Characterization of a novel thiosulfate-forming enzyme isolated from Desulfovibrio vulgaris.

An enzyme that formed thiosulfate from bisulfite and trithionate was purified from extracts of Desulfovibrio vulgaris. This enzyme, designated as "thiosulfate-forming" enzyme, required the presence of both bisulfite and trithionate. Various 35S-labeling studies showed that thiosulfate was formed from bisulfite and the inner sulfur atom of trithionate. This involved a nucleophilic attack by the bisulfite ion, resulting in the displacement of the two outer sulfonate groups of trithionate that recycled to participate as free bisulfite in subsequent reactions. This reaction required a reduction, presumably by a concerted mechanism with thiosulfate formation. The natural electron carrier cytochrome c3 participated in this reductive formation of thiosulfate. This reaction was coupled to the bisulfite reductase-catalyzed reaction, which resulted in the reconstruction of a thiosulfate-forming pathway from bisulfite.     

H2, a temperate bacteriophage isolated from Bacillus amyloliquefaciens strain H

Bacillus amyloliquefaciens strain H is lysogenic for a large temperate phage we call H2. H2 has a polyhedral head 85 nm in diameter and a tail of about 17 x 434 nm. H2 lysogenizes Bacillus subtilis between the tyrA and metB genes, and gives specialized transduction of metB and, at lower frequencies, of ilvD and ilvA. The phage carries a thymidylate synthase gene and converts thymine auxotrophs of B. subtilis to prototrophy. The H2 genome is a linear DNA molecule about 129 kb in length. DNA extracted from phage particles grown in B. subtilis is not cut by the restriction endonucleases HaeIII, Fnu4HI, Bsp1286I, and BamHI; the latter enzyme is produced by B. amyloliquefaciens strain H. The prophage in lysogenic B. subtilis cells can be cut by these enzymes. We have isolated H2 mutants that carry the transposon Tn917, or a mutation resulting in clear-plaque morphology, or both.     

Several new substrates for Desulfovibrio vulgaris strain Marburg and a spontaneous mutant from it

The ability of Desulfovibrio vulgaris strain Marburg (DSM 2119) to oxidize alcohols was surveyed in the presence and absence of hydrogen-scavenging anaerobes, Acetobacterium woodii and Methanospirillum hungatei. In the presence of sulfate, D. vulgaris grew not only on ethanol, 1-propanol, and 1-butanol, but also on isobutanol, 1-pentanol, ethyleneglycol, and 1,3-propanediol. Metabolism of these alcohols was simple oxidation to the corresponding acids, except with the last two substrates: ethyleneglycol was oxidized to glycolate plus acetate, 1,3-propanediol to 3-hydroxypropionate plus acetate. Experimental evidence was obtained, suggesting that 2-methoxyethanol was not utilized by all the cells of strain marburg, but by a spontaneous mutant. 2-Methoxyethanol was oxidized to methoxyacetate by the mutant. Co-culture of strain Marburg plus A. woodii grew on ethanol, 1-propanol, 1-butanol, and 1,3-propanediol in the absence of sulfate. Co-culture of strain Marburg plus M. hungatei grew on ethanol, 1-propanol, and 1-butanol, but not on ethyleneglycol and 1,3-propanediol, Co-culture of the mutant plus A. woodii or M. hungatei did not grow on 2-methoxyethanol.     

Rubrerythrin and rubredoxin oxidoreductase in Desulfovibrio vulgaris: a novel oxidative stress protection system

Evidence is presented for an alternative to the superoxide dismutase (SOD)-catalase oxidative stress defense system in Desulfovibrio vulgaris (strain Hildenborough). This alternative system consists of the nonheme iron proteins, rubrerythrin (Rbr) and rubredoxin oxidoreductase (Rbo), the product of the rbo gene (also called desulfoferrodoxin). A Deltarbo strain of D. vulgaris was found to be more sensitive to internal superoxide exposure than was the wild type. Unlike Rbo, expression of plasmid-borne Rbr failed to restore the aerobic growth of a SOD-deficient strain of Escherichia coli. Conversely, plasmid-borne expression of two different Rbrs from D. vulgaris increased the viability of a catalase-deficient strain of E. coli that had been exposed to hydrogen peroxide whereas Rbo actually decreased the viability. A previously undescribed D. vulgaris gene was found to encode a protein having 50% sequence identity to that of E. coli Fe-SOD. This gene also encoded an extended N-terminal sequence with high homologies to export signal peptides of periplasmic redox proteins. The SOD activity of D. vulgaris is not affected by the absence of Rbo and is concentrated in the periplasmic fraction of cell extracts. These results are consistent with a superoxide reductase rather than SOD activity of Rbo and with a peroxidase activity of Rbr. A joint role for Rbo and Rbr as a novel cytoplasmic oxidative stress protection system in D. vulgaris and other anaerobic microorganisms is proposed.     

Thiosulfate Reductase of Desulfovibrio vulgaris

The thiosulfate reductase of Desulfovibrio vulgaris has been purified and some of its properties have been determined. Only one protein component was detected when the purified enzyme was subjected to polyacrylamide gel electrophoresis at pH values of 8.9, 8.0, and 7.6. In the presence of H(2), the enzyme, when coupled to hydrogenase and with methyl viologen as an electron carrier, catalyzed the reduction of thiosulfate to hydogen sulfide. The use of specifically labeled (35)S-thiosulfate revealed that the outer sulfur atom was reduced to sulfide and the inner sulfur atom was released as sulfite. Thus, the enzyme catalyzes the reductive dismutation of thiosulfate to sulfide and sulfite. The molecular weight of the enzyme was determined by sedimentation equilibrium (16,300) and amino acid analysis (15,500). The enzyme sedimented as a single, symmetrical component with a calculated sedimentation coefficient of 2.21S. Amino acid analysis revealed the presence of two half-cystine residues per mole of enzyme and a total of 128 amino acid residues. Carbohydrate and organic phosphorus analyses revealed the presence of 9.2 moles of carbohydrate and 4.8 moles of phosphate per mole of enzyme. The substrate specificity of the enzyme was studied.     

Characteristics of a novel temperate bacteriophage against Staphylococcus arlettae (vB_SarS_BM31)

International Microbiology - Staphylococcus arlettae is a rarely reported coagulase-negative staphylococcus (CoNS) isolated from infected humans and livestock. Observing phage-bacteria interaction...     

Generation of a proton gradient in Desulfovibrio vulgaris

Washed cells of Desulfovibrio vulgaris strain Marburg oxidized H₂, formate, lactate or pyruvate with sulfate, sulfite, trithionate, thiosulfate or oxygen as electron acceptor. CuCl₂ as an inhibitor of periplasmic hydrogenase inhibited H₂ and formate oxidation with sulfur compounds, and lactate oxidation in H₂-grown, but not in lactate-grown cells. H₂ oxidation was sensitive to O₂ concentrations above 2% saturation. Carbon monoxide inhibited the oxidation of all substrates tested. Additions of micromolar H₂ pulses to cells incubated in KCl in the presence of various sulfur compounds (reductant pulse method) resulted in a reversible acidification. This proton release was stimulated by thiocyanate, methyl triphenylphosphonium (MTPP⁺) or valinomycin plus EDTA, and completely inhibited by the uncoupler carbonylcyanide m-chlorophenylhydrazone (CCCP), CuCl₂ or carbon monoxide. The extrapolated H⁺/H₂ ratios obtained with sulfate, sulfite, trithionate or thiosulfate varied from 1.0 to 1.7. Micromolar additions of O₂ to cells incubated in the presence of excess of electron donor (oxidant pulse method) caused proton translocation with extrapolated H⁺/H₂ ratios of 3.9 with H₂, 1.6 with lactate and 2.4 with pyruvate. Since a periplasmic hydrogenase can release at maximum 2 H⁺/H₂, it is concluded that D. vulgaris is able to generate a proton gradient by vectorial proton translocation across the cytoplasmic membrane and by extracellular proton release by a periplasmic hydrogenase.     

Coordination and redox properties of a novel triheme cytochrome from Desulfovibrio vulgaris (Hildenborough)

A high molecular weight multiheme c-type cytochrome from the sulfate-reducing bacterium Desulfovibrio vulgaris (Hildenborough) has been spectroscopically characterized and compared with the tetraheme cytochrome c3. The protein contains a pentacoordinate high-spin heme (gz 6.0) and two hexacoordinate low-spin hemes (gz 2.95, gy 2.27, gx 1.48). From analysis of the g values for the low-spin hemes by the procedure of Blumberg and Peisach (Palmer, 1983) and comparison with with the optical spectra from a variety of c-type cytochromes, it is likely that these low-spin hemes are bound by two histidine residues. The NO derivative displayed typical rhombic EPR features (gx 2.07, gz 2.02, gy 1.99). Addition of azide does not lead to coupling between heme chromophores, but the ligand is accessible to the high-spin heme. The use of a glassy-carbon electrode to perform direct (no promoter) electrochemistry on the cytochrome is illustrated. Differential pulse polarography of the native protein gave two waves with reduction potentials of -59 (5) and -400 (8) mV (versus NHE). The cyanide adduct gave two waves with reduction potentials of -263 (8) and -401 (8) mV. The cytochrome was found to catalyze the reduction of nitrite and hydroxylamine.     

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.     

Homology of Ribosomal Ribonucleic Acid of Desulfovibrio Species with Desulfovibrio vulgaris

Three species of Desulfovibrio were found to have a high degree of ribosomal ribonucleic acid homology with Desulfovibrio vulgaris. Desulfotomaculum nigrificans, which is also a sulfate-reducing anaerobe, had only 38% ribosomal ribonucleic acid homology with D. vulgaris. The homologies of six other unrelated genera were determined and found to be lower than 50%.     

A novel antivirulence element in the temperate bacteriophage HK022.

Lysogens of the temperate lambdoid phage HK022 are immune to superinfection by HK022. Superinfection immunity is conferred in part by the action of the HK022 CI repressor at the O.R operators. In this work, we have identified an additional regulatory element involved in immunity. This site, termed OFR (operator far right), is located just downstream of the cro gene, more than 250 nucleotides distant from OR. The behavior of phage containing a mutation in OFR suggests that the wild-type site functions as an antivirulence element. HK022 OFR- mutants were able to form turbid plaques indistinguishable from those of the wild type. However, they gave rise to virulent derivatives at a far higher frequency than the wild type (approximately 10(-5) for OFR- versus about 10(-9) for the wild type). This frequency was so high that cultures of HK022 OFR- lysogens were rapidly overgrown by virulent derivatives. Whereas virulent mutants arising from a wild-type OFR+ background contained mutations in both OR1 and OR2, virulent derivatives of the OFR- mutant phage contained a single mutation in either OR1 or OR2. We conclude that the wild-type OFR site functions to prevent single mutations in OR from conferring virulence. The mechanism by which OFR acts is not yet clear. Both CI and Cro bound to OFR and repressed a very weak rightward promoter (PFR). It is unlikely that repression of PFR by CI or Cro binding to OFR can account in full for the antivirulence phenotype conferred by this element, since PFR is such a weak promoter. Other models for the possible action of OFR are discussed.     

Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics.

The response of Desulfovibrio vulgaris Hildenborough (DvH), a sulphate-reducing bacterium, to nitrate stress was examined using quantitative proteomic analysis. DvH was stressed with 105 mM sodium nitrate (NaNO(3)), a level that caused a 50% inhibition in growth. The protein profile of stressed cells was compared with that of cells grown in the absence of nitrate using the iTRAQ peptide labelling strategy and tandem liquid chromatography separation coupled with mass spectrometry (quadrupole time-of-flight) detection. A total of 737 unique proteins were identified by two or more peptides, representing 22% of the total DvH proteome and spanning every functional category. The results indicate that this was a mild stress, as proteins involved in central metabolism and the sulphate reduction pathway were unperturbed. Proteins involved in the nitrate reduction pathway increased. Increases seen in transport systems for proline, glycine-betaine and glutamate indicate that the NaNO(3) exposure led to both salt stress and nitrate stress. Up-regulation observed in oxidative stress response proteins (Rbr, RbO, etc.) and a large number of ABC transport systems as well as in iron-sulphur-cluster-containing proteins, however, appear to be specific to nitrate exposure. Finally, a number of hypothetical proteins were among the most significant changers, indicating that there may be unknown mechanisms initiated upon nitrate stress in DvH.     

Isolation and characterization of bacteriophage BCJA1, a novel temperate bacteriophage active against the alkaliphilic bacterium, Bacillus clarkii

The isolation and characterization of a novel bacteriophage active against the obligately alkaliphilic bacterium Bacillus clarkii is described. The bacteriophage, designated BCJA1, is a member of the Siphoviridae family with a B1 morphology. It possesses an isometric head, which measures 65 nm between opposite apices, and a noncontractile tail of 195 nm length. It had a buoyant density of 1.518 g/ml and an estimated particle mass of 37 × 10⁷ daltons. BCJA1 was stable over the pH range of 6–11. A one-step growth experiment conducted at pH 10 demonstrated a latent period of about 40 min and a burst size of approximately 40. The purified bacteriophage appeared to consist of 10 proteins with the major head and tail proteins likely to be of molecular weight 36 500 and 28 000, respectively. The genome size was estimated to be between 32.1 and 34.8 kb. The percent G + C content of purified bacteriophage DNA was 45.6. The wildtype bacteriophage is temperate but a clear plaque mutant was isolated. Received: May 25, 1997 / Accepted: August 5, 1997     

Purification and characterization of desulfoferrodoxin. A novel protein from Desulfovibrio desulfuricans (ATCC 27774) and from Desulfovibrio vulgaris (strain Hildenborough) that contains a distorted rubredoxin center and a mononuclear ferrous center

A new type of non-heme iron protein was purified to homogeneity from extracts of Desulfovibrio desulfuricans (ATCC 27774) and Desulfovibrio vulgaris (strain Hildenborough). This protein is a monomer of 16-kDa containing two iron atoms per molecule. The visible spectrum has maxima at 495, 368, and 279 nm and the EPR spectrum of the native form shows resonances at g = 7.7, 5.7, 4.1 and 1.8 characteristic of a high-spin ferric ion (S = 5/2) with E/D = 0.08. M?ssbauer data indicates the presence of two types of iron: an FeS4 site very similar to that found in desulforedoxin from Desulfovibrio gigas and an octahedral coordinated high-spin ferrous site most probably with nitrogen/oxygen-containing ligands. Due to this rather unusual combination of active centers, this novel protein is named desulfoferrodoxin. Based on NH2-terminal amino acid sequence determined so far, the desulfoferrodoxin isolated from D. desulfuricans (ATCC 27774) appears to be a close analogue to a recently discovered gene product from D. vulgaris (Brumlik, M.J., and Voordouw, G. (1989) J. Bacteriol. 171, 49996-50004), which was suggested to be a rubredoxin oxidoreductase. However, reduced pyridine nucleotides failed to reduce the desulforedoxin-like center of this new protein.     

The adaptive genome of Desulfovibrio vulgaris Hildenborough

Peculiar attributes revealed by sequencing the genome of Desulfovibrio vulgaris Hildenborough are analyzed, particularly in relation to the presence of a phosphotransferase system (PTS). The PTS is a typical bacterial carbohydrate transport system functioning via group translocation. Novel avenues for investigations are proposed emphasizing the metabolic diversity of D. vulgaris Hildenborough, especially the likely utilization of mannose-type sugars. Comparative analysis with PTS from other Gram-negative and Gram-positive bacteria indicates regulatory functions for the PTS of D. vulgaris Hildenborough, including catabolite repression and inducer exclusion. Chemotaxis towards PTS substrates is considered. Evidence suggests that this organism may not be a strict anaerobic sulfate reducer typical of the ocean, but a versatile organism capable of bidirectional transmigration and adaptation to both water and terrestrial environments.     

Ferroxidase activity of recombinant Desulfovibrio vulgaris rubrerythrin

 Rubrerythrin (Rr) is the trivial name given to a non-heme iron protein of unknown function which has been found in anaerobic sulfate-reducing bacteria. Rr is unique in containing both rubredoxin-type FeS₄ and diiron-oxo sites in the same protein. The results described here demonstrate for the recombinant protein that: (a) Rr catalyzes oxidation of Fe²⁺ to Fe³⁺ by O₂, i.e., Rr has ferroxidase activity, (b) both FeS₄ and diiron domains of the Rr protein are required for ferroxidase activity, (c) with excess Fe²⁺ and O₂ the initial rate of this oxidation appears to be first order in [Rr] and independent of starting [Fe²⁺] above 30 μM, (d) the Fe³⁺ is produced in a form which is capable of rapid incorporation into the iron-binding site of ovotransferrin, and (e) the ferroxidase activity of Rr is comparable to that of published ferroxidase activities of apoferritins on a subunit basis. Ferroxidase activity of Rr was monitored either by the rate of increase in absorbance at 315 nm (which lies near an isosbestic point for oxidized and reduced Rr) or by using apoovotransferrin as Fe³⁺ acceptor, and measuring the rate and extent of diferric transferrin formation at 460 nm. No polyironoxyhydroxide aggregates appeared to associate with Rr after the ferroxidase reaction. A truncated form of Rr containing only the diiron domain had little or no ferroxidase activity. Rr could function as one component of a set of enzymes which channels the reaction products of O₂ and Fe²⁺ onto a non-toxic pathway during transient exposure of the bacteria to air.     

Characterization of a trithionate reductase system from Desulfovibrio vulgaris.

A trithionate reductase system was isolated and purified from extracts of Desulfovibrio vulgaris. This system reduced trithionate to thiosulfate and consisted of two proteins. One was bisulfite reductase, an enzyme that reduces bisulfite to trithionate, and the second component was designated TR-1. Both enzymes were required to reduce trithionate to thiosulfate. Flavodoxin and cytochrome c3 from D. vulgaris were tested for their ability to function as electron carriers during trithionate reduction. When molecular hydrogen was the source of electrons for the reduction, both flavodoxin and cytochrome c3 were required. In contrast, when the pyruvate phosphoroclastic system was the reductant, flavodoxin alone participated as the electron carrier. The results indicate that flavodoxin, but not cytochrome c3, interacted with the trithionate reductase system. The cytochrome in the hydrogenase-linked assay functioned as an electron carrier between hydrogenase and flavodoxin.     

Magnetic susceptibility of hydrogenase from Desulfovibrio vulgaris

Magnetization and magnetic susceptibility measurements revealed that the hydrogenase [EC 1.12.2.1] from Desulfovibrio vulgaris Miyazaki F has an independent unpaired electron in its iron-sulfur cluster. The paramagnetic center of the Desulfovibrio hydrogenase is, therefore, different from that in the Chromatium hydrogenase which interacts with another paramagnetic center, probably nickel.