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Quinson J, Hidalgo R, Ash PA, Dillon F, Grobert N, Vincent KA. Comparison of carbon materials as electrodes for enzyme electrocatalysis: hydrogenase as a case study. Faraday Discuss 2014; 172:473-96. [DOI: 10.1039/c4fd00058g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We present a study of electrocatalysis by an enzyme adsorbed on a range of carbon materials, with different size, surface area, morphology and graphitic structure, which are either commercially available or prepared via simple, established protocols. We choose as our model enzyme the hydrogenase I from E. coli (Hyd-1), which is an active catalyst for H2 oxidation, is relatively robust and has been demonstrated in H2 fuel cells and H2-driven chemical synthesis. The carbon materials were characterised according to their surface area, surface morphology and graphitic character, and we use the electrocatalytic H2 oxidation current for Hyd-1 adsorbed on these materials to evaluate their effectiveness as enzyme electrodes. Here, we show that a variety of carbon materials are suitable for adsorbing hydrogenases in an electroactive configuration. This unified study provides insight into selection and design of carbon materials for study of redox enzymes and different applications of enzyme electrocatalysis.
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Affiliation(s)
- Jonathan Quinson
- Department of Materials
- University of Oxford
- Oxford OX1 3PH, UK
- Department of Chemistry
- University of Oxford
| | - Ricardo Hidalgo
- Department of Chemistry
- University of Oxford
- Inorganic Chemistry Laboratory
- Oxford, UK
| | - Philip A. Ash
- Department of Chemistry
- University of Oxford
- Inorganic Chemistry Laboratory
- Oxford, UK
| | - Frank Dillon
- Department of Materials
- University of Oxford
- Oxford OX1 3PH, UK
| | - Nicole Grobert
- Department of Materials
- University of Oxford
- Oxford OX1 3PH, UK
| | - Kylie A. Vincent
- Department of Chemistry
- University of Oxford
- Inorganic Chemistry Laboratory
- Oxford, UK
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Wang V, Ragsdale SW, Armstrong FA. Investigations of the efficient electrocatalytic interconversions of carbon dioxide and carbon monoxide by nickel-containing carbon monoxide dehydrogenases. Met Ions Life Sci 2014; 14:71-97. [PMID: 25416391 PMCID: PMC4261625 DOI: 10.1007/978-94-017-9269-1_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Carbon monoxide dehydrogenases (CODH) play an important role in utilizing carbon monoxide (CO) or carbon dioxide (CO2) in the metabolism of some microorganisms. Two distinctly different types of CODH are distinguished by the elements constituting the active site. A Mo-Cu containing CODH is found in some aerobic organisms, whereas a Ni-Fe containing CODH (henceforth simply Ni-CODH) is found in some anaerobes. Two members of the simplest class (IV) of Ni-CODH behave as efficient, reversible electrocatalysts of CO2/CO interconversion when adsorbed on a graphite electrode. Their intense electroactivity sets an important benchmark for the standard of performance at which synthetic molecular and material electrocatalysts comprised of suitably attired abundant first-row transition elements must be able to operate. Investigations of CODHs by protein film electrochemistry (PFE) reveal how the enzymes respond to the variable electrode potential that can drive CO2/CO interconversion in each direction, and identify the potential thresholds at which different small molecules, both substrates and inhibitors, enter or leave the catalytic cycle. Experiments carried out on a much larger (Class III) enzyme CODH/ACS, in which CODH is complexed tightly with acetyl-CoA synthase, show that some of these characteristics are retained, albeit with much slower rates of interfacial electron transfer, attributable to the difficulty in making good electronic contact at the electrode. The PFE results complement and clarify investigations made using spectroscopic investigations.
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103
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Hexter SV, Esterle TF, Armstrong FA. A unified model for surface electrocatalysis based on observations with enzymes. Phys Chem Chem Phys 2014; 16:11822-33. [DOI: 10.1039/c3cp55230f] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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104
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Trchounian A, Gary Sawers R. Novel insights into the bioenergetics of mixed-acid fermentation: Can hydrogen and proton cycles combine to help maintain a proton motive force? IUBMB Life 2013; 66:1-7. [DOI: 10.1002/iub.1236] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/04/2013] [Accepted: 12/08/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Armen Trchounian
- Department of Microbiology; Plants and Microbes Biotechnology, Faculty of Biology, Yerevan State University; Yerevan Armenia
| | - R. Gary Sawers
- Institute of Biology/Microbiology; Martin Luther University of Halle-Wittenberg; Halle (Saale) Germany
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105
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Contribution of hydrogenase 2 to stationary phase H2 production by Escherichia coli during fermentation of glycerol. Cell Biochem Biophys 2013; 66:103-8. [PMID: 23090790 DOI: 10.1007/s12013-012-9458-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Escherichia coli has four hydrogenases (Hyd), three genes of which are encoded by the hya, hyb, and hyc operons. The proton-reducing and hydrogen-oxidizing activities of Hyd-2 (hyb) were analyzed in whole cells grown to stationary phase and cell extracts, respectively, during glycerol fermentation using novel double mutants. H2 production rate at pH 7.5 was decreased by ~3.5- and ~7-fold in hya and hyc (HDK 103) or hyb and hyc (HDK 203) operon double mutants, respectively, compared with the wild type. At pH 6.5, H2 production decreased by ~2- and ~5-fold in HDK103 and HDK203, respectively, compared with the wild type. At pH 5.5, H2 production was reduced by ~4.5-fold in the mutants compared with the wild type. The total hydrogen-oxidizing activity was shown to depend on the pH of the growth medium in agreement with previous findings and was significantly reduced in the HDK103 or HDK203 mutants. At pH 7.5, Hyd-2 activity was 0.26 U (mg protein)(-1) and Hyd-1 activity was 0.1 U (mg protein)(-1). As the pH of the growth medium decreased to 6.5, Hyd-2 activity was 0.16 U (mg protein)(-1), and Hyd-1 was absent. Surprisingly, at pH 5.5, there was an increase in Hyd-2 activity (0.33 U mg protein)(-1) but not in that of Hyd-1. These findings show a major contribution of Hyd-2 to H2 production during glycerol fermentation that resulted from altered metabolism which surprisingly influenced proton reduction.
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106
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Poladyan A, Trchounian K, Sawers RG, Trchounian A. Hydrogen-oxidizing hydrogenases 1 and 2 ofEscherichia coliregulate the onset of hydrogen evolution and ATPase activity, respectively, during glucose fermentation at alkaline pH. FEMS Microbiol Lett 2013; 348:143-8. [DOI: 10.1111/1574-6968.12281] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 09/17/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Anna Poladyan
- Department of Microbiology, Plants and Microbes Biotechnology; Faculty of Biology; Yerevan State University; Yerevan Armenia
| | - Karen Trchounian
- Department of Biophysics; Faculty of Biology; Yerevan State University; Yerevan Armenia
- Institute of Biology/Microbiology; Martin Luther University of Halle-Wittenberg; Halle Germany
| | - R. Gary Sawers
- Institute of Biology/Microbiology; Martin Luther University of Halle-Wittenberg; Halle Germany
| | - Armen Trchounian
- Department of Microbiology, Plants and Microbes Biotechnology; Faculty of Biology; Yerevan State University; Yerevan Armenia
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107
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Trchounian K, Trchounian A. Escherichia colimultiple [Ni-Fe]-hydrogenases are sensitive to osmotic stress during glycerol fermentation but at different pHs. FEBS Lett 2013; 587:3562-6. [DOI: 10.1016/j.febslet.2013.09.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022]
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108
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Bowman L, Palmer T, Sargent F. A regulatory domain controls the transport activity of a twin-arginine signal peptide. FEBS Lett 2013; 587:3365-70. [PMID: 24036452 DOI: 10.1016/j.febslet.2013.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/02/2013] [Accepted: 09/03/2013] [Indexed: 11/25/2022]
Abstract
The twin-arginine translocation (Tat) pathway is used by bacteria for the transmembrane transport of folded proteins. Proteins are targeted to the Tat translocase by signal peptides that have common tripartite structures consisting of polar n-regions, hydrophobic h-regions, and polar c-regions. In this work, the signal peptide of [NiFe] hydrogenase-1 from Escherichia coli has been studied. The hydrogenase-1 signal peptide contains an extended n-region that has a conserved primary structure. Genetic and biochemical approaches reveal that the signal peptide n-region is essential for hydrogenase assembly and acts as a regulatory domain controlling transport activity of the signal peptide.
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Affiliation(s)
- Lisa Bowman
- College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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109
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James MJ, Coulthurst SJ, Palmer T, Sargent F. Signal peptide etiquette during assembly of a complex respiratory enzyme. Mol Microbiol 2013; 90:400-14. [PMID: 23961722 DOI: 10.1111/mmi.12373] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2013] [Indexed: 12/25/2022]
Abstract
Salmonella enterica serovar Typhimurium is a Gram-negative pathogen capable of respiration with a number of terminal electron acceptors. Tetrathionate reductase is important for the infection process and is encoded by the ttrBCA operon where TtrA and TtrB are metallocofactor-containing proteins targeted to the periplasmic side of the membrane by two different Tat targeting peptides. In this work, the inter-relationship between these two signal peptides has been explored. Molecular genetics and biochemical approaches reveal that the processing of the TtrB Tat signal peptide is dependent on the successful assembly of its partner protein, TtrA. Inactivation of either the TtrA or the TtrB Tat targeting peptides individually was observed to have limited overall effects on assembly of the enzyme or on cellular tetrathionate reductase activity. However, inactivation of both signal peptides simultaneously was found to completely abolish physiological tetrathionate reductase activity. These data suggest both signals are normally active during assembly of the enzyme, and imply a code of conduct exists between the signal peptides where one can compensate for inactivity in the other. Since it appears likely that tetrathionate reductase presents itself for export as a multi-signal complex, these observations also have implications for the mechanism of the bacterial Tat translocase.
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Affiliation(s)
- Martyn J James
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
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110
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Trchounian A. Mechanisms for hydrogen production by different bacteria during mixed-acid and photo-fermentation and perspectives of hydrogen production biotechnology. Crit Rev Biotechnol 2013; 35:103-13. [DOI: 10.3109/07388551.2013.809047] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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111
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Yonemoto IT, Matteri CW, Nguyen TA, Smith HO, Weyman PD. Dual organism design cycle reveals small subunit substitutions that improve [NiFe] hydrogenase hydrogen evolution. J Biol Eng 2013; 7:17. [PMID: 23819621 PMCID: PMC3701524 DOI: 10.1186/1754-1611-7-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 06/26/2013] [Indexed: 01/21/2023] Open
Abstract
Background Photosynthetic microorganisms that directly channel solar energy to the production of molecular hydrogen are a potential future biofuel system. Building such a system requires installation of a hydrogenase in the photosynthetic organism that is both tolerant to oxygen and capable of hydrogen production. Toward this end, we have identified the [NiFe] hydrogenase from the marine bacterium Alteromonas macleodii “Deep ecotype” that is able to be heterologously expressed in cyanobacteria and has tolerance to partial oxygen. The A. macleodii enzyme shares sequence similarity with the uptake hydrogenases that favor hydrogen uptake activity over hydrogen evolution. To improve hydrogen evolution from the A. macleodii hydrogenase, we examined the three Fe-S clusters found in the small subunit of many [NiFe] uptake hydrogenases that presumably act as a molecular wire to guide electrons to or from the active site of the enzyme. Studies by others altering the medial cluster of a Desulfovibrio fructosovorans hydrogenase from 3Fe-4S to 4Fe-4S resulted in two-fold improved hydrogen evolution activity. Results We adopted a strategy of screening for improved hydrogenase constructs using an Escherichia coli expression system before testing in slower growing cyanobacteria. From the A. macleodii enzyme, we created a mutation in the gene encoding the hydrogenase small subunit that in other systems is known to convert the 3Fe-4S medial cluster to 4Fe-4S. The medial cluster substitution did not improve the hydrogen evolution activity of our hydrogenase. However, modifying both the medial cluster and the ligation of the distal Fe-S cluster improved in vitro hydrogen evolution activity relative to the wild type hydrogenase by three- to four-fold. Other properties of the enzyme including thermostability and tolerance to partial oxygen did not appear to be affected by the substitutions. Conclusions Our results show that substitution of amino acids altering the ligation of Fe-S clusters in the A. macleodii [NiFe] uptake hydrogenase resulted in increased hydrogen evolution activity. This activity can be recapitulated in multiple host systems and with purified protein. These results validate the approach of using an E. coli-cyanobacteria shuttle system for enzyme expression and improvement.
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Affiliation(s)
- Isaac T Yonemoto
- J, Craig Venter Institute, 10355 Science Center Dr, San Diego, CA 92121, USA.
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112
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Chenevier P, Mugherli L, Darbe S, Darchy L, DiManno S, Tran PD, Valentino F, Iannello M, Volbeda A, Cavazza C, Artero V. Hydrogenase enzymes: Application in biofuel cells and inspiration for the design of noble-metal free catalysts for H2 oxidation. CR CHIM 2013. [DOI: 10.1016/j.crci.2012.11.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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113
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Nonaka K, Nguyen NT, Yoon KS, Ogo S. Novel H2-oxidizing [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F. J Biosci Bioeng 2013. [DOI: 10.1016/j.jbiosc.2012.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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114
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Evans RM, Parkin A, Roessler MM, Murphy BJ, Adamson H, Lukey MJ, Sargent F, Volbeda A, Fontecilla-Camps JC, Armstrong FA. Principles of sustained enzymatic hydrogen oxidation in the presence of oxygen--the crucial influence of high potential Fe-S clusters in the electron relay of [NiFe]-hydrogenases. J Am Chem Soc 2013; 135:2694-707. [PMID: 23398301 DOI: 10.1021/ja311055d] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
"Hyd-1", produced by Escherichia coli , exemplifies a special class of [NiFe]-hydrogenase that can sustain high catalytic H(2) oxidation activity in the presence of O(2)-an intruder that normally incapacitates the sulfur- and electron-rich active site. The mechanism of "O(2) tolerance" involves a critical role for the Fe-S clusters of the electron relay, which is to ensure the availability-for immediate transfer back to the active site-of all of the electrons required to reduce an attacking O(2) molecule completely to harmless H(2)O. The unique [4Fe-3S] cluster proximal to the active site is crucial because it can rapidly transfer two of the electrons needed. Here we investigate and establish the equally crucial role of the high potential medial [3Fe-4S] cluster, located >20 Å from the active site. A variant, P242C, in which the medial [3Fe-4S] cluster is replaced by a [4Fe-4S] cluster, is unable to sustain steady-state H(2) oxidation activity in 1% O(2). The [3Fe-4S] cluster is essential only for the first stage of complete O(2) reduction, ensuring the supply of all three electrons needed to form the oxidized inactive state "Ni-B" or "Ready" (Ni(III)-OH). Potentiometric titrations show that Ni-B is easily reduced (E(m) ≈ +0.1 V at pH 6.0); this final stage of the O(2)-tolerance mechanism regenerates active enzyme, effectively completing a competitive four-electron oxidase cycle and is fast regardless of alterations at the proximal or medial clusters. As a consequence of all these factors, the enzyme's response to O(2), viewed by its electrocatalytic activity in protein film electrochemistry (PFE) experiments, is merely to exhibit attenuated steady-state H(2) oxidation activity; thus, O(2) behaves like a reversible inhibitor rather than an agent that effectively causes irreversible inactivation. The data consolidate a rich picture of the versatile role of Fe-S clusters in electron relays and suggest that Hyd-1 can function as a proficient hydrogen oxidase.
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115
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[NiFe] hydrogenases: a common active site for hydrogen metabolism under diverse conditions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:986-1002. [PMID: 23399489 DOI: 10.1016/j.bbabio.2013.01.015] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/06/2012] [Accepted: 01/26/2013] [Indexed: 01/05/2023]
Abstract
Hydrogenase proteins catalyze the reversible conversion of molecular hydrogen to protons and electrons. The most abundant hydrogenases contain a [NiFe] active site; these proteins are generally biased towards hydrogen oxidation activity and are reversibly inhibited by oxygen. However, there are [NiFe] hydrogenase that exhibit unique properties, including aerobic hydrogen oxidation and preferential hydrogen production activity; these proteins are highly relevant in the context of biotechnological devices. This review describes four classes of these "nonstandard" [NiFe] hydrogenases and discusses the electrochemical, spectroscopic, and structural studies that have been used to understand the mechanisms behind this exceptional behavior. A revised classification protocol is suggested in the conclusions, particularly with respect to the term "oxygen-tolerance". This article is part of a special issue entitled: metals in bioenergetics and biomimetics systems.
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116
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117
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Mouesca JM, Fontecilla-Camps JC, Amara P. The Structural Plasticity of the Proximal [4Fe3S] Cluster is Responsible for the O2Tolerance of Membrane-Bound [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2013; 52:2002-6. [DOI: 10.1002/anie.201209063] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Indexed: 11/08/2022]
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118
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Mouesca JM, Fontecilla-Camps JC, Amara P. The Structural Plasticity of the Proximal [4Fe3S] Cluster is Responsible for the O2
Tolerance of Membrane-Bound [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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119
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Ciaccafava A, Hamon C, Infossi P, Marchi V, Giudici-Orticoni MT, Lojou E. Light-induced reactivation of O2-tolerant membrane-bound [Ni–Fe] hydrogenase from the hyperthermophilic bacterium Aquifex aeolicus under turnover conditions. Phys Chem Chem Phys 2013; 15:16463-7. [DOI: 10.1039/c3cp52596a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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120
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Kim K, Kishima T, Matsumoto T, Nakai H, Ogo S. Selective Redox Activation of H2 or O2 in a [NiRu] Complex by Aromatic Ligand Effects. Organometallics 2012. [DOI: 10.1021/om300833m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Kyoungmok Kim
- International Institute for Carbon-Neutral
Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku,
Fukuoka 819-0395, Japan
- Department of Chemistry and Biochemistry, Graduate School
of Engineering, Kyushu University, 744
Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takahiro Kishima
- Department of Chemistry and Biochemistry, Graduate School
of Engineering, Kyushu University, 744
Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takahiro Matsumoto
- International Institute for Carbon-Neutral
Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku,
Fukuoka 819-0395, Japan
- Department of Chemistry and Biochemistry, Graduate School
of Engineering, Kyushu University, 744
Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hidetaka Nakai
- International Institute for Carbon-Neutral
Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku,
Fukuoka 819-0395, Japan
- Department of Chemistry and Biochemistry, Graduate School
of Engineering, Kyushu University, 744
Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Seiji Ogo
- International Institute for Carbon-Neutral
Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku,
Fukuoka 819-0395, Japan
- Department of Chemistry and Biochemistry, Graduate School
of Engineering, Kyushu University, 744
Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
- Core Research for
Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi
Center Building, 4-1-8 Honcho, Kawaguchi-shi, Saitama
332-0012, Japan
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Volbeda A, Darnault C, Parkin A, Sargent F, Armstrong FA, Fontecilla-Camps JC. Crystal structure of the O(2)-tolerant membrane-bound hydrogenase 1 from Escherichia coli in complex with its cognate cytochrome b. Structure 2012; 21:184-190. [PMID: 23260654 DOI: 10.1016/j.str.2012.11.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/10/2012] [Accepted: 11/15/2012] [Indexed: 10/27/2022]
Abstract
We report the 3.3 Å resolution structure of dimeric membrane-bound O(2)-tolerant hydrogenase 1 from Escherichia coli in a 2:1 complex with its physiological partner, cytochrome b. From the short distance between distal [Fe(4)S(4)] clusters, we predict rapid transfer of H(2)-derived electrons between hydrogenase heterodimers. Thus, under low O(2) levels, a functional active site in one heterodimer can reductively reactivate its O(2)-exposed counterpart in the other. Hydrogenase 1 is maximally expressed during fermentation, when electron acceptors are scarce. These conditions are achieved in the lower part of the host's intestinal tract when E. coli is soon to be excreted and undergo an anaerobic-to-aerobic metabolic transition. The apparent paradox of having an O(2)-tolerant hydrogenase expressed under anoxia makes sense if the enzyme functions to keep intracellular O(2) levels low by reducing it to water, protecting O(2)-sensitive enzymes during the transition. Cytochrome b's main role may be anchoring the hydrogenase to the membrane.
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Affiliation(s)
- Anne Volbeda
- Metalloproteins Unit, Institut de Biologie Structurale J.-P. Ebel CEA-CNRS-Université Joseph Fourier, UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble, France
| | - Claudine Darnault
- Metalloproteins Unit, Institut de Biologie Structurale J.-P. Ebel CEA-CNRS-Université Joseph Fourier, UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble, France
| | - Alison Parkin
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Frank Sargent
- College of Life Sciences, University of Dundee, Dow Street, Dundee DD15EH, Scotland, UK
| | - Fraser A Armstrong
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Juan C Fontecilla-Camps
- Metalloproteins Unit, Institut de Biologie Structurale J.-P. Ebel CEA-CNRS-Université Joseph Fourier, UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble, France.
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122
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Relation between anaerobic inactivation and oxygen tolerance in a large series of NiFe hydrogenase mutants. Proc Natl Acad Sci U S A 2012; 109:19916-21. [PMID: 23169623 DOI: 10.1073/pnas.1212258109] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nickel-containing hydrogenases, the biological catalysts of oxidation and production, reversibly inactivate under anaerobic, oxidizing conditions. We aim at understanding the mechanism of (in)activation and what determines its kinetics, because there is a correlation between fast reductive reactivation and oxygen tolerance, a property of some hydrogenases that is very desirable from the point of view of biotechnology. Direct electrochemistry is potentially very useful for learning about the redox-dependent conversions between active and inactive forms of hydrogenase, but the voltammetric signals are complex and often misread. Here we describe simple analytical models that we used to characterize and compare 16 mutants, obtained by substituting the position-74 valine of the -sensitive NiFe hydrogenase from Desulfovibrio fructosovorans. We observed that this substitution can accelerate reactivation up to 1,000-fold, depending on the polarity of the position 74 amino acid side chain. In terms of kinetics of anaerobic (in)activation and oxygen tolerance, the valine-to-histidine mutation has the most spectacular effect: The V74H mutant compares favorably with the -tolerant hydrogenase from Aquifex aeolicus, which we use here as a benchmark.
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Albareda M, Manyani H, Imperial J, Brito B, Ruiz-Argüeso T, Böck A, Palacios JM. Dual role of HupF in the biosynthesis of [NiFe] hydrogenase in Rhizobium leguminosarum. BMC Microbiol 2012; 12:256. [PMID: 23136881 PMCID: PMC3534401 DOI: 10.1186/1471-2180-12-256] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/24/2012] [Indexed: 11/16/2022] Open
Abstract
Background [NiFe] hydrogenases are enzymes that catalyze the oxidation of hydrogen into protons and electrons, to use H2 as energy source, or the production of hydrogen through proton reduction, as an escape valve for the excess of reduction equivalents in anaerobic metabolism. Biosynthesis of [NiFe] hydrogenases is a complex process that occurs in the cytoplasm, where a number of auxiliary proteins are required to synthesize and insert the metal cofactors into the enzyme structural units. The endosymbiotic bacterium Rhizobium leguminosarum requires the products of eighteen genes (hupSLCDEFGHIJKhypABFCDEX) to synthesize an active hydrogenase. hupF and hupK genes are found only in hydrogenase clusters from bacteria expressing hydrogenase in the presence of oxygen. Results HupF is a HypC paralogue with a similar predicted structure, except for the C-terminal domain present only in HupF. Deletion of hupF results in the inability to process the hydrogenase large subunit HupL, and also in reduced stability of this subunit when cells are exposed to high oxygen tensions. A ΔhupF mutant was fully complemented for hydrogenase activity by a C-terminal deletion derivative under symbiotic, ultra low-oxygen tensions, but only partial complementation was observed in free living cells under higher oxygen tensions (1% or 3%). Co-purification experiments using StrepTag-labelled HupF derivatives and mass spectrometry analysis indicate the existence of a major complex involving HupL and HupF, and a less abundant HupF-HupK complex. Conclusions The results indicate that HupF has a dual role during hydrogenase biosynthesis: it is required for hydrogenase large subunit processing and it also acts as a chaperone to stabilize HupL when hydrogenase is synthesized in the presence of oxygen.
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Affiliation(s)
- Marta Albareda
- Centro de Biotecnología y Genómica de Plantas-CBGP, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40- km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain
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ArcA and AppY antagonize IscR repression of hydrogenase-1 expression under anaerobic conditions, revealing a novel mode of O2 regulation of gene expression in Escherichia coli. J Bacteriol 2012; 194:6892-9. [PMID: 23065979 DOI: 10.1128/jb.01757-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription of the Escherichia coli hydrogenase-1 operon (hyaABCDEF) is increased by the transcription factors ArcA and AppY under anaerobic growth conditions. However, IscR, which represses transcription of the hyaA promoter (P(hyaA)) under aerobic conditions, was not known to repress transcription of this promoter under anaerobic conditions. Here, we report that ArcA and AppY increase P(hyaA) expression under anaerobic conditions by antagonizing IscR binding at P(hyaA), since IscR repression is observed when either ArcA or AppY is eliminated. The ability of ArcA and AppY to act as antirepressors of IscR repression of P(hyaA) depended on IscR levels, suggesting that IscR competes with ArcA and/or AppY for binding. In support of this competition model, electrophoretic mobility shift assays and DNase I footprinting showed that the ArcA and IscR binding sites overlap and that binding of ArcA and IscR is mutually exclusive. Unexpectedly, IscR with a C92A mutation (IscR-C92A), which mimics the clusterless form of the protein that is present predominantly under aerobic conditions, was a better repressor under anaerobic conditions of both P(hyaA) and a constitutive promoter containing the IscR binding site from P(hyaA) than wild-type IscR, which is predominantly in the [2Fe-2S] form under anaerobic conditions. This observation could not be explained by differences in DNA binding affinities or IscR levels, so we conclude that [2Fe-2S]-IscR is a weaker repressor of P(hyaA) than clusterless IscR. In sum, a combination of ArcA and AppY antirepression of IscR function, lower levels of IscR, and weak repression by [2Fe-2S]-IscR leads to increased P(hyaA) expression under anaerobic conditions.
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125
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Roessler MM, Evans RM, Davies RA, Harmer J, Armstrong FA. EPR Spectroscopic Studies of the Fe–S Clusters in the O2-Tolerant [NiFe]-Hydrogenase Hyd-1 from Escherichia coli and Characterization of the Unique [4Fe–3S] Cluster by HYSCORE. J Am Chem Soc 2012; 134:15581-94. [DOI: 10.1021/ja307117y] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Maxie M. Roessler
- Department of Chemistry and ‡Center for Advanced Electron Spin Resonance, Oxford University, South Parks Road,
OX1 3QR Oxford, United Kingdom
| | - Rhiannon M. Evans
- Department of Chemistry and ‡Center for Advanced Electron Spin Resonance, Oxford University, South Parks Road,
OX1 3QR Oxford, United Kingdom
| | - Rosalind A. Davies
- Department of Chemistry and ‡Center for Advanced Electron Spin Resonance, Oxford University, South Parks Road,
OX1 3QR Oxford, United Kingdom
| | - Jeffrey Harmer
- Department of Chemistry and ‡Center for Advanced Electron Spin Resonance, Oxford University, South Parks Road,
OX1 3QR Oxford, United Kingdom
| | - Fraser A. Armstrong
- Department of Chemistry and ‡Center for Advanced Electron Spin Resonance, Oxford University, South Parks Road,
OX1 3QR Oxford, United Kingdom
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Pandelia ME, Lubitz W, Nitschke W. Evolution and diversification of Group 1 [NiFe] hydrogenases. Is there a phylogenetic marker for O2-tolerance? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1565-75. [DOI: 10.1016/j.bbabio.2012.04.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 04/21/2012] [Accepted: 04/24/2012] [Indexed: 10/28/2022]
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127
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Trchounian K. Transcriptional control of hydrogen production during mixed carbon fermentation by hydrogenases 4 (hyf) and 3 (hyc) in Escherichia coli. Gene 2012; 506:156-60. [DOI: 10.1016/j.gene.2012.06.084] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 06/25/2012] [Indexed: 01/07/2023]
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128
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Electrocatalytic mechanism of reversible hydrogen cycling by enzymes and distinctions between the major classes of hydrogenases. Proc Natl Acad Sci U S A 2012; 109:11516-21. [PMID: 22802675 DOI: 10.1073/pnas.1204770109] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extraordinary ability of Fe- and Ni-containing enzymes to catalyze rapid and efficient H(+)/H(2) interconversion--a property otherwise exclusive to platinum metals--has been investigated in a series of experiments combining variable-temperature protein film voltammetry with mathematical modeling. The results highlight important differences between the catalytic performance of [FeFe]-hydrogenases and [NiFe]-hydrogenases and justify a simple model for reversible catalytic electron flow in enzymes and electrocatalysts that should be widely applicable in fields as diverse as electrochemistry, catalysis, and bioenergetics. The active site of [FeFe]-hydrogenases, an intricate Fe-carbonyl complex known as the "H cluster," emerges as a supreme catalyst.
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129
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Trchounian K, Pinske C, Sawers RG, Trchounian A. Characterization of Escherichia coli [NiFe]-hydrogenase distribution during fermentative growth at different pHs. Cell Biochem Biophys 2012; 62:433-40. [PMID: 22095389 DOI: 10.1007/s12013-011-9325-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The contribution made by each of the three active [NiFe]-hydrogenases (Hyd) of Escherichia coli during fermentation of glucose or glycerol in peptone-based medium at different pHs was analysed. The activities of the hydrogen-oxidizing Hyd-1 and Hyd-2 enzymes showed a reciprocal dependence on the pH of the medium while Hyd-3, a key component of the hydrogen-evolving formate hydrogenlyase complex, was mainly active at pH 6.5. Our findings identify the conditions during fermentation of glucose or glycerol under which each [NiFe]-hydrogenase is optimally active and demonstrate a previously unrecognized dependence on Hyd-1 activity at low pH.
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Affiliation(s)
- Karen Trchounian
- Department of Biophysics, Yerevan State University, 1 A. Manoukian Str., 0025 Yerevan, Armenia
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130
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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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131
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Howlett RM, Hughes BM, Hitchcock A, Kelly DJ. Hydrogenase activity in the foodborne pathogen Campylobacter jejuni depends upon a novel ABC-type nickel transporter (NikZYXWV) and is SlyD-independent. MICROBIOLOGY-SGM 2012; 158:1645-1655. [PMID: 22403188 DOI: 10.1099/mic.0.054130-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Campylobacter jejuni is a human pathogen of worldwide significance. It is commensal in the gut of many birds and mammals, where hydrogen is a readily available electron donor. The bacterium possesses a single membrane-bound, periplasmic-facing NiFe uptake hydrogenase that depends on the acquisition of environmental nickel for activity. The periplasmic binding protein Cj1584 (NikZ) of the ATP binding cassette (ABC) transporter encoded by the cj1584c-cj1580c (nikZYXWV) operon in C. jejuni strain NCTC 11168 was found to be nickel-repressed and to bind free nickel ions with a submicromolar K(d) value, as measured by fluorescence spectroscopy. Unlike the Escherichia coli NikA protein, NikZ did not bind EDTA-chelated nickel and lacks key conserved residues implicated in metallophore interaction. A C. jejuni cj1584c null mutant strain showed an approximately 22-fold decrease in intracellular nickel content compared with the wild-type strain and a decreased rate of uptake of (63)NiCl(2). The inhibition of residual nickel uptake at higher nickel concentrations in this mutant by hexa-ammine cobalt (III) chloride or magnesium ions suggests that low-affinity uptake occurs partly through the CorA magnesium transporter. Hydrogenase activity was completely abolished in the cj1584c mutant after growth in unsupplemented media, but was fully restored after growth with 0.5 mM nickel chloride. Mutation of the putative metallochaperone gene slyD (cj0115) had no effect on either intracellular nickel accumulation or hydrogenase activity. Our data reveal a strict dependence of hydrogenase activity in C. jejuni on high-affinity nickel uptake through an ABC transporter that has distinct properties compared with the E. coli Nik system.
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Affiliation(s)
- Robert M Howlett
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Bethan M Hughes
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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132
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Pinske C, McDowall JS, Sargent F, Sawers RG. Analysis of hydrogenase 1 levels reveals an intimate link between carbon and hydrogen metabolism in Escherichia coli K-12. Microbiology (Reading) 2012; 158:856-868. [DOI: 10.1099/mic.0.056622-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Constanze Pinske
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | | | - Frank Sargent
- Division of Molecular Microbiology, University of Dundee, Dundee DD1 5EH, UK
| | - R. Gary Sawers
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
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133
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Simple Ligand Effects Switch a Hydrogenase Mimic between H2and O2Activation. Chem Asian J 2012; 7:1394-400. [DOI: 10.1002/asia.201101020] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Indexed: 12/31/2022]
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134
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Parkin A, Sargent F. The hows and whys of aerobic H2 metabolism. Curr Opin Chem Biol 2012; 16:26-34. [PMID: 22366384 DOI: 10.1016/j.cbpa.2012.01.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 01/16/2012] [Accepted: 01/25/2012] [Indexed: 01/08/2023]
Abstract
The bacterial [NiFe]-hydrogenases have been classified as either 'standard' or 'O2-tolerant' based on their ability to function in the presence of O2. Typically, these enzymes contain four redox-active metal centers: a Ni-Fe-CO-2CN- active site and three electron-transferring Fe-S clusters. Recent research suggests that, rather than differences at the catalytic active site, it is a novel Fe-S cluster electron transfer (ET) relay that controls how [NiFe]-hydrogenases recover from O2 attack. In light of recent structural data and mutagenic studies this article reviews the molecular mechanism of O2-tolerance in [NiFe]-hydrogenases and discusses the biosynthesis of the unique Fe-S relay.
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Affiliation(s)
- Alison Parkin
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford OX1 3QR, UK
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135
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Role of the NiFe hydrogenase Hya in oxidative stress defense in Geobacter sulfurreducens. J Bacteriol 2012; 194:2248-53. [PMID: 22366414 DOI: 10.1128/jb.00044-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Geobacter sulfurreducens, an Fe(III)-reducing deltaproteobacterium found in anoxic subsurface environments, contains 4 NiFe hydrogenases. Hyb, a periplasmically oriented membrane-bound NiFe hydrogenase, is essential for hydrogen-dependent growth. The functions of the three other hydrogenases are unknown. We show here that the other periplasmically oriented membrane-bound NiFe hydrogenase, Hya, is necessary for growth after exposure to oxidative stress when hydrogen or a highly limiting concentration of acetate is the electron source. The beneficial impact of Hya on growth was dependent on the presence of H(2) in the atmosphere. Moreover, the Hya-deficient strain was more sensitive to the presence of superoxide or hydrogen peroxide. Hya was also required to safeguard Hyb hydrogen oxidation activity after exposure to O(2). Overexpression studies demonstrated that Hya was more resistant to oxidative stress than Hyb. Overexpression of Hya also resulted in the creation of a recombinant strain better fitted for exposure to oxidative stress than wild-type G. sulfurreducens. These results demonstrate that one of the physiological roles of the O(2)-resistant Hya is to participate in the oxidative stress defense of G. sulfurreducens.
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136
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Trchounian K, Poladyan A, Vassilian A, Trchounian A. Multiple and reversible hydrogenases for hydrogen production byEscherichia coli: dependence on fermentation substrate, pH and the F0F1-ATPase. Crit Rev Biochem Mol Biol 2012; 47:236-49. [DOI: 10.3109/10409238.2012.655375] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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137
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Krishnan S, Armstrong FA. Order-of-magnitude enhancement of an enzymatic hydrogen-air fuel cell based on pyrenyl carbon nanostructures. Chem Sci 2012. [DOI: 10.1039/c2sc01103d] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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138
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139
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Lojou E. Hydrogenases as catalysts for fuel cells: Strategies for efficient immobilization at electrode interfaces. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.03.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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140
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Healy AJ, Reeve HA, Parkin A, Vincent KA. Electrically conducting particle networks in polymer electrolyte as three-dimensional electrodes for hydrogenase electrocatalysis. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.01.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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141
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Trchounian K, Pinske C, Sawers RG, Trchounian A. Dependence on the F0F1-ATP synthase for the activities of the hydrogen-oxidizing hydrogenases 1 and 2 during glucose and glycerol fermentation at high and low pH in Escherichia coli. J Bioenerg Biomembr 2011; 43:645-50. [DOI: 10.1007/s10863-011-9397-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Accepted: 10/20/2011] [Indexed: 11/24/2022]
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142
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Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase. Nature 2011; 479:253-6. [PMID: 22002607 DOI: 10.1038/nature10504] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 08/23/2011] [Indexed: 01/26/2023]
Abstract
Membrane-bound respiratory [NiFe]-hydrogenase (MBH), a H(2)-uptake enzyme found in the periplasmic space of bacteria, catalyses the oxidation of dihydrogen: H(2) → 2H(+) + 2e(-) (ref. 1). In contrast to the well-studied O(2)-sensitive [NiFe]-hydrogenases (referred to as the standard enzymes), MBH has an O(2)-tolerant H(2) oxidation activity; however, the mechanism of O(2) tolerance is unclear. Here we report the crystal structures of Hydrogenovibrio marinus MBH in three different redox conditions at resolutions between 1.18 and 1.32 Å. We find that the proximal iron-sulphur (Fe-S) cluster of MBH has a [4Fe-3S] structure coordinated by six cysteine residues--in contrast to the [4Fe-4S] cubane structure coordinated by four cysteine residues found in the proximal Fe-S cluster of the standard enzymes--and that an amide nitrogen of the polypeptide backbone is deprotonated and additionally coordinates the cluster when chemically oxidized, thus stabilizing the superoxidized state of the cluster. The structure of MBH is very similar to that of the O(2)-sensitive standard enzymes except for the proximal Fe-S cluster. Our results give a reasonable explanation why the O(2) tolerance of MBH is attributable to the unique proximal Fe-S cluster; we propose that the cluster is not only a component of the electron transfer for the catalytic cycle, but that it also donates two electrons and one proton crucial for the appropriate reduction of O(2) in preventing the formation of an unready, inactive state of the enzyme.
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143
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Fritsch J, Scheerer P, Frielingsdorf S, Kroschinsky S, Friedrich B, Lenz O, Spahn CMT. The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron-sulphur centre. Nature 2011; 479:249-52. [PMID: 22002606 DOI: 10.1038/nature10505] [Citation(s) in RCA: 259] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 08/23/2011] [Indexed: 11/10/2022]
Abstract
Hydrogenases are abundant enzymes that catalyse the reversible interconversion of H(2) into protons and electrons at high rates. Those hydrogenases maintaining their activity in the presence of O(2) are considered to be central to H(2)-based technologies, such as enzymatic fuel cells and for light-driven H(2) production. Despite comprehensive genetic, biochemical, electrochemical and spectroscopic investigations, the molecular background allowing a structural interpretation of how the catalytic centre is protected from irreversible inactivation by O(2) has remained unclear. Here we present the crystal structure of an O(2)-tolerant [NiFe]-hydrogenase from the aerobic H(2) oxidizer Ralstonia eutropha H16 at 1.5 Å resolution. The heterodimeric enzyme consists of a large subunit harbouring the catalytic centre in the H(2)-reduced state and a small subunit containing an electron relay consisting of three different iron-sulphur clusters. The cluster proximal to the active site displays an unprecedented [4Fe-3S] structure and is coordinated by six cysteines. According to the current model, this cofactor operates as an electronic switch depending on the nature of the gas molecule approaching the active site. It serves as an electron acceptor in the course of H(2) oxidation and as an electron-delivering device upon O(2) attack at the active site. This dual function is supported by the capability of the novel iron-sulphur cluster to adopt three redox states at physiological redox potentials. The second structural feature is a network of extended water cavities that may act as a channel facilitating the removal of water produced at the [NiFe] active site. These discoveries will have an impact on the design of biological and chemical H(2)-converting catalysts that are capable of cycling H(2) in air.
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Affiliation(s)
- Johannes Fritsch
- Mikrobiologie, Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestraße 117, 10115 Berlin, Germany
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144
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Lauterbach L, Idris Z, Vincent KA, Lenz O. Catalytic properties of the isolated diaphorase fragment of the NAD-reducing [NiFe]-hydrogenase from Ralstonia eutropha. PLoS One 2011; 6:e25939. [PMID: 22016788 PMCID: PMC3189943 DOI: 10.1371/journal.pone.0025939] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 09/14/2011] [Indexed: 11/19/2022] Open
Abstract
The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha H16 catalyzes the H2-driven reduction of NAD+, as well as reverse electron transfer from NADH to H+, in the presence of O2. It comprises six subunits, HoxHYFUI2, and incorporates a [NiFe] H+/H2 cycling catalytic centre, two non-covalently bound flavin mononucleotide (FMN) groups and an iron-sulfur cluster relay for electron transfer. This study provides the first characterization of the diaphorase sub-complex made up of HoxF and HoxU. Sequence comparisons with the closely related peripheral subunits of Complex I in combination with UV/Vis spectroscopy and the quantification of the metal and FMN content revealed that HoxFU accommodates a [2Fe2S] cluster, FMN and a series of [4Fe4S] clusters. Protein film electrochemistry (PFE) experiments show clear electrocatalytic activity for both NAD+ reduction and NADH oxidation with minimal overpotential relative to the potential of the NAD+/NADH couple. Michaelis-Menten constants of 56 µM and 197 µM were determined for NADH and NAD+, respectively. Catalysis in both directions is product inhibited with KI values of around 0.2 mM. In PFE experiments, the electrocatalytic current was unaffected by O2, however in aerobic solution assays, a moderate superoxide production rate of 54 nmol per mg of protein was observed, meaning that the formation of reactive oxygen species (ROS) observed for the native SH can be attributed mainly to HoxFU. The results are discussed in terms of their implications for aerobic functioning of the SH and possible control mechanism for the direction of catalysis.
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Affiliation(s)
- Lars Lauterbach
- Institute of Biology, Department of Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Zulkifli Idris
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Kylie A. Vincent
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
- * E-mail: (KAV); (OL)
| | - Oliver Lenz
- Institute of Biology, Department of Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
- * E-mail: (KAV); (OL)
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145
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Reeve HA, Lauterbach L, Ash PA, Lenz O, Vincent KA. A modular system for regeneration of NAD cofactors using graphite particles modified with hydrogenase and diaphorase moieties. Chem Commun (Camb) 2011; 48:1589-91. [PMID: 21986817 DOI: 10.1039/c1cc14826e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyrolytic graphite particles modified with hydrogenase and an NAD(+)/NADH cycling enzyme provide a modular heterogeneous catalyst system for regeneration of oxidised or reduced nicotinamide cofactors using H(2) and H(+) as electron source or sink. Particles can be tuned for cofactor supply under different conditions by appropriate choice of hydrogenase.
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Affiliation(s)
- Holly A Reeve
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
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Lukey MJ, Roessler MM, Parkin A, Evans RM, Davies RA, Lenz O, Friedrich B, Sargent F, Armstrong FA. Oxygen-Tolerant [NiFe]-Hydrogenases: The Individual and Collective Importance of Supernumerary Cysteines at the Proximal Fe-S Cluster. J Am Chem Soc 2011; 133:16881-92. [DOI: 10.1021/ja205393w] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Oliver Lenz
- Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Baerbel Friedrich
- Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Frank Sargent
- College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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147
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Pinske C, Sawers G. Iron restriction induces preferential down-regulation of H(2)-consuming over H(2)-evolving reactions during fermentative growth of Escherichia coli. BMC Microbiol 2011; 11:196. [PMID: 21880124 PMCID: PMC3176205 DOI: 10.1186/1471-2180-11-196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 08/31/2011] [Indexed: 12/22/2022] Open
Abstract
Background Escherichia coli synthesizes three anaerobically inducible [NiFe]-hydrogenases (Hyd). All three enzymes have a [NiFe]-cofactor in the large subunit and each enzyme also has an iron-sulfur-containing small subunit that is required for electron transfer. In order to synthesize functionally active Hyd enzymes iron must be supplied to the maturation pathways for both the large and small subunits. The focus of this study was the analysis of the iron uptake systems required for synthesis of active Hyd-1, Hyd-2 and Hyd-3 during fermentative growth. Results A transposon-insertion mutant impaired in hydrogenase enzyme activity was isolated. The mutation was in the feoB gene encoding the ferrous iron transport system. The levels of both hydrogen-oxidizing enzymes Hyd-1 and Hyd-2 as determined by specific in-gel activity staining were reduced at least 10-fold in the mutant after anaerobic fermentative growth in minimal medium, while the hydrogen-evolving Hyd-3 activity was less severely affected. Supplementation of the growth medium with ferric iron, which is taken up by e.g. the siderophore enterobactin, resulted in phenotypic complementation of the feoB mutant. Growth in rich medium demonstrated that a mutant lacking both the ferrous iron transport system and enterobactin biosynthesis (entC) was devoid of Hyd-1 and Hyd-2 activity but retained some hydrogen-evolving Hyd-3 activity. Analysis of crude extracts derived from the feoB entC double null mutant revealed that the large subunits of the hydrogen-oxidizing enzymes Hyd-1 and Hyd-2 were absent. Analysis of lacZ fusions demonstrated, however, that expression of the hya, hyb and hyc operons was reduced only by maximally 50% in the mutants compared with the wild type. Conclusions Our findings demonstrate that the ferrous iron transport system is the principal route of iron uptake for anaerobic hydrogenase biosynthesis, with a contribution from the ferric-enterobactin system. Hydrogen-oxidizing enzyme function was abolished in a feoB entC double mutant and this appears to be due to post-translational effects. The retention of residual hydrogen-evolving activity, even in the feoB entC double null mutant suggests that sufficient iron can be scavenged to synthesize this key fermentative enzyme complex in preference to the hydrogen-uptake enzymes.
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Affiliation(s)
- Constanze Pinske
- Institute for Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str, 3, 06120 Halle (Saale), Germany
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148
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Reversibility and efficiency in electrocatalytic energy conversion and lessons from enzymes. Proc Natl Acad Sci U S A 2011; 108:14049-54. [PMID: 21844379 DOI: 10.1073/pnas.1103697108] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Enzymes are long established as extremely efficient catalysts. Here, we show that enzymes can also be extremely efficient electrocatalysts (catalysts of redox reactions at electrodes). Despite being large and electronically insulating through most of their volume, some enzymes, when attached to an electrode, catalyze electrochemical reactions that are otherwise extremely sluggish (even with the best synthetic catalysts) and require a large overpotential to achieve a useful rate. These enzymes produce high electrocatalytic currents, displayed in single bidirectional voltammetric waves that switch direction (between oxidation and reduction) sharply at the equilibrium potential for the substrate redox couple. Notoriously irreversible processes such as CO(2) reduction are thereby rendered electrochemically reversible--a consequence of molecular evolution responding to stringent biological drivers for thermodynamic efficiency. Enzymes thus set high standards for the catalysts of future energy technologies.
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149
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HowSalmonellaoxidises H2under aerobic conditions. FEBS Lett 2011; 586:536-44. [DOI: 10.1016/j.febslet.2011.07.044] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 07/22/2011] [Accepted: 07/28/2011] [Indexed: 11/22/2022]
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150
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McIntosh CL, Germer F, Schulz R, Appel J, Jones AK. The [NiFe]-hydrogenase of the cyanobacterium Synechocystis sp. PCC 6803 works bidirectionally with a bias to H2 production. J Am Chem Soc 2011; 133:11308-19. [PMID: 21675712 DOI: 10.1021/ja203376y] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein film electrochemistry (PFE) was utilized to characterize the catalytic activity and oxidative inactivation of a bidirectional [NiFe]-hydrogenase (HoxEFUYH) from the cyanobacterium Synechocystis sp. PCC 6803. PFE provides precise control of the redox potential of the adsorbed enzyme so that its activity can be monitored under changing experimental conditions as current. The properties of HoxEFUYH are different from those of both the standard uptake and the "oxygen-tolerant" [NiFe]-hydrogenases. First, HoxEFUYH is biased toward proton reduction as opposed to hydrogen oxidation. Second, despite being expressed under aerobic conditions in vivo, HoxEFUYH is clearly not oxygen-tolerant. Aerobic inactivation of catalytic hydrogen oxidation by HoxEFUYH is total and nearly instantaneous, producing two inactive states. However, unlike the Ni-A and Ni-B inactive states of standard [NiFe]-hydrogenases, both of these states are quickly (<90 s) reactivated by removal of oxygen and exposure to reducing conditions. Third, proton reduction continues at 25-50% of the maximal rate in the presence of 1% oxygen. Whereas most previously characterized [NiFe]-hydrogenases seem to be preferential hydrogen oxidizing catalysts, the cyanobacterial enzyme works effectively in both directions. This unusual catalytic bias as well as the ability to be quickly reactivated may be essential to fulfilling the physiological role in cyanobacteria, organisms expected to experience swings in cellular reduction potential as they switch between aerobic conditions in the light and dark anaerobic conditions. Our results suggest that the uptake [NiFe]-hydrogenases alone are not representative of the catalytic diversity of [NiFe]-hydrogenases, and the bidirectional heteromultimeric enzymes may serve as valuable models to understand the diverse mechanisms of tuning the reactivity of the hydrogen activating site.
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Affiliation(s)
- Chelsea L McIntosh
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
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