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Liduino V, Galvão M, Brasil S, Sérvulo E. SRB-mediated corrosion of marine submerged AISI 1020 steel under impressed current cathodic protection. Colloids Surf B Biointerfaces 2021; 202:111701. [PMID: 33756296 DOI: 10.1016/j.colsurfb.2021.111701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
Metallic corrosion is a recurrent and costly problem to almost every industry; therefore, prevention strategies might be well-defined on a case-by-case basis. Commonly, cathodic protection (CP) is the world's most widely-adopted technique to guarantee the integrity of buried or submerged structures from corrosion. However, as current potential values are dependent on metal-structure and environmental features, the target shall be well-identified; otherwise, the intended effect will not be reached. In seawater, a protective current potential of -800 mVAg/AgCl is recommended by technical standards, while a more negative potential (-900 mVAg/AgCl) is the suggested criterion for the control of corrosion induced by sulfate-reducing bacteria (SRB), even though without proper scientific support. Thus, this study focused on evaluating the efficiency of different cathodic protection potentials (-800, -900 and, -1000 mVAg/AgCl) on inhibiting SRB-mediated corrosion of AISI 1020 steel. Both unprotected and impressed current cathodically protected steel specimens were exposed to indigenous microorganisms in seawater for 7 days. The Most Probable Number (MPN) enumeration of sessile aerobic heterotrophic bacteria, acid-producing bacteria and, sulfate-reducing bacteria was performed at the beginning and at the end of the assays. Also, the reducing activity of hydrogenase-positive SRB strains was measured. Although the microbial colonization was greater on unprotected steel surfaces than on the cathodically protected ones, biofilm quantification of CP specimens did not show important differences regardless of the potential. However, hydrogenase-positive SRB counts increased with the reduction of CP potential value, promoting an increase in the number and depth of pits on specimens protected at -1000 mVAg/AgCl when compared with those protected at -800 mVAg/AgCl and unprotected ones.
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Affiliation(s)
- Vitor Liduino
- School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Mariana Galvão
- School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Simone Brasil
- School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eliana Sérvulo
- School of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Zymographic differentiation of [NiFe]-hydrogenases 1, 2 and 3 of Escherichia coli K-12. BMC Microbiol 2012; 12:134. [PMID: 22769583 PMCID: PMC3431244 DOI: 10.1186/1471-2180-12-134] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 06/25/2012] [Indexed: 11/10/2022] Open
Abstract
Background When grown under anaerobic conditions, Escherichia coli K-12 is able to synthesize three active [NiFe]-hydrogenases (Hyd1-3). Two of these hydrogenases are respiratory enzymes catalysing hydrogen oxidation, whereby Hyd-1 is oxygen-tolerant and Hyd-2 is considered a standard oxygen-sensitive hydrogenase. Hyd-3, together with formate dehydrogenase H (Fdh-H), forms the formate hydrogenlyase (FHL) complex, which is responsible for H2 evolution by intact cells. Hydrogen oxidation activity can be assayed for all three hydrogenases using benzyl viologen (BV; Eo′ = -360 mV) as an artificial electron acceptor; however ascribing activities to specific isoenzymes is not trivial. Previously, an in-gel assay could differentiate Hyd-1 and Hyd-2, while Hyd-3 had long been considered too unstable to be visualized on such native gels. This study identifies conditions allowing differentiation of all three enzymes using simple in-gel zymographic assays. Results Using a modified in-gel assay hydrogen-dependent BV reduction catalyzed by Hyd-3 has been described for the first time. High hydrogen concentrations facilitated visualization of Hyd-3 activity. The activity was membrane-associated and although not essential for visualization of Hyd-3, the activity was maximal in the presence of a functional Fdh-H enzyme. Furthermore, through the use of nitroblue tetrazolium (NBT; Eo′ = -80 mV) it was demonstrated that Hyd-1 reduces this redox dye in a hydrogen-dependent manner, while neither Hyd-2 nor Hyd-3 could couple hydrogen oxidation to NBT reduction. Hydrogen-dependent reduction of NBT was also catalysed by an oxygen-sensitive variant of Hyd-1 that had a supernumerary cysteine residue at position 19 of the small subunit substituted for glycine. This finding suggests that tolerance toward oxygen is not the main determinant that governs electron donation to more redox-positive electron acceptors such as NBT. Conclusions The utilization of particular electron acceptors at different hydrogen concentrations and redox potentials correlates with the known physiological functions of the respective hydrogenase. The ability to rapidly distinguish between oxygen-tolerant and standard [NiFe]-hydrogenases provides a facile new screen for the discovery of novel enzymes. A reliable assay for Hyd-3 will reinvigorate studies on the characterisation of the hydrogen-evolving FHL complex.
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[NiFe] hydrogenase from Alteromonas macleodii with unusual stability in the presence of oxygen and high temperature. Appl Environ Microbiol 2011; 77:1990-8. [PMID: 21257809 DOI: 10.1128/aem.01559-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydrogenases are enzymes involved in the bioproduction of hydrogen, a clean alternative energy source whose combustion generates water as the only end product. In this article we identified and characterized a [NiFe] hydrogenase from the marine bacterium Alteromonas macleodii "deep ecotype" with unusual stability toward oxygen and high temperature. The A. macleodii hydrogenase (HynSL) can catalyze both H(2) evolution and H(2) uptake reactions. HynSL was expressed in A. macleodii under aerobic conditions and reached the maximum activity when the cells entered the late exponential phase. The higher level of hydrogenase activity was accompanied by a greater abundance of the HynSL protein in the late-log or stationary phase. The addition of nickel to the growth medium significantly enhanced the hydrogenase activity. Ni treatment affected the level of the protein, but not the mRNA, indicating that the effect of Ni was exerted at the posttranscriptional level. Hydrogenase activity was distributed ∼30% in the membrane fraction and ∼70% in the cytoplasmic fraction. Thus, HynSL appears to be loosely membrane-bound. Partially purified A. macleodii hydrogenase demonstrated extraordinary stability. It retained 84% of its activity after exposure to 80°C for 2 h. After exposure to air for 45 days at 4°C, it retained nearly 100% of its activity when assayed under anaerobic conditions. Its catalytic activity in the presence of O(2) was evaluated by the hydrogen-deuterium (H-D) exchange assay. In 1% O(2), 20.4% of its H-D exchange activity was retained. The great stability of HynSL makes it a potential candidate for biotechnological applications.
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Cammack R. K. Krishna Rao-a lifetime study of ferredoxins and solar hydrogen. PHOTOSYNTHESIS RESEARCH 2006; 90:97-9. [PMID: 16917667 DOI: 10.1007/s11120-006-9080-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Richard Cammack
- Department of Biochemistry, King's College London, Franklin-Wilkins Building 150, Stamford St, London, SE1 9NH, UK.
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Long M, Liu J, Chen Z, Bleijlevens B, Roseboom W, Albracht SPJ. Characterization of a HoxEFUYH type of [NiFe] hydrogenase from Allochromatium vinosum and some EPR and IR properties of the hydrogenase module. J Biol Inorg Chem 2006; 12:62-78. [PMID: 16969669 DOI: 10.1007/s00775-006-0162-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 08/11/2006] [Indexed: 10/24/2022]
Abstract
A soluble hydrogenase from Allochromatium vinosum was purified. It consisted of a large (M (r) = 52 kDa) and a small (M (r) = 23 kDa) subunit. The genes encoding for both subunits were identified. They belong to an open reading frame where they are preceded by three more genes. A DNA fragment containing all five genes was cloned and sequenced. The deduced amino acid sequences of the products characterized the complex as a member of the HoxEFUYH type of [NiFe] hydrogenases. Detailed sequence analyses revealed binding sites for eight Fe-S clusters, three [2Fe-2S] clusters and five [4Fe-4S] clusters, six of which are also present in homologous subunits of [FeFe] hydrogenases and NADH:ubiquione oxidoreductases (complex I). This makes the HoxEFUYH type of hydrogenases the one that is evolutionary closest to complex I. The relative positions of six of the potential Fe-S clusters are predicted on the basis of the X-ray structures of the Clostridium pasteurianum [FeFe] hydrogenase I and the hydrophilic domain of complex I from Thermus thermophilus. Although the HoxF subunit contains binding sites for flavin mononucleotide and NAD(H), cell-free extracts of A. vinosum did not catalyse a H(2)-dependent reduction of NAD(+). Only the hydrogenase module (HoxYH) could be purified. Its electron paramagnetic resonance (EPR) and IR spectral properties showed the presence of a Ni-Fe active site and a [4Fe-4S] cluster. Its activity was sensitive to carbon monoxide. No EPR signals from a light-sensitive Ni(a)-C* state could be observed. This study presents the first IR spectroscopic data on the HoxYH module of a HoxEFUYH type of [NiFe] hydrogenase.
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Affiliation(s)
- Minnan Long
- School of Life Sciences, Bio-energy Center, Xiamen University, Xiamen, 361005, People's Republic of China.
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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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Llama MJ, Serra JL, Rao KK, Hall DO. Isolation of two hydrogenase activities in Chromatium. EUROPEAN JOURNAL OF BIOCHEMISTRY 2005; 114:89-96. [PMID: 7011805 DOI: 10.1111/j.1432-1033.1981.tb06176.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Kinetic, chromatographic and electrophoretic studies of Chromatium hydrogenase show the existence in vitro of two different activities (I and II). The two hydrogenases exhibit different kinetic parameters and properties. Using reduced methyl viologen, Km and [S]0.5 values of about 20 microM and 360 microM were calculated for the hydrogenases I and II, respectively. Hill plots revealed that hydrogenase I followed classical hyperbolic (Michaelis-Menten) kinetics. However, a Hill coefficient (h = 0.68) indicating non-hyperbolic kinetics could be shown for hydrogenase II. After several purification steps hydrogenase II still showed kinetics typical of the action of either (a) two enzymes each of which shows Michaelis-Menten kinetics but with different substrate affinities or (b) only one enzyme which shows apparent negative cooperative regulation. The molecular weights of the hydrogenases were about 37,000 (I) and 55,000 (II) when determined by gel filtration. Sodium dodecyl sulphate/polyacrylamide gel electrophoresis revealed that both enzymes give a coincidental single protein band with the same relative mobility indicating a molecular weight of 31,000. Both hydrogenases were able to catalyse the reversible activation of H2 in the presence of artificial electron carriers but with different rates, hydrogenase II being much more active in the H2-uptake mode. The kinetic properties and molecular weight of hydrogenase II are partially modified by high ionic strength resulting in an increased substrate affinity and Hill coefficient and thus resembling hydrogenase I. These results are interpreted as due to the existence in vitro of monomeric and dimeric forms of Chromatium hydrogenase.
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Coppi MV, O'Neil RA, Lovley DR. Identification of an uptake hydrogenase required for hydrogen-dependent reduction of Fe(III) and other electron acceptors by Geobacter sulfurreducens. J Bacteriol 2004; 186:3022-8. [PMID: 15126463 PMCID: PMC400607 DOI: 10.1128/jb.186.10.3022-3028.2004] [Citation(s) in RCA: 72] [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
Geobacter sulfurreducens, a representative of the family Geobacteraceae that predominates in Fe(III)-reducing subsurface environments, can grow by coupling the oxidation of hydrogen to the reduction of a variety of electron acceptors, including Fe(III), fumarate, and quinones. An examination of the G. sulfurreducens genome revealed two operons, hya and hyb, which appeared to encode periplasmically oriented respiratory uptake hydrogenases. In order to assess the roles of these two enzymes in hydrogen-dependent growth, Hya- and Hyb-deficient mutants were generated by gene replacement. Hyb was found to be required for hydrogen-dependent reduction of Fe(III), anthraquinone-2,6-disulfonate, and fumarate by resting cell suspensions and to be essential for growth with hydrogen and these three electron acceptors. Hya, in contrast, was not. These findings suggest that Hyb is an essential respiratory hydrogenase in G. sulfurreducens.
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Affiliation(s)
- Maddalena V Coppi
- Department of Microbiology, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, USA.
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Brugna-Guiral M, Tron P, Nitschke W, Stetter KO, Burlat B, Guigliarelli B, Bruschi M, Giudici-Orticoni MT. [NiFe] hydrogenases from the hyperthermophilic bacterium Aquifex aeolicus: properties, function, and phylogenetics. Extremophiles 2003; 7:145-57. [PMID: 12664267 DOI: 10.1007/s00792-002-0306-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2002] [Accepted: 11/07/2002] [Indexed: 11/26/2022]
Abstract
Genes potentially coding for three distinct [NiFe] hydrogenases are present in the genome of Aquifex aeolicus. We have demonstrated that all three hydrogenases are expressed under standard growth conditions of the organism. Two hydrogenases were further purified to homogeneity. A periplasmically oriented hydrogenase was obtained in two forms, i.e., as a soluble enzyme containing only the two essential subunits and as a detergent-solubilized complex additionally containing a membrane-integral b-type cytochrome. The second hydrogenase purified was identified as a soluble cytoplasmic enzyme. The isolated enzymes were characterized with respect to biochemical/biophysical parameters, activity, thermostability, and substrate specificity. The phylogenetic positioning of all three hydrogenases was analyzed. A model for the metabolic roles of the three enzymes is proposed on the basis of the obtained results.
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Affiliation(s)
- Marianne Brugna-Guiral
- Bioénergétique et Ingénierie des Protéines, CNRS, IBSM, 31 chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
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10
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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] [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.
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Affiliation(s)
- Brant K J Pohorelic
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
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Asada Y, Koike Y, Schnackenberg J, Miyake M, Uemura I, Miyake J. Heterologous expression of clostridial hydrogenase in the Cyanobacterium synechococcus PCC7942. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1490:269-78. [PMID: 10684972 DOI: 10.1016/s0167-4781(00)00010-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Clostridium pasteurianum hydrogenase I has been expressed in the cyanobacterium Synechococcus PCC7942. The Shine-Dalgarno sequence of the structural gene encoding hydrogenase I from C. pasteurianum was changed to that of the cat (chloramphenicol acetyltransferase) gene. The hydrogenase gene was cloned downstream of a strong promoter, isolated from Synechococcus PCC7942, with the cat gene as a reporter gene. Expression of clostridial hydrogenase was confirmed by Western and Northern blot analyses in Synechococcus and Escherichia coli, whereas in vivo/in vitro measurements and activity staining of soluble proteins separated on non-denaturing polyacrylamide gels revealed functional expression of hydrogenase only in cyanobacterial cells. The changed Shine-Dalgarno sequence appeared to be essential for the functional expression of clostridial hydrogenase in Synechococcus, but had no influence on the expression and activity of clostridial hydrogenase expressed in E. coli.
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Affiliation(s)
- Y Asada
- Industrial Technology Center of Okayama Prefecture, 5301 Haga, Okayama-shi, Japan
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12
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Brugna M, Nitschke W, Toci R, Bruschi M, Giudici-Orticoni MT. First evidence for the presence of a hydrogenase in the sulfur-reducing bacterium Desulfuromonas acetoxidans. J Bacteriol 1999; 181:5505-8. [PMID: 10464227 PMCID: PMC94062 DOI: 10.1128/jb.181.17.5505-5508.1999] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/1999] [Accepted: 06/22/1999] [Indexed: 11/20/2022] Open
Abstract
Hydrogenases, which are ubiquitous in sulfate-reducing bacteria, were previously thought to be absent from Desulfuromonas acetoxidans. For the first time, a hydrogenase from the strict anaerobic sulfur-respiring bacterium D. acetoxidans, grown on ethanol-malate, was detected and enriched. To assay the role of the hydrogenase in the energetic metabolism of D. acetoxidans, we examined the reactivity of the enzyme with polyheme cytochromes from the same bacterium.
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Affiliation(s)
- M Brugna
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036 CNRS, Institut de Biologie Structurale et Microbiologie, 13402 Marseille Cedex 20, France
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13
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Brugna M, Giudici-Orticoni M, Spinelli S, Brown K, Tegoni M, Bruschi M. Kinetics and interaction studies between cytochrome c3 and Fe-only hydrogenase fromDesulfovibrio vulgaris hildenborough. Proteins 1998. [DOI: 10.1002/(sici)1097-0134(19981201)33:4<590::aid-prot11>3.0.co;2-i] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Casalot L, Hatchikian CE, Forget N, de Philip P, Dermoun Z, Bélaïch JP, Rousset M. Molecular Study and Partial Characterization of Iron-only Hydrogenase inDesulfovibrio fructosovorans. Anaerobe 1998; 4:45-55. [PMID: 16887623 DOI: 10.1006/anae.1997.0137] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/1997] [Accepted: 11/26/1997] [Indexed: 11/22/2022]
Abstract
An iron-only hydrogenase was partially purified and characterized from Desulfovibrio fructosovorans wild-type strain. The enzyme exhibits a molecular mass of 56 kDa and is composed of two distinct subunits HydA and HydB (46 and 13 kDa, respectively). The N-terminal amino acid sequences of the two subunits of the enzyme were determined with the aim of designing degenerate oligonucleotides. Direct and inverse polymerase chain reaction techniques were used to clone the hydrogenase encoding genes. A 9-nucleotide region located 75 bp upstream from the translational start codon of the D. fructosovorans hydA gene was found to be highly conserved. The analysis of the deduced amino acid sequence of these genes showed the presence of a signal sequence located in the small subunit, exhibiting the consensus sequence which is likely to be involved in the specific export mechanism of hydrogenases. Two ferredoxin-like motives involved in the coordination of [4Fe-4S] clusters were identified in the N-terminal domain of the large subunit. The amino acid sequence of the [Fe] hydrogenase from D. fructosovorans was compared with the amino acid sequences from eight other hydrogenases (cytoplasmic and periplasmic). These enzymes share an overall 18% identity and 28% similarity. The identity reached 73% and 69% when the D. fructosovorans hydrogenase sequence was compared with the hydrogenase sequences from Desulfovibrio vulgaris Hildenborough and Desulfovibrio vulgaris oxamicus Monticello, respectively.
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Affiliation(s)
- L Casalot
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036-CNRS, Marseille, France
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Hatchikian EC, Forget N, Bernadac A, Alazard D, Ollivier B. Involvement of a single periplasmic hydrogenase for both hydrogen uptake and production in some Desulfovibrio species. Res Microbiol 1995; 146:129-41. [PMID: 7652207 DOI: 10.1016/0923-2508(96)80891-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Various sulphate-reducing bacteria differing in the number of genes encoding hydrogenase were shown to ferment lactate in coculture with Methanospirillum hungatei, in the absence of sulphate. The efficiency of interspecies H2 transfer carried out by these species of sulphate-reducing bacteria does not appear to correlate with the distribution of genes coding for hydrogenase. Desulfovibrio vulgaris Groningen, which possesses only the gene for [NiFe] hydrogenase, oxidizes hydrogen in the presence of sulphate and produces some hydrogen during fermentation of pyruvate without electron acceptor. The hydrogenase of D. vulgaris was purified and characterized. It exhibits a molecular mass of 87 kDa and is composed of two different subunits (60 and 28 kDa). D. vulgaris hydrogenase contains 10.6 iron atoms, 0.9 nickel atom and 12 acid-labile sulphur atoms/molecule, and the absorption spectrum of the enzyme is characteristic of an iron-sulphur protein. Maximal H2 uptake and H2 evolution activities were 332 and 230 units/mg protein, respectively. D. vulgaris cells contain exclusively the [NiFe] hydrogenase, whatever the growth conditions, as shown by biochemical and immunological studies. Immunocytolocalization in ultrathin frozen sections of cells grown on lactate and sulphate, on H2 and sulphate and on pyruvate showed that the [NiFe] hydrogenase was located in the periplasmic space. Labelling was enhanced in cells grown on H2 and sulphate and on pyruvate. The results enable us to conclude that D. vulgaris Groningen contains a single hydrogenase of the [NiFe] type, located in the periplasmic space like that described for D. gigas. This enzyme appears to be involved in both H2 uptake and H2 production, depending on the growth conditions.
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Affiliation(s)
- E C Hatchikian
- Unité de Bioénergétique et Ingéniérie des Protéines, CNRS, Marseille, France
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Albracht SP. Nickel hydrogenases: in search of the active site. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1188:167-204. [PMID: 7803444 DOI: 10.1016/0005-2728(94)90036-1] [Citation(s) in RCA: 341] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- S P Albracht
- E.C. Slater Institute, BioCentrum Amsterdam, University of Amsterdam, The Netherlands
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Abstract
Escherichia coli has the capacity to synthesise three distinct formate dehydrogenase isoenzymes and three hydrogenase isoenzymes. All six are multisubunit, membrane-associated proteins that are functional in the anaerobic metabolism of the organism. One of the formate dehydrogenase isoenzymes is also synthesised in aerobic cells. Two of the formate dehydrogenase enzymes and two hydrogenases have a respiratory function while the formate dehydrogenase and hydrogenase associated with the formate hydrogenlyase pathway are not involved in energy conservation. The three formate dehydrogenases are molybdo-selenoproteins while the three hydrogenases are nickel enzymes; all six enzymes have an abundance of iron-sulfur clusters. These metal requirements alone invoke the necessity for a profusion of ancillary enzymes which are involved in the preparation and incorporation of these cofactors. The characterisation of a large number of pleiotropic mutants unable to synthesise either functionally active formate dehydrogenases or hydrogenases has led to the identification of a number of these enzymes. However, it is apparent that there are many more accessory proteins involved in the biosynthesis of these isoenzymes than originally anticipated. The biochemical function of the vast majority of these enzymes is not understood. Nevertheless, through the construction and study of defined mutants, together with sequence comparisons with homologous proteins from other organisms, it has been possible at least to categorise them with regard to a general requirement for the biosynthesis of all three isoenzymes or whether they have a specific function in the assembly of a particular enzyme. The identification of the structural genes encoding the formate dehydrogenase and hydrogenase isoenzymes has enabled a detailed dissection of how their expression is coordinated to the metabolic requirement for their products. Slowly, a picture is emerging of the extremely complex and involved path of events leading to the regulated synthesis, processing and assembly of catalytically active formate dehydrogenase and hydrogenase isoenzymes. This article aims to review the current state of knowledge regarding the biochemistry, genetics, molecular biology and physiology of these enzymes.
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Affiliation(s)
- G Sawers
- Lehrstuhl für Mikrobiologie der Universität München, Germany
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18
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Hatchikian EC, Forget N, Fernandez VM, Williams R, Cammack R. Further characterization of the [Fe]-hydrogenase from Desulfovibrio desulfuricans ATCC 7757. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 209:357-65. [PMID: 1327776 DOI: 10.1111/j.1432-1033.1992.tb17297.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The properties of the periplasmic hydrogenase from Desulfovibrio desulfuricans ATCC 7757, previously reported to be a single-subunit protein [Glick, B. R., Martin, W. G., and Martin, S. M. (1980) Can. J. Microbiol. 26, 1214-1223] were reinvestigated. The pure enzyme exhibited a molecular mass of 53.5 kDa as measured by analytical ultracentrifugation and was found to comprise two different subunits of 42.5 kDa and 11 kDa, with serine and alanine as N-terminal residues, respectively. The N-terminal amino acid sequences of its large and small subunits, determined up to 25 residues, were identical to those of the Desulfovibrio vulgaris Hildenborough [Fe]-hydrogenase. D. desulfuricans ATCC 7757 hydrogenase was free of nickel and contained 14.0 atoms of iron and 14.4 atoms of acid-labile sulfur/molecule and had E400, 52.5 mM-1.cm-1. The purified hydrogenase showed a specific activity of 62 kU/mg of protein in the H2-uptake assay, and the H2-uptake activity was higher than H2-evolution activity. The enzyme isolated under aerobic conditions required incubation under reducing conditions to express its maximum activity both in the H2-uptake and 2H2/1H2 exchange reaction. The ratio of the activity of activated to as-isolated hydrogenase was approximately 3. EPR studies allowed the identification of two ferredoxin-type [4Fe-4S]1+ clusters in hydrogenase samples reduced by hydrogen. In addition, an atypical cluster exhibiting a rhombic signal (g values 2.10, 2.038, 1.994) assigned to the H2-activating site in other [Fe]-hydrogenases was detected in partially reduced samples. Molecular properties, EPR spectroscopy, catalytic activities with different substrates and sensitivity to hydrogenase inhibitors indicated that D. desulfuricans ATCC 7757 periplasmic hydrogenase is a [Fe]-hydrogenase, similar in most respects to the well characterized [Fe]-hydrogenase from D. vulgaris Hildenborough.
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Affiliation(s)
- E C Hatchikian
- Laboratoire de Chimie Bacterienne, Centre National de la Recherche Scientifique, Marseille, France
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19
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MOMOSHIMA N, TJAHAJA PI, TAKASHIMA Y. HT Oxidation Activity of Soil Irradiated with Gamma Radiation. J NUCL SCI TECHNOL 1992. [DOI: 10.1080/18811248.1992.9731626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Koch HG, Kern M, Klemme JH. Reinvestigation of regulation of biosynthesis and subunit composition of nickel-dependent Hup-hydrogenase ofRhodospirillum rubrum. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05208.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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21
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Rousset M, Dermoun Z, Chippaux M, Bélaich JP. Marker exchange mutagenesis of the hydN genes in Desulfovibrio fructosovorans. Mol Microbiol 1991; 5:1735-40. [PMID: 1943706 DOI: 10.1111/j.1365-2958.1991.tb01922.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A strain of Desulfovibrio fructosovorans deleted from the hydN [NiFe]hydrogenase structural gene was constructed. A plasmid carrying a 7 kb DNA fragment on which the hydN gene had been replaced by the npt reporter gene (kanamycin-resistant, KnR) was introduced into D. fructosovorans by electroporation. Southern analysis of one KnR clone demonstrated that the hydN gene had been eliminated by marker exchange. This mutant, which was devoid of the [NiFe]hydrogenase gene, still showed a 10% residual hydrogenase activity. Its ability to grow efficiently with H2 as sole energy source is discussed. This is the first report, in a member of the sulphate-reducing bacteria, of a successful transformation and concomitant homologous recombination leading to a fully controlled genotype.
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Affiliation(s)
- M Rousset
- Laboratoire de Chimie Bactérienne, CNRS, Marseille, France
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22
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Kovács KL, Tigyi G, Thanh LT, Lakatos S, Kiss Z, Bagyinka C. Structural rearrangements in active and inactive forms of hydrogenase from Thiocapsa roseopersicina. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(17)35265-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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23
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Abstract
Hydrogenases devoid of nickel and containing only Fe-S clusters have been found so far only in some strictly anaerobic bacteria. Four Fe-hydrogenases have been characterized: from Megasphaera elsdenii, Desulfovibrio vulgaris (strain Hildenborough), and two from Clostridium pasteurianum. All contain two or more [4Fe-4S]1+,2+ or F clusters and a unique type of Fe-S center termed the H cluster. The H cluster appears to be remarkably similar in all the hydrogenases, and is proposed as the site of H2 oxidation and H2 production. The F clusters serve to transfer electrons between the H cluster and the external electron carrier. In all of the hydrogenases the H cluster is comprised of at least three Fe atoms, and possibly six. In the oxidized state it contains two types of magnetically distinct Fe atoms, has an S = 1/2 spin state, and exhibits a novel rhombic EPR signal. The reduced cluster is diamagnetic (S = 0). The oxidized H cluster appears to undergo a conformation change upon reduction with H2 with an increase in Fe-Fe distances of about 0.5 A. Studies using resonance Raman, magnetic circular dichroism and electron spin echo spectroscopies suggest that the H cluster has significant non-sulfur coordination. The H cluster has two binding sites for CO, at least one of which can also bind O2. Binding to one site changes the EPR properties of the cluster and gives a photosensitive adduct, but does not affect catalytic activity. Binding to the other site, which only becomes exposed during the catalytic cycle, leads to loss of catalytic activity. Mechanisms of H2 activation and electron transfer are proposed to explain the effects of CO binding and the ability of one of the hydrogenases to preferentially catalyze H2 oxidation.
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Affiliation(s)
- M W Adams
- Department of Biochemistry, University of Georgia, Athens 30602
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24
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Hatchikian CE, Traore AS, Fernandez VM, Cammack R. Characterization of the nickel-iron periplasmic hydrogenase from Desulfovibrio fructosovorans. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 187:635-43. [PMID: 2154378 DOI: 10.1111/j.1432-1033.1990.tb15347.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The periplasmic hydrogenase from Desulfovibrio fructosovorans grown on fructose/sulfate medium was purified to homogeneity. It exhibits a molecular mass of 88 kDa and is composed of two different subunits of 60 kDa and 28.5 kDa. The absorption spectrum of the enzyme is characteristic of an iron-sulfur protein and its absorption coefficients at 400 and 280 nm are 50 and 180 mM-1 cm-1, respectively. D. fructosovorans hydrogenase contains 11 +/- 1 iron atoms, 0.9 +/- 0.15 nickel atom and 12 +/- 1 acid-labile sulfur atoms/molecule but does not contain selenium. The amino acid composition of the protein and of its subunits, as well as the N-terminal sequences of the small and large subunits, have been determined. The cysteine residues of the protein are distributed between the large (9 residues) and the small subunits (11 residues). Electron spin resonance (ESR) properties of the enzyme are consistent with the presence of nickel(III), [3Fe-4S] and [4Fe-4S] clusters. The hydrogenase of D. fructosovorans isolated under aerobic conditions required an incubation with hydrogen or other reductants in order to express its full catalytic activity. H2 uptake and H2 evolution activities doubled after a 3-h incubation under reducing conditions. Comparison with the (NiFe) hydrogenase from D. gigas shows great structural similarities between the two proteins. However, there are significant differences between the catalytic properties of the two enzymes which can be related to the respective state of their nickel atom. ESR showed a higher proportion of the Ni-B species (g = 2.33, 2.16, 2.01) which can be related to a more facile conversion to the ready state. The periplasmic location of the enzyme and the presence of hydrogenase activity in other cellular compartments are discussed in relation to the ability of D. fructosovorans to participate actively in interspecies hydrogen transfer.
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Affiliation(s)
- C E Hatchikian
- Laboratoire de Chimie Bactérienne, Centre National de la Recherche Scientifique, Marseille, France
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25
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Fauque G, Peck HD, Moura JJ, Huynh BH, Berlier Y, DerVartanian DV, Teixeira M, Przybyla AE, Lespinat PA, Moura I. The three classes of hydrogenases from sulfate-reducing bacteria of the genus Desulfovibrio. FEMS Microbiol Rev 1988; 4:299-344. [PMID: 3078655 DOI: 10.1111/j.1574-6968.1988.tb02748.x] [Citation(s) in RCA: 163] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Three types of hydrogenases have been isolated from the sulfate-reducing bacteria of the genus Desulfovibrio. They differ in their subunit and metal compositions, physico-chemical characteristics, amino acid sequences, immunological reactivities, gene structures and their catalytic properties. Broadly, the hydrogenases can be considered as 'iron only' hydrogenases and nickel-containing hydrogenases. The iron-sulfur-containing hydrogenase ([Fe] hydrogenase) contains two ferredoxin-type (4Fe-4S) clusters and an atypical iron-sulfur center believed to be involved in the activation of H2. The [Fe] hydrogenase has the highest specific activity in the evolution and consumption of hydrogen and in the proton-deuterium exchange reaction and this enzyme is the most sensitive to CO and NO2-. It is not present in all species of Desulfovibrio. The nickel-(iron-sulfur)-containing hydrogenases [( NiFe] hydrogenases) possess two (4Fe-4S) centers and one (3Fe-xS) cluster in addition to nickel and have been found in all species of Desulfovibrio so far investigated. The redox active nickel is ligated by at least two cysteinyl thiolate residues and the [NiFe] hydrogenases are particularly resistant to inhibitors such as CO and NO2-. The genes encoding the large and small subunits of a periplasmic and a membrane-bound species of the [NiFe] hydrogenase have been cloned in Escherichia (E.) coli and sequenced. Their derived amino acid sequences exhibit a high degree of homology (70%); however, they show no obvious metal-binding sites or homology with the derived amino acid sequence of the [Fe] hydrogenase. The third class is represented by the nickel-(iron-sulfur)-selenium-containing hydrogenases [( NiFe-Se] hydrogenases) which contain nickel and selenium in equimolecular amounts plus (4Fe-4S) centers and are only found in some species of Desulfovibrio. The genes encoding the large and small subunits of the periplasmic hydrogenase from Desulfovibrio (D.) baculatus (DSM 1743) have been cloned in E. coli and sequenced. The derived amino acid sequence exhibits homology (40%) with the sequence of the [NiFe] hydrogenase and the carboxy-terminus of the gene for the large subunit contains a codon (TGA) for selenocysteine in a position homologous to a codon (TGC) for cysteine in the large subunit of the [NiFe] hydrogenase. EXAFS and EPR studies with the 77Se-enriched D. baculatus hydrogenase indicate that selenium is a ligand to nickel and suggest that the redox active nickel is ligated by at least two cysteinyl thiolate and one selenocysteine selenolate residues.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- G Fauque
- Section Enzymologie et Biochimie Bactérienne, ARBS, CEN Cadarache, Saint-Paul-Lez-Durance, France
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26
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Proteolytic resistance and its utilization in purification of hydrogenase from Thiocapsa roseopersicina. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1988. [DOI: 10.1016/0005-2728(88)90213-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Stoker K, Oltmann LF, Stouthamer AH. Partial characterization of an electrophoretically labile hydrogenase activity of Escherichia coli K-12. J Bacteriol 1988; 170:1220-6. [PMID: 3277948 PMCID: PMC210895 DOI: 10.1128/jb.170.3.1220-1226.1988] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A mutant of Escherichia coli K-12 is described that is specifically impaired in only one hydrogenase isoenzyme. By means of Tn5-mediated insertional mutagenesis, a class of mutants was isolated (class I) that had retained 20% of the overall hydrogenase activity. As determined by neutral polyacrylamide gel electrophoresis, the mutant contained normal amounts of the hydrogenase isoenzymes 1 and 2. Therefore, the hydrogenase activity affected seemed to be electrophoretically labile and was called hydrogenase L. The presence of such an activity was recently suggested in various papers and was called isoenzyme 3. Hydrogenase L might be identical or part of the latter isoenzyme. By DEAE ion-exchange chromatography it could be separated from hydrogenases 1 and 2. Hydrogenase activity in the parent strain HB101, determined manometrically with cell-free preparations and methylviologen as the electron acceptor, immediately showed maximal activity. However, class I mutants showed a lag phase which was dependent on the protein concentration utilized in the assay. This suggested that the fast initial activity of HB101 was due to hydrogenase L. The enzyme or enzyme complex showed an Mr around 300,000 and a pH optimum between 7 and 8. Strong indications about its physiological role were provided by the finding that in class I mutants H2 production by the formate-hydrogen lyase pathway was unimpaired, whereas fumarate-dependent H2 uptake was essentially zero. Complementation with F-prime factor F'116 but not with F'143 and coconjugation and cotransduction experiments localized the mutation (hydL) close to metC at approximately 64.8 min.
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Affiliation(s)
- K Stoker
- Department of Microbiology, Vrije Universiteit, Amsterdam, The Netherlands
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28
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[53] Hydrogenases: Isolation and assay. Methods Enzymol 1988. [DOI: 10.1016/0076-6879(88)67056-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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29
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Li C, Peck HD, LeGall J, Przybyla AE. Cloning, characterization, and sequencing of the genes encoding the large and small subunits of the periplasmic [NiFe]hydrogenase of Desulfovibrio gigas. DNA (MARY ANN LIEBERT, INC.) 1987; 6:539-51. [PMID: 3322743 DOI: 10.1089/dna.1987.6.539] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The structural genes for the large and small subunits of Desulfovibrio gigas periplasmic [NiFe]hydrogenase were identified and isolated by immunological and oligonucleotide screening. The gene for the small subunit codes for a 266-amino-acid, 28,724-dalton polypeptide which is separated by 63 nucleotides from the large subunit gene that codes for a 560-amino-acid, 61,707-dalton polypeptide. A putative signal peptide precedes the small subunit coding region, which may direct transport of the enzyme into the periplasmic compartment. Comparison of the amino acid sequence of this enzyme with those of two other classes of hydrogenase found in Desulfovibrio revealed that the D. gigas periplasmic hydrogenase has some homologies to the periplasmic [NiFeSe]hydrogenase of D. baculatus but none to the periplasmic [Fe]hydrogenase of D. vulgaris. The genes for the large and small subunits of the D. gigas hydrogenase hybridize strongly to genomic DNAs from several species of Desulfovibrio, indicating molecular similarity of the [NiFe]hydrogenase among sulfate reducers.
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Affiliation(s)
- C Li
- Department of Biochemistry, School of Chemical Sciences, University of Georgia, Athens 30602
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30
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Lissolo T, Choi ES, LeGall J, Peck HD. The presence of multiple intrinsic membrane nickel-containing hydrogenases in Desulfovibrio vulgaris (Hildenborough). Biochem Biophys Res Commun 1986; 139:701-8. [PMID: 3533065 DOI: 10.1016/s0006-291x(86)80047-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Three intrinsic membrane proteins exhibiting oxygen stable hydrogenase activity have been isolated from D. vulgaris. In contrast to the periplasmic exclusively non-heme iron hydrogenase, all three hydrogenases contain Ni in addition to non-heme iron, have low specific activities and are insensitive to inhibition by CO. None of the three hydrogenases cross react with IgA against the periplasmic hydrogenase of D. vulgaris but two of the new hydrogenases cross react with IgA against the periplasmic nickel containing hydrogenase of D. gigas and the other new hydrogenase cross reacts with IgA against the periplasmic nickel and selenium hydrogenase of D. desulfuricans (Norway -4).
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31
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Prickril BC, Czechowski MH, Przybyla AE, Peck HD, LeGall J. Putative signal peptide on the small subunit of the periplasmic hydrogenase from Desulfovibrio vulgaris. J Bacteriol 1986; 167:722-5. [PMID: 3525521 PMCID: PMC212951 DOI: 10.1128/jb.167.2.722-725.1986] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We sequenced the NH2 terminus of the large and small subunits of the periplasmic hydrogenase from the sulfate-reducing bacterium Desulfovibrio vulgaris (Hildenborough) and found that the small subunit lacks a region of 34 NH4-terminal amino acids coded by the gene for the small subunit (G. Voordouw and S. Brenner, Eur. J. Biochem. 148:515-520, 1985). We suggest that this region constitutes a signal peptide based on comparison with known procaryotic signal peptides.
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32
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Waugh R, Boxer DH. Pleiotropic hydrogenase mutants of Escherichia coli K12: growth in the presence of nickel can restore hydrogenase activity. Biochimie 1986; 68:157-66. [PMID: 3015243 DOI: 10.1016/s0300-9084(86)81080-x] [Citation(s) in RCA: 107] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Anaerobic growth in the presence of 0.6 mM NiCl2 was able to restore hydrogenase and benzyl-viologen-linked formate dehydrogenase activities to a mutant (FD12), which is normally defective in these activities. This mutant carries a mutation located near minute 58 in the genome. Hydrogenase isoenzyme I and II activities were restored along with the hydrogenase activity that forms part of the formate hydrogen lyase system. A plasmid (pRW1) was constructed, containing a 4.8 kb chromosomal DNA insert, which was able to complement the lesion in mutant FD12. Further mutants with mutations near 58 minutes on the chromosome, and which lacked hydrogenase and formate dehydrogenase activities were isolated. These mutants were divided into three groups. Class I mutants were restored to the wild-type phenotype either by growth with 0.6 mM NiCl2 or following transformation with pRW1. Class II mutants were also complemented by pRW1 but were unaffected by growth with NiCl2. Class III mutants were unaffected by both pRW1 and growth with NiCl2. The cloned 4.8 kb fragment of chromosomal DNA therefore encodes two genes essential for hydrogenase activity. Restriction analysis indicates that the cloned DNA is the same as a fragment that has previously been cloned and which complements the hydB locus (Sankar et al. (1985) J. Bacteriol., 162, 353-360). None of the three classes of mutants possess mutations in hydrogenase structural genes.
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33
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Tigyi G, Bagyinka C, Kovács KL. Protein structural changes associated with active and inactive states of hydrogenase from Thiocapsa roseopersicina. Biochimie 1986; 68:69-74. [PMID: 3089316 DOI: 10.1016/s0300-9084(86)81070-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Electrophoretic and isoelectrofocusing behavior of the hydrogenase from Thiocapsa roseopersicina under various conditions revealed remarkable properties of this enzyme: there are two active forms which differ in their molecular masses as well as in oxygen sensitivity; the apparent molecular masses of the active hydrogenase forms (90 and 49 kDa) differ considerably from those in the inactive state (64, 34, and 15 kDa); the active forms and some of the inactivated ones can be transformed into each other reversibly; urea can unfold the 64 and 34 kDa proteins but not the 49 kDa form at room temperature; the pI of these proteins are different in the presence of urea. The results suggest large rearrangements in the hydrogenase protein structure which are associated with the enzymatically active and inactive states. It is concluded that reversible formation of disulfide bonds cannot be the major cause for maintaining the enzyme conformation. Strong hydrophobic interactions are suggested to be primarily responsible for the structural stability and for the rearrangements.
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34
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Ballantine SP, Boxer DH. Nickel-containing hydrogenase isoenzymes from anaerobically grown Escherichia coli K-12. J Bacteriol 1985; 163:454-9. [PMID: 3894325 PMCID: PMC219143 DOI: 10.1128/jb.163.2.454-459.1985] [Citation(s) in RCA: 186] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Two membrane-bound hydrogenase isoenzymes present in Escherichia coli during anaerobic growth have been resolved. The isoenzymes are immunologically and electrophoretically distinct. The physically more abundant isoenzyme (hydrogenase 1) contains a subunit of Mr 64,000 and is not released from the membrane by exposure to either trypsin or pancreatin. The second isoenzyme (hydrogenase 2) apparently contributes the greater part of the membrane-bound hydrogen:benzyl viologen oxidoreductase activity and exists in two electrophoretic forms revealed by nondenaturing polyacrylamide gel analysis. This isoenzyme is irreversibly inactivated at alkaline pH and gives rise to an active, soluble derivative when the membrane-bound enzyme is exposed to either trypsin or pancreatin. Both hydrogenase isoenzymes contain nickel.
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35
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Sankar P, Lee JH, Shanmugam KT. Cloning of hydrogenase genes and fine structure analysis of an operon essential for H2 metabolism in Escherichia coli. J Bacteriol 1985; 162:353-60. [PMID: 3884595 PMCID: PMC218996 DOI: 10.1128/jb.162.1.353-360.1985] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Escherichia coli has two unlinked genes that code for hydrogenase synthesis and activity. The DNA fragments containing the two genes (hydA and hydB) were cloned into a plasmid vector, pBR322. The plasmids containing the hyd genes (pSE-290 and pSE-111 carrying the hydA and hydB genes, respectively) were used to genetically map a total of 51 mutant strains with defects in hydrogenase activity. A total of 37 mutants carried a mutation in the hydB gene, whereas the remaining 14 hyd were hydA. This complementation analysis also established the presence of two new genes, so far unidentified, one coding for formate dehydrogenase-2 (fdv) and another producing an electron transport protein (fhl) coupling formate dehydrogenase-2 to hydrogenase. Three of the four genes, hydB, fhl, and fdv, may constitute a single operon, and all three genes are carried by a 5.6-kilobase-pair chromosomal DNA insert in plasmid pSE-128. Plasmids carrying a part of this 5.6-kilobase-pair DNA (pSE-130) or fragments derived from this DNA in different orientations (pSE-126 and pSE-129) inhibited the production of active formate hydrogenlyase. This inhibition occurred even in a prototrophic E. coli, strain K-10, but only during an early induction period. These results, based on complementation analysis with cloned DNA fragments, show that both hydA and hydB genes are essential for the production of active hydrogenase. For the expression of active formate hydrogenlyase, two other gene products, fhl and fdv are also needed. All four genes map between 58 and 59 min in the E. coli chromosome.
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36
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Czechowski MH, He SH, Nacro M, DerVartanian DV, Peck HD, LeGall J. A cytoplasmic nickel-iron hydrogenase with high specific activity from Desulfovibrio multispirans sp. N., a new species of sulfate reducing bacterium. Biochem Biophys Res Commun 1984; 125:1025-32. [PMID: 6097250 DOI: 10.1016/0006-291x(84)91386-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A hydrogenase from a new species of sulfate reducing bacterium has been isolated and characterized. In contrast to other hydrogenases isolated from Desulfovibrio, this enzyme is found in the cytoplasmic fraction rather than in the periplasm. The specific activity of the enzyme, as measured in the hydrogen evolution assay, is twice as high as the specific activity of the hydrogenase from D. gigas. It also differentiates itself from the periplasmic Desulfovibrio hydrogenases by being more active in the hydrogen evolution rather than in the hydrogen uptake assay. The enzyme was shown to contain 0.9 atoms of nickel, 11 atoms of iron and 10 atoms of labile sulfide per mole of enzyme. It exhibits an unusually low intensity of the g = 2.31 nickel EPR signal in the isolated enzyme but shows a normal intensity for the g = 2.19 nickel EPR signal when reduced under hydrogen.
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37
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Rieder R, Cammack R, Hall DO. Purification and properties of the soluble hydrogenase from Desulfovibrio desulfuricans (strain Norway 4). EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 145:637-43. [PMID: 6096145 DOI: 10.1111/j.1432-1033.1984.tb08604.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A soluble hydrogenase has been isolated from Desulfovibrio desulfuricans (strain Norway 4) grown on Postgate's medium. The enzyme differs significantly from a membrane-bound hydrogenase previously purified from the same organism grown on Starkey's medium. The enzyme consisted of two subunits of 56 kDa and 29 kDa compared with masses of 60 kDa and 27 kDa for the membrane-bound enzyme. Analysis of preparations of the soluble enzyme by various methods gave values of 5-10 iron atoms, 6 labile sulphur atoms and 0.45-0.8 nickel atom per molecule. The enzyme was unusual in that it contained selenium, in quantities equivalent to nickel. The highly purified active enzyme produced no electron-spin-resonance (ESR) signals in the oxidized state. ESR signals due to a [3Fe-xS] cluster and nickel were observed only in some of the less active fractions of the enzyme, demonstrating that neither of these ESR-detectable components is a prerequisite for hydrogenase activity. Treatment of D. desulfuricans (Norway) cells with EDTA released a minor fraction with hydrogenase activity, which might indicate the presence of a periplasmic enzyme.
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Tigyi GJ, Kovács KL. Monoclonal antibodies to the hydrogenase ofThiocapsa roseopersicina. Curr Microbiol 1984. [DOI: 10.1007/bf01567701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Zinoni F, Beier A, Pecher A, Wirth R, Böck A. Regulation of the synthesis of hydrogenase (formate hydrogen-lyase linked) of E. coli. Arch Microbiol 1984; 139:299-304. [PMID: 6440507 DOI: 10.1007/bf00408370] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The regulation of synthesis of the hydrogenase which is a component of the formate hydrogen-lyase complex was studied by means of a strain of Escherichia coli possessing a transcriptional fusion of the hydrogenase gene (hyd) with the lacZ gene (hyd::lac fusion). Formation of active hydrogenase in the wild strain requires the presence of nickel in the medium; transcription of the hyd gene, however, is independent from the presence of Ni2+. Ni2+ addition to Ni2+-prestarved cells did not lead to any activation of presumptive hydrogenase apoprotein. Regulatory mutants were isolated in which nitrate repression of hyd::lac expression was relieved. Two main classes of regulatory mutants were identified: (i) Mutants with a defect in nitrate reductase; (ii) mutants with a cis-dominant regulatory mutation closely linked to the hyd::lac fusion. In the presence of formate which acts as an inducer, the hyd::lac fusion was also expressed under aerobic conditions. The results infer that nitrate repression of transcription of the hydrogenase structural gene is not effected by nitrate itself but requires the function of the electron transport chain leading to nitrate and that mutations in the promoter/operator region of the hyd cistron may confer insensitivity to redox control both by oxygen and nitrate.
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Lalla-Maharajh WV, Hall DO, Cammack R, Rao KK, Le Gall J. Purification and properties of the membrane-bound by hydrogenase from Desulfovibrio desulfuricans. Biochem J 1983; 209:445-54. [PMID: 6303306 PMCID: PMC1154111 DOI: 10.1042/bj2090445] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The membrane-bound hydrogenase from the anaerobic sulphate-reducing bacterium Desulfovibrio desulfuricans (Norway strain) has been purified to homogeneity, with an overall 80-fold purification and a specific activity of 70 mumol of H2 evolved/min per mg of protein. The hydrogenase had a relative molecular mass of 58 000 as determined by gel filtration and was estimated to contain six iron atoms and six acid-labile sulphur groups per molecule. The absorption spectrum of the enzyme was characteristic of an iron-sulphur protein. The E400 and E280 were 28 500 and 109 000 M-1.cm-1 respectively. The e.s.r. of the oxidized protein indicated the presence of [4Fe-4S]3+ or [3Fe-3S]3+, and another paramagnetic centre, probably Ni(III). The hydrogenase was inhibited by heavy-metal salts, carbon monoxide and high ionic strength. However, it was resistant to inhibition by thiol-blocking and metal-complexing reagents. N-Bromosuccinimide totally inhibited the enzyme activity at low concentrations. The enzyme was stable to O2 over long periods and to high temperatures. It catalyses both H2-evolution and H2-uptake with a variety of artificial electron carriers. D. desulfuricans cytochrome C3, its natural electron carrier, had a high affinity for the enzyme (Km = 2 microns). Rate enhancement was observed when cytochrome C3 was added to Methyl Viologen in the H2-evolution assay. The pH optimum for H2-evolution was 6.5.
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Urano N, Karube I, Suzuki S, Yamada T, Hirochika H, Sakaguchi K. Isolation and partial characterization of large plasmids in hydrogen-evolving bacterium Clostridium butyricum. ACTA ACUST UNITED AC 1983. [DOI: 10.1007/bf00499502] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Peck HD, LeGall J. Biochemistry of dissimilatory sulphate reduction. Philos Trans R Soc Lond B Biol Sci 1982; 298:443-66. [PMID: 6127735 DOI: 10.1098/rstb.1982.0091] [Citation(s) in RCA: 115] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Extensive information is available on the enzymology of respiratory sulphate reduction and the structure of electron transfer proteins isolated from the sulphate-reducing bacteria; however, it has not yet been possible to delineate satisfactorily the function of these electron transfer proteins in terms of the enzymes involved in respiratory sulphate reduction. New information about differences in pyrophosphate metabolism by Desulfovibrio and Desulfotomaculum, cellular localizations of electron transfer proteins and enzymes, and the concepts of vectorial electron transfer plus hydrogen cycling suggest that previous data on the function of electron transfer proteins must be re-evaluated and new experimental approaches designed before the problem is resolved. New information on the enzymology of lactate dehydrogenase, pyruvate dehydrogenase, adenylyl sulphate reductase, bisulphite reductase and hydrogenase is presented and discussed in the context of enzyme localization and specifically for electron transfer proteins. The function of cytochrome c3 (Mr = 13000) in the mechanism of the periplasmic hydrogenase and the role of the new [3Fe-3S] non-haem iron centres in electron transfer is emphasized.
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LAMBERT GRANTR, SMITH GEOFFREYD. THE HYDROGEN METABOLISM OF CYANOBACTERIA (BLUE-GREEN ALGAE). Biol Rev Camb Philos Soc 1981. [DOI: 10.1111/j.1469-185x.1981.tb00360.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Glick BR, Zeisler J, Banaszuk AM, Friesen JD, Martin WG. The identification and partial characterization of a plasmid containing the gene for the membrane-associated hydrogenase from E. coli. Gene 1981; 15:201-6. [PMID: 6271643 DOI: 10.1016/0378-1119(81)90129-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Escherichia coli DNA was digested with restriction endonuclease PstI and ligated into the PstI site of plasmid pBR322. Recombinant plasmids that were constructed in this manner were used to transform E. coli H61, a mutant with a decreased level of hydrogenase activity. Complementation of this hydrogenase mutation identified a bacterial clone carrying the gene for the membrane-associated E. coli hydrogenase in plasmid pBL101. In E. coli minicells, the pBL101 DNA directed the synthesis of a protein of a size corresponding to that of the precursor of the E. coli membrane-associated hydrogenase, which appears to contain an uncleaved leader peptide. A restriction map of the cloned DNA was determined for 14 endonucleases.
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van Heerikhuizen H, Albracht SP, Slater EC, van Rheenen PS. Purification and some properties of the soluble hydrogenase from Chromatium vinosum. BIOCHIMICA ET BIOPHYSICA ACTA 1981; 657:26-39. [PMID: 6260199 DOI: 10.1016/0005-2744(81)90127-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A routine procedure for the growth and harvesting of large (600 1) batches of Chromatium vinosum and the isolation of hydrogenase (hydrogen: (acceptor) oxidoreductase, EC 1.12.-.-) are described. The enzyme is pure according to polyacrylamide gel electrophoresis, has a molecular weight of 61,000-63,000 and consists of a single polypeptide chain. The enzyme is stable in air but not active. Activity is obtained only after complete removal of oxygen. EPR spectroscopy at 9 GHz shows a signal indicative for a [4Fe-4S]3+(3+,2+) cluster and in addition a rather complex signal of unknown origin. This additional signal completely disappears upon removal of oxygen, by incubation with 2-mercaptoethanol or by reduction with ferrocytochrome c. No EPR signals are detected in the enzyme reduced with H2 or dithionite. The intensity of the EPR signal of the [4Fe-4S] cluster corresponds to one-quarter of the enzyme concentration, both in the untreated as well as in the He- or N2-activated enzyme. If the enzyme is activated under He and then brought in contact with air the signal increases 4-fold and represents about one free spin/enzyme molecule. When measured at 35 GHz the line shape and peak positions of the additional signal change, indicating that the signal is not originating from a simple S = 1/2 system. None of the inhibitors of the hydrogenase activity has any effect on the shape or intensity o the EPR signal fo the Fe-S cluster, 2H2O also has no effect. All EPR signals disappear after reduction with NADH or ascorbate in the presence of phenazine methosulphate. It is suggested that the Fe-S cluster is not the primary site of interaction of H2 with the enzyme.
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Abstract
For a variety of reasons, including the potential industrial applications of hydrogenase, we are interested in the isolation and analysis of hydrogenase genes. In a program focusing on the hydrogen bacterium A. eutrophus H1 and E. coli, we have developed a preliminary concept of the interaction of hydrogenase in cellular metabolism, constructed mutants deficient in hydrogenase activity, and begun the isolation of hydrogenase genes utilizing the technology allowing the in vitro manipulation of DNA. We hope to pursue this project to its ultimate goal: the analysis of the molecular mechanisms involved in the control of expression of these genes and the development of the ability to manipulate the production of hydrogenase.
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Abstract
The membrane-bound hydrogenase (EC class 1.12) of aerobically grown Escherichia coli cells was solubilized by treatment with deoxycholate and pancreatin. The enzyme was further purified to electrophoretic homogeneity by chromoatographic methods, including hydrophobic-interaction chromatography, with a yield of 10% as judged by activity and an overall purification of 2140-fold. The hydrogenase was a dimer of identical subunits with a mol.wt. of 113,000 and contained 12 iron and 12 acid-labile sulphur atoms per molecule. The epsilon 400 was 49,000M-1 . cm-1. The hydrogenase catalysed both H2 evolution and H2 uptake with a variety of artificial electron carriers, but would not interact with flavodoxin, ferredoxin or nicotinamide and flavin nucleotides. We were unable to identify any physiological electron carrier for the hydrogenase. With Methyl Viologen as the electron carrier, the pH optimum for H2 evolution and H2 uptake was 6.5 and 8.5 respectively. The enzyme was stable for long periods at neutral pH, low temperatures and under anaerobic conditions. The half-life of the hydrogenase under air at room temperature was about 12 h, but it could be stabilized by Methyl Viologen and Benzyl Viologen, both of which are electron carriers for the enzyme, and by bovine serum albumin. The hydrogenase was strongly inhibited by carbon monoxide (Ki = 1870Pa), heavy-metal salts and high concentrations of buffers, but was resistant to inhibition by thiol-blocking and metal-complexing reagents. These aerobically grown E. coli cells lacked formate hydrogenlyase activity and cytochrome c552.
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