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Angenent SC, Schuttinga JH, van Efferen MFH, Kuizenga B, van Bree B, van der Krieken RO, Verhoeven TJ, Wijffels RH. Hydrogen Oxidizing Bacteria as Novel Protein Source for Human Consumption: An Overview. Open Microbiol J 2022. [DOI: 10.2174/18742858-v16-e2207270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The increasing threat of climate change combined with the prospected growth in the world population puts an enormous pressure on the future demand for sustainable protein sources for human consumption. In this review, hydrogen oxidizing bacteria (HOB) are presented as a novel protein source that could play a role in fulfilling this future demand. HOB are species of bacteria that merely require an inflow of the gasses hydrogen, oxygen, carbon dioxide, and a nitrogen source to grow in a conventional bioreactor. Cupriavidus necator is proposed as HOB for industrial cultivation due to its remarkably high protein content (up to 70% of mass), suitability for cultivation in a bioreactor, and the vast amount of available background information. A broad overview of the unique aspects of the bacteria will be provided, from the production process, amino acid composition, and source of the required gasses to the future acceptance of HOB into the market.
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Li Z, Xin X, Xiong B, Zhao D, Zhang X, Bi C. Engineering the Calvin-Benson-Bassham cycle and hydrogen utilization pathway of Ralstonia eutropha for improved autotrophic growth and polyhydroxybutyrate production. Microb Cell Fact 2020; 19:228. [PMID: 33308236 PMCID: PMC7733298 DOI: 10.1186/s12934-020-01494-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/05/2020] [Indexed: 12/24/2022] Open
Abstract
Background CO2 is fixed by all living organisms with an autotrophic metabolism, among which the Calvin–Benson–Bassham (CBB) cycle is the most important and widespread carbon fixation pathway. Thus, studying and engineering the CBB cycle with the associated energy providing pathways to increase the CO2 fixation efficiency of cells is an important subject of biological research with significant application potential. Results In this work, the autotrophic microbe Ralstonia eutropha (Cupriavidus necator) was selected as a research platform for CBB cycle optimization engineering. By knocking out either CBB operon genes on the operon or mega-plasmid of R. eutropha, we found that both CBB operons were active and contributed almost equally to the carbon fixation process. With similar knock-out experiments, we found both soluble and membrane-bound hydrogenases (SH and MBH), belonging to the energy providing hydrogenase module, were functional during autotrophic growth of R. eutropha. SH played a more significant role. By introducing a heterologous cyanobacterial RuBisCO with the endogenous GroES/EL chaperone system(A quality control systems for proteins consisting of molecular chaperones and proteases, which prevent protein aggregation by either refolding or degrading misfolded proteins) and RbcX(A chaperone in the folding of Rubisco), the culture OD600 of engineered strain increased 89.2% after 72 h of autotrophic growth, although the difference was decreased at 96 h, indicating cyanobacterial RuBisCO with a higher activity was functional in R. eutropha and lead to improved growth in comparison to the host specific enzyme. Meanwhile, expression of hydrogenases was optimized by modulating the expression of MBH and SH, which could further increase the R. eutropha H16 culture OD600 to 93.4% at 72 h. Moreover, the autotrophic yield of its major industrially relevant product, polyhydroxybutyrate (PHB), was increased by 99.7%. Conclusions To our best knowledge, this is the first report of successfully engineering the CBB pathway and hydrogenases of R. eutropha for improved activity, and is one of only a few cases where the efficiency of CO2 assimilation pathway was improved. Our work demonstrates that R. eutropha is a useful platform for studying and engineering the CBB for applications.
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Affiliation(s)
- Zhongkang Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiuqing Xin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Bin Xiong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part IV. Canonical, non-canonical and hybrid iron-sulfur proteins. J Struct Biol 2019; 205:103-120. [PMID: 30677521 DOI: 10.1016/j.jsb.2019.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 12/26/2022]
Abstract
A plethora of proteins are able to express iron-sulfur clusters, but have a clear picture of the different types of proteins and the different iron-sulfur clusters they harbor it is not easy. In the last five years we have reviewed structure/electrochemistry of metalloproteins expressing: (i) single types of iron-sulfur clusters (namely: {Fe(Cys)4}, {[Fe2S2](Cys)4}, {[Fe2S2](Cys)3(X)} (X = Asp, Arg, His), {[Fe2S2](Cys)2(His)2}, {[Fe3S4](Cys)3}, {[Fe4S4](Cys)4} and {[Fe4S4](Cys)3(nonthiolate ligand)} cores); (ii) metalloproteins harboring iron-sulfur centres of different nuclearities (namely: [4Fe-4S] and [2Fe-2S], [4Fe-4S] and [3Fe-4S], and [4Fe-4S], [3Fe-4S] and [2Fe-2S] clusters. Our target is now to review structure and electrochemistry of proteins harboring canonical, non-canonical and hybrid iron-sulfur proteins.
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Affiliation(s)
- Piero Zanello
- Dipartimento di Biotecnologie, Chimica e Farmacia dell'Università di Siena, Via A. De Gasperi 2, 53100 Siena, Italy
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4
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Campbell BJ, Sessions AL, Fox DN, Paul BG, Qin Q, Kellermann MY, Valentine DL. Minimal Influence of [NiFe] Hydrogenase on Hydrogen Isotope Fractionation in H 2-Oxidizing Cupriavidus necator. Front Microbiol 2017; 8:1886. [PMID: 29085342 PMCID: PMC5649130 DOI: 10.3389/fmicb.2017.01886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 09/14/2017] [Indexed: 11/25/2022] Open
Abstract
Fatty acids produced by H2-metabolizing bacteria are sometimes observed to be more D-depleted than those of photoautotrophic organisms, a trait that has been suggested as diagnostic for chemoautotrophic bacteria. The biochemical reasons for such a depletion are not known, but are often assumed to involve the strong D-depletion of H2. Here, we cultivated the bacterium Cupriavidus necator H16 (formerly Ralstonia eutropha H16) under aerobic, H2-consuming, chemoautotrophic conditions and measured the isotopic compositions of its fatty acids. In parallel with the wild type, two mutants of this strain, each lacking one of two key hydrogenase enzymes, were also grown and measured. In all three strains, fractionations between fatty acids and water ranged from -173‰ to -235‰, and averaged -217‰, -196‰, and -226‰, respectively, for the wild type, SH- mutant, and MBH- mutant. There was a modest increase in δD as a result of loss of the soluble hydrogenase enzyme. Fractionation curves for all three strains were constructed by growing parallel cultures in waters with δDwater values of approximately -25‰, 520‰, and 1100‰. These curves indicate that at least 90% of the hydrogen in fatty acids is derived from water, not H2. Published details of the biochemistry of the soluble and membrane-bound hydrogenases confirm that these enzymes transfer electrons rather than intact hydride (H-) ions, providing no direct mechanism to connect the isotopic composition of H2 to that of lipids. Multiple lines of evidence thus agree that in this organism, and presumably others like it, environmental H2 plays little or no direct role in controlling lipid δD values. The observed fractionations must instead result from isotope effects in the reduction of NAD(P)H by reductases with flavin prosthetic groups, which transfer two electrons and acquire H+ (or D+) from solution. Parallels to NADPH reduction in photosynthesis may explain why D/H fractionations in C. necator are nearly identical to those in many photoautotrophic algae and bacteria. We conclude that strong D-depletion is not a diagnostic feature of chemoautotrophy.
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Affiliation(s)
- Brian J Campbell
- Department of Earth Science, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Daniel N Fox
- Undergraduate College of Letters and Sciences, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Blair G Paul
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Qianhui Qin
- Interdepartmental Graduate Program in Marine Science, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Matthias Y Kellermann
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Wilhelmshaven, Germany
| | - David L Valentine
- Department of Earth Science, University of California, Santa Barbara, Santa Barbara, CA, United States.,Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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5
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Radu V, Frielingsdorf S, Evans SD, Lenz O, Jeuken LJC. Enhanced oxygen-tolerance of the full heterotrimeric membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha. J Am Chem Soc 2014; 136:8512-5. [PMID: 24866391 PMCID: PMC4073834 DOI: 10.1021/ja503138p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hydrogenases are oxygen-sensitive enzymes that catalyze the conversion between protons and hydrogen. Water-soluble subcomplexes of membrane-bound [NiFe]-hydrogenases (MBH) have been extensively studied for applications in hydrogen-oxygen fuel cells as they are relatively tolerant to oxygen, although even these catalysts are still inactivated in oxidative conditions. Here, the full heterotrimeric MBH of Ralstonia eutropha, including the membrane-integral cytochrome b subunit, was investigated electrochemically using electrodes modified with planar tethered bilayer lipid membranes (tBLM). Cyclic voltammetry and chronoamperometry experiments show that MBH, in equilibrium with the quinone pool in the tBLM, does not anaerobically inactivate under oxidative redox conditions. In aerobic environments, the MBH is reversibly inactivated by O2, but reactivation was found to be fast even under oxidative redox conditions. This enhanced resistance to inactivation is ascribed to the oligomeric state of MBH in the lipid membrane.
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Affiliation(s)
- Valentin Radu
- School of Biomedical Sciences, the Astbury Centre for Structural Molecular Biology, and School of Physics & Astronomy, University of Leeds , Leeds LS2 9JT, United Kingdom
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6
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Frielingsdorf S, Fritsch J, Schmidt A, Hammer M, Löwenstein J, Siebert E, Pelmenschikov V, Jaenicke T, Kalms J, Rippers Y, Lendzian F, Zebger I, Teutloff C, Kaupp M, Bittl R, Hildebrandt P, Friedrich B, Lenz O, Scheerer P. Reversible [4Fe-3S] cluster morphing in an O2-tolerant [NiFe] hydrogenase. Nat Chem Biol 2014; 10:378-85. [DOI: 10.1038/nchembio.1500] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 03/13/2014] [Indexed: 12/27/2022]
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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8
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Fritsch J, Siebert E, Priebe J, Zebger I, Lendzian F, Teutloff C, Friedrich B, Lenz O. Rubredoxin-related maturation factor guarantees metal cofactor integrity during aerobic biosynthesis of membrane-bound [NiFe] hydrogenase. J Biol Chem 2014; 289:7982-93. [PMID: 24448806 DOI: 10.1074/jbc.m113.544668] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The membrane-bound [NiFe] hydrogenase (MBH) supports growth of Ralstonia eutropha H16 with H2 as the sole energy source. The enzyme undergoes a complex biosynthesis process that proceeds during cell growth even at ambient O2 levels and involves 14 specific maturation proteins. One of these is a rubredoxin-like protein, which is essential for biosynthesis of active MBH at high oxygen concentrations but dispensable under microaerobic growth conditions. To obtain insights into the function of HoxR, we investigated the MBH protein purified from the cytoplasmic membrane of hoxR mutant cells. Compared with wild-type MBH, the mutant enzyme displayed severely decreased hydrogenase activity. Electron paramagnetic resonance and infrared spectroscopic analyses revealed features resembling those of O2-sensitive [NiFe] hydrogenases and/or oxidatively damaged protein. The catalytic center resided partially in an inactive Niu-A-like state, and the electron transfer chain consisting of three different Fe-S clusters showed marked alterations compared with wild-type enzyme. Purification of HoxR protein from its original host, R. eutropha, revealed only low protein amounts. Therefore, recombinant HoxR protein was isolated from Escherichia coli. Unlike common rubredoxins, the HoxR protein was colorless, rather unstable, and essentially metal-free. Conversion of the atypical iron-binding motif into a canonical one through genetic engineering led to a stable reddish rubredoxin. Remarkably, the modified HoxR protein did not support MBH-dependent growth at high O2. Analysis of MBH-associated protein complexes points toward a specific interaction of HoxR with the Fe-S cluster-bearing small subunit. This supports the previously made notion that HoxR avoids oxidative damage of the metal centers of the MBH, in particular the unprecedented Cys6[4Fe-3S] cluster.
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Affiliation(s)
- Johannes Fritsch
- From the Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin
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9
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Yu J. Bio-based products from solar energy and carbon dioxide. Trends Biotechnol 2013; 32:5-10. [PMID: 24315481 DOI: 10.1016/j.tibtech.2013.11.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/24/2013] [Accepted: 11/04/2013] [Indexed: 12/20/2022]
Abstract
Producing bio-based products directly from CO₂ and solar energy is a desirable alternative to the conventional biorefining that relies on biomass feedstocks. The production paradigm is based on an artificial photosynthetic system that converts sunlight to electricity and H₂ via water electrolysis. An autotrophic H₂-oxidizing bacterium fixes CO₂ in dark conditions. The assimilated CO₂ is stored in bacterial cells as polyhydroxybutyrate (PHB), from which a range of products can be derived. Compared with natural photosynthesis of a fast-growing cyanobacterium, the artificial photosynthetic system has much higher energy efficiency and productivity of bio-based products. The new technology looks promising because of possible cost reduction in feedstock, equipment, and operation.
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Affiliation(s)
- Jian Yu
- Hawaii Natural Energy Institute, University of Hawaii at Manoa, 1680 East-West Road POST 104, Honolulu, HI 96822, USA.
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10
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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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12
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Jugder BE, Welch J, Aguey-Zinsou KF, Marquis CP. Fundamentals and electrochemical applications of [Ni–Fe]-uptake hydrogenases. RSC Adv 2013. [DOI: 10.1039/c3ra22668a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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13
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O2-stable membrane-bound [NiFe]hydrogenase from a newly isolated Citrobacter sp. S-77. J Biosci Bioeng 2012; 114:479-84. [DOI: 10.1016/j.jbiosc.2012.05.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 05/22/2012] [Accepted: 05/24/2012] [Indexed: 12/11/2022]
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14
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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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15
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Sprecher BN, Gittings ME, Ludwig RA. Respiratory membrane endo-hydrogenase activity in the microaerophile Azorhizobium caulinodans is bidirectional. PLoS One 2012; 7:e36744. [PMID: 22662125 PMCID: PMC3357923 DOI: 10.1371/journal.pone.0036744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 04/12/2012] [Indexed: 11/19/2022] Open
Abstract
Background The microaerophilic bacterium Azorhizobium caulinodans, when fixing N2 both in pure cultures held at 20 µM dissolved O2 tension and as endosymbiont of Sesbania rostrata legume nodules, employs a novel, respiratory-membrane endo-hydrogenase to oxidize and recycle endogenous H2 produced by soluble Mo-dinitrogenase activity at the expense of O2. Methods and Findings From a bioinformatic analysis, this endo-hydrogenase is a core (6 subunit) version of (14 subunit) NADH:ubiquinone oxidoreductase (respiratory complex I). In pure A. caulinodans liquid cultures, when O2 levels are lowered to <1 µM dissolved O2 tension (true microaerobic physiology), in vivo endo-hydrogenase activity reverses and continuously evolves H2 at high rates. In essence, H+ ions then supplement scarce O2 as respiratory-membrane electron acceptor. Paradoxically, from thermodynamic considerations, such hydrogenic respiratory-membrane electron transfer need largely uncouple oxidative phosphorylation, required for growth of non-phototrophic aerobic bacteria, A. caulinodans included. Conclusions A. caulinodans in vivo endo-hydrogenase catalytic activity is bidirectional. To our knowledge, this study is the first demonstration of hydrogenic respiratory-membrane electron transfer among aerobic (non-fermentative) bacteria. When compared with O2 tolerant hydrogenases in other organisms, A. caulinodans in vivo endo-hydrogenase mediated H2 production rates (50,000 pmol 109·cells−1 min−1) are at least one-thousandfold higher. Conceivably, A. caulinodans respiratory-membrane hydrogenesis might initiate H2 crossfeeding among spatially organized bacterial populations whose individual cells adopt distinct metabolic states in response to variant O2 availability. Such organized, physiologically heterogeneous cell populations might benefit from augmented energy transduction and growth rates of the populations, considered as a whole.
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Affiliation(s)
- Brittany N. Sprecher
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Margo E. Gittings
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Robert A. Ludwig
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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Frielingsdorf S, Schubert T, Pohlmann A, Lenz O, Friedrich B. A Trimeric Supercomplex of the Oxygen-Tolerant Membrane-Bound [NiFe]-Hydrogenase from Ralstonia eutropha H16. Biochemistry 2011; 50:10836-43. [DOI: 10.1021/bi201594m] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefan Frielingsdorf
- Institut für Biologie-Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestraβe
117, 10115 Berlin, Germany
| | - Torsten Schubert
- Institut für Biologie-Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestraβe
117, 10115 Berlin, Germany
| | - Anne Pohlmann
- Institut für Biologie-Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestraβe
117, 10115 Berlin, Germany
| | - Oliver Lenz
- Institut für Biologie-Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestraβe
117, 10115 Berlin, Germany
| | - Bärbel Friedrich
- Institut für Biologie-Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestraβe
117, 10115 Berlin, Germany
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17
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Bürstel I, Hummel P, Siebert E, Wisitruangsakul N, Zebger I, Friedrich B, Lenz O. Probing the origin of the metabolic precursor of the CO ligand in the catalytic center of [NiFe] hydrogenase. J Biol Chem 2011; 286:44937-44. [PMID: 22049085 DOI: 10.1074/jbc.m111.309351] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The O(2)-tolerant [NiFe] hydrogenases of Ralstonia eutropha are capable of H(2) conversion in the presence of ambient O(2). Oxygen represents not only a challenge for catalysis but also for the complex assembling process of the [NiFe] active site. Apart from nickel and iron, the catalytic center contains unusual diatomic ligands, namely two cyanides (CN(-)) and one carbon monoxide (CO), which are coordinated to the iron. One of the open questions of the maturation process concerns the origin and biosynthesis of the CO group. Isotope labeling in combination with infrared spectroscopy revealed that externally supplied gaseous (13)CO serves as precursor of the carbonyl group of the regulatory [NiFe] hydrogenase in R. eutropha. Corresponding (13)CO titration experiments showed that a concentration 130-fold higher than ambient CO (0.1 ppmv) caused a 50% labeling of the carbonyl ligand in the [NiFe] hydrogenase, leading to the conclusion that the carbonyl ligand originates from an intracellular metabolite. A novel setup allowed us to the study effects of CO depletion on maturation in vivo. Upon induction of CO depletion by addition of the CO scavenger PdCl(2), cells cultivated on H(2), CO(2), and O(2) showed severe growth retardation at low cell concentrations, which was on the basis of partially arrested hydrogenase maturation, leading to reduced hydrogenase activity. This suggests gaseous CO as a metabolic precursor under these conditions. The addition of PdCl(2) to cells cultivated heterotrophically on organic substrates had no effect on hydrogenase maturation. These results indicate at least two different pathways for biosynthesis of the CO ligand of [NiFe] hydrogenase.
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Affiliation(s)
- Ingmar Bürstel
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, Chausseestrasse 117, 10115 Berlin, Germany
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18
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Sezer M, Frielingsdorf S, Millo D, Heidary N, Utesch T, Mroginski MA, Friedrich B, Hildebrandt P, Zebger I, Weidinger IM. Role of the HoxZ Subunit in the Electron Transfer Pathway of the Membrane-Bound [NiFe]-Hydrogenase from Ralstonia eutropha Immobilized on Electrodes. J Phys Chem B 2011; 115:10368-74. [DOI: 10.1021/jp204665r] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Murat Sezer
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | | | - Diego Millo
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Nina Heidary
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Tillman Utesch
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Maria-Andrea Mroginski
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Bärbel Friedrich
- Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany
| | - Peter Hildebrandt
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Ingo Zebger
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
| | - Inez M. Weidinger
- Insitut für Chemie, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany
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Fritsch J, Löscher S, Sanganas O, Siebert E, Zebger I, Stein M, Ludwig M, De Lacey AL, Dau H, Friedrich B, Lenz O, Haumann M. [NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O2-Tolerant H2 Cleavage. Biochemistry 2011; 50:5858-69. [DOI: 10.1021/bi200367u] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Johannes Fritsch
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, 10115 Berlin, Germany
| | - Simone Löscher
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Oliver Sanganas
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Elisabeth Siebert
- Technische Universität Berlin, Max-Volmer Institut, 10623 Berlin, Germany
| | - Ingo Zebger
- Technische Universität Berlin, Max-Volmer Institut, 10623 Berlin, Germany
| | - Matthias Stein
- Max-Planck-Institut für Dynamik komplexer technischer Systeme, 39106 Magdeburg, Germany
| | - Marcus Ludwig
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, 10115 Berlin, Germany
| | | | - Holger Dau
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Bärbel Friedrich
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, 10115 Berlin, Germany
| | - Oliver Lenz
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, 10115 Berlin, Germany
| | - Michael Haumann
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
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The maturation factors HoxR and HoxT contribute to oxygen tolerance of membrane-bound [NiFe] hydrogenase in Ralstonia eutropha H16. J Bacteriol 2011; 193:2487-97. [PMID: 21441514 DOI: 10.1128/jb.01427-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha H16 undergoes a complex maturation process comprising cofactor assembly and incorporation, subunit oligomerization, and finally twin-arginine-dependent membrane translocation. Due to its outstanding O(2) and CO tolerance, the MBH is of biotechnological interest and serves as a molecular model for a robust hydrogen catalyst. Adaptation of the enzyme to oxygen exposure has to take into account not only the catalytic reaction but also biosynthesis of the intricate redox cofactors. Here, we report on the role of the MBH-specific accessory proteins HoxR and HoxT, which are key components in MBH maturation at ambient O(2) levels. MBH-driven growth on H(2) is inhibited or retarded at high O(2) partial pressure (pO(2)) in mutants inactivated in the hoxR and hoxT genes. The ratio of mature and nonmature forms of the MBH small subunit is shifted toward the precursor form in extracts derived from the mutant cells grown at high pO(2). Lack of hoxR and hoxT can phenotypically be restored by providing O(2)-limited growth conditions. Analysis of copurified maturation intermediates leads to the conclusion that the HoxR protein is a constituent of a large transient protein complex, whereas the HoxT protein appears to function at a final stage of MBH maturation. UV-visible spectroscopy of heterodimeric MBH purified from hoxR mutant cells points to alterations of the Fe-S cluster composition. Thus, HoxR may play a role in establishing a specific Fe-S cluster profile, whereas the HoxT protein seems to be beneficial for cofactor stability under aerobic conditions.
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Goris T, Wait AF, Saggu M, Fritsch J, Heidary N, Stein M, Zebger I, Lendzian F, Armstrong FA, Friedrich B, Lenz O. A unique iron-sulfur cluster is crucial for oxygen tolerance of a [NiFe]-hydrogenase. Nat Chem Biol 2011; 7:310-8. [PMID: 21390036 DOI: 10.1038/nchembio.555] [Citation(s) in RCA: 196] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 03/01/2011] [Indexed: 12/11/2022]
Abstract
Hydrogenases are essential for H(2) cycling in microbial metabolism and serve as valuable blueprints for H(2)-based biotechnological applications. However, most hydrogenases are extremely oxygen sensitive and prone to inactivation by even traces of O(2). The O(2)-tolerant membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha H16 is one of the few examples that can perform H(2) uptake in the presence of ambient O(2). Here we show that O(2) tolerance is crucially related to a modification of the internal electron-transfer chain. The iron-sulfur cluster proximal to the active site is surrounded by six instead of four conserved coordinating cysteines. Removal of the two additional cysteines alters the electronic structure of the proximal iron-sulfur cluster and renders the catalytic activity sensitive to O(2) as shown by physiological, biochemical, spectroscopic and electrochemical studies. The data indicate that the mechanism of O(2) tolerance relies on the reductive removal of oxygenic species guided by the unique architecture of the electron relay rather than a restricted access of O(2) to the active site.
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Affiliation(s)
- Tobias Goris
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany
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Ciccolella CO, Raynard NA, Mei JHM, Church DC, Ludwig RA. Symbiotic legume nodules employ both rhizobial exo- and endo-hydrogenases to recycle hydrogen produced by nitrogen fixation. PLoS One 2010; 5:e12094. [PMID: 20838423 PMCID: PMC2930871 DOI: 10.1371/journal.pone.0012094] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Accepted: 07/16/2010] [Indexed: 11/19/2022] Open
Abstract
Background In symbiotic legume nodules, endosymbiotic rhizobia (bacteroids) fix atmospheric N2, an ATP-dependent catalytic process yielding stoichiometric ammonium and hydrogen gas (H2). While in most legume nodules this H2 is quantitatively evolved, which loss drains metabolic energy, certain bacteroid strains employ uptake hydrogenase activity and thus evolve little or no H2. Rather, endogenous H2 is efficiently respired at the expense of O2, driving oxidative phosphorylation, recouping ATP used for H2 production, and increasing the efficiency of symbiotic nodule N2 fixation. In many ensuing investigations since its discovery as a physiological process, bacteroid uptake hydrogenase activity has been presumed a single entity. Methodology/Principal Findings Azorhizobium caulinodans, the nodule endosymbiont of Sesbania rostrata stems and roots, possesses both orthodox respiratory (exo-)hydrogenase and novel (endo-)hydrogenase activities. These two respiratory hydrogenases are structurally quite distinct and encoded by disparate, unlinked gene-sets. As shown here, in S. rostrata symbiotic nodules, haploid A. caulinodans bacteroids carrying single knockout alleles in either exo- or-endo-hydrogenase structural genes, like the wild-type parent, evolve no detectable H2 and thus are fully competent for endogenous H2 recycling. Whereas, nodules formed with A. caulinodans exo-, endo-hydrogenase double-mutants evolve endogenous H2 quantitatively and thus suffer complete loss of H2 recycling capability. More generally, from bioinformatic analyses, diazotrophic microaerophiles, including rhizobia, which respire H2 may carry both exo- and endo-hydrogenase gene-sets. Conclusions/Significance In symbiotic S. rostrata nodules, A. caulinodans bacteroids can use either respiratory hydrogenase to recycle endogenous H2 produced by N2 fixation. Thus, H2 recycling by symbiotic legume nodules may involve multiple respiratory hydrogenases.
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Affiliation(s)
- Christopher O. Ciccolella
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Nathan A. Raynard
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - John H-M. Mei
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Derek C. Church
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Robert A. Ludwig
- Sinsheimer Laboratories, Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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Lenz O, Ludwig M, Schubert T, Bürstel I, Ganskow S, Goris T, Schwarze A, Friedrich B. H2 conversion in the presence of O2 as performed by the membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha. Chemphyschem 2010; 11:1107-19. [PMID: 20186906 DOI: 10.1002/cphc.200901002] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
[NiFe]-hydrogenases catalyze the oxidation of H(2) to protons and electrons. This reversible reaction is based on a complex interplay of metal cofactors including the Ni-Fe active site and several [Fe-S] clusters. H(2) catalysis of most [NiFe]-hydrogenases is sensitive to dioxygen. However, some bacteria contain hydrogenases that activate H(2) even in the presence of O(2). There is now compelling evidence that O(2) affects hydrogenase on three levels: 1) H(2) catalysis, 2) hydrogenase maturation, and 3) H(2)-mediated signal transduction. Herein, we summarize the genetic, biochemical, electrochemical, and spectroscopic properties related to the O(2) tolerance of hydrogenases resident in the facultative chemolithoautotroph Ralstonia eutropha H16. A focus is given to the membrane-bound [NiFe]-hydogenase, which currently represents the best-characterized member of O(2)-tolerant hydrogenases.
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Affiliation(s)
- Oliver Lenz
- Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany.
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Saggu M, Ludwig M, Friedrich B, Hildebrandt P, Bittl R, Lendzian F, Lenz O, Zebger I. Impact of Amino Acid Substitutions near the Catalytic Site on the Spectral Properties of an O2-Tolerant Membrane-Bound [NiFe] Hydrogenase. Chemphyschem 2010; 11:1215-24. [DOI: 10.1002/cphc.200900988] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Requirements for construction of a functional hybrid complex of photosystem I and [NiFe]-hydrogenase. Appl Environ Microbiol 2010; 76:2641-51. [PMID: 20154103 DOI: 10.1128/aem.02700-09] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The development of cellular systems in which the enzyme hydrogenase is efficiently coupled to the oxygenic photosynthesis apparatus represents an attractive avenue to produce H(2) sustainably from light and water. Here we describe the molecular design of the individual components required for the direct coupling of the O(2)-tolerant membrane-bound hydrogenase (MBH) from Ralstonia eutropha H16 to the acceptor site of photosystem I (PS I) from Synechocystis sp. PCC 6803. By genetic engineering, the peripheral subunit PsaE of PS I was fused to the MBH, and the resulting hybrid protein was purified from R. eutropha to apparent homogeneity via two independent affinity chromatographical steps. The catalytically active MBH-PsaE (MBH(PsaE)) hybrid protein could be isolated only from the cytoplasmic fraction. This was surprising, since the MBH is a substrate of the twin-arginine translocation system and was expected to reside in the periplasm. We conclude that the attachment of the additional PsaE domain to the small, electron-transferring subunit of the MBH completely abolished the export competence of the protein. Activity measurements revealed that the H(2) production capacity of the purified MBH(PsaE) fusion protein was very similar to that of wild-type MBH. In order to analyze the specific interaction of MBH(PsaE) with PS I, His-tagged PS I lacking the PsaE subunit was purified via Ni-nitrilotriacetic acid affinity and subsequent hydrophobic interaction chromatography. Formation of PS I-hydrogenase supercomplexes was demonstrated by blue native gel electrophoresis. The results indicate a vital prerequisite for the quantitative analysis of the MBH(PsaE)-PS I complex formation and its light-driven H(2) production capacity by means of spectroelectrochemistry.
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Saggu M, Teutloff C, Ludwig M, Brecht M, Pandelia ME, Lenz O, Friedrich B, Lubitz W, Hildebrandt P, Lendzian F, Bittl R. Comparison of the membrane-bound [NiFe] hydrogenases from R. eutropha H16 and D. vulgaris Miyazaki F in the oxidized ready state by pulsed EPR. Phys Chem Chem Phys 2010; 12:2139-48. [DOI: 10.1039/b922236g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Decolorization of malachite green by cytochrome c in the mitochondria of the fungus Cunninghamella elegans. Arch Biochem Biophys 2009; 494:159-65. [PMID: 19944668 DOI: 10.1016/j.abb.2009.11.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 11/20/2009] [Accepted: 11/21/2009] [Indexed: 11/20/2022]
Abstract
We studied the decolorization of malachite green (MG) by the fungus Cunninghamella elegans. The mitochondrial activity for MG reduction was increased with a simultaneous increase of a 9-kDa protein, called CeCyt. The presence of cytochrome c in CeCyt protein was determined by optical absorbance spectroscopy with an extinction coefficient (E(550-535)) of 19.7+/-6.3 mM(-1) cm(-1) and reduction potential of + 261 mV. When purified CeCyt was added into the mitochondria, the specific activity of CeCyt reached 440 +/- 122 micromol min(-1) mg(-1) protein. The inhibition of MG reduction by stigmatellin, but not by antimycin A, indicated a possible linkage of CeCyt activity to the Qo site of the bc1 complex. The RT-PCR results showed tight regulation of the cecyt gene expression by reactive oxygen species. We suggest that CeCyt acts as a protein reductant for MG under oxidative stress in a stationary or secondary growth stage of this fungus.
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Lukey MJ, Parkin A, Roessler MM, Murphy BJ, Harmer J, Palmer T, Sargent F, Armstrong FA. How Escherichia coli is equipped to oxidize hydrogen under different redox conditions. J Biol Chem 2009; 285:3928-3938. [PMID: 19917611 DOI: 10.1074/jbc.m109.067751] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The enterobacterium Escherichia coli synthesizes two H(2) uptake enzymes, Hyd-1 and Hyd-2. We show using precise electrochemical kinetic measurements that the properties of Hyd-1 and Hyd-2 contrast strikingly, and may be individually optimized to function under distinct environmental conditions. Hyd-2 is well suited for fast and efficient catalysis in more reducing environments, to the extent that in vitro it behaves as a bidirectional hydrogenase. In contrast, Hyd-1 is active for H(2) oxidation under more oxidizing conditions and cannot function in reverse. Importantly, Hyd-1 is O(2) tolerant and can oxidize H(2) in the presence of air, whereas Hyd-2 is ineffective for H(2) oxidation under aerobic conditions. The results have direct relevance for physiological roles of Hyd-1 and Hyd-2, which are expressed in different phases of growth. The properties that we report suggest distinct technological applications of these contrasting enzymes.
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Affiliation(s)
- Michael J Lukey
- From the Department of Inorganic Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom and
| | - Alison Parkin
- From the Department of Inorganic Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom and
| | - Maxie M Roessler
- From the Department of Inorganic Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom and
| | - Bonnie J Murphy
- From the Department of Inorganic Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom and
| | - Jeffrey Harmer
- From the Department of Inorganic Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom and
| | - Tracy Palmer
- the College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - Frank Sargent
- the College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom.
| | - Fraser A Armstrong
- From the Department of Inorganic Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom and.
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Saggu M, Zebger I, Ludwig M, Lenz O, Friedrich B, Hildebrandt P, Lendzian F. Spectroscopic insights into the oxygen-tolerant membrane-associated [NiFe] hydrogenase of Ralstonia eutropha H16. J Biol Chem 2009; 284:16264-16276. [PMID: 19304663 DOI: 10.1074/jbc.m805690200] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study provides the first spectroscopic characterization of the membrane-bound oxygen-tolerant [NiFe] hydrogenase (MBH) from Ralstonia eutropha H16 in its natural environment, the cytoplasmic membrane. The H2-converting MBH is composed of a large subunit, harboring the [NiFe] active site, and a small subunit, capable in coordinating one [3Fe4S] and two [4Fe4S] clusters. The hydrogenase dimer is electronically connected to a membrane-integral cytochrome b. EPR and Fourier transform infrared spectroscopy revealed a strong similarity of the MBH active site with known [NiFe] centers from strictly anaerobic hydrogenases. Most redox states characteristic for anaerobic [NiFe] hydrogenases were identified except for one remarkable difference. The formation of the oxygen-inhibited Niu-A state was never observed. Furthermore, EPR data showed the presence of an additional paramagnetic center at high redox potential (+290 mV), which couples magnetically to the [3Fe4S] center and indicates a structural and/or redox modification at or near the proximal [4Fe4S] cluster. Additionally, significant differences regarding the magnetic coupling between the Nia-C state and [4Fe4S] clusters were observed in the reduced form of the MBH. The spectroscopic properties are discussed with regard to the unusual oxygen tolerance of this hydrogenase and in comparison with those of the solubilized, dimeric form of the MBH.
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Affiliation(s)
- Miguel Saggu
- From the Institut für Chemie, Technische Universität Berlin, PC14, Strasse des 17. Juni 135, D-10623 Berlin
| | - Ingo Zebger
- From the Institut für Chemie, Technische Universität Berlin, PC14, Strasse des 17. Juni 135, D-10623 Berlin.
| | - Marcus Ludwig
- Institute of Biology, Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
| | - Oliver Lenz
- Institute of Biology, Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
| | - Bärbel Friedrich
- Institute of Biology, Department of Microbiology, Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
| | - Peter Hildebrandt
- From the Institut für Chemie, Technische Universität Berlin, PC14, Strasse des 17. Juni 135, D-10623 Berlin
| | - Friedhelm Lendzian
- From the Institut für Chemie, Technische Universität Berlin, PC14, Strasse des 17. Juni 135, D-10623 Berlin.
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A novel endo-hydrogenase activity recycles hydrogen produced by nitrogen fixation. PLoS One 2009; 4:e4695. [PMID: 19277114 PMCID: PMC2650096 DOI: 10.1371/journal.pone.0004695] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2008] [Accepted: 01/16/2009] [Indexed: 12/17/2022] Open
Abstract
Background Nitrogen (N2) fixation also yields hydrogen (H2) at 1∶1 stoichiometric amounts. In aerobic diazotrophic (able to grow on N2 as sole N-source) bacteria, orthodox respiratory hupSL-encoded hydrogenase activity, associated with the cell membrane but facing the periplasm (exo-hydrogenase), has nevertheless been presumed responsible for recycling such endogenous hydrogen. Methods and Findings As shown here, for Azorhizobium caulinodans diazotrophic cultures open to the atmosphere, exo-hydrogenase activity is of no consequence to hydrogen recycling. In a bioinformatic analysis, a novel seven-gene A. caulinodans hyq cluster encoding an integral-membrane, group-4, Ni,Fe-hydrogenase with homology to respiratory complex I (NADH : quinone dehydrogenase) was identified. By analogy, Hyq hydrogenase is also integral to the cell membrane, but its active site faces the cytoplasm (endo-hydrogenase). An A. caulinodans in-frame hyq operon deletion mutant, constructed by “crossover PCR”, showed markedly decreased growth rates in diazotrophic cultures; normal growth was restored with added ammonium—as expected of an H2-recycling mutant phenotype. Using A. caulinodans hyq merodiploid strains expressing β-glucuronidase as promoter-reporter, the hyq operon proved strongly and specifically induced in diazotrophic culture; as well, hyq operon induction required the NIFA transcriptional activator. Therefore, the hyq operon is constituent of the nif regulon. Conclusions Representative of aerobic N2-fixing and H2-recycling α-proteobacteria, A. caulinodans possesses two respiratory Ni,Fe-hydrogenases: HupSL exo-hydrogenase activity drives exogenous H2 respiration, and Hyq endo-hydrogenase activity recycles endogenous H2, specifically that produced by N2 fixation. To benefit human civilization, H2 has generated considerable interest as potential renewable energy source as its makings are ubiquitous and its combustion yields no greenhouse gases. As such, the reversible, group-4 Ni,Fe-hydrogenases, such as the A. caulinodans Hyq endo-hydrogenase, offer promise as biocatalytic agents for H2 production and/or consumption.
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Yoon KS, Sakai Y, Tsukada N, Fujisawa K, Nishihara H. Purification and biochemical characterization of a membrane-bound [NiFe]-hydrogenase from a hydrogen-oxidizing, lithotrophic bacterium, Hydrogenophaga sp. AH-24. FEMS Microbiol Lett 2008; 290:114-20. [PMID: 19025569 DOI: 10.1111/j.1574-6968.2008.01417.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Membrane-bound [NiFe]-hydrogenase from Hydrogenophaga sp. AH-24 was purified to homogeneity. The molecular weight was estimated as 100+/-10 kDa, consisting of two different subunits (62 and 37 kDa). The optimal pH values for H(2) oxidation and evolution were 8.0 and 4.0, respectively, and the activity ratio (H(2) oxidation/H(2) evolution) was 1.61 x 10(2) at pH 7.0. The optimal temperature was 75 degrees C. The enzyme was quite stable under air atmosphere (the half-life of activity was c. 48 h at 4 degrees C), which should be important to function in the aerobic habitat of the strain. The enzyme showed high thermal stability under anaerobic conditions, which retained full activity for over 5 h at 50 degrees C. The activity increased up to 2.5-fold during incubation at 50 degrees C under H(2). Using methylene blue as an electron acceptor, the kinetic constants of the purified membrane-bound homogenase (MBH) were V(max)=336 U mg(-1), k(cat)=560 s(-1), and k(cat)/K(m)=2.24 x 10(7) M(-1) s(-1). The MBH exhibited prominent electron paramagnetic resonance signals originating from [3Fe-4S](+) and [4Fe-4S](+) clusters. On the other hand, signals originating from Ni of the active center were very weak, as observed in other oxygen-stable hydrogenases from aerobic H(2)-oxidizing bacteria. This is the first report of catalytic and biochemical characterization of the respiratory MBH from Hydrogenophaga.
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Affiliation(s)
- Ki-Seok Yoon
- Department of Bioresource Science, School of Agriculture, Ibaraki University, Ibaraki, Japan
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Ueda Y, Yamamoto M, Urasaki T, Arai H, Ishii M, Igarashi Y. Sequencing and Reverse Transcription-Polymerase Chain Reaction (RT-PCR) Analysis of Four Hydrogenase Gene Clusters from an Obligately Autotrophic Hydrogen-Oxidizing Bacterium, Hydrogenobacter thermophilus TK-6. J Biosci Bioeng 2007; 104:470-5. [DOI: 10.1263/jbb.104.470] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Accepted: 09/08/2007] [Indexed: 11/17/2022]
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Yoon KS, Tsukada N, Sakai Y, Ishii M, Igarashi Y, Nishihara H. Isolation and characterization of a new facultatively autotrophic hydrogen-oxidizing Betaproteobacterium, Hydrogenophaga sp. AH-24. FEMS Microbiol Lett 2007; 278:94-100. [PMID: 18031533 DOI: 10.1111/j.1574-6968.2007.00983.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
A hydrogen-oxidizing bacterium strain AH-24 was isolated, which was classified in the genus Hydrogenophaga, based on the 16S rRNA gene sequence. The isolate possessed a typical yellow pigment of Hydrogenophaga species. Its closest relative was Hydrogenophaga pseudoflava, but the assimilation profile of sugar compounds resembled that of no species of Hydrogenophaga. The optimum temperature and pH for autotrophic growth were, respectively, 33-35 degrees C and 7.0. Most hydrogenase activity (benzyl viologen reducing activity) was localized in the membrane fraction (MF), but NAD(P)-reducing hydrogenase activity was detected in neither the membrane nor the soluble fractions. Cytochromes b561 and c551 were present in MF; both were reduced when hydrogen was supplied to the oxidized MF, suggesting involvement in respiratory H2 oxidation as electron carriers. Cytochrome b561 was inferred to function as the redox partner of the membrane-bound hydrogenase.
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Affiliation(s)
- Ki-Seok Yoon
- Department of Bioresource Science, School of Agriculture, Ibaraki University, Inashiki-gun, Ibaraki, Japan
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Schubert T, Lenz O, Krause E, Volkmer R, Friedrich B. Chaperones specific for the membrane-bound [NiFe]-hydrogenase interact with the Tat signal peptide of the small subunit precursor in Ralstonia eutropha H16. Mol Microbiol 2007; 66:453-67. [PMID: 17850259 DOI: 10.1111/j.1365-2958.2007.05933.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Periplasmic membrane-bound [NiFe]-hydrogenases undergo a complex maturation pathway, including cofactor incorporation, subunit assembly, and finally twin-arginine-dependent membrane translocation (Tat). In this study, the role of the two accessory proteins HoxO and HoxQ in the maturation of the membrane-bound [NiFe]-hydrogenase (MBH) of Ralstonia eutropha H16 was investigated. MBH activity was absent in soluble as well as membrane fractions of cells with deletions in the respective genes. The absence of HoxO and HoxQ led to degradation of the small subunit precursor (preHoxK) of the MBH. The two accessory proteins directly interacted with preHoxK prior to assembly of active MBH dimer in the cytoplasm. MBH mutants with modified Tat signal peptides were disrupted in preHoxK/HoxO/HoxQ complex formation. Isolated HoxO and HoxQ proteins formed a complex in vitro with the chemically synthesized HoxK Tat signal peptide. Two functions of the two chaperones are discussed: (i) protection of the Fe-S cluster containing HoxK subunit under oxygenic conditions, and (ii) avoidance of HoxK export prior to dimerization with the large MBH subunit HoxG.
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Affiliation(s)
- Torsten Schubert
- Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestr. 117, D-10115 Berlin, Germany
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Gebler A, Burgdorf T, De Lacey AL, Rüdiger O, Martinez-Arias A, Lenz O, Friedrich B. Impact of alterations near the [NiFe] active site on the function of the H(2) sensor from Ralstonia eutropha. FEBS J 2007; 274:74-85. [PMID: 17222178 DOI: 10.1111/j.1742-4658.2006.05565.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In proteobacteria capable of H(2) oxidation under (micro)aerobic conditions, hydrogenase gene expression is often controlled in response to the availability of H(2). The H(2)-sensing signal transduction pathway consists of a heterodimeric regulatory [NiFe]-hydrogenase (RH), a histidine protein kinase and a response regulator. To gain insights into the signal transmission from the Ni-Fe active site in the RH to the histidine protein kinase, conserved amino acid residues in the L0 motif near the active site of the RH large subunit of Ralstonia eutropha H16 were exchanged. Replacement of the strictly conserved Glu13 (E13N, E13L) resulted in loss of the regulatory, H(2)-oxidizing and D(2)/H(+) exchange activities of the RH. According to EPR and FTIR analysis, these RH derivatives contained fully assembled [NiFe] active sites, and para-/ortho-H(2) conversion activity showed that these centres were still able to bind H(2). This indicates that H(2) binding at the active site is not sufficient for the regulatory function of H(2) sensors. Replacement of His15, a residue unique in RHs, by Asp restored the consensus of energy-linked [NiFe]-hydrogenases. The respective RH mutant protein showed only traces of H(2)-oxidizing activity, whereas its D(2)/H(+)-exchange activity and H(2)-sensing function were almost unaffected. H(2)-dependent signal transduction in this mutant was less sensitive to oxygen than in the wild-type strain. These results suggest that H(2) turnover is not crucial for H(2) sensing. It may even be detrimental for the function of the H(2) sensor under high O(2) concentrations.
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Affiliation(s)
- Antje Gebler
- Institut für Biologie, Humboldt Universität zu Berlin, Germany
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36
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Abstract
Hydrogenases are metalloenzymes subdivided into two classes that contain iron-sulfur clusters and catalyze the reversible oxidation of hydrogen gas (H(2)[Symbol: see text]left arrow over right arrow[Symbol: see text]2H(+)[Symbol: see text]+[Symbol: see text]2e(-)). Two metal atoms are present at their active center: either a Ni and an Fe atom in the [NiFe]hydrogenases, or two Fe atoms in the [FeFe]hydrogenases. They are phylogenetically distinct classes of proteins. The catalytic core of [NiFe]hydrogenases is a heterodimeric protein associated with additional subunits in many of these enzymes. The catalytic core of [FeFe]hydrogenases is a domain of about 350 residues that accommodates the active site (H cluster). Many [FeFe]hydrogenases are monomeric but possess additional domains that contain redox centers, mostly Fe-S clusters. A third class of hydrogenase, characterized by a specific iron-containing cofactor and by the absence of Fe-S cluster, is found in some methanogenic archaea; this Hmd hydrogenase has catalytic properties different from those of [NiFe]- and [FeFe]hydrogenases. The [NiFe]hydrogenases can be subdivided into four subgroups: (1) the H(2) uptake [NiFe]hydrogenases (group 1); (2) the cyanobacterial uptake hydrogenases and the cytoplasmic H(2) sensors (group 2); (3) the bidirectional cytoplasmic hydrogenases able to bind soluble cofactors (group 3); and (4) the membrane-associated, energy-converting, H(2) evolving hydrogenases (group 4). Unlike the [NiFe]hydrogenases, the [FeFe]hydrogenases form a homogeneous group and are primarily involved in H(2) evolution. This review recapitulates the classification of hydrogenases based on phylogenetic analysis and the correlation with hydrogenase function of the different phylogenetic groupings, discusses the possible role of the [FeFe]hydrogenases in the genesis of the eukaryotic cell, and emphasizes the structural and functional relationships of hydrogenase subunits with those of complex I of the respiratory electron transport chain.
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Affiliation(s)
- Paulette M Vignais
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, UMR CEA/CNRS/UJF no. 5092, Institut de Recherches en Technologies et Sciences pour le Vivant, Grenoble cedex 9, France.
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Deppenmeier U, Müller V. Life close to the thermodynamic limit: how methanogenic archaea conserve energy. Results Probl Cell Differ 2007; 45:123-52. [PMID: 17713742 DOI: 10.1007/400_2006_026] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methane-forming archaea are strictly anaerobic, ancient microbes that are widespread in nature. These organisms are commonly found in anaerobic environments such as rumen, anaerobic sediments of rivers and lakes, hyperthermal deep sea vents and even hypersaline environments. From an evolutionary standpoint they are close to the origin of life. Common to all methanogens is the biological production of methane by a unique pathway currently only found in archaea. Methanogens can grow on only a limited number of substrates such as H(2) + CO(2), formate, methanol and other methyl group-containing substrates and some on acetate. The free energy change associated with methanogenesis from these compounds allows for the synthesis of 1 (acetate) to a maximum of only 2 mol of ATP under standard conditions while under environmental conditions less than one ATP can be synthesized. Therefore, methanogens live close to the thermodynamic limit. To cope with this problem, they have evolved elaborate mechanisms of energy conservation using both protons and sodium ions as the coupling ion in one pathway. These energy conserving mechanisms are comprised of unique enzymes, cofactors and electron carriers present only in methanogens. This review will summarize the current knowledge of energy conservation of methanogens and focus on recent insights into structure and function of ion translocating enzymes found in these organisms.
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Affiliation(s)
- Uwe Deppenmeier
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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Burgdorf T, Lenz O, Buhrke T, van der Linden E, Jones AK, Albracht SPJ, Friedrich B. [NiFe]-Hydrogenases of Ralstonia eutropha H16: Modular Enzymes for Oxygen-Tolerant Biological Hydrogen Oxidation. J Mol Microbiol Biotechnol 2006; 10:181-96. [PMID: 16645314 DOI: 10.1159/000091564] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recent research on hydrogenases has been notably motivated by a desire to utilize these remarkable hydrogen oxidation catalysts in biotechnological applications. Progress in the development of such applications is substantially hindered by the oxygen sensitivity of the majority of hydrogenases. This problem tends to inspire the study of organisms such as Ralstonia eutropha H16 that produce oxygen-tolerant [NiFe]-hydrogenases. R. eutropha H16 serves as an excellent model system in that it produces three distinct [NiFe]-hydrogenases that each serve unique physiological roles: a membrane-bound hydrogenase (MBH) coupled to the respiratory chain, a cytoplasmic, soluble hydrogenase (SH) able to generate reducing equivalents by reducing NAD+ at the expense of hydrogen, and a regulatory hydrogenase (RH) which acts in a signal transduction cascade to control hydrogenase gene transcription. This review will present recent results regarding the biosynthesis, regulation, structure, activity, and spectroscopy of these enzymes. This information will be discussed in light of the question how do organisms adapt the prototypical [NiFe]-hydrogenase system to function in the presence of oxygen.
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Affiliation(s)
- Tanja Burgdorf
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
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39
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Abe T, Kobayashi T, Saito T. Properties of a novel intracellular poly(3-hydroxybutyrate) depolymerase with high specific activity (PhaZd) in Wautersia eutropha H16. J Bacteriol 2005; 187:6982-90. [PMID: 16199568 PMCID: PMC1251622 DOI: 10.1128/jb.187.20.6982-6990.2005] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel intracellular poly(3-hydroxybutyrate) (PHB) depolymerase (PhaZd) of Wautersia eutropha (formerly Ralstonia eutropha) H16 which shows similarity with the catalytic domain of the extracellular PHB depolymerase in Ralstonia pickettii T1 was identified. The positions of the catalytic triad (Ser190-Asp266-His330) and oxyanion hole (His108) in the amino acid sequence of PhaZd deduced from the nucleotide sequence roughly accorded with those of the extracellular PHB depolymerase of R. pickettii T1, but a signal peptide, a linker domain, and a substrate binding domain were missing. The PhaZd gene was cloned and the gene product was purified from Escherichia coli. The specific activity of PhaZd toward artificial amorphous PHB granules was significantly greater than that of other known intracellular PHB depolymerase or 3-hydroxybutyrate (3HB) oligomer hydrolases of W. eutropha H16. The enzyme degraded artificial amorphous PHB granules and mainly released various 3-hydroxybutyrate oligomers. PhaZd distributed nearly equally between PHB inclusion bodies and the cytosolic fraction. The amount of PHB was greater in phaZd deletion mutant cells than the wild-type cells under various culture conditions. These results indicate that PhaZd is a novel intracellular PHB depolymerase which participates in the mobilization of PHB in W. eutropha H16 along with other PHB depolymerases.
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Affiliation(s)
- Tomoko Abe
- Laboratory of Molecular Microbiology, Department of Biological Sciences, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
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40
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Lenz O, Gleiche A, Strack A, Friedrich B. Requirements for heterologous production of a complex metalloenzyme: the membrane-bound [NiFe] hydrogenase. J Bacteriol 2005; 187:6590-5. [PMID: 16159796 PMCID: PMC1236620 DOI: 10.1128/jb.187.18.6590-6595.2005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
By taking advantage of the tightly clustered genes for the membrane-bound [NiFe] hydrogenase of Ralstonia eutropha H16, broad-host-range recombinant plasmids were constructed carrying the entire membrane-bound hydrogenase (MBH) operon encompassing 21 genes. We demonstrate that the complex MBH biosynthetic apparatus is actively produced in hydrogenase-free hosts yielding fully assembled and functional MBH protein.
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Affiliation(s)
- Oliver Lenz
- Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestrasse 117, D-10115 Berlin, Germany
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41
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Buhrke T, Lenz O, Krauss N, Friedrich B. Oxygen tolerance of the H2-sensing [NiFe] hydrogenase from Ralstonia eutropha H16 is based on limited access of oxygen to the active site. J Biol Chem 2005; 280:23791-6. [PMID: 15849358 DOI: 10.1074/jbc.m503260200] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hydrogenases, abundant proteins in the microbial world, catalyze cleavage of H2 into protons and electrons or the evolution of H2 by proton reduction. Hydrogen metabolism predominantly occurs in anoxic environments mediated by hydrogenases, which are sensitive to inhibition by oxygen. Those microorganisms, which thrive in oxic habitats, contain hydrogenases that operate in the presence of oxygen. We have selected the H2-sensing regulatory [NiFe] hydrogenase of Ralstonia eutropha H16 to investigate the molecular background of its oxygen tolerance. Evidence is presented that the shape and size of the intramolecular hydrophobic cavities leading to the [NiFe] active site of the regulatory hydrogenase are crucial for oxygen insensitivity. Expansion of the putative gas channel by site-directed mutagenesis yielded mutant derivatives that are sensitive to inhibition by oxygen, presumably because the active site has become accessible for oxygen. The mutant proteins revealed characteristics typical of standard [NiFe] hydrogenases as described for Desulfovibrio gigas and Allochromatium vinosum. The data offer a new strategy how to engineer oxygen-tolerant hydrogenases for biotechnological application.
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Affiliation(s)
- Thorsten Buhrke
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany
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42
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Buhrke T, Lenz O, Porthun A, Friedrich B. The H2-sensing complex of Ralstonia eutropha: interaction between a regulatory [NiFe] hydrogenase and a histidine protein kinase. Mol Microbiol 2004; 51:1677-89. [PMID: 15009894 DOI: 10.1111/j.1365-2958.2003.03933.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two [NiFe] hydrogenases enable the proteobacterium Ralstonia eutropha H16 to grow on molecular hydrogen as the sole energy source. A third [NiFe] hydrogenase (RH) acts as an H2 sensor in a multiple component signal transduction chain that controls hydrogenase gene transcription. The RH forms a dimeric heterodimer (HoxBC)2 in which HoxC contains the H2-sensing active site and HoxB the electron-transferring components including an organic, not yet identified redox cofactor. This oligomer forms a tight complex with the histidine protein kinase HoxJ. Both the sensor and the kinase were analysed by mutagenesis for functional domains that are instrumental in H2 signal transmission. A mutant deleted for a C-terminal peptide of 55 amino acids in HoxB lost its H2-sensing ability but still catalysed H2 oxidation. The mutant protein failed to form the dimeric heterodimer and a complex with HoxJ. The organic redox cofactor was no longer detectable in the truncated sensor. H2 sensing was also abolished by deletion of the PAS domain of HoxJ, indicating that this domain is involved in signal transduction. A truncated version of HoxJ consisting of only the input domain of the kinase was still capable of forming a complex with the RH. Mass determination of the purified HoxJ protein revealed that the kinase forms a homotetramer. The unique oligomeric structure of the H2-sensing complex with respect to its regulatory function is discussed.
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Affiliation(s)
- Thorsten Buhrke
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestr 117, 10115 Berlin, Germany
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43
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Berks BC, Palmer T, Sargent F. The Tat protein translocation pathway and its role in microbial physiology. Adv Microb Physiol 2003; 47:187-254. [PMID: 14560665 DOI: 10.1016/s0065-2911(03)47004-5] [Citation(s) in RCA: 192] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Tat (twin arginine translocation) protein transport system functions to export folded protein substrates across the bacterial cytoplasmic membrane and to insert certain integral membrane proteins into that membrane. It is entirely distinct from the Sec pathway. Here, we describe our current knowledge of the molecular features of the Tat transport system. In addition, we discuss the roles that the Tat pathway plays in the bacterial cell, paying particular attention to the involvement of the Tat pathway in the biogenesis of cofactor-containing proteins, in cell wall biosynthesis and in bacterial pathogenicity.
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Affiliation(s)
- Ben C Berks
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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44
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Schwartz E, Henne A, Cramm R, Eitinger T, Friedrich B, Gottschalk G. Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis. J Mol Biol 2003; 332:369-83. [PMID: 12948488 DOI: 10.1016/s0022-2836(03)00894-5] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The self-transmissible megaplasmid pHG1 carries essential genetic information for the facultatively lithoautotrophic and facultatively anaerobic lifestyles of its host, the Gram-negative soil bacterium Ralstonia eutropha H16. We have determined the complete nucleotide sequence of pHG1. This megaplasmid is 452,156 bp in size and carries 429 potential genes. Groups of functionally related genes form loose clusters flanked by mobile elements. The largest functional group consists of lithoautotrophy-related genes. These include a set of 41 genes for the biosynthesis of the three previously identified hydrogenases and of a fourth, novel hydrogenase. Another large cluster carries the genetic information for denitrification. In addition to a dissimilatory nitrate reductase, both specific and global regulators were identified. Also located in the denitrification region is a set of genes for cytochrome c biosynthesis. Determinants for several enzymes involved in the mineralization of aromatic compounds were found. The genes for conjugative plasmid transfer predict that R.eutropha forms two types of pili. One of them is related to the type IV pili of pathogenic enterobacteria. pHG1 also carries an extensive "junkyard" region encompassing 17 remnants of mobile elements and 22 partial or intact genes for phage-type integrase. Among the mobile elements is a novel member of the IS5 family, in which the transposase gene is interrupted by a group II intron.
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Affiliation(s)
- Edward Schwartz
- Institut für Biologie, Mikrobiologie, Humboldt-Universität zu Berlin, Chausseestr. 117, 10115 Berlin, Germany.
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45
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Hatzixanthis K, Palmer T, Sargent F. A subset of bacterial inner membrane proteins integrated by the twin-arginine translocase. Mol Microbiol 2003; 49:1377-90. [PMID: 12940994 DOI: 10.1046/j.1365-2958.2003.03642.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A group of bacterial exported proteins are synthesized with N-terminal signal peptides containing a SRRxFLK 'twin-arginine' amino acid motif. Proteins bearing twin-arginine signal peptides are targeted post-translationally to the twin-arginine translocation (Tat) system which transports folded substrates across the inner membrane. In Escherichia coli, most integral inner membrane proteins are assembled by a co-translational process directed by SRP/FtsY, the SecYEG translocase, and YidC. In this work we define a novel class of integral membrane proteins assembled by a Tat-dependent mechanism. We show that at least five E. coli Tat substrate proteins contain hydrophobic C-terminal transmembrane helices (or 'C-tails'). Fusions between the identified transmembrane C-tails and the exclusively Tat-dependent reporter proteins TorA and SufI render the resultant chimeras membrane-bound. Export-linked signal peptide processing and membrane integration of the chimeras is shown to be both Tat-dependent and YidC-independent. It is proposed that the mechanism of membrane integration of proteins by the Tat system is fundamentally distinct from that employed for other bacterial inner membrane proteins.
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Affiliation(s)
- Kostas Hatzixanthis
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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46
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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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47
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Stanley NR, Sargent F, Buchanan G, Shi J, Stewart V, Palmer T, Berks BC. Behaviour of topological marker proteins targeted to the Tat protein transport pathway. Mol Microbiol 2002; 43:1005-21. [PMID: 11929547 DOI: 10.1046/j.1365-2958.2002.02797.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Escherichia coli Tat system mediates Sec-independent export of protein precursors bearing twin arginine signal peptides. Formate dehydrogenase-N is a three-subunit membrane-bound enzyme, in which localization of the FdnG subunit to the membrane is Tat dependent. FdnG was found in the periplasmic fraction of a mutant lacking the membrane anchor subunit FdnI, confirming that FdnG is located at the periplasmic face of the cytoplasmic membrane. However, the phenotypes of gene fusions between fdnG and the subcellular reporter genes phoA (encoding alkaline phosphatase) or lacZ (encoding beta-galactosidase) were the opposite of those expected for analogous fusions targeted to the Sec translocase. PhoA fusion experiments have previously been used to argue that the peripheral membrane DmsAB subunits of the Tat-dependent enzyme dimethyl sulphoxide reductase are located at the cytoplasmic face of the inner membrane. Biochemical data are presented that instead show DmsAB to be at the periplasmic side of the membrane. The behaviour of reporter proteins targeted to the Tat system was analysed in more detail. These data suggest that the Tat and Sec pathways differ in their ability to transport heterologous passenger proteins. They also suggest that caution should be observed when using subcellular reporter fusions to determine the topological organization of Tat-dependent membrane protein complexes.
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Affiliation(s)
- Nicola R Stanley
- Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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48
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Buhrke T, Bleijlevens B, Albracht SP, Friedrich B. Involvement of hyp gene products in maturation of the H(2)-sensing [NiFe] hydrogenase of Ralstonia eutropha. J Bacteriol 2001; 183:7087-93. [PMID: 11717266 PMCID: PMC95556 DOI: 10.1128/jb.183.24.7087-7093.2001] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The biosynthesis of [NiFe] hydrogenases is a complex process that requires the function of the Hyp proteins HypA, HypB, HypC, HypD, HypE, HypF, and HypX for assembly of the H(2)-activating [NiFe] site. In this study we examined the maturation of the regulatory hydrogenase (RH) of Ralstonia eutropha. The RH is a H(2)-sensing [NiFe] hydrogenase and is required as a constituent of a signal transduction chain for the expression of two energy-linked [NiFe] hydrogenases. Here we demonstrate that the RH regulatory activity was barely affected by mutations in hypA, hypB, hypC, and hypX and was not substantially diminished in hypD- and hypE-deficient strains. The lack of HypF, however, resulted in a 90% decrease of the RH regulatory activity. Fourier transform infrared spectroscopy and the incorporation of (63)Ni into the RH from overproducing cells revealed that the assembly of the [NiFe] active site is dependent on all Hyp functions, with the exception of HypX. We conclude that the entire Hyp apparatus (HypA, HypB, HypC, HypD, HypE, and HypF) is involved in an efficient incorporation of the [NiFe] center into the RH.
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Affiliation(s)
- T Buhrke
- Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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49
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Magnani P, Doussiere J, Lissolo T. Diphenylene iodonium as an inhibitor for the hydrogenase complex of Rhodobacter capsulatus. Evidence for two distinct electron donor sites. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1459:169-78. [PMID: 10924909 DOI: 10.1016/s0005-2728(00)00145-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The photosynthetic bacterium Rhodobacter capsulatus synthesises a membrane-bound [NiFe] hydrogenase encoded by the H2 uptake hydrogenase (hup)SLC structural operon. The hupS and hupL genes encode the small and large subunits of hydrogenase, respectively; hupC encodes a membrane electron carrier protein which may be considered as the third subunit of the uptake hydrogenase. In Wolinella succinogenes, the hydC gene, homologous to hupC, has been shown to encode a low potential cytochrome b which mediates electron transfer from H2 to the quinone pool of the bacterial membrane. In whole cells of R. capsulatus or intact membrane preparation of the wild type strain B10, methylene blue but not benzyl viologen can be used as acceptor of the electrons donated by H2 to hydrogenase; on the other hand, membranes of B10 treated with Triton X-100 or whole cells of a HupC- mutant exhibit both benzyl viologen and methylene blue reductase activities. We report the effect of diphenylene iodonium (Ph2I), a known inhibitor of mitochondrial complex I and of various monooxygenases on R. capsulatus hydrogenase activity. With H2 as electron donor, Ph2I inhibited partially the methylene blue reductase activity in an uncompetitive manner, and totally benzyl viologen reductase activity in a competitive manner. Furthermore, with benzyl viologen as electron acceptor, Ph2I increased dramatically the observed lagtime for dye reduction. These results suggest that two different sites exist on the electron donor side of the membrane-bound [NiFe] hydrogenase of R. capsulatus, both located on the small subunit. A low redox potential site which reduces benzyl viologen, binds Ph2I and could be located on the distal [Fe4S4] cluster. A higher redox potential site which can reduce methylene blue in vitro could be connected to the high potential [Fe3S4] cluster and freely accessible from the periplasm.
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Affiliation(s)
- P Magnani
- Laboratoire TEPE, ESIGEC, Université de Savoie, Le Bourget Du Lac, France
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50
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Meek L, Arp DJ. The hydrogenase cytochrome b heme ligands of Azotobacter vinelandii are required for full H(2) oxidation capability. J Bacteriol 2000; 182:3429-36. [PMID: 10852874 PMCID: PMC101916 DOI: 10.1128/jb.182.12.3429-3436.2000] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hydrogenase in Azotobacter vinelandii, like other membrane-bound [NiFe] hydrogenases, consists of a catalytic heterodimer and an integral membrane cytochrome b. The histidines ligating the hemes in this cytochrome b were identified by H(2) oxidation properties of altered proteins produced by site-directed mutagenesis. Four fully conserved and four partially conserved histidines in HoxZ were substituted with alanine or tyrosine. The roles of these histidines in HoxZ heme binding and hydrogenase were characterized by O(2)-dependent H(2) oxidation and H(2)-dependent methylene blue reduction in vivo. Mutants H33A/Y (H33 replaced by A or Y), H74A/Y, H194A, H208A/Y, and H194,208A lost O(2)-dependent H(2) oxidation activity, H194Y and H136A had partial activity, and H97Y,H98A and H191A had full activity. These results suggest that the fully conserved histidines 33, 74, 194, and 208 are ligands to the hemes, tyrosine can serve as an alternate ligand in position 194, and H136 plays a role in H(2) oxidation. In mutant H194A/Y, imidazole (Imd) rescued H(2) oxidation activity in intact cells, which suggests that Imd acts as an exogenous ligand. The heterodimer activity, quantitatively determined as H(2)-dependent methylene blue reduction, indicated that the heterodimers of all mutants were catalytically active. H33A/Y had wild-type levels of methylene blue reduction, but the other HoxZ ligand mutants had significantly less than wild-type levels. Imd reconstituted full methylene blue reduction activity in mutants H194A/Y and H208A/Y and partial activity in H194,208A. These results indicate that structural and functional integrity of HoxZ is required for physiologically relevant H(2) oxidation, and structural integrity of HoxZ is necessary for full heterodimer-catalyzed H(2) oxidation.
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Affiliation(s)
- L Meek
- Biochemistry and Biophysics Department, Oregon State University, Corvallis 97331-2902, USA
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