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Fida TT, Voordouw J, Ataeian M, Kleiner M, Okpala G, Mand J, Voordouw G. Synergy of Sodium Nitroprusside and Nitrate in Inhibiting the Activity of Sulfate Reducing Bacteria in Oil-Containing Bioreactors. Front Microbiol 2018; 9:981. [PMID: 29867883 PMCID: PMC5965020 DOI: 10.3389/fmicb.2018.00981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/26/2018] [Indexed: 11/13/2022] Open
Abstract
Sodium nitroprusside (SNP) disrupts microbial biofilms through the release of nitric oxide (NO). The actions of SNP on bacteria have been mostly limited to the genera Pseudomonas, Clostridium, and Bacillus. There are no reports of its biocidal action on sulfate-reducing bacteria (SRB), which couple the reduction of sulfate to sulfide with the oxidation of organic electron donors. Here, we report the inhibition and kill of SRB by low SNP concentrations [0.05 mM (15 ppm)] depending on biomass concentration. Chemical reaction of SNP with sulfide did not compromise its efficacy. SNP was more effective than five biocides commonly used to control SRB. Souring, the SRB activity in oil reservoirs, is often controlled by injection of nitrate. Control of SRB-mediated souring in oil-containing bioreactors was inhibited by 4 mM (340 ppm) of sodium nitrate, but required only 0.05 mM (15 ppm) of SNP. Interestingly, nitrate and SNP were found to be highly synergistic with 0.003 mM (1 ppm) of SNP and 1 mM (85 ppm) of sodium nitrate being sufficient in inhibiting souring. Hence, using SNP as an additive may greatly increase the efficacy of nitrate injection in oil reservoirs.
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Affiliation(s)
- Tekle T Fida
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Johanna Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Maryam Ataeian
- Department of Geosciences, University of Calgary, Calgary, AB, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Gloria Okpala
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jaspreet Mand
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Gerrit Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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Leavitt WD, Bradley AS, Santos AA, Pereira IAC, Johnston DT. Sulfur Isotope Effects of Dissimilatory Sulfite Reductase. Front Microbiol 2015; 6:1392. [PMID: 26733949 PMCID: PMC4690157 DOI: 10.3389/fmicb.2015.01392] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/23/2015] [Indexed: 12/01/2022] Open
Abstract
The precise interpretation of environmental sulfur isotope records requires a quantitative understanding of the biochemical controls on sulfur isotope fractionation by the principle isotope-fractionating process within the S cycle, microbial sulfate reduction (MSR). Here we provide the only direct observation of the major (34S/32S) and minor (33S/32S, 36S/32S) sulfur isotope fractionations imparted by a central enzyme in the energy metabolism of sulfate reducers, dissimilatory sulfite reductase (DsrAB). Results from in vitro sulfite reduction experiments allow us to calculate the in vitro DsrAB isotope effect in 34S/32S (hereafter, 34εDsrAB) to be 15.3 ± 2‰, 2σ. The accompanying minor isotope effect in 33S, described as 33λDsrAB, is calculated to be 0.5150 ± 0.0012, 2σ. These observations facilitate a rigorous evaluation of the isotopic fractionation associated with the dissimilatory MSR pathway, as well as of the environmental variables that govern the overall magnitude of fractionation by natural communities of sulfate reducers. The isotope effect induced by DsrAB upon sulfite reduction is a factor of 0.3–0.6 times prior indirect estimates, which have ranged from 25 to 53‰ in 34εDsrAB. The minor isotope fractionation observed from DsrAB is consistent with a kinetic or equilibrium effect. Our in vitro constraints on the magnitude of 34εDsrAB is similar to the median value of experimental observations compiled from all known published work, where 34εr−p = 16.1‰ (r–p indicates reactant vs. product, n = 648). This value closely matches those of MSR operating at high sulfate reduction rates in both laboratory chemostat experiments (34εSO4−H2S = 17.3 ± 1.5‰, 2σ) and in modern marine sediments (34εSO4−H2S = 17.3 ± 3.8‰). Targeting the direct isotopic consequences of a specific enzymatic processes is a fundamental step toward a biochemical foundation for reinterpreting the biogeochemical and geobiological sulfur isotope records in modern and ancient environments.
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Affiliation(s)
- William D Leavitt
- Department of Earth and Planetary Sciences, Harvard UniversityCambridge, MA, USA; Department of Earth and Planetary Sciences, Washington University in St. LouisSt. Louis, MO, USA
| | - Alexander S Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis St. Louis, MO, USA
| | - André A Santos
- Bacterial Energy Metabolism Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Inês A C Pereira
- Bacterial Energy Metabolism Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - David T Johnston
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
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3
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Lobo SA, Lawrence AD, Romão CV, Warren MJ, Teixeira M, Saraiva LM. Characterisation of Desulfovibrio vulgaris haem b synthase, a radical SAM family member. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1238-47. [DOI: 10.1016/j.bbapap.2014.03.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 11/27/2022]
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4
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Zhou C, Vannela R, Hyun SP, Hayes KF, Rittmann BE. Growth of Desulfovibrio vulgaris when respiring U(VI) and characterization of biogenic uraninite. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:6928-6937. [PMID: 24871825 DOI: 10.1021/es501404h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The capacity of Desulfovibrio vulgaris to reduce U(VI) was studied previously with nongrowth conditions involving a high biomass concentration; thus, bacterial growth through respiration of U(VI) was not proven. In this study, we conducted a series of batch tests on U(VI) reduction by D. vulgaris at a low initial biomass (10 to 20 mg/L of protein) that could reveal biomass growth. D. vulgaris grew with U(VI) respiration alone, as well as with simultaneous sulfate reduction. Patterns of growth kinetics and solids production were affected by sulfate and Fe(2+). Biogenic sulfide nonenzymatically reduced 76% of the U(VI) and greatly enhanced the overall reduction rate in the absence of Fe(2+) but was rapidly scavenged by Fe(2+) to form FeS in the presence of Fe(2+). Biogenic U solids were uraninite (UO2) nanocrystallites associated with 20 mg/g biomass as protein. The crystallite thickness of UO2 was 4 to 5 nm without Fe(2+) but was <1.4 nm in the presence of Fe(2+), indicating poor crystallization inhibited by adsorbed Fe(2+) and other amorphous Fe solids, such as FeS or FeCO3. This work fills critical gaps in understanding the metabolic utilization of U by microorganisms and formation of UO2 solids in bioremediation sites.
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Affiliation(s)
- Chen Zhou
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University , Tempe, Arizona 85207-5701, United States
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5
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da Silva SM, Pacheco I, Pereira IAC. Electron transfer between periplasmic formate dehydrogenase and cytochromes c in Desulfovibrio desulfuricans ATCC 27774. J Biol Inorg Chem 2012; 17:831-8. [DOI: 10.1007/s00775-012-0900-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 04/08/2012] [Indexed: 10/28/2022]
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6
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Marques M, Coelho R, Pereira IAC, Matias PM. Purification, crystallization and preliminary crystallographic analysis of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:920-2. [PMID: 19724133 PMCID: PMC2795601 DOI: 10.1107/s1744309109031261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 08/07/2009] [Indexed: 11/11/2022]
Abstract
The [NiFeSe] hydrogenases belong to a subgroup of the [NiFe] proteins in which a selenocysteine is a ligand of the Ni. These enzymes demonstrate interesting catalytic properties, showing a very high H(2)-producing activity that is sustained in the presence of low O(2) concentrations. The purification, crystallization and preliminary X-ray diffraction analysis of the [NiFeSe] hydrogenase isolated from Desulfovibrio vulgaris Hildenborough are reported. Crystals of the soluble form of this hydrogenase were obtained using 20% PEG 1500 as a precipitant and belonged to the monoclinic space group P2(1), with unit-cell parameters a = 60.57, b = 91.05, c = 66.85 A, beta = 101.46 degrees. Using an in-house X-ray diffraction system, they were observed to diffract X-rays to 2.4 A resolution.
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Affiliation(s)
- Marta Marques
- ITQB – Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Ricardo Coelho
- ITQB – Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Inês A. C. Pereira
- ITQB – Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Pedro M. Matias
- ITQB – Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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7
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The tetraheme cytochrome from Shewanella oneidensis MR-1 shows thermodynamic bias for functional specificity of the hemes. J Biol Inorg Chem 2008; 14:375-85. [DOI: 10.1007/s00775-008-0455-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2008] [Accepted: 11/14/2008] [Indexed: 10/21/2022]
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8
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The haem–copper oxygen reductase of Desulfovibrio vulgaris contains a dihaem cytochrome c in subunit II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1528-34. [DOI: 10.1016/j.bbabio.2008.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 09/02/2008] [Accepted: 09/15/2008] [Indexed: 11/20/2022]
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9
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Purification, crystallization and preliminary crystallographic analysis of a dissimilatory DsrAB sulfite reductase in complex with DsrC. J Struct Biol 2008; 164:236-9. [DOI: 10.1016/j.jsb.2008.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 07/22/2008] [Indexed: 11/18/2022]
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10
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Paquete CM, Pereira PM, Catarino T, Turner DL, Louro RO, Xavier AV. Functional properties of type I and type II cytochromes c3 from Desulfovibrio africanus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:178-88. [PMID: 17316553 DOI: 10.1016/j.bbabio.2007.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Revised: 01/09/2007] [Accepted: 01/17/2007] [Indexed: 10/23/2022]
Abstract
Type I cytochrome c(3) is a key protein in the bioenergetic metabolism of Desulfovibrio spp., mediating electron transfer between periplasmic hydrogenase and multihaem cytochromes associated with membrane bound complexes, such as type II cytochrome c(3). This work presents the NMR assignment of the haem substituents in type I cytochrome c(3) isolated from Desulfovibrio africanus and the thermodynamic and kinetic characterisation of type I and type II cytochromes c(3) belonging to the same organism. It is shown that the redox properties of the two proteins allow electrons to be transferred between them in the physiologically relevant direction with the release of energised protons close to the membrane where they can be used by the ATP synthase.
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Affiliation(s)
- Catarina M Paquete
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6, Apt. 127, 2780-156 Oeiras, Portugal
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11
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Louro RO. Proton thrusters: overview of the structural and functional features of soluble tetrahaem cytochromes c 3. J Biol Inorg Chem 2006; 12:1-10. [PMID: 16964504 DOI: 10.1007/s00775-006-0165-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Accepted: 08/21/2006] [Indexed: 10/24/2022]
Abstract
Tetrahaem cytochromes c (3) from sulfate-reducing bacteria have revealed exquisite complexity in their ligand binding properties and they couple the cooperative binding of two electrons with the binding of protons. In this review, the molecular mechanisms for these cooperative effects are described, and the functional consequences of these cooperativities are discussed in the context of the general mechanisms of biological energy transduction and the specific physiological metabolism of Desulfovibrio.
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Affiliation(s)
- Ricardo O Louro
- Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
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12
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Valente FMA, Oliveira ASF, Gnadt N, Pacheco I, Coelho AV, Xavier AV, Teixeira M, Soares CM, Pereira IAC. Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase. J Biol Inorg Chem 2005; 10:667-82. [PMID: 16187073 DOI: 10.1007/s00775-005-0022-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2005] [Accepted: 08/11/2005] [Indexed: 10/25/2022]
Abstract
The genome of Desulfovibrio vulgaris Hildenborough (DvH) encodes for six hydrogenases (Hases), making it an interesting organism to study the role of these proteins in sulphate respiration. In this work we address the role of the [NiFeSe] Hase, found to be the major Hase associated with the cytoplasmic membrane. The purified enzyme displays interesting catalytic properties, such as a very high H(2) production activity, which is dependent on the presence of phospholipids or detergent, and resistance to oxygen inactivation since it is isolated aerobically in a Ni(II) oxidation state. Evidence was obtained that the [NiFeSe] Hase is post-translationally modified to include a hydrophobic group bound to the N-terminal, which is responsible for its membrane association. Cleavage of this group originates a soluble, less active form of the enzyme. Sequence analysis shows that [NiFeSe] Hases from Desulfovibrionacae form a separate family from the [NiFe] enzymes of these organisms, and are more closely related to [NiFe] Hases from more distant bacterial species that have a medial [4Fe4S](2+/1+) cluster, but not a selenocysteine. The interaction of the [NiFeSe] Hase with periplasmic cytochromes was investigated and is similar to the [NiFe](1) Hase, with the Type I cytochrome c (3) as the preferred electron acceptor. A model of the DvH [NiFeSe] Hase was generated based on the structure of the Desulfomicrobium baculatum enzyme. The structures of the two [NiFeSe] Hases are compared with the structures of [NiFe] Hases, to evaluate the consensual structural differences between the two families. Several conserved residues close to the redox centres were identified, which may be relevant to the higher activity displayed by [NiFeSe] Hases.
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Affiliation(s)
- Filipa M A Valente
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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13
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Sani RK, Peyton BM, Dohnalkova A, Amonette JE. Reoxidation of reduced uranium with iron(III) (hydr)oxides under sulfate-reducing conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2005; 39:2059-66. [PMID: 15871237 DOI: 10.1021/es0494297] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In cultures of Desulfovibrio desulfuricans 620 the effects of iron(III) (hydr)oxides (hematite, goethite, and ferrihydrite) on microbial reduction and reoxidation of uranium (U) were evaluated under lactate-limited sulfate-reducing conditions. With lactate present, G20 reduced U(VI) in both 1,4-piperazinediethanesulfonate (PIPES) and bicarbonate buffer. Once lactate was depleted, however, microbially reduced U served as an electron donor to reduce Fe(III) present in iron(III) (hydr)oxides. With the same initial amount of Fe(III) (10 mmol/L) for each iron(III) (hydr)oxide, reoxidation of U(IV) was greater with hematite than with goethite orferrihydrite. As the initial mass loading of hematite increased from 0 to 20 mmol of Fe(III)/L, the rate and extent of U(IV) reoxidation increased. Subsequent addition of hematite [15 mmol of Fe(III)/L] to stationary-phase cultures containing microbially reduced U(IV) also resulted in rapid reoxidation to U(VI). Analysis by U L3-edge X-ray absorption near-edge spectroscopy (XANES) of microbially reduced U particles yielded spectra similar to that of natural uraninite. Observations by high-resolution transmission electron microscopy, selected area electron diffraction, and energy-dispersive X-ray spectroscopic analysis confirmed that precipitated U associated with cells was uraninite with particle diameters of 3-5 nm. By the same techniques, iron sulfide precipitates were found to have a variable Fe and S stoichiometry and were not associated with cells.
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Affiliation(s)
- Rajesh K Sani
- Department of Chemical Engineering, Center for Multiphase Environmental Research, Washington State University, Pullman, Washington 99164-2710, USA
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14
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Beyenal H, Lewandowski Z. Dynamics of lead immobilization in sulfate reducing biofilms. WATER RESEARCH 2004; 38:2726-2736. [PMID: 15207603 DOI: 10.1016/j.watres.2004.03.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2003] [Revised: 11/11/2003] [Accepted: 03/18/2004] [Indexed: 05/24/2023]
Abstract
We have evaluated the effects of selected minerals present in subsoil environment on the efficiency of lead removal from contaminated groundwaters using biofilms composed of sulfate-reducing microorganisms, and examined the stability of metal deposits after the biofilms had been temporarily exposed to the air. To quantify the studied effects, lead was immobilized in biofilms of Desulfovibrio desulfuricans grown anaerobically in two flat-plate flow reactors, one filled with hematite and the other with quartz. While the biofilms in both reactors were heterogeneous and consisted of voids and channels, the biofilms grown on hematite were denser, thicker, and more porous than those grown on quartz. The average H2S concentrations, measured using microelectrodes, were higher in the biofilms grown on quartz than those measured in the biofilms grown on hematite. During 18 weeks of operation, iron was continuously released from the hematite. Lead was immobilized more efficiently in the biofilms grown on quartz than it was in the biofilms grown on hematite. Lead deposits were partially reoxidized, especially in biofilms grown on hematite, and the biofilms in both reactors responded to the presence of oxygen by lowering their density and increasing the H2S production rate.
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Affiliation(s)
- Haluk Beyenal
- Center for Biofilm Engineering, Montana State University, P. O. 173980, Bozeman 59717, USA
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15
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De Luca G, de Philip P, Dermoun Z, Rousset M, Verméglio A. Reduction of technetium(VII) by Desulfovibrio fructosovorans is mediated by the nickel-iron hydrogenase. Appl Environ Microbiol 2001; 67:4583-7. [PMID: 11571159 PMCID: PMC93206 DOI: 10.1128/aem.67.10.4583-4587.2001] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Resting cells of the sulfate-reducing bacterium Desulfovibrio fructosovorans grown in the absence of sulfate had a very high Tc(VII)-reducing activity, which led to the formation of an insoluble black precipitate. The involvement of a periplasmic hydrogenase in Tc(VII) reduction was indicated (i) by the requirement for hydrogen as an electron donor, (ii) by the tolerance of this activity to oxygen, and (iii) by the inhibition of this activity by Cu(II). Moreover, a mutant carrying a deletion in the nickel-iron hydrogenase operon showed a dramatic decrease in the rate of Tc(VII) reduction. The restoration of Tc(VII) reduction by complementation of this mutation with nickel-iron hydrogenase genes demonstrated the specific involvement of the periplasmic nickel-iron hydrogenase in the mechanism in vivo. The Tc(VII)-reducing activity was also observed with cell extracts in the presence of hydrogen. Under these conditions, Tc(VII) was reduced enzymatically to soluble Tc(V) or precipitated to an insoluble black precipitate, depending on the chemical nature of the buffer used. The purified nickel-iron hydrogenase performed Tc(VII) reduction and precipitation at high rates. These series of genetic and biochemical approaches demonstrated that the periplasmic nickel-iron hydrogenase of sulfate-reducing bacteria functions as a Tc(VII) reductase. The role of cytochrome c(3) in the mechanism is also discussed.
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Affiliation(s)
- G De Luca
- CEA Cadarache, DSV/DEVM/Laboratoire de Bioénergétique Cellulaire, 13108 Saint Paul-Lez-Durance, France
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16
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da Costa PN, Marujo PE, van Dongen WM, Arraiano CM, Saraiva LM. Cloning, sequencing and expression of the tetraheme cytochrome c(3) from Desulfovibrio gigas. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1492:271-5. [PMID: 11004501 DOI: 10.1016/s0167-4781(00)00099-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The gene encoding the tetraheme cytochrome c(3) from Desulfovibrio gigas was cloned and sequenced from a 2.7-kb EcoRI-PstI insert of D. gigas DNA. The derived amino acid sequence showed that the D. gigas cytochrome c(3) is synthesized as a precursor protein with an N-terminal signal peptide sequence of 25 residues and allowed the correction of the previous reported amino acid sequence (Matias et al. Protein Science 5 (1996) 1342-1354). Expression in D. vulgaris (Hildenborough) was possible by conjugal transfer of a recombinant broad-host-range vector pSUP104 containing a SmaI fragment of the D. gigas cytochrome c(3) gene. Biochemical, immunological and spectroscopic analysis of the purified protein showed that the recombinant cytochrome is identical to that isolated from D. gigas.
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Affiliation(s)
- P N da Costa
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado, 127, 2780-156 Oeiras, Potugal
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17
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Saraiva LM, da Costa PN, LeGall J. Sequencing the gene encoding desulfovibrio desulfuricans ATCC 27774 nine-heme cytochrome c. Biochem Biophys Res Commun 1999; 262:629-34. [PMID: 10471375 DOI: 10.1006/bbrc.1999.1238] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Contradicting early suggestions, the sequencing of the gene encoding the Desulfovibrio desulfuricans (ATCC 27774) nine-heme cytochrome c proves that this cytochrome is not the product of the degradation of the 16-heme containing cytochrome c [Coelho et al. (1996) Acta Cryst. D52, 1202-1208]. However, preliminary data indicate that the cytochrome gene is part of an operon similar to the DvH hmc operon, which contains the gene coding for the 16-heme cytochrome c [Rossi et al. (1993) J. Bacteriol. 175, 4699-4711]. Also, the amino acid sequence deduced from the DNA sequence shows four residues in the C-terminal not predicted in the amino acid sequence obtained by X-ray methods [Matias et al. (1999) Structure 7, 119-130].
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Affiliation(s)
- L M Saraiva
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, Oeiras, 2780, Portugal.
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18
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Nørager S, Legrand P, Pieulle L, Hatchikian C, Roth M. Crystal structure of the oxidised and reduced acidic cytochrome c3from Desulfovibrio africanus. J Mol Biol 1999; 290:881-902. [PMID: 10398589 DOI: 10.1006/jmbi.1999.2917] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Unique among sulphate-reducing bacteria, Desulfovibrio africanus has two periplasmic tetraheme cytochromes c3, one with an acidic isoelectric point which exhibits an unusually low reactivity towards hydrogenase, and another with a basic isoelectric point which shows the usual cytochrome c3reactivity. The crystal structure of the oxidised acidic cytochrome c3of Desulfovibrio africanus (Dva.a) was solved by the multiple anomalous diffraction (MAD) method and refined to 1.6 A resolution. Its structure clearly belongs to the same family as the other known cytochromes c3, but with weak parentage with those of the Desulfovibrio genus and slightly closer to the cytochromes c3of Desulfomicrobium norvegicum. In Dva.a, one edge of heme I is completely exposed to the solvent and surrounded by a negatively charged protein surface. Heme I thus seems to play an important role in electron exchange, in addition to heme III or heme IV which are the electron exchange ports in the other cytochromes c3. The function of Dva.a and the nature of its redox partners in the cell are thus very likely different. By alignment of the seven known 3D structures including Dva.a, it is shown that the structure which is most conserved in all cytochromes c3is the four-heme cluster itself. There is no conserved continuous protein structure which could explain the remarkable invariance of the four-heme cluster. On the contrary, the proximity of the heme edges is such that they interact directly by hydrophobic and van der Waals contacts. This direct interaction, which always involves a pyrrole CA-CB side-chain and its bound protein cysteine Sgammaatom, is probably the main origin of the four-heme cluster stability. The same kind of interaction is found in the chaining of the hemes in other multihemic redox proteins.The crystal structure of reduced Dva. a was solved at 1.9 A resolution. The comparison of the oxidised and reduced structures reveals changes in the positions of water molecules and polar residues which probably result from changes in the protonation state of amino acids and heme propionates. Water molecules are found closer to the hemes and to the iron atoms in the reduced than in the oxidised state. A global movement of a chain fragment in the vicinity of hemes III and IV is observed which result very likely from the electrostatic reorganization of the polypeptide chain induced by reduction.
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Affiliation(s)
- S Nørager
- Laboratoire de Cristallographie et Cristallogénèse des Protéines Institut de Biologie Structurale J.P.Ebel, CEA-CNRS, rue Jules Horowitz, Grenoble, Cedex 1, 38027, France
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Evidence for an Atypical Tetrapyrrole Biosynthetic Pathway inDesulfovibrio: Back Conversion of Sirohydrochlorin into Porphyrins. Bioorg Chem 1998. [DOI: 10.1006/bioo.1998.1099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Desulfoviridin, the dissimilatory sulfite reductase from Desulfovibrio desulfuricans (Essex): new structural and functional aspects of the membranous enzyme. Inorganica Chim Acta 1998. [DOI: 10.1016/s0020-1693(97)06143-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Romão CV, Pereira IA, Xavier AV, LeGall J, Teixeira M. Characterization of the [NiFe] hydrogenase from the sulfate reducer Desulfovibrio vulgaris Hildenborough. Biochem Biophys Res Commun 1997; 240:75-9. [PMID: 9367885 DOI: 10.1006/bbrc.1997.7598] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The [NiFe] hydrogenase from Desulfovibrio vulgaris Hildenborough was isolated from the cytoplasmic membranes and characterized by EPR spectroscopy. It has a total molecular mass of 98.7 kDa (subunits of 66.4 and 32.3 kDa), and contains 1 nickel and 12 Fe atoms per heterodimer. The catalytic activities for hydrogen consumption and production were determined to be 174 and 89 mumol H2.min-1.mg-1, respectively. As isolated, under aerobic conditions, this hydrogenase exhibits EPR signals characteristic of the nickel centers in [NiFe] hydrogenases (Ni-A signal at gx,y,z = 2.32, 2.23 and approximately 2.0 and Ni-B signal at gx,y,z = 2.33, 2.16 and approximately 2.0) as well as an intense quasi-isotropic signal centered at g = 2.02 due to the oxidized [3Fe-4S] center. The redox profile under hydrogen atmosphere is remarkably similar to that of other [NiFe] hydrogenases. The signals observed for the oxidized state disappear, first being substituted by the Ni-C type signal (gx,y,z = 2.19, 2.14, approximately 2.01), which upon long incubation under hydrogen yields the split Ni-C signal due to interaction with the reduced [4Fe-4S] centers.
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Affiliation(s)
- C V Romão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Ozawa K, Mogi T, Suzuki M, Kitamura M, Nakaya T, Anraku Y, Akutsu H. Membrane-Bound Cytochromes in a Sulfate-Reducing Strict AnaerobeDesulfovibrio vulgarisMiyazaki F. Anaerobe 1997; 3:339-46. [PMID: 16887609 DOI: 10.1006/anae.1997.0114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/1997] [Accepted: 07/16/1997] [Indexed: 11/22/2022]
Abstract
Cytoplasmic membranes were isolated from the cells of a sulfate-reducing strict anaerobe Desulfovibrio vulgaris Miyazaki F and membrane-bound cytochromes were characterized. Redox difference spectra at 77 K revealed the presence of cytochromes with the alpha peaks at 552 and 556 nm while CO-binding difference spectra showed the presence of o-type cytochrome(s). Partial purification of the cytochromes demonstrated that the membranes contain cytochromes c550, c551, c556 and possibly d1 besides high molecular mass cytochrome c and cytochrome c3. It turned out that two kinds of novel CO-binding c-type cytochromes are present in the membrane. The membranes and a partially purified fraction showed weak ubiquinol-1 oxidase activity but no cytochrome c oxidase activity. Results suggest that D. vulgaris does not express the heme-copper terminal oxidase under our growth conditions in spite of the presence of the col gene, which is homologous to the gene of subunit I of the aa3-type oxidase.
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Affiliation(s)
- K Ozawa
- Department of Bioengineering, Faculty of Engineering, Yokohama National University, Hodogaya-ku, Yokohama, 240, Japan
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Aubert C, Leroy G, Bruschi M, Wall JD, Dolla A. A single mutation in the heme 4 environment of Desulfovibrio desulfuricans Norway cytochrome c3 (Mr 26,000) greatly affects the molecule reactivity. J Biol Chem 1997; 272:15128-34. [PMID: 9182533 DOI: 10.1074/jbc.272.24.15128] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
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.
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Affiliation(s)
- C Aubert
- Unité de Bioénergétique et Ingéniérie des Protéines, IFR1-Centre National de la Recherche Scientifique, 13402 Marseille Cedex 20, France
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Pieulle L, Haladjian J, Bonicel J, Hatchikian EC. Biochemical studies of the c-type cytochromes of the sulfate reducer Desulfovibrio africanus. Characterization of two tetraheme cytochromes c3 with different specificity. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1273:51-61. [PMID: 8573595 DOI: 10.1016/0005-2728(95)00129-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
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.
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Affiliation(s)
- L Pieulle
- Unité de Bioénergétique et Ingénierie des Protéines, CNRS, Marseille, France
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