1
|
Shen Y, Agrawal A, Suri NK, An D, Voordouw JK, Clark RG, Jack TR, Miner K, Pederzolli R, Benko A, Voordouw G. Control of microbial sulfide production by limiting sulfate dispersal in a water-injected oil field. J Biotechnol 2018; 266:14-19. [PMID: 29197544 DOI: 10.1016/j.jbiotec.2017.11.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/25/2017] [Accepted: 11/28/2017] [Indexed: 11/16/2022]
Abstract
Oil production by water injection often involves the use of makeup water to replace produced oil. Sulfate in makeup water is reduced by sulfate-reducing bacteria to sulfide, a process referred to as souring. In the MHGC field souring was caused by using makeup water with 4mM (384ppm) sulfate. Mixing with sulfate-free produced water gave injection water with 0.8mM sulfate. This was amended with nitrate to limit souring and was then distributed fieldwide. The start-up of an enhanced-oil-recovery pilot caused all sulfate-containing makeup water to be used for dissolution of polymer, which was then injected into a limited region of the field. Produced water from this pilot contained 10% of the injected sulfate concentration as sulfide, but was free of sulfate. Its use as makeup water in the main water plant of the field caused injection water sulfate to drop to zero. This in turn strongly decreased produced sulfide concentrations throughout the field and allowed a decreased injection of nitrate. The decreased injection of sulfate and nitrate caused major changes in the microbial community of produced waters. Limiting sulfate dispersal into a reservoir, which acts as a sulfate-removing biofilter, is thus a powerful method to decrease souring.
Collapse
Affiliation(s)
- Y Shen
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - A Agrawal
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - N K Suri
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - D An
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - J K Voordouw
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - R G Clark
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - T R Jack
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - K Miner
- Baker Hughes, Redcliff, AB, T0J 2P0, Canada
| | | | - A Benko
- Enerplus Corporation, Calgary, AB, T2P 2Z1, Canada
| | - G Voordouw
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| |
Collapse
|
2
|
Hubert CRJ, Oldenburg TBP, Fustic M, Gray ND, Larter SR, Penn K, Rowan AK, Seshadri R, Sherry A, Swainsbury R, Voordouw G, Voordouw JK, Head IM. Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil. Environ Microbiol 2011; 14:387-404. [PMID: 21824242 PMCID: PMC3490369 DOI: 10.1111/j.1462-2920.2011.02521.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The subsurface microbiology of an Athabasca oil sands reservoir in western Canada containing severely biodegraded oil was investigated by combining 16S rRNA gene- and polar lipid-based analyses of reservoir formation water with geochemical analyses of the crude oil and formation water. Biomass was filtered from formation water, DNA was extracted using two different methods, and 16S rRNA gene fragments were amplified with several different primer pairs prior to cloning and sequencing or community fingerprinting by denaturing gradient gel electrophoresis (DGGE). Similar results were obtained irrespective of the DNA extraction method or primers used. Archaeal libraries were dominated by Methanomicrobiales (410 of 414 total sequences formed a dominant phylotype affiliated with a Methanoregula sp.), consistent with the proposed dominant role of CO(2) -reducing methanogens in crude oil biodegradation. In two bacterial 16S rRNA clone libraries generated with different primer pairs, > 99% and 100% of the sequences were affiliated with Epsilonproteobacteria (n = 382 and 72 total clones respectively). This massive dominance of Epsilonproteobacteria sequences was again obtained in a third library (99% of sequences; n = 96 clones) using a third universal bacterial primer pair (inosine-341f and 1492r). Sequencing of bands from DGGE profiles and intact polar lipid analyses were in accordance with the bacterial clone library results. Epsilonproteobacterial OTUs were affiliated with Sulfuricurvum, Arcobacter and Sulfurospirillum spp. detected in other oil field habitats. The dominant organism revealed by the bacterial libraries (87% of all sequences) is a close relative of Sulfuricurvum kujiense - an organism capable of oxidizing reduced sulfur compounds in crude oil. Geochemical analysis of organic extracts from bitumen at different reservoir depths down to the oil water transition zone of these oil sands indicated active biodegradation of dibenzothiophenes, and stable sulfur isotope ratios for elemental sulfur and sulfate in formation waters were indicative of anaerobic oxidation of sulfur compounds. Microbial desulfurization of crude oil may be an important metabolism for Epsilonproteobacteria indigenous to oil reservoirs with elevated sulfur content and may explain their prevalence in formation waters from highly biodegraded petroleum systems.
Collapse
Affiliation(s)
- Casey R J Hubert
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Voordouw G, Voordouw JK, Jack TR, Foght J, Fedorak PM, Westlake DW. Identification of distinct communities of sulfate-reducing bacteria in oil fields by reverse sample genome probing. Appl Environ Microbiol 2010; 58:3542-52. [PMID: 16348801 PMCID: PMC183142 DOI: 10.1128/aem.58.11.3542-3552.1992] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thirty-five different standards of sulfate-reducing bacteria, identified by reverse sample genome probing and defined as bacteria with genomes showing little or no cross-hybridization, were in part characterized by Southern blotting, using 16S rRNA and hydrogenase gene probes. Samples from 56 sites in seven different western Canadian oil field locations were collected and enriched for sulfate-reducing bacteria by using different liquid media containing one of the following carbon sources: lactate, ethanol, benzoate, decanoate, propionate, or acetate. DNA was isolated from the enrichments and probed by reverse sample genome probing using master filters containing denatured chromosomal DNAs from the 35 sulfate-reducing bacterial standards. Statistical analysis of the microbial compositions at 44 of the 56 sites indicated the presence of two distinct communities of sulfate-reducing bacteria. The discriminating factor between the two communities was the salt concentration of the production waters, which were either fresh water or saline. Of 34 standards detected, 10 were unique to the fresh water and 18 were unique to the saline oil field environment, while only 6 organisms were cultured from both communities.
Collapse
Affiliation(s)
- G Voordouw
- Division of Biochemistry, Department of Biological Sciences, The University of Calgary, Calgary, Alberta, Canada T2N 1N4; NOVA HUSKY Research Corporation, Calgary, Alberta, Canada T2E 7K7 ; and Department of Microbiology, University of Alberta, Edmonton, Alberta, Canada T6G 2E9
| | | | | | | | | | | |
Collapse
|
4
|
Voordouw G, Voordouw JK, Karkhoff-Schweizer RR, Fedorak PM, Westlake DW. Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples. Appl Environ Microbiol 2010; 57:3070-8. [PMID: 16348574 PMCID: PMC183929 DOI: 10.1128/aem.57.11.3070-3078.1991] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel method for the identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a "standard") to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples.
Collapse
Affiliation(s)
- G Voordouw
- Division of Biochemistry, Department of Biological Sciences, The University of Calgary, Calgary, Alberta T2N 1N4, and Department of Microbiology, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | | | | | | | | |
Collapse
|
5
|
Johnston S, Lin S, Lee P, Caffrey SM, Wildschut J, Voordouw JK, da Silva SM, Pereira IAC, Voordouw G. A genomic island of the sulfate-reducing bacteriumDesulfovibrio vulgarisHildenborough promotes survival under stress conditions while decreasing the efficiency of anaerobic growth. Environ Microbiol 2009; 11:981-91. [DOI: 10.1111/j.1462-2920.2008.01823.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
6
|
Caffrey SM, Park HS, Voordouw JK, He Z, Zhou J, Voordouw G. Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J Bacteriol 2007; 189:6159-67. [PMID: 17601789 PMCID: PMC1951932 DOI: 10.1128/jb.00747-07] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe] hydrogenase, an [NiFeSe] hydrogenase, and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1, and hyn2 genes, respectively. In order to understand their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in defined media in which lactate or hydrogen at either 5 or 50% (vol/vol) was used as the sole electron donor for sulfate reduction. Only strains missing the [Fe] hydrogenase were significantly affected during growth with lactate or with 50% (vol/vol) hydrogen as the sole electron donor. When the cells were grown at low (5% [vol/vol]) hydrogen concentrations, those missing the [NiFeSe] hydrogenase suffered the greatest impairment. The growth rate data correlated strongly with gene expression results obtained from microarray hybridizations and real-time PCR using mRNA extracted from cells grown under the three conditions. Expression of the hys genes followed the order 5% hydrogen>50% hydrogen>lactate, whereas expression of the hyd genes followed the reverse order. These results suggest that growth with lactate and 50% hydrogen is associated with high intracellular hydrogen concentrations, which are best captured by the higher activity, lower affinity [Fe] hydrogenase. In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase.
Collapse
Affiliation(s)
- Sean M Caffrey
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | | | | | | | | | | |
Collapse
|
7
|
Wildschut JD, Lang RM, Voordouw JK, Voordouw G. Rubredoxin:oxygen oxidoreductase enhances survival of Desulfovibrio vulgaris hildenborough under microaerophilic conditions. J Bacteriol 2006; 188:6253-60. [PMID: 16923892 PMCID: PMC1595363 DOI: 10.1128/jb.00425-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genes for superoxide reductase (Sor), rubredoxin (Rub), and rubredoxin:oxygen oxidoreductase (Roo) are located in close proximity in the chromosome of Desulfovibrio vulgaris Hildenborough. Protein blots confirmed the absence of Roo from roo mutant and sor-rub-roo (srr) mutant cells and its presence in sor mutant and wild-type cells grown under anaerobic conditions. Oxygen reduction rates of the roo and srr mutants were 20 to 40% lower than those of the wild type and the sor mutant, indicating that Roo functions as an O2 reductase in vivo. Survival of single cells incubated for 5 days on agar plates under microaerophilic conditions (1% air) was 85% for the sor, 4% for the roo, and 0.7% for the srr mutant relative to that of the wild type (100%). The similar survival rates of sor mutant and wild-type cells suggest that O2 reduction by Roo prevents the formation of reactive oxygen species (ROS) under these conditions; i.e., the ROS-reducing enzyme Sor is only needed for survival when Roo is missing. In contrast, the sor mutant was inactivated much more rapidly than the roo mutant when liquid cultures were incubated in 100% air, indicating that O2 reduction by Roo and other terminal oxidases did not prevent ROS formation under these conditions. Competition of Sor and Roo for limited reduced Rub was suggested by the observation that the roo mutant survived better than the wild type under fully aerobic conditions. The roo mutant was more strongly inhibited than the wild type by the nitric oxide (NO)-generating compound S-nitrosoglutathione, indicating that Roo may also serve as an NO reductase in vivo.
Collapse
Affiliation(s)
- Janine D Wildschut
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | | | | | | |
Collapse
|
8
|
Goenka A, Voordouw JK, Lubitz W, Gärtner W, Voordouw G. Construction of a [NiFe]-hydrogenase deletion mutant of Desulfovibrio vulgaris Hildenborough. Biochem Soc Trans 2005; 33:59-60. [PMID: 15667264 DOI: 10.1042/bst0330059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A mutant of Desulfovibrio vulgaris Hildenborough lacking a gene for [NiFe] hydrogenase was generated. Growth studies, performed for the mutant in comparison with the wild-type, showed no strong differences during the exponential growth phase. However, the mutant cells died more rapidly in the stationary growth phase.
Collapse
Affiliation(s)
- A Goenka
- Max-Planck Institut für Bioanorganische Chemie, Stiftstr. 34-36, 45470 Mülheim a.d. Ruhr, Germany
| | | | | | | | | |
Collapse
|
9
|
Haveman SA, Greene EA, Stilwell CP, Voordouw JK, Voordouw G. Physiological and gene expression analysis of inhibition of Desulfovibrio vulgaris hildenborough by nitrite. J Bacteriol 2004; 186:7944-50. [PMID: 15547266 PMCID: PMC529081 DOI: 10.1128/jb.186.23.7944-7950.2004] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Desulfovibrio vulgaris Hildenborough mutant lacking the nrfA gene for the catalytic subunit of periplasmic cytochrome c nitrite reductase (NrfHA) was constructed. In mid-log phase, growth of the wild type in medium containing lactate and sulfate was inhibited by 10 mM nitrite, whereas 0.6 mM nitrite inhibited the nrfA mutant. Lower concentrations (0.04 mM) inhibited the growth of both mutant and wild-type cells on plates. Macroarray hybridization indicated that nitrite upregulates the nrfHA genes and downregulates genes for sulfate reduction enzymes catalyzing steps preceding the reduction of sulfite to sulfide by dissimilatory sulfite reductase (DsrAB), for two membrane-bound electron transport complexes (qmoABC and dsrMKJOP) and for ATP synthase (atp). DsrAB is known to bind and slowly reduce nitrite. The data support a model in which nitrite inhibits DsrAB (apparent dissociation constant K(m) for nitrite = 0.03 mM), and in which NrfHA (K(m) for nitrite = 1.4 mM) limits nitrite entry by reducing it to ammonia when nitrite concentrations are at millimolar levels. The gene expression data and consideration of relative gene locations suggest that QmoABC and DsrMKJOP donate electrons to adenosine phosphosulfate reductase and DsrAB, respectively. Downregulation of atp genes, as well as the recorded cell death following addition of inhibitory nitrite concentrations, suggests that the proton gradient collapses when electrons are diverted from cytoplasmic sulfate to periplasmic nitrite reduction.
Collapse
Affiliation(s)
- Shelley A Haveman
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | | | | | | | | |
Collapse
|
10
|
Haveman SA, Brunelle V, Voordouw JK, Voordouw G, Heidelberg JF, Rabus R. Gene expression analysis of energy metabolism mutants of Desulfovibrio vulgaris Hildenborough indicates an important role for alcohol dehydrogenase. J Bacteriol 2003; 185:4345-53. [PMID: 12867442 PMCID: PMC165767 DOI: 10.1128/jb.185.15.4345-4353.2003] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Comparison of the proteomes of the wild-type and Fe-only hydrogenase mutant strains of Desulfovibrio vulgaris Hildenborough, grown in lactate-sulfate (LS) medium, indicated the near absence of open reading frame 2977 (ORF2977)-coded alcohol dehydrogenase in the hyd mutant. Hybridization of labeled cDNA to a macroarray of 145 PCR-amplified D. vulgaris genes encoding proteins active in energy metabolism indicated that the adh gene was among the most highly expressed in wild-type cells grown in LS medium. Relative to the wild type, expression of the adh gene was strongly downregulated in the hyd mutant, in agreement with the proteomic data. Expression was upregulated in ethanol-grown wild-type cells. An adh mutant was constructed and found to be incapable of growth in media in which ethanol was both the carbon source and electron donor for sulfate reduction or was only the carbon source, with hydrogen serving as electron donor. The hyd mutant also grew poorly on ethanol, in agreement with its low level of adh gene expression. The adh mutant grew to a lower final cell density on LS medium than the wild type. These results, as well as the high level of expression of adh in wild-type cells on media in which lactate, pyruvate, formate, or hydrogen served as the sole electron donor for sulfate reduction, indicate that ORF2977 Adh contributes to the energy metabolism of D. vulgaris under a wide variety of metabolic conditions. A hydrogen cycling mechanism is proposed in which protons and electrons originating from cytoplasmic ethanol oxidation by ORF2977 Adh are converted to hydrogen or hydrogen equivalents, possibly by a putative H(2)-heterodisulfide oxidoreductase complex, which is then oxidized by periplasmic Fe-only hydrogenase to generate a proton gradient.
Collapse
Affiliation(s)
- Shelley A Haveman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | | | | | | | | | | |
Collapse
|
11
|
Fournier M, Zhang Y, Wildschut JD, Dolla A, Voordouw JK, Schriemer DC, Voordouw G. Function of oxygen resistance proteins in the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris hildenborough. J Bacteriol 2003; 185:71-9. [PMID: 12486042 PMCID: PMC141827 DOI: 10.1128/jb.185.1.71-79.2003] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two mutant strains of Desulfovibrio vulgaris Hildenborough lacking either the sod gene for periplasmic superoxide dismutase or the rbr gene for rubrerythrin, a cytoplasmic hydrogen peroxide (H(2)O(2)) reductase, were constructed. Their resistance to oxidative stress was compared to that of the wild-type and of a sor mutant lacking the gene for the cytoplasmic superoxide reductase. The sor mutant was more sensitive to exposure to air or to internally or externally generated superoxide than was the sod mutant, which was in turn more sensitive than the wild-type strain. No obvious oxidative stress phenotype was found for the rbr mutant, indicating that H(2)O(2) resistance may also be conferred by two other rbr genes in the D. vulgaris genome. Inhibition of Sod activity by azide and H(2)O(2), but not by cyanide, indicated it to be an iron-containing Sod. The positions of Fe-Sod and Sor were mapped by two-dimensional gel electrophoresis (2DE). A strong decrease of Sor in continuously aerated cells, indicated by 2DE, may be a critical factor in causing cell death of D. vulgaris. Thus, Sor plays a key role in oxygen defense of D. vulgaris under fully aerobic conditions, when superoxide is generated mostly in the cytoplasm. Fe-Sod may be more important under microaerophilic conditions, when the periplasm contains oxygen-sensitive, superoxide-producing targets.
Collapse
Affiliation(s)
- Marjorie Fournier
- Department of Biological Sciences. Department of Biochemistry and Molecular Biology, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | | | | | | | | | | | | |
Collapse
|
12
|
Pohorelic BKJ, Voordouw JK, Lojou E, Dolla A, Harder J, Voordouw G. Effects of deletion of genes encoding Fe-only hydrogenase of Desulfovibrio vulgaris Hildenborough on hydrogen and lactate metabolism. J Bacteriol 2002; 184:679-86. [PMID: 11790737 PMCID: PMC139517 DOI: 10.1128/jb.184.3.679-686.2002] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The physiological properties of a hyd mutant of Desulfovibrio vulgaris Hildenborough, lacking periplasmic Fe-only hydrogenase, have been compared with those of the wild-type strain. Fe-only hydrogenase is the main hydrogenase of D. vulgaris Hildenborough, which also has periplasmic NiFe- and NiFeSe-hydrogenases. The hyd mutant grew less well than the wild-type strain in media with sulfate as the electron acceptor and H(2) as the sole electron donor, especially at a high sulfate concentration. Although the hyd mutation had little effect on growth with lactate as the electron donor for sulfate reduction when H(2) was also present, growth in lactate- and sulfate-containing media lacking H(2) was less efficient. The hyd mutant produced, transiently, significant amounts of H(2) under these conditions, which were eventually all used for sulfate reduction. The results do not confirm the essential role proposed elsewhere for Fe-only hydrogenase as a hydrogen-producing enzyme in lactate metabolism (W. A. M. van den Berg, W. M. A. M. van Dongen, and C. Veeger, J. Bacteriol. 173:3688-3694, 1991). This role is more likely played by a membrane-bound, cytoplasmic Ech-hydrogenase homolog, which is indicated by the D. vulgaris genome sequence. The physiological role of periplasmic Fe-only hydrogenase is hydrogen uptake, both when hydrogen is and when lactate is the electron donor for sulfate reduction.
Collapse
Affiliation(s)
- Brant K J Pohorelic
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
| | | | | | | | | | | |
Collapse
|
13
|
Dolla A, Pohorelic BK, Voordouw JK, Voordouw G. Deletion of the hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough hampers hydrogen metabolism and low-redox-potential niche establishment. Arch Microbiol 2000; 174:143-51. [PMID: 11041344 DOI: 10.1007/s002030000183] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
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.
Collapse
Affiliation(s)
- A Dolla
- Department of Biological Sciences, The University of Calgary, Alberta, Canada
| | | | | | | |
Collapse
|
14
|
Voordouw JK, Voordouw G. Deletion of the rbo gene increases the oxygen sensitivity of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 1998; 64:2882-7. [PMID: 9687445 PMCID: PMC106787 DOI: 10.1128/aem.64.8.2882-2887.1998] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The rbo gene of Desulfovibrio vulgaris Hildenborough encodes rubredoxin oxidoreductase (Rbo), a 14-kDa iron sulfur protein; forms an operon with the gene for rubredoxin; and is preceded by the gene for the oxygen-sensing protein DcrA. We have deleted the rbo gene from D. vulgaris with the sacB mutagenesis procedure developed previously (R. Fu and G. Voordouw, Microbiology 143:1815-1826, 1997). The absence of the rbo-gene in the resulting mutant, D. vulgaris L2, was confirmed by PCR and protein blotting with Rbo-specific polyclonal antibodies. D. vulgaris L2 grows like the wild type under anaerobic conditions. Exposure to air for 24 h caused a 100-fold drop in CFU of L2 relative to the wild type. The lag times of liquid cultures of inocula exposed to air were on average also greater for L2 than for the wild type. These results demonstrate that Rbo, which is not homologous with superoxide dismutase or catalase, acts as an oxygen defense protein in the anaerobic, sulfate-reducing bacterium D. vulgaris Hildenborough and likely also in other sulfate-reducing bacteria and anaerobic archaea in which it has been found.
Collapse
Affiliation(s)
- J K Voordouw
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | | |
Collapse
|
15
|
Stevenson KJ, Voordouw JK. Characterization of trypsin and elastase from the moose (Alces alces). I. Amino acid composition and specificity towards polypeptides. Biochim Biophys Acta 1975; 386:324-31. [PMID: 1125277 DOI: 10.1016/0005-2795(75)90274-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Trypsin and elastase isolated from the pancreas of the moose (Alces alces), a member of the Cervidae (deer) family, were characterized with respect to their amino acid composition and specificity towards polypeptides. Moose trypsin possessed 234 residues, based on alanine recoveries equal to 16.0 residues, with a molecular weight calculated at 24 476. Moose trypsin readily hydrolysed peptide bonds in which the carbonyl group was contributed by arginine, lysine and S-2-aminoethylcysteine as indicated by the peptides isolated following hydrolysis of the oxidized and the S-aminoethylated B-chain of insulin. Moose elastase possessed 231 residues, based on alanine recoveries equal to 17.0 residues, with a molecular weight calculated as 24 201. The high lysine (9 residues), low arginine (3 residues) content was in contrast to the opposite situation with porcine elastase and the elastase-like, alpha-lytic protease from Sorangium. The hydrolysis of the oxidized B-chain of insulin by moose elastase was similar to that produced by porcine elastase with major cleavages occurring at Val-12-Glu-13, Ala-14-Leu-15 and Val-18-Cys(O-3H)-19 and minor cleavages occurring at Ser-9-His-10 and Arg-21-Gly-22. The hydrolysis of glucagon with moose elastase produced major cleavages at Thr-7-Ser-8, Ser-11-Lys-12, Val-23-Gln-24 and Leu-26-Met-27. The facile hydrolysis of Arg-17-Arg-18 was also observed and attributed, in part, to trypsin.
Collapse
|