Spectroscopic investigation and determination of reactivity and structure of the tetraheme cytochrome c3 from Desulfovibrio desulfuricans Essex 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.     

Toxicity of Al to Desulfovibrio desulfuricans

The toxicity of Al to Desulfovibrio desulfuricans G20 was assessed over a period of 8 weeks in a modified lactate C medium buffered at four initial pHs (5.0, 6.5, 7.2, and 8.3) and treated with five levels of added Al (0, 0.01, 0.1, 1.0, and 10 mM). At pH 5, cell population densities decreased significantly and any effect of Al was negligible compared to that of the pH. At pHs 6.5 and 7.2, the cell population densities increased by 30-fold during the first few days and then remained stable for soluble-Al concentrations of <5 x 10(-5) M. In treatments having total-Al concentrations of > or =1 mM, soluble-Al concentrations exceeded 5 x 10(-5) M and limited cell population growth substantially and proportionally. At pH 8.3, soluble-Al concentrations were below the 5 x 10(-5) M toxicity threshold and cell population density increases of 20- to 40-fold were observed. An apparent cell population response to added Al at pH 8.3 was attributed to the presence of large, spirilloidal bacteria (accounting for as much as 80% of the cells at the 10 mM added Al level). Calculations of soluble-Al speciation for the pH 6.5 and 7.2 treatments that showed Al toxicity suggested the possible presence of the Al(13)O(4)(OH)(24)(H(2)O)(12)(7+) "tridecamer" cation and an inverse correlation of the tridecamer concentration and the cell population density. Analysis by (27)Al nuclear magnetic resonance spectroscopy, however, yielded no evidence of this species in freshly prepared samples or those taken 800 days after inoculation. Exclusion of the tridecamer species from the aqueous speciation calculations at pHs 6.5 and 7.2 yielded inverse correlations of the neutral Al(OH)(3) and anionic Al(OH)(4)(-) monomeric species with cell population density, suggesting that one or both of these ions bear primary responsibility for the toxicity observed.     

Toxicity of Al to Desulfovibrio desulfuricans

The toxicity of Al to Desulfovibrio desulfuricans G20 was assessed over a period of 8 weeks in a modified lactate C medium buffered at four initial pHs (5.0, 6.5, 7.2, and 8.3) and treated with five levels of added Al (0, 0.01, 0.1, 1.0, and 10 mM). At pH 5, cell population densities decreased significantly and any effect of Al was negligible compared to that of the pH. At pHs 6.5 and 7.2, the cell population densities increased by 30-fold during the first few days and then remained stable for soluble-Al concentrations of <5 × 10⁻⁵ M. In treatments having total-Al concentrations of ≥1 mM, soluble-Al concentrations exceeded 5 × 10⁻⁵ M and limited cell population growth substantially and proportionally. At pH 8.3, soluble-Al concentrations were below the 5 × 10⁻⁵ M toxicity threshold and cell population density increases of 20- to 40-fold were observed. An apparent cell population response to added Al at pH 8.3 was attributed to the presence of large, spirilloidal bacteria (accounting for as much as 80% of the cells at the 10 mM added Al level). Calculations of soluble-Al speciation for the pH 6.5 and 7.2 treatments that showed Al toxicity suggested the possible presence of the Al₁₃O₄(OH)₂₄(H₂O)₁₂⁷⁺ “tridecamer” cation and an inverse correlation of the tridecamer concentration and the cell population density. Analysis by ²⁷Al nuclear magnetic resonance spectroscopy, however, yielded no evidence of this species in freshly prepared samples or those taken 800 days after inoculation. Exclusion of the tridecamer species from the aqueous speciation calculations at pHs 6.5 and 7.2 yielded inverse correlations of the neutral Al(OH)₃ and anionic Al(OH)₄⁻ monomeric species with cell population density, suggesting that one or both of these ions bear primary responsibility for the toxicity observed.     

Characterization of sulfate transport in Desulfovibrio desulfuricans

Uptake of ³⁵S-labelled sulfate was studied with a new isolate of Desulfovibrio desulfuricans, strain CSN. Micromolar additions of sulfate (1–10 M or nmol/mg protein) to cell suspensions incubated in 150 mM KCl at-1°C were almost completely taken up and accumulated about 5,000-fold. Accumulation was not influenced by incubation in NaCl instead of KCl, by acidic pH (5.5) or by incubation under air for 10 min. In alkaline milieu (pH 8.5), after prolonged contact with air (2 h), or after growth with excess sulfate or thiosulfate as electron acceptor, the amount taken up was diminished approximately by half. Pasteurization inhibited sulfate uptake completely. With increasing concentrations of added sulfate (0.1 to 2.5 mM) the intracellular concentration increased only slowly up to 25 mM, and the accumulation factor decreased down to 8. Sulfate transport was reversible. Accumulated sulfate was rapidly lost from the cells after addition of excess non-labelled sulfate or after addition of the uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP). The ATPase inhibitor dicyclohexylcarbodiimide (DCCD) specifically inhibited sulfate reduction but had no immediate influence on sulfate accumulation. Addition of the phosphate analogue arsenate (5 mM) was without effect. These results were not in favour of an ATP-dependent transport system. The K⁺-H⁺-antiporter nigericin (in 150 mM KCl) and the Na⁺-H⁺-antiporter monensin (in 150 mM NaCl) caused partial inhibition of sulfate accumulation, whereas the K⁺-transporter valinomycin (in 150 mM KCl) and the Na⁺-H⁺ exchange inhibitor amiloride (2 mM) were without effect. The permeant thiocyanate anion (150 mM) inhibited sulfate uptake by 60% at pH 7, and completely at pH 8.5. Although the effects of the different ionophores on the chemiosmotic gradients have not been studied so far, the results indicated that probably both, pH and drive sulfate accumulation and that sulfate is taken up electrogenically in symport with more than 2 protons. The structural sulfate analogues tungstate and molybdate (0.1 mM, each) did not affect sulfate accumulation, although molybdate inhibited sulfate reduction. Chromate completely blocked both of these activities. Sulfite and selenite caused little or no decrease of sulfate accumulation, whereas with thiosulfate and selenate significant inhibition was observed.Abbreviations CCCP carbonyl cyanide m-chlorophenylhydrazone - DCCD dicyclohexylcarbodiimide     

Reduction of uranium by Desulfovibrio desulfuricans.

The possibility that sulfate-reducing microorganisms contribute to U(VI) reduction in sedimentary environments was investigated. U(VI) was reduced to U(IV) when washed cells of sulfate-grown Desulfovibrio desulfuricans were suspended in a bicarbonate buffer with lactate or H2 as the electron donor. There was no U(VI) reduction in the absence of an electron donor or when the cells were killed by heat prior to the incubation. The rates of U(VI) reduction were comparable to those in respiratory Fe(III)-reducing microorganisms. Azide or prior exposure of the cells to air did not affect the ability of D. desulfuricans to reduce U(VI). Attempts to grow D. desulfuricans with U(VI) as the electron acceptor were unsuccessful. U(VI) reduction resulted in the extracellular precipitation of the U(IV) mineral uraninite. The presence of sulfate had no effect on the rate of U(VI) reduction. Sulfate and U(VI) were reduced simultaneously. Enzymatic reduction of U(VI) by D. desulfuricans was much faster than nonenzymatic reduction of U(VI) by sulfide, even when cells of D. desulfuricans were added to provide a potential catalytic surface for the nonenzymatic reaction. The results indicate that enzymatic U(VI) reduction by sulfate-reducing microorganisms may be responsible for the accumulation of U(IV) in sulfidogenic environments. Furthermore, since the reduction of U(VI) to U(IV) precipitates uranium from solution, D. desulfuricans might be a useful organism for recovering uranium from contaminated waters and waste streams.     

Reduction of uranium by Desulfovibrio desulfuricans.

The possibility that sulfate-reducing microorganisms contribute to U(VI) reduction in sedimentary environments was investigated. U(VI) was reduced to U(IV) when washed cells of sulfate-grown Desulfovibrio desulfuricans were suspended in a bicarbonate buffer with lactate or H2 as the electron donor. There was no U(VI) reduction in the absence of an electron donor or when the cells were killed by heat prior to the incubation. The rates of U(VI) reduction were comparable to those in respiratory Fe(III)-reducing microorganisms. Azide or prior exposure of the cells to air did not affect the ability of D. desulfuricans to reduce U(VI). Attempts to grow D. desulfuricans with U(VI) as the electron acceptor were unsuccessful. U(VI) reduction resulted in the extracellular precipitation of the U(IV) mineral uraninite. The presence of sulfate had no effect on the rate of U(VI) reduction. Sulfate and U(VI) were reduced simultaneously. Enzymatic reduction of U(VI) by D. desulfuricans was much faster than nonenzymatic reduction of U(VI) by sulfide, even when cells of D. desulfuricans were added to provide a potential catalytic surface for the nonenzymatic reaction. The results indicate that enzymatic U(VI) reduction by sulfate-reducing microorganisms may be responsible for the accumulation of U(IV) in sulfidogenic environments. Furthermore, since the reduction of U(VI) to U(IV) precipitates uranium from solution, D. desulfuricans might be a useful organism for recovering uranium from contaminated waters and waste streams.     

Cytochrome c3 Mutants of Desulfovibrio desulfuricans

To explore the physiological role of tetraheme cytochrome c₃ 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 c₃ in the electron transport pathway from pyruvate to sulfate or sulfite in D. desulfuricans G20.     

Pyruvate-carbon dioxide exchange reaction of Desulfovibrio desulfuricans

Suh, Byungse (University of Kansas, Lawrence), and J. M. Akagi. Pyruvate-carbon dioxide exchange reaction of Desulfovibrio desulfuricans. J. Bacteriol. 91:2281-2285. 1966.-The pyruvate-CO(2) exchange reaction, catalyzed by Desulfovibrio desulfuricans, required the presence of phosphate and coenzyme A. However, the requirement for phosphate disappeared when the concentration of coenzyme A was increased to a level of 3.8 x 10(-3)m. Passing crude extracts through a diethylaminoethyl-cellulose column and an Amberlite CG-50 ion-exchange column, to remove ferredoxin and cytochrome c(3), resulted in a marked decrease in exchange activity; full activity was restored by the addition of ferredoxin or cytochrome c(3). Fe(++) or Co(++) stimulated the exchange of CO(2) into pyruvate.     

Purification and properties of L-alanine dehydrogenase from Desulfovibrio desulfuricans

The l-alanine dehydrogenase from cell-free extracts of Desulfovibrio desulfuricans was purified approximately 56-fold. The Michaelis constants for the substrates of the amination reaction and the pH optima for the reactions catalyzed by this enzyme closely agree with those reported for other l-alanine dehydrogenases. Pyruvate was found to inhibit the amination reaction. The enzyme was absolutely specific for l-alanine and nicotinamide adenine dinucleotide. Its sensitivity to para-chloromecuribenzoate suggests that sulfhydryl groups may be necessary for enzymatic activity. These extracts also contained a nicotinamide adenine dinucleotide phosphate-specific glutamic dehydrogenase which was separated from the l-alanine dehydrogenase during purification.     

Biorecovery of gold by Escherichia coli and Desulfovibrio desulfuricans

Microbial precipitation of gold was achieved using Escherichia coli and Desulfovibrio desulfuricans provided with H2 as the electron donor. No precipitation was observed using H2 alone or with heat-killed cells. Reduction of aqueous AuIII ions by both strains was demonstrated at pH 7 using 2 mM HAuCl4 solution and the concept was successfully applied to recover 100% of the gold from acidic leachate (115 ppm of AuIII) obtained from jewelry waste. Bioreductive recovery of gold from aqueous solution was achieved within 2 h, giving crystalline Au0 particles (20-50 nm), in the periplasmic space and on the cell surface, and small intracellular nanoparticles. The nanoparticle size was smaller (red suspension) at acidic pH (2.0) as compared to that obtained at pH 6.0 and 7.0 (purple) and 9.0 (dark blue). Comparable nanoparticles were obtained from AuIII test solutions and jewelry leachate.     

The preferred electron acceptor of Desulfovibrio desulfuricans CSN

Abstract: The sulfate-reducing bacterium Desulfovibrio desulfuricans strain CSN (DSM 104) oxidized H₂ with thiosulfate, sulfate, sulfite, nitrite, nitrate and oxygen with rates increasing (in the order listed) from 20 to 525 nmol H₂ min⁻¹ mg⁻¹ protein. Nitrate reduction was induced by nitrate or limiting concentrations of sulfate during growth, while all other activities were constitutive. Oxygen prevented reduction of all other electron acceptors, while nitrate and nitrite blocked the reduction of the sulfur compounds. In the presence of H₂ and reduced sulfur compounds, H₂ was the preferred electron donor. The cells oxidized thiosulfate or sulfite coupled to the reduction of nitrate to ammonia. This represents a novel type of metabolism connecting the sulfur and nitrogen cycles. It is concluded that oxygen is the preferred electron acceptor of D. desulfuricans . Sulfate reduction in oxic environments must be due to different organisms or mechanisms.     

Purification and Properties of a Hydrogenase from Desulfovibrio vulgaris

The soluble hydrogenase of Desulfovibrio vulgaris was purified and some of its properties are described. The molecular weight was determined for the enzyme by sedimentation equilibrium (45,400) and amino acid analysis (44,800). The hydrogenase appears to be a loosely coiled molecule or to have a high axial ratio, which is reflected in an unusually low sedimentation coefficient (2.58S) and a low diffusion coefficient (D 5.85). The molecular weight of the hydrogenase (41,000), as calculated by the Svedberg equation, was in general agreement with the sedimentation equilibrium molecular weight. Amino acid analysis revealed the presence of six halfcystine residues per mole of enzyme and a total of 417 amino acid residues. The specificity of the hydrogenase and its capacity to reduce certain low potential dyes and cytochrome c(3) was studied. Metal analysis of the hydrogenase indicated the presence of 1 mole of ferrous iron per mole of enzyme.     

Biomass-supported palladium catalysts on Desulfovibrio desulfuricans and Rhodobacter sphaeroides

A Rhodobacter sphaeroides-supported dried, ground palladium catalyst ("Rs-Pd(0)") was compared with a Desulfovibrio desulfuricans-supported catalyst ("Dd-Pd(0)") and with unsupported palladium metal particles made by reduction under H2 ("Chem-Pd(0)"). Cell surface-located clusters of Pd(0) nanoparticles were detected on both D. desulfuricans and R. sphaeroides but the size and location of deposits differed among comparably loaded preparations. These differences may underlie the observation of different activities of Dd-Pd(0) and Rs-Pd(0) when compared with respect to their ability to promote hydrogen release from hypophosphite and to catalyze chloride release from chlorinated aromatic compounds. Dd-Pd(0) was more effective in the reductive dehalogenation of polychlorinated biphenyls (PCBs), whereas Rs-Pd(0) was more effective in the initial dehalogenation of pentachlorophenol (PCP) although the rate of chloride release from PCP was comparable with both preparations after 2 h.     

Three-dimensional structure of the nonaheme cytochrome c from Desulfovibrio desulfuricans Essex in the Fe(III) state at 1.89 A resolution

A nine heme group containing cytochrome c isolated from the soluble and membrane fractions of Desulfovibrio desulfuricans Essex, termed nonaheme cytochrome c, was crystallized, and the structure was solved using the multiple wavelength anomalous dispersion (MAD) phasing method. Refinement was carried out to a resolution of 1.89 A, and anisotropic temperature factors were addressed to the iron and sulfur atoms in the model. The structure revealed two cytochrome c(3) like domains with the typical arrangement of four heme centers. Both domains flanked an extra heme buried under the protein surface. This heme is held in position by loop extensions in each of the two domains. Although both the N- and C-terminal tetraheme domains exhibit a fold and heme arrangement very similar to that of cytochrome c(3), they differ considerably in their loop extensions and electrostatic surface. Analysis of the structure provides evidence for a different function of both domains, namely, anchoring the protein in a transmembranous complex with the N-terminal domain and formation of an electron-transfer complex with hydrogenase by the C-terminal domain.