway tetra-heme cytochrome c3, the chemical modification of arginine 73 residue, was performed. Biochemical and biophysical studies have shown that the modified cytochrome retains its ability to both interact and act as an electron carrier with its redox partners, ferredoxin and hydrogenase. Moreover, the chemical modification effects on the cytochrome c3 1H NMR spectrum were similar to that induced by the presence of ferredoxin. This suggests that arginine 73 is localized on the cytochrome c3 ferredoxin interacting site. The identification of heme 4, the closest heme to arginine 73, as the ferredoxin interacting heme helps us to hypothesize about the role of the three other hemes in the molecule. A structural hypothesis for an intramolecular electron transfer pathway, involving hemes 4, 3 and 1, is proposed on the basis of the crystal structures of D. vulgaris Miyazaki and D. desulfuricans Norway cytochromes c3. The unique role of some structural features (alpha helix, aromatic residues) intervening between the heme groups, is proposed.

Structural assignment of the heme potentials of cytochrome c3, using a specifically modified arginine

In view of the assignment of the four redox potentials values to the four heme groups in the crystallographic structure of Desulfovibrio desulfuricans Norway cytochrome c3, a biochemical approach is reported. A singly modified cytochrome c3 on arginine 73 has been prepared. The study of the redox properties of the modified cytochrome by electrochemistry together with the graphic modelisation of the molecule allow to assign the highest redox potential (-165 mV) to the heme 4 in the three dimensional structure.