1
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Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. mSystems 2023; 8:e0003823. [PMID: 37882557 PMCID: PMC10734462 DOI: 10.1128/msystems.00038-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study, we show the Gallionellaceae FeOB genomes encode both characterized iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it would be advantageous for them to have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.
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Affiliation(s)
- Rene L. Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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2
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Gerlach MS, Neubauer P, Gimpel M. Improved preculture management for Cupriavidus necator cultivations. Biotechnol Lett 2023; 45:1487-1493. [PMID: 37828291 PMCID: PMC10635987 DOI: 10.1007/s10529-023-03436-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/30/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
OBJECTIVES Research on hydrogenases from Cupriavidus necator has been ongoing for more than two decades and still today the common methods for culture inoculation are used. These methods were never adapted to the requirements of modified bacterial strains, resulting in different physiological states of the bacteria in the precultures, which in turn lead prolonged and different lag-phases. RESULTS In order to obtain uniform and always equally fit precultures for inoculation, we have established in this study an optimized protocol for precultures of the derivative of C. necator HF210 (C. necator HP80) which is used for homologous overexpression of the genes for the NAD+-reducing soluble hydrogenase (SH). We compared different media for preculture growth and determined the optimal time point for harvest. The protocol obtained in this study is based on two subsequent precultures, the first one in complex nutrient broth medium (NB) and a second one in fructose -nitrogen mineral salt medium (FN). CONCLUSION Despite having two subsequent precultures our protocol reduces the preculture time to less than 30 h and provides reproducible precultures for cultivation of C. necator HP80.
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Affiliation(s)
- Michelle-Sophie Gerlach
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstr. 76, ACK24, 13355, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstr. 76, ACK24, 13355, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Institute of Biotechnology, Technische Universität Berlin, Ackerstr. 76, ACK24, 13355, Berlin, Germany.
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3
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Al-Shameri A, Siebert DL, Sutiono S, Lauterbach L, Sieber V. Hydrogenase-based oxidative biocatalysis without oxygen. Nat Commun 2023; 14:2693. [PMID: 37258512 DOI: 10.1038/s41467-023-38227-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/21/2023] [Indexed: 06/02/2023] Open
Abstract
Biocatalysis-based synthesis can provide a sustainable and clean platform for producing chemicals. Many oxidative biocatalytic routes require the cofactor NAD+ as an electron acceptor. To date, NADH oxidase (NOX) remains the most widely applied system for NAD+ regeneration. However, its dependence on O2 implies various technical challenges in terms of O2 supply, solubility, and mass transfer. Here, we present the suitability of a NAD+ regeneration system in vitro based on H2 evolution. The efficiency of the hydrogenase-based system is demonstrated by integrating it into a multi-enzymatic cascade to produce ketoacids from sugars. The total NAD+ recycled using the hydrogenase system outperforms NOX in all different setups reaching up to 44,000 mol per mol enzyme. This system proves to be scalable and superior to NOX in terms of technical simplicity, flexibility, and total output. Furthermore, the system produces only green H2 as a by-product even in the presence of O2.
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Affiliation(s)
- Ammar Al-Shameri
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Dominik L Siebert
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Lars Lauterbach
- RWTH Universität Aachen, Institute of Applied Microbiology, Worringerweg 1, 52074, Aachen, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany.
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, 85748, Garching, Germany.
- SynBiofoundry@TUM, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany.
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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4
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Partipilo M, Claassens NJ, Slotboom DJ. A Hitchhiker's Guide to Supplying Enzymatic Reducing Power into Synthetic Cells. ACS Synth Biol 2023; 12:947-962. [PMID: 37052416 PMCID: PMC10127272 DOI: 10.1021/acssynbio.3c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Indexed: 04/14/2023]
Abstract
The construction from scratch of synthetic cells by assembling molecular building blocks is unquestionably an ambitious goal from a scientific and technological point of view. To realize functional life-like systems, minimal enzymatic modules are required to sustain the processes underlying the out-of-equilibrium thermodynamic status hallmarking life, including the essential supply of energy in the form of electrons. The nicotinamide cofactors NAD(H) and NADP(H) are the main electron carriers fueling reductive redox reactions of the metabolic network of living cells. One way to ensure the continuous availability of reduced nicotinamide cofactors in a synthetic cell is to build a minimal enzymatic module that can oxidize an external electron donor and reduce NAD(P)+. In the diverse world of metabolism there is a plethora of potential electron donors and enzymes known from living organisms to provide reducing power to NAD(P)+ coenzymes. This perspective proposes guidelines to enable the reduction of nicotinamide cofactors enclosed in phospholipid vesicles, while avoiding high burdens of or cross-talk with other encapsulated metabolic modules. By determining key requirements, such as the feasibility of the reaction and transport of the electron donor into the cell-like compartment, we select a shortlist of potentially suitable electron donors. We review the most convenient proteins for the use of these reducing agents, highlighting their main biochemical and structural features. Noting that specificity toward either NAD(H) or NADP(H) imposes a limitation common to most of the analyzed enzymes, we discuss the need for specific enzymes─transhydrogenases─to overcome this potential bottleneck.
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Affiliation(s)
- Michele Partipilo
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nico J. Claassens
- Laboratory
of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Jan Slotboom
- Department
of Biochemistry, Groningen Institute of Biomolecular Sciences &
Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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5
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Unique H 2-utilizing lithotrophy in serpentinite-hosted systems. THE ISME JOURNAL 2023; 17:95-104. [PMID: 36207493 PMCID: PMC9751293 DOI: 10.1038/s41396-022-01197-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 01/08/2022] [Accepted: 01/17/2022] [Indexed: 11/08/2022]
Abstract
Serpentinization of ultramafic rocks provides molecular hydrogen (H2) that can support lithotrophic metabolism of microorganisms, but also poses extremely challenging conditions, including hyperalkalinity and limited electron acceptor availability. Investigation of two serpentinization-active systems reveals that conventional H2-/CO2-dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, "Ca. Lithacetigenota", that exclusively inhabits serpentinite-hosted systems and harbors genes encoding alternative modes of H2-utilizing lithotrophy. Rather than CO2, these putative metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein-the glycine reductase. A survey of microbiomes shows that glycine reductases are diverse and nearly ubiquitous in serpentinite-hosted environments. "Ca. Lithacetigenota" glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation by Terrabacteria for gaining energy from geogenic H2 even under hyperalkaline, CO2-poor conditions. Unique non-CO2-reducing metabolisms presented here shed light on potential strategies that extremophiles may employ for overcoming a crucial obstacle in serpentinization-associated environments, features potentially relevant to primordial lithotrophy in early Earth.
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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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7
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Evidence for Electron Transfer from the Bidirectional Hydrogenase to the Photosynthetic Complex I (NDH-1) in the Cyanobacterium Synechocystis sp. PCC 6803. Microorganisms 2022; 10:microorganisms10081617. [PMID: 36014035 PMCID: PMC9414918 DOI: 10.3390/microorganisms10081617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 12/12/2022] Open
Abstract
The cyanobacterial bidirectional [NiFe]-hydrogenase is a pentameric enzyme. Apart from the small and large hydrogenase subunits (HoxYH) it contains a diaphorase module (HoxEFU) that interacts with NAD(P)+ and ferredoxin. HoxEFU shows strong similarity to the outermost subunits (NuoEFG) of canonical respiratory complexes I. Photosynthetic complex I (NDH-1) lacks these three subunits. This led to the idea that HoxEFU might interact with NDH-1 instead. HoxEFUYH utilizes excited electrons from PSI for photohydrogen production and it catalyzes the reverse reaction and feeds electrons into the photosynthetic electron transport. We analyzed hydrogenase activity, photohydrogen evolution and hydrogen uptake, the respiration and photosynthetic electron transport of ΔhoxEFUYH, and a knock-out strain with dysfunctional NDH-1 (ΔndhD1/ΔndhD2) of the cyanobacterium Synechocystis sp. PCC 6803. Photohydrogen production was prolonged in ΔndhD1/ΔndhD2 due to diminished hydrogen uptake. Electrons from hydrogen oxidation must follow a different route into the photosynthetic electron transport in this mutant compared to wild type cells. Furthermore, respiration was reduced in ΔhoxEFUYH and the ΔndhD1/ΔndhD2 localization of the hydrogenase to the membrane was impaired. These data indicate that electron transfer from the hydrogenase to the NDH-1 complex is either direct, by the binding of the hydrogenase to the complex, or indirect, via an additional mediator.
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8
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Yang J, Peng Z, Zhu Q, Zhang J, Du G. [NiFe] Hydrogenase Accessory Proteins HypB-HypC Accelerate Proton Conversion to Enhance the Acid Resistance and d-Lactic Acid Production of Escherichia coli. ACS Synth Biol 2022; 11:1521-1530. [PMID: 35271275 DOI: 10.1021/acssynbio.1c00599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli is a major industrial producer of d-lactic acid due to its well-known advantages, such as short cycle times and low demand. However, acid sensitivity limits production capacity and increases costs. Enhancing the resistance of E. coli to acid stress is essential for improving the cell performance and production value. Here, we propose a feasible strategy to increase the acid tolerance of cells by strengthening intracellular proton conversion. The transcriptome test of the acid-tolerant adaptive evolution strain identified the hydrogenase accessory proteins HypB and HypC as a class of acid-tolerant factors that can assist the hydrogenase in catalyzing the reduction of protons to produce hydrogen. Strengthening the expression of HypB and HypC can increase the cell survival rate by 336.3 times during the lethal stress of d-lactate. In addition, HypB and HypC will assist d-lactate-producing strains to show higher sustainable productivity in an acidic fermentation environment, and d-lactate titer will increase by 113.6%. In order to further improve the expression system of the hydrogenase accessory protein, the introduction of a strong acid stress-driven promoter tdcAp can reduce the demand for neutralizer delivery in the fermentation process by about 26.7% while maintaining the maximum intensity of d-lactic acid production. Therefore, this research developed a method to improve the acid resistance of E. coli cells and reduce the cost of organic acid production by transforming protons.
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Affiliation(s)
- Jinhua Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Qi Zhu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
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9
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Lupacchini S, Appel J, Stauder R, Bolay P, Klähn S, Lettau E, Adrian L, Lauterbach L, Bühler B, Schmid A, Toepel J. Rewiring cyanobacterial photosynthesis by the implementation of an oxygen-tolerant hydrogenase. Metab Eng 2021; 68:199-209. [PMID: 34673236 DOI: 10.1016/j.ymben.2021.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/11/2021] [Accepted: 10/16/2021] [Indexed: 10/20/2022]
Abstract
Molecular hydrogen (H2) is considered as an ideal energy carrier to replace fossil fuels in future. Biotechnological H2 production driven by oxygenic photosynthesis appears highly promising, as biocatalyst and H2 syntheses rely mainly on light, water, and CO2 and not on rare metals. This biological process requires coupling of the photosynthetic water oxidizing apparatus to a H2-producing hydrogenase. However, this strategy is impeded by the simultaneous release of oxygen (O2) which is a strong inhibitor of most hydrogenases. Here, we addressed this challenge, by the introduction of an O2-tolerant hydrogenase into phototrophic bacteria, namely the cyanobacterial model strain Synechocystis sp. PCC 6803. To this end, the gene cluster encoding the soluble, O2-tolerant, and NAD(H)-dependent hydrogenase from Ralstonia eutropha (ReSH) was functionally transferred to a Synechocystis strain featuring a knockout of the native O2 sensitive hydrogenase. Intriguingly, photosynthetically active cells produced the O2 tolerant ReSH, and activity was confirmed in vitro and in vivo. Further, ReSH enabled the constructed strain Syn_ReSH+ to utilize H2 as sole electron source to fix CO2. Syn_ReSH+ also was able to produce H2 under dark fermentative conditions as well as in presence of light, under conditions fostering intracellular NADH excess. These findings highlight a high level of interconnection between ReSH and cyanobacterial redox metabolism. This study lays a foundation for further engineering, e.g., of electron transfer to ReSH via NADPH or ferredoxin, to finally enable photosynthesis-driven H2 production.
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Affiliation(s)
- Sara Lupacchini
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Jens Appel
- Department of Biology, Botanical Institute, University Kiel, 24118, Kiel, Germany
| | - Ron Stauder
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Paul Bolay
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Stephan Klähn
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Elisabeth Lettau
- Institute for Chemistry, Technische Universität Berlin, 10623, Berlin, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, 10923, Berlin, Germany
| | - Lars Lauterbach
- Institute for Chemistry, Technische Universität Berlin, 10623, Berlin, Germany; Institute of Applied Microbiology, Rheinisch-Westfälische Technische Hochschule Aachen, 52074, Aachen, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Andreas Schmid
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany
| | - Jörg Toepel
- Department of Solar Materials, Helmholtz Centre for Environmental Research -UFZ, 04318, Leipzig, Germany.
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10
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Joseph Srinivasan S, Cleary SE, Ramirez MA, Reeve HA, Paul CE, Vincent KA. E. coli Nickel-Iron Hydrogenase 1 Catalyses Non-native Reduction of Flavins: Demonstration for Alkene Hydrogenation by Old Yellow Enzyme Ene-reductases*. Angew Chem Int Ed Engl 2021; 60:13824-13828. [PMID: 33721401 PMCID: PMC8252551 DOI: 10.1002/anie.202101186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/26/2021] [Indexed: 11/10/2022]
Abstract
A new activity for the [NiFe] uptake hydrogenase 1 of Escherichia coli (Hyd1) is presented. Direct reduction of biological flavin cofactors FMN and FAD is achieved using H2 as a simple, completely atom-economical reductant. The robust nature of Hyd1 is exploited for flavin reduction across a broad range of temperatures (25-70 °C) and extended reaction times. The utility of this system as a simple, easy to implement FMNH2 or FADH2 regenerating system is then demonstrated by supplying reduced flavin to Old Yellow Enzyme "ene-reductases" to support asymmetric alkene reductions with up to 100 % conversion. Hyd1 turnover frequencies up to 20.4 min-1 and total turnover numbers up to 20 200 were recorded during flavin recycling.
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Affiliation(s)
- Shiny Joseph Srinivasan
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Sarah E Cleary
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Miguel A Ramirez
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Holly A Reeve
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
| | - Caroline E Paul
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, The Netherlands
| | - Kylie A Vincent
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QR, United Kingdom
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11
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Furusawa G, Diyana T, Lau NS. Metabolic strategies of dormancy of a marine bacterium Microbulbifer aggregans CCB-MM1: Its alternative electron transfer chain and sulfate-reducing pathway. Genomics 2021; 114:443-455. [PMID: 33689784 DOI: 10.1016/j.ygeno.2021.02.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/26/2021] [Accepted: 02/28/2021] [Indexed: 12/26/2022]
Abstract
Bacterial dormancy plays a crucial role in maintaining the functioning and diversity of microbial communities in natural environments. However, the metabolic regulations of the dormancy of bacteria in natural habitats, especially marine habitats, have remained largely unknown. A marine bacterium, Microbulbifer aggregans CCB-MM1 exhibits rod-to-coccus cell shape change during the dormant state. Therefore, to clarify the metabolic regulation of the dormancy, differential gene expression analysis based on RNA-Seq was performed between rod- (vegetative), intermediate, and coccus-shaped cells (dormancy). The RNA-Seq data revealed that one of two distinct electron transfer chains was upregulated in the dormancy. Dissimilatory sulfite reductase and soluble hydrogenase were also highly upregulated in the dormancy. In addition, induction of the dormancy of MM1 in the absence of MgSO4 was slower than that in the presence of MgSO4. These results indicate that the sulfate-reducing pathway plays an important role in entering the dormancy of MM1.
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Affiliation(s)
- Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.
| | - Tarmizi Diyana
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
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12
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Preissler J, Reeve HA, Zhu T, Nicholson J, Urata K, Lauterbach L, Wong LL, Vincent KA, Lenz O. Dihydrogen‐Driven NADPH Recycling in Imine Reduction and P450‐Catalyzed Oxidations Mediated by an Engineered O
2
‐Tolerant Hydrogenase. ChemCatChem 2020. [DOI: 10.1002/cctc.202000763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Janina Preissler
- Institute of Chemistry, Biophysical Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Holly A. Reeve
- Department of Chemistry University of Oxford Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Tianze Zhu
- Department of Chemistry University of Oxford Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Jake Nicholson
- Department of Chemistry University of Oxford Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Kouji Urata
- Department of Chemistry University of Oxford Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Lars Lauterbach
- Institute of Chemistry, Biophysical Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Luet L. Wong
- Department of Chemistry University of Oxford Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Kylie A. Vincent
- Department of Chemistry University of Oxford Inorganic Chemistry Laboratory South Parks Road Oxford OX1 3QR UK
| | - Oliver Lenz
- Institute of Chemistry, Biophysical Chemistry Technische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
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13
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Al-Shameri A, Willot SJP, Paul CE, Hollmann F, Lauterbach L. H 2 as a fuel for flavin- and H 2O 2-dependent biocatalytic reactions. Chem Commun (Camb) 2020; 56:9667-9670. [PMID: 32696786 DOI: 10.1039/d0cc03229h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The soluble hydrogenase from Ralstonia eutropha provides an atom efficient regeneration system for reduced flavin cofactors using H2 as an electron source. We demonstrated this system for highly selective ene-reductase-catalyzed C[double bond, length as m-dash]C-double bond reductions and monooxygenase-catalyzed epoxidation. Reactions were expanded to aerobic conditions to supply H2O2 for peroxygenase-catalyzed hydroxylations.
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Affiliation(s)
- Ammar Al-Shameri
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17, Juni 135, 10623 Berlin, Germany.
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14
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Abstract
A number of self-sufficient hydride transfer processes have been reported in biocatalysis, with a common feature being the dependence on nicotinamide as a cofactor. This cofactor is provided in catalytic amounts and serves as a hydride shuttle to connect two or more enzymatic redox events, usually ensuring overall redox neutrality. Creative systems were designed to produce synthetic sequences characterized by high hydride economy, typically going in hand with excellent atom economy. Several redox enzymes have been successfully combined in one-pot one-step to allow functionalization of a large variety of molecules while preventing by-product formation. This review analyzes and classifies the various strategies, with a strong focus on efficiency, which is evaluated here in terms of the hydride economy and measured by the turnover number of the nicotinamide cofactor(s). The review ends with a critical evaluation of the reported systems and highlights areas where further improvements might be desirable.
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Affiliation(s)
- Erika Tassano
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria.
| | - Mélanie Hall
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria.
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15
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Ash PA, Kendall-Price SET, Vincent KA. Unifying Activity, Structure, and Spectroscopy of [NiFe] Hydrogenases: Combining Techniques To Clarify Mechanistic Understanding. Acc Chem Res 2019; 52:3120-3131. [PMID: 31675209 DOI: 10.1021/acs.accounts.9b00293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Achieving a unified understanding of the mechanism of a multicenter redox enzyme such as [NiFe] hydrogenase is complicated by difficulties in reconciling information obtained by using different techniques and on samples in different physical forms. Measurements of the activity of the enzyme, and of factors which perturb activity, are generally carried out using biochemical assays in solution or with electrode-immobilized enzymes using protein film electrochemistry (PFE). Conversely, spectroscopy aimed at reporting on features of the metalloclusters in the enzyme, such as electron paramagnetic resonance (EPR) or X-ray absorption spectroscopy (XAS), is often conducted on frozen samples and is thus difficult to relate to catalytically relevant states as information about turnover and activity has been lost. To complicate matters further, most of our knowledge of the atomic-level structure of metalloenzymes comes from X-ray diffraction studies in the solid, crystalline state, which are again difficult to link to turnover conditions. Taking [NiFe] hydrogenases as our case study, we show here how it is possible to apply infrared (IR) spectroscopic sampling approaches to unite direct spectroscopic study with catalytic turnover. Using a method we have named protein film IR electrochemistry (PFIRE), we reveal the steady-state distribution of intermediates during catalysis and identify catalytic "bottlenecks" introduced by site-directed mutagenesis. We also show that it is possible to study dynamic transitions between active site states of enzymes in single crystals, uniting solid state and solution spectroscopic information. In all of these cases, the spectroscopic data complement and enhance interpretation of purely activity-based measurements by providing direct chemical insight that is otherwise hidden. The [NiFe] hydrogenases possess a bimetallic [NiFe] active site, coordinated by CO and CN- ligands, linked to the protein via bridging and terminal cysteine sulfur ligands, as well as an electron relay chain of iron sulfur clusters. Infrared spectroscopy is ideal for probing hydrogenases because the CO and CN- ligands are strong IR absorbers, but the suite of IR-based approaches we describe here will be equally valuable in studying substrate- or intermediate-bound states of other metalloenzymes where key mechanistic questions remain open, such as nitrogenase, formate dehydrogenase, or carbon monoxide dehydrogenase. We therefore hope that this Account will encourage future studies which unify information from different techniques across bioinorganic chemistry.
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Affiliation(s)
- Philip A. Ash
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
- School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | | | - Kylie A. Vincent
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
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16
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Wilkening S, Schmitt FJ, Lenz O, Zebger I, Horch M, Friedrich T. Discriminating changes in intracellular NADH/NAD + levels due to anoxicity and H 2 supply in R. eutropha cells using the Frex fluorescence sensor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148062. [PMID: 31419395 DOI: 10.1016/j.bbabio.2019.148062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/23/2019] [Accepted: 08/10/2019] [Indexed: 12/19/2022]
Abstract
The hydrogen-oxidizing "Knallgas" bacterium Ralstonia eutropha can thrive in aerobic and anaerobic environments and readily switches between heterotrophic and autotrophic metabolism, making it an attractive host for biotechnological applications including the sustainable H2-driven production of hydrocarbons. The soluble hydrogenase (SH), one out of four different [NiFe]-hydrogenases in R. eutropha, mediates H2 oxidation even in the presence of O2, thus providing an ideal model system for biological hydrogen production and utilization. The SH reversibly couples H2 oxidation with the reduction of NAD+ to NADH, thereby enabling the sustainable regeneration of this biotechnologically important nicotinamide cofactor. Thus, understanding the interaction of the SH with the cellular NADH/NAD+ pool is of high interest. Here, we applied the fluorescent biosensor Frex to measure changes in cytoplasmic [NADH] in R. eutropha cells under different gas supply conditions. The results show that Frex is well-suited to distinguish SH-mediated changes in the cytoplasmic redox status from effects of general anaerobiosis of the respiratory chain. Upon H2 supply, the Frex reporter reveals a robust fluorescence response and allows for monitoring rapid changes in cellular [NADH]. Compared to the Peredox fluorescence reporter, Frex displays a diminished NADH affinity, which prevents the saturation of the sensor under typical bacterial [NADH] levels. Thus, Frex is a valuable reporter for on-line monitoring of the [NADH]/[NAD+] redox state in living cells of R. eutropha and other proteobacteria. Based on these results, strategies for a rational optimization of fluorescent NADH sensors are discussed.
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Affiliation(s)
- S Wilkening
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - F-J Schmitt
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - O Lenz
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - I Zebger
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - M Horch
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany; Department of Chemistry and York Biomedical Research Institute, University of York, YO10 5DD, United Kingdom
| | - T Friedrich
- Technische Universität Berlin, Institut für Chemie PC 14, Straße des 17. Juni 135, 10623 Berlin, Germany.
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17
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Lauterbach L, Lenz O. How to make the reducing power of H 2 available for in vivo biosyntheses and biotransformations. Curr Opin Chem Biol 2018; 49:91-96. [PMID: 30544016 DOI: 10.1016/j.cbpa.2018.11.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/15/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022]
Abstract
Solar-driven electrolysis enables sustainable production of molecular hydrogen (H2), which represents a cheap and carbon-free reductant. Knallgas bacteria like Ralstonia eutropha are able to split H2 to supply energy in form of ATP and NADH, which can be subsequently used to power reactions of interest. R. eutropha employs the Calvin-Benson-Bassham cycle for the fixation of CO2, which is considered as an abundant and non-competing raw material. In this article, we summarize state-of-the-art approaches for H2-driven biosyntheses using engineered R. eutropha. Furthermore, we describe strategies for synthetic H2-driven NADH recycling. Major challenges for technical application and future perspectives are discussed.
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Affiliation(s)
- Lars Lauterbach
- Technische Universität Berlin, Department of Chemistry, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Oliver Lenz
- Technische Universität Berlin, Department of Chemistry, Straße des 17. Juni 135, 10623 Berlin, Germany
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18
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Shomura Y, Taketa M, Nakashima H, Tai H, Nakagawa H, Ikeda Y, Ishii M, Igarashi Y, Nishihara H, Yoon KS, Ogo S, Hirota S, Higuchi Y. Structural basis of the redox switches in the NAD +-reducing soluble [NiFe]-hydrogenase. Science 2018; 357:928-932. [PMID: 28860386 DOI: 10.1126/science.aan4497] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/03/2017] [Indexed: 11/03/2022]
Abstract
NAD+ (oxidized form of NAD:nicotinamide adenine dinucleotide)-reducing soluble [NiFe]-hydrogenase (SH) is phylogenetically related to NADH (reduced form of NAD+):quinone oxidoreductase (complex I), but the geometrical arrangements of the subunits and Fe-S clusters are unclear. Here, we describe the crystal structures of SH in the oxidized and reduced states. The cluster arrangement is similar to that of complex I, but the subunits orientation is not, which supports the hypothesis that subunits evolved as prebuilt modules. The oxidized active site includes a six-coordinate Ni, which is unprecedented for hydrogenases, whose coordination geometry would prevent O2 from approaching. In the reduced state showing the normal active site structure without a physiological electron acceptor, the flavin mononucleotide cofactor is dissociated, which may be caused by the oxidation state change of nearby Fe-S clusters and may suppress production of reactive oxygen species.
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Affiliation(s)
- Y Shomura
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan.
| | - M Taketa
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan and Science Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - H Nakashima
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - H Tai
- Core Research for Evolutional Science and Technology (CREST), Japan and Science Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.,Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - H Nakagawa
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Y Ikeda
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - M Ishii
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Y Igarashi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - H Nishihara
- Department of Bioresource Science, College of Agriculture, Ibaraki University, 3-21-1, Chu-ou, Ami, Ibaraki 300-0393, Japan
| | - K-S Yoon
- World Premier International Research Center Initiative-International Institute for Carbon Neutral Energy Research (WPI-ICNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.,SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - S Ogo
- World Premier International Research Center Initiative-International Institute for Carbon Neutral Energy Research (WPI-ICNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.,SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - S Hirota
- Core Research for Evolutional Science and Technology (CREST), Japan and Science Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.,Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Y Higuchi
- Department of Picobiology, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan and Science Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.,SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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19
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Lenz O, Lauterbach L, Frielingsdorf S. O2-tolerant [NiFe]-hydrogenases of Ralstonia eutropha H16: Physiology, molecular biology, purification, and biochemical analysis. Methods Enzymol 2018; 613:117-151. [DOI: 10.1016/bs.mie.2018.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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20
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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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21
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Enzymatic and spectroscopic properties of a thermostable [NiFe]‑hydrogenase performing H 2-driven NAD +-reduction in the presence of O 2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1859:8-18. [PMID: 28970007 DOI: 10.1016/j.bbabio.2017.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/17/2017] [Accepted: 09/28/2017] [Indexed: 12/18/2022]
Abstract
Biocatalysts that mediate the H2-dependent reduction of NAD+ to NADH are attractive from both a fundamental and applied perspective. Here we present the first biochemical and spectroscopic characterization of an NAD+-reducing [NiFe]‑hydrogenase that sustains catalytic activity at high temperatures and in the presence of O2, which usually acts as an inhibitor. We isolated and sequenced the four structural genes, hoxFUYH, encoding the soluble NAD+-reducing [NiFe]‑hydrogenase (SH) from the thermophilic betaproteobacterium, Hydrogenophilus thermoluteolus TH-1T (Ht). The HtSH was recombinantly overproduced in a hydrogenase-free mutant of the well-studied, H2-oxidizing betaproteobacterium Ralstonia eutropha H16 (Re). The enzyme was purified and characterized with various biochemical and spectroscopic techniques. Highest H2-mediated NAD+ reduction activity was observed at 80°C and pH6.5, and catalytic activity was found to be sustained at low O2 concentrations. Infrared spectroscopic analyses revealed a spectral pattern for as-isolated HtSH that is remarkably different from those of the closely related ReSH and other [NiFe]‑hydrogenases. This indicates an unusual configuration of the oxidized catalytic center in HtSH. Complementary electron paramagnetic resonance spectroscopic analyses revealed spectral signatures similar to related NAD+-reducing [NiFe]‑hydrogenases. This study lays the groundwork for structural and functional analyses of the HtSH as well as application of this enzyme for H2-driven cofactor recycling under oxic conditions at elevated temperatures.
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22
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Tejwani V, Schmitt FJ, Wilkening S, Zebger I, Horch M, Lenz O, Friedrich T. Investigation of the NADH/NAD + ratio in Ralstonia eutropha using the fluorescence reporter protein Peredox. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:86-94. [PMID: 27816420 DOI: 10.1016/j.bbabio.2016.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/11/2016] [Accepted: 11/02/2016] [Indexed: 10/20/2022]
Abstract
Ralstonia eutropha is a hydrogen-oxidizing ("Knallgas") bacterium that can easily switch between heterotrophic and autotrophic metabolism to thrive in aerobic and anaerobic environments. Its versatile metabolism makes R. eutropha an attractive host for biotechnological applications, including H2-driven production of biodegradable polymers and hydrocarbons. H2 oxidation by R. eutropha takes place in the presence of O2 and is mediated by four hydrogenases, which represent ideal model systems for both biohydrogen production and H2 utilization. The so-called soluble hydrogenase (SH) couples reversibly H2 oxidation with the reduction of NAD+ to NADH and has already been applied successfully in vitro and in vivo for cofactor regeneration. Thus, the interaction of the SH with the cellular NADH/NAD+ pool is of major interest. In this work, we applied the fluorescent biosensor Peredox to measure the [NADH]:[NAD+] ratio in R. eutropha cells under different metabolic conditions. The results suggest that the sensor operates close to saturation level, indicating a rather high [NADH]:[NAD+] ratio in aerobically grown R. eutropha cells. Furthermore, we demonstrate that multicomponent analysis of spectrally-resolved fluorescence lifetime data of the Peredox sensor response to different [NADH]:[NAD+] ratios represents a novel and sensitive tool to determine the redox state of cells.
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Affiliation(s)
- Vijay Tejwani
- SUNY Polytechnic Institute, College of Nanoscale Science and Engineering, 257 Fuller Road, Albany, NY, 12203, U.S.A
| | - Franz-Josef Schmitt
- Technische Universität Berlin, Institut für Chemie, PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Svea Wilkening
- Technische Universität Berlin, Institut für Chemie, PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Ingo Zebger
- Technische Universität Berlin, Institut für Chemie, PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Marius Horch
- Technische Universität Berlin, Institut für Chemie, PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Oliver Lenz
- Technische Universität Berlin, Institut für Chemie, PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Thomas Friedrich
- Technische Universität Berlin, Institut für Chemie, PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany.
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23
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Production and purification of a soluble hydrogenase from Ralstonia eutropha H16 for potential hydrogen fuel cell applications. MethodsX 2016; 3:242-50. [PMID: 27077052 PMCID: PMC4816682 DOI: 10.1016/j.mex.2016.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/07/2016] [Indexed: 11/22/2022] Open
Abstract
The soluble hydrogenase (SH) from Ralstonia eutropha H16 is a promising candidate enzyme for H2-based biofuel application as it favours H2 oxidation and is relatively oxygen-tolerant. In this report, bioprocess development studies undertaken to produce and purify an active SH are described, based on the methods previously reported [1], [2], [3], [4]. Our modifications are: Upstream method optimizations were undertaken on heterotrophic growth media and cell lysis involving ultrasonication. Two anion exchangers (Q Sepharose and RESOURCE Q) and size exclusion chromatographic (Superdex 200) matrices were successfully employed for purification of a hexameric SH from R. eutropha. The H2 oxidizing activity of the SH was demonstrated spectrophotometrically in solution and also immobilized on an EPG electrode using cyclic voltammetry.
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24
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Arunasri K, Annie Modestra J, Yeruva DK, Vamshi Krishna K, Venkata Mohan S. Polarized potential and electrode materials implication on electro-fermentative di-hydrogen production: Microbial assemblages and hydrogenase gene copy variation. BIORESOURCE TECHNOLOGY 2016; 200:691-698. [PMID: 26556403 DOI: 10.1016/j.biortech.2015.10.091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 06/05/2023]
Abstract
This study examined the changes in microbial diversity in response to different electrode materials viz., stainless steel mesh (SS) and graphite plate as anodes in two microbial electrolysis cell (MEC) each poised at 0.2V, 0.4V, 0.6V and 0.8V. Changes in microbiota prior to and after pretreatment along with microbiota enriched in response to various poised potentials with SS and graphite are monitored by 16S rRNA gene based DGGE profiling. Significant shifts in microbial community were noticed at all these experimental conditions. Correspondingly, the level of hydrogenase belonging to genera Bacillus, Pseudomonas, Rhodopseudomonas and Clostridium was studied by quantitative real time PCR (RT-PCR) at various applied potentials. DGGE based 16S rRNA gene profiling revealed enriched members belonging to phylum Firmicutes predominantly present at 0.8V in both MECs contributing to high hydrogen production. This study first time explored the growth behavior of mixed consortia in response to poised potentials and electrode materials.
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Affiliation(s)
- Kotakonda Arunasri
- Bioengineering and Environmental Sciences, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - J Annie Modestra
- Bioengineering and Environmental Sciences, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Dileep Kumar Yeruva
- Bioengineering and Environmental Sciences, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - K Vamshi Krishna
- Bioengineering and Environmental Sciences, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - S Venkata Mohan
- Bioengineering and Environmental Sciences, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India.
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25
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Kwan P, McIntosh CL, Jennings DP, Hopkins RC, Chandrayan SK, Wu CH, Adams MWW, Jones AK. The [NiFe]-Hydrogenase of Pyrococcus furiosus Exhibits a New Type of Oxygen Tolerance. J Am Chem Soc 2015; 137:13556-65. [PMID: 26436715 DOI: 10.1021/jacs.5b07680] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report the first direct electrochemical characterization of the impact of oxygen on the hydrogen oxidation activity of an oxygen-tolerant, group 3, soluble [NiFe]-hydrogenase: hydrogenase I from Pyrococcus furiosus (PfSHI), which grows optimally near 100 °C. Chronoamperometric experiments were used to probe the sensitivity of PfSHI hydrogen oxidation activity to both brief and prolonged exposure to oxygen. For experiments between 15 and 80 °C, following short (<200 s) exposure to 14 μM O2 under oxidizing conditions, PfSHI always maintains some fraction of its initial hydrogen oxidation activity; i.e., it is oxygen-tolerant. Reactivation experiments show that two inactive states are formed by interaction with oxygen and both can be quickly (<150 s) reactivated. Analogous experiments, in which the interval of oxygen exposure is extended to 900 s, reveal that the response is highly temperature-dependent. At 25 °C, under sustained 1% O2/ 99% H2 exposure, the H2oxidation activity drops nearly to zero. However, at 80 °C, up to 32% of the enzyme's oxidation activity is retained. Reactivation of PfSHI following sustained exposure to oxygen occurs on a much longer time scale (tens of minutes), suggesting that a third inactive species predominates under these conditions. These results stand in contrast to the properties of oxygen-tolerant, group 1 [NiFe]-hydrogenases, which form a single state upon reaction with oxygen, and we propose that this new type of hydrogenase should be referred to as oxygen-resilient. Furthermore, PfSHI, like other group 3 [NiFe]-hydrogenases, does not possess the proximal [4Fe3S] cluster associated with the oxygen tolerance of some group 1 enzymes. Thus, a new mechanism is necessary to explain the observed oxygen tolerance in soluble, group 3 [NiFe]-hydrogenases, and we present a model integrating both electrochemical and spectroscopic results to define the relationships of these inactive states.
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Affiliation(s)
- Patrick Kwan
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Chelsea L McIntosh
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - David P Jennings
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - R Chris Hopkins
- Department of Biochemistry and Molecular Biology, The University of Georgia , Athens, Georgia 30602, United States
| | - Sanjeev K Chandrayan
- Department of Biochemistry and Molecular Biology, The University of Georgia , Athens, Georgia 30602, United States
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology, The University of Georgia , Athens, Georgia 30602, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, The University of Georgia , Athens, Georgia 30602, United States
| | - Anne K Jones
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
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26
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Löwenstein J, Lauterbach L, Teutloff C, Lenz O, Bittl R. Active Site of the NAD(+)-Reducing Hydrogenase from Ralstonia eutropha Studied by EPR Spectroscopy. J Phys Chem B 2015. [PMID: 26214595 DOI: 10.1021/acs.jpcb.5b04144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pulsed ENDOR and HYSCORE measurements were carried out to characterize the active site of the oxygen-tolerant NAD(+)-reducing hydrogenase of Ralstonia eutropha. The catalytically active Nia-C state exhibits a bridging hydride between iron and nickel in the active site, which is photodissociated upon illumination. Its hyperfine coupling is comparable to that of standard hydrogenases. In addition, a histidine residue could be identified, which shows hyperfine and nuclear quadrupole parameters in significant variance from comparable histidine residues that are conserved in standard [NiFe] hydrogenases, and might be related to the O2 tolerance of the enzyme.
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Affiliation(s)
- Julia Löwenstein
- Fachbereich Physik, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - Lars Lauterbach
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin , Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Teutloff
- Fachbereich Physik, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin , Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Robert Bittl
- Fachbereich Physik, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
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Ash PA, Liu J, Coutard N, Heidary N, Horch M, Gudim I, Simler T, Zebger I, Lenz O, Vincent KA. Electrochemical and Infrared Spectroscopic Studies Provide Insight into Reactions of the NiFe Regulatory Hydrogenase from Ralstonia eutropha with O2 and CO. J Phys Chem B 2015; 119:13807-15. [PMID: 26115011 DOI: 10.1021/acs.jpcb.5b04164] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The regulatory hydrogenase (RH) from Ralstonia eutropha acts as the H2-sensing unit of a two-component system that regulates biosynthesis of the energy conserving hydrogenases of the organism according to the availability of H2. The H2 oxidation activity, which was so far determined in vitro with artificial electron acceptors, has been considered to be insensitive to O2 and CO. It is assumed that bulky isoleucine and phenylalanine amino acid residues close to the NiFe active site "gate" gas access, preventing molecules larger than H2 interacting with the active site. We have carried out sensitive electrochemical measurements to demonstrate that O2 is in fact an inhibitor of H2 oxidation by the RH, and that both H(+) reduction and H2 oxidation are inhibited by CO. Furthermore, we have demonstrated that the inhibitory effect of O2 arises due to interaction of O2 with the active site. Using protein film infrared electrochemistry (PFIRE) under H2 oxidation conditions, in conjunction with solution infrared measurements, we have identified previously unreported oxidized inactive and catalytically active reduced states of the RH active site. These findings suggest that the RH has a rich active site chemistry similar to that of other NiFe hydrogenases.
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Affiliation(s)
- Philip A Ash
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Juan Liu
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Nathan Coutard
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Nina Heidary
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Marius Horch
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Ingvild Gudim
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Thomas Simler
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Technische Universität Berlin , PC14, Berlin, Germany
| | - Kylie A Vincent
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford , South Parks Road, Oxford, OX1 3QR, U.K
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28
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Schiffels J, Selmer T. A flexible toolbox to study protein-assisted metalloenzyme assembly in vitro. Biotechnol Bioeng 2015; 112:2360-72. [PMID: 25994231 DOI: 10.1002/bit.25658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/11/2015] [Indexed: 11/06/2022]
Abstract
A number of metalloenzymes harbor unique cofactors, which are incorporated into the apo-enzymes via protein-assisted maturation. In the case of [NiFe]-hydrogenases, minimally seven maturation factors (HypABCDEF and a specific endopeptidase) are involved, making these enzymes an excellent example for studying metallocenter assembly in general. Here, we describe an innovative toolbox to study maturation involving multiple putative gene products. The two core elements of the system are a modular, combinatorial cloning system and a cell-free maturation system, which is based on recombinant Escherichia coli extracts and/or purified maturases. Taking maturation of the soluble, oxygen-tolerant [NiFe]-hydrogenase (SH) from Cupriavidus necator as an example, the capacities of the toolbox are illustrated. In total 18 genes from C. necator were analyzed, including four SH-structural genes, the SH-dedicated hyp-genes and a second set of hyp-genes putatively involved in maturation of the Actinobacterium-like hydrogenase (AH). The two hyp-sets were either expressed in their entirety from single vectors or split into functional modules, which enabled flexible approaches to investigate limitations, specificities and the capabilities of individual constituents to functionally substitute each other. Affinity-tagged Hyp-Proteins were used in pull-down experiments to demonstrate direct interactions between dedicated or non-related constituents. The dedicated Hyp-set from C. necator exhibited the highest maturation efficiency in vitro. Constituents of non-related maturation machineries were found to interact with and to accomplish partial activation of SH. In contrast to homologues of the Hyp-family, omission of the SH-specific endopeptidase HoxW completely abolished in vitro maturation. We detected stoichiometric imbalances inside the recombinant production system, which point to limitations by the cyanylation complex HypEF and the premature subunit HoxH. Purification of HoxW revealed strong indications for the presence of a putative [4Fe-4S]-cluster, which is unique among this class of maturases. Results are discussed in the context of [NiFe]-hydrogenase maturation, and in light of the capacity of the novel toolbox.
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Affiliation(s)
- Johannes Schiffels
- From the Aachen University of Applied Sciences, Campus Juelich, Department of Chemistry and Biotechnology, Heinrich-Mussmann-Str. 1, D-52428 Juelich, Germany
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29
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Holzer AK, Hiebler K, Mutti FG, Simon RC, Lauterbach L, Lenz O, Kroutil W. Asymmetric Biocatalytic Amination of Ketones at the Expense of NH3 and Molecular Hydrogen. Org Lett 2015; 17:2431-3. [DOI: 10.1021/acs.orglett.5b01154] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anja K. Holzer
- Department
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Katharina Hiebler
- Department
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Francesco G. Mutti
- Department
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Robert C. Simon
- Department
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Lars Lauterbach
- Department
of Chemistry, Technische Universität Berlin, Straße des
17. Juni 135, 10623 Berlin, Germany
| | - Oliver Lenz
- Department
of Chemistry, Technische Universität Berlin, Straße des
17. Juni 135, 10623 Berlin, Germany
| | - Wolfgang Kroutil
- Department
of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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30
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Jugder BE, Chen Z, Ping DTT, Lebhar H, Welch J, Marquis CP. An analysis of the changes in soluble hydrogenase and global gene expression in Cupriavidus necator (Ralstonia eutropha) H16 grown in heterotrophic diauxic batch culture. Microb Cell Fact 2015; 14:42. [PMID: 25880663 PMCID: PMC4377017 DOI: 10.1186/s12934-015-0226-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/12/2015] [Indexed: 12/20/2022] Open
Abstract
Background Soluble hydrogenases (SH) are enzymes that catalyse the oxidation of molecular hydrogen. The SH enzyme from Cupriavidus necator H16 is relatively oxygen tolerant and makes an attractive target for potential application in biochemical hydrogen fuel cells. Expression of the enzyme can be mediated by derepression of the hox promoter system under heterotrophic conditions. However, the overall impact of hox derepression, from a transcriptomic perspective, has never been previously reported. Results Derepression of hydrogenase gene expression upon fructose depletion was confirmed in replicate experiments. Using qRT-PCR, hoxF was 4.6-fold up-regulated, hypF2 was up-regulated in the cells grown 2.2-fold and the regulatory gene hoxA was up-regulated by a mean factor of 4.5. A full transcriptomic evaluation revealed a substantial shift in the global pattern of gene expression. In addition to up-regulation of genes associated with hydrogenase expression, significant changes were observed in genes associated with energy transduction, amino acid metabolism, transcription and translation (and regulation thereof), genes associated with cell stress, lipid and cell wall biogenesis and other functions, including cell motility. Conclusions We report the first full transcriptome analysis of C. necator H16 grown heterotrophically on fructose and glycerol in diauxic batch culture, which permits expression of soluble hydrogenase under heterotrophic conditions. The data presented deepens our understanding of the changes in global gene expression patterns that occur during the switch to growth on glycerol and suggests that energy deficit is a key driver for induction of hydrogenase expression in this organism. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0226-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bat-Erdene Jugder
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Zhiliang Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. .,Systems Biology Initiative, University of New South Wales, Sydney, 2052, Australia.
| | - Darren Tan Tek Ping
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Helene Lebhar
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Jeffrey Welch
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
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Horch M, Lauterbach L, Mroginski MA, Hildebrandt P, Lenz O, Zebger I. Reversible active site sulfoxygenation can explain the oxygen tolerance of a NAD+-reducing [NiFe] hydrogenase and its unusual infrared spectroscopic properties. J Am Chem Soc 2015; 137:2555-64. [PMID: 25647259 DOI: 10.1021/ja511154y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Oxygen-tolerant [NiFe] hydrogenases are metalloenzymes that represent valuable model systems for sustainable H2 oxidation and production. The soluble NAD(+)-reducing [NiFe] hydrogenase (SH) from Ralstonia eutropha couples the reversible cleavage of H2 with the reduction of NAD(+) and displays a unique O2 tolerance. Here we performed IR spectroscopic investigations on purified SH in various redox states in combination with density functional theory to provide structural insights into the catalytic [NiFe] center. These studies revealed a standard-like coordination of the active site with diatomic CO and cyanide ligands. The long-lasting discrepancy between spectroscopic data obtained in vitro and in vivo could be solved on the basis of reversible cysteine oxygenation in the fully oxidized state of the [NiFe] site. The data are consistent with a model in which the SH detoxifies O2 catalytically by means of an NADH-dependent (per)oxidase reaction involving the intermediary formation of stable cysteine sulfenates. The occurrence of two catalytic activities, hydrogen conversion and oxygen reduction, at the same cofactor may inspire the design of novel biomimetic catalysts performing H2-conversion even in the presence of O2.
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Affiliation(s)
- Marius Horch
- Institut für Chemie, Technische Universität Berlin , Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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Karstens K, Wahlefeld S, Horch M, Grunzel M, Lauterbach L, Lendzian F, Zebger I, Lenz O. Impact of the iron-sulfur cluster proximal to the active site on the catalytic function of an O2-tolerant NAD(+)-reducing [NiFe]-hydrogenase. Biochemistry 2015; 54:389-403. [PMID: 25517969 DOI: 10.1021/bi501347u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The soluble NAD(+)-reducing hydrogenase (SH) from Ralstonia eutropha H16 belongs to the O2-tolerant subtype of pyridine nucleotide-dependent [NiFe]-hydrogenases. To identify molecular determinants for the O2 tolerance of this enzyme, we introduced single amino acids exchanges in the SH small hydrogenase subunit. The resulting mutant strains and proteins were investigated with respect to their physiological, biochemical, and spectroscopic properties. Replacement of the four invariant conserved cysteine residues, Cys41, Cys44, Cys113, and Cys179, led to unstable protein, strongly supporting their involvement in the coordination of the iron-sulfur cluster proximal to the catalytic [NiFe] center. The Cys41Ser exchange, however, resulted in an SH variant that displayed up to 10% of wild-type activity, suggesting that the coordinating role of Cys41 might be partly substituted by the nearby Cys39 residue, which is present only in O2-tolerant pyridine nucleotide-dependent [NiFe]-hydrogenases. Indeed, SH variants carrying glycine, alanine, or serine in place of Cys39 showed increased O2 sensitivity compared to that of the wild-type enzyme. Substitution of further amino acids typical for O2-tolerant SH representatives did not greatly affect the H2-oxidizing activity in the presence of O2. Remarkably, all mutant enzymes investigated by electron paramagnetic resonance spectroscopy did not reveal significant spectral changes in relation to wild-type SH, showing that the proximal iron-sulfur cluster does not contribute to the wild-type spectrum. Interestingly, exchange of Trp42 by serine resulted in a completely redox-inactive [NiFe] site, as revealed by infrared spectroscopy and H2/D(+) exchange experiments. The possible role of this residue in electron and/or proton transfer is discussed.
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Affiliation(s)
- Katja Karstens
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin , Chausseestr. 117, 10115 Berlin, Germany
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Taketa M, Nakagawa H, Habukawa M, Osuka H, Kihira K, Komori H, Shibata N, Ishii M, Igarashi Y, Nishihara H, Yoon KS, Ogo S, Shomura Y, Higuchi Y. Crystallization and preliminary X-ray analysis of the NAD+-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus TH-1. Acta Crystallogr F Struct Biol Commun 2015; 71:96-9. [PMID: 25615977 PMCID: PMC4304756 DOI: 10.1107/s2053230x14026521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/02/2014] [Indexed: 11/10/2022] Open
Abstract
NAD+-reducing [NiFe] hydrogenases catalyze the oxidoreduction of dihydrogen concomitant with the interconversion of NAD+ and NADH. Here, the isolation, purification and crystallization of the NAD+-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus TH-1 are reported. Crystals of the NAD+-reducing [NiFe] hydrogenase were obtained within one week from a solution containing polyethylene glycol using the sitting-drop vapour-diffusion method and micro-seeding. The crystal diffracted to 2.58 Å resolution and belonged to space group C2, with unit-cell parameters a=131.43, b=189.71, c=124.59 Å, β=109.42°. Assuming the presence of two NAD+-reducing [NiFe] hydrogenase molecules in the asymmetric unit, VM was calculated to be 2.2 Å3 Da(-1), which corresponds to a solvent content of 43%. Initial phases were determined by the single-wavelength anomalous dispersion method using the anomalous signal from the Fe atoms.
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Affiliation(s)
- Midori Taketa
- Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan and Science Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hanae Nakagawa
- Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Mao Habukawa
- Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hisao Osuka
- Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Kiyohito Kihira
- Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Hirofumi Komori
- Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Naoki Shibata
- Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Masaharu Ishii
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Igarashi
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hirofumi Nishihara
- Department of Bioresource Science, Ibaraki University, 3-21-1 Chu-ou, Ami, Ibaraki 300-0393, Japan
| | - Ki-Seok Yoon
- International Institute for Carbon Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Seiji Ogo
- International Institute for Carbon Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
- Department of Chemistry and Biochemistry, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yasuhito Shomura
- Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Higuchi
- Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan and Science Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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Horch M, Hildebrandt P, Zebger I. Concepts in bio-molecular spectroscopy: vibrational case studies on metalloenzymes. Phys Chem Chem Phys 2015; 17:18222-37. [DOI: 10.1039/c5cp02447a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Challenges and chances in bio-molecular spectroscopy are exemplified by vibrational case studies on metalloenzymes.
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Affiliation(s)
- M. Horch
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
| | - P. Hildebrandt
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
| | - I. Zebger
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin
- Germany
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35
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Herzberg M, Schüttau M, Reimers M, Große C, Hans-Günther-Schlegel HGS, Nies DH. Synthesis of nickel–iron hydrogenase in Cupriavidus metallidurans is controlled by metal-dependent silencing and un-silencing of genomic islands. Metallomics 2015; 7:632-49. [DOI: 10.1039/c4mt00297k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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The growth and survival of Mycobacterium smegmatis is enhanced by co-metabolism of atmospheric H2. PLoS One 2014; 9:e103034. [PMID: 25058581 PMCID: PMC4109961 DOI: 10.1371/journal.pone.0103034] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 06/27/2014] [Indexed: 02/04/2023] Open
Abstract
The soil bacterium Mycobacterium smegmatis is able to scavenge the trace concentrations of H2 present in the atmosphere, but the physiological function and importance of this activity is not understood. We have shown that atmospheric H2 oxidation in this organism depends on two phylogenetically and kinetically distinct high-affinity hydrogenases, Hyd1 (MSMEG_2262-2263) and Hyd2 (MSMEG_2720-2719). In this study, we explored the effect of deleting Hyd2 on cellular physiology by comparing the viability, energetics, transcriptomes, and metabolomes of wild-type vs. Δhyd2 cells. The long-term survival of the Δhyd2 mutant was significantly reduced compared to the wild-type. The mutant additionally grew less efficiently in a range of conditions, most notably during metabolism of short-chain fatty acids; there was a twofold reduction in growth rate and growth yield of the Δhyd2 strain when acetate served as the sole carbon source. Hyd1 compensated for loss of Hyd2 when cells were grown in a high H2 atmosphere. Analysis of cellular parameters showed that Hyd2 was not necessary to generate the membrane potential, maintain intracellular pH homeostasis, or sustain redox balance. However, microarray analysis indicated that Δhyd2 cells were starved for reductant and compensated by rewiring central metabolism; transcripts encoding proteins responsible for oxidative decarboxylation pathways, the urea cycle, and ABC transporter-mediated import were significantly more abundant in the Δhyd2 mutant. Metabolome profiling consistently revealed an increase in intracellular amino acids in the Δhyd2 mutant. We propose that atmospheric H2 oxidation has two major roles in mycobacterial cells: to generate reductant during mixotrophic growth and to sustain the respiratory chain during dormancy.
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Herr N, Ratzka J, Lauterbach L, Lenz O, Ansorge-Schumacher MB. Stability enhancement of an O2-tolerant NAD+-reducing [NiFe]-hydrogenase by a combination of immobilisation and chemical modification. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Lauterbach L, Lenz O. Catalytic production of hydrogen peroxide and water by oxygen-tolerant [NiFe]-hydrogenase during H2 cycling in the presence of O2. J Am Chem Soc 2013; 135:17897-905. [PMID: 24180286 DOI: 10.1021/ja408420d] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydrogenases control the H2-related metabolism in many microbes. Most of these enzymes are prone to immediate inactivation by O2. However, a few members of the subclass of [NiFe]-hydrogenases are able to convert H2 into protons and electrons even in the presence of O2, making them attractive for biotechnological application. Recent studies on O2-tolerant membrane-bound hydrogenases indicate that the mechanism of O2 tolerance relies on their capability to completely reduce O2 with four electrons to harmless water. In order to verify this hypothesis, we probed the O2 reduction capacity of the soluble, NAD(+)-reducing [NiFe]-hydrogenase (SH) from Ralstonia eutropha H16. A newly established, homologous overexpression allowed the purification of up to 90 mg of homogeneous and highly active enzyme from 10 g of cell material. We showed that the SH produces trace amounts of superoxide in the course of H2-driven NAD(+) reduction in the presence of O2. However, the major products of the SH-mediated oxidase activity was in fact hydrogen peroxide and water as shown by the mass spectrometric detection of H2(18)O formed from H2 and isotopically labeled (18)O2. Water release was also observed when the enzyme was incubated with NADH and (18)O2, demonstrating the importance of reverse electron flow to the [NiFe] active site for O2 reduction. A comparison of the turnover rates for H2 and O2 revealed that in the presence of twice the ambient level of O2, up to 3% of the electrons generated through H2 oxidation serve as "health insurance" and are reused for O2 reduction.
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Affiliation(s)
- Lars Lauterbach
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin , Chausseestrasse 117, 10115 Berlin, Germany
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39
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Schiffels J, Pinkenburg O, Schelden M, Aboulnaga EHAA, Baumann MEM, Selmer T. An innovative cloning platform enables large-scale production and maturation of an oxygen-tolerant [NiFe]-hydrogenase from Cupriavidus necator in Escherichia coli. PLoS One 2013; 8:e68812. [PMID: 23861944 PMCID: PMC3702609 DOI: 10.1371/journal.pone.0068812] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 05/31/2013] [Indexed: 11/18/2022] Open
Abstract
Expression of multiple heterologous genes in a dedicated host is a prerequisite for approaches in synthetic biology, spanning from the production of recombinant multiprotein complexes to the transfer of tailor-made metabolic pathways. Such attempts are often exacerbated, due in most cases to a lack of proper directional, robust and readily accessible genetic tools. Here, we introduce an innovative system for cloning and expression of multiple genes in Escherichia coli BL21 (DE3). Using the novel methodology, genes are equipped with individual promoters and terminators and subsequently assembled. The resulting multiple gene cassettes may either be placed in one vector or alternatively distributed among a set of compatible plasmids. We demonstrate the effectiveness of the developed tool by production and maturation of the NAD(+)reducing soluble [NiFe]-hydrogenase (SH) from Cupriavidus necator H16 (formerly Ralstonia eutropha H16) in E. coli BL21Star™ (DE3). The SH (encoded in hoxFUYHI) was successfully matured by co-expression of a dedicated set of auxiliary genes, comprising seven hyp genes (hypC1D1E1A2B2F2X) along with hoxW, which encodes a specific endopeptidase. Deletion of genes involved in SH maturation reduced maturation efficiency substantially. Further addition of hoxN1, encoding a high-affinity nickel permease from C. necator, considerably increased maturation efficiency in E. coli. Carefully balanced growth conditions enabled hydrogenase production at high cell-densities, scoring mg·(Liter culture)(-1) yields of purified functional SH. Specific activities of up to 7.2±1.15 U·mg(-1) were obtained in cell-free extracts, which is in the range of the highest activities ever determined in C. necator extracts. The recombinant enzyme was isolated in equal purity and stability as previously achieved with the native form, yielding ultrapure preparations with anaerobic specific activities of up to 230 U·mg(-1). Owing to the combinatorial power exhibited by the presented cloning platform, the system might represent an important step towards new routes in synthetic biology.
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Affiliation(s)
- Johannes Schiffels
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Juelich, Germany
| | - Olaf Pinkenburg
- Institute for Immunology, Biomedical Research Centre (BMFZ), Philipps University of Marburg, Marburg (Lahn), Germany
| | - Maximilian Schelden
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Juelich, Germany
| | | | - Marcus E. M. Baumann
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Juelich, Germany
| | - Thorsten Selmer
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Juelich, Germany
- * E-mail:
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Novel, oxygen-insensitive group 5 [NiFe]-hydrogenase in Ralstonia eutropha. Appl Environ Microbiol 2013; 79:5137-45. [PMID: 23793632 DOI: 10.1128/aem.01576-13] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, a novel group of [NiFe]-hydrogenases has been defined that appear to have a great impact in the global hydrogen cycle. This so-called group 5 [NiFe]-hydrogenase is widespread in soil-living actinobacteria and can oxidize molecular hydrogen at atmospheric levels, which suggests a high affinity of the enzyme toward H2. Here, we provide a biochemical characterization of a group 5 hydrogenase from the betaproteobacterium Ralstonia eutropha H16. The hydrogenase was designated an actinobacterial hydrogenase (AH) and is catalytically active, as shown by the in vivo H2 uptake and by activity staining in native gels. However, the enzyme does not sustain autotrophic growth on H2. The AH was purified to homogeneity by affinity chromatography and consists of two subunits with molecular masses of 65 and 37 kDa. Among the electron acceptors tested, nitroblue tetrazolium chloride was reduced by the AH at highest rates. At 30°C and pH 8, the specific activity of the enzyme was 0.3 μmol of H2 per min and mg of protein. However, an unexpectedly high Michaelis constant (Km) for H2 of 3.6 ± 0.5 μM was determined, which is in contrast to the previously proposed low Km of group 5 hydrogenases and makes atmospheric H2 uptake by R. eutropha most unlikely. Amperometric activity measurements revealed that the AH maintains full H2 oxidation activity even at atmospheric oxygen concentrations, showing that the enzyme is insensitive toward O2.
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Lauterbach L, Lenz O, Vincent KA. H₂-driven cofactor regeneration with NAD(P)⁺-reducing hydrogenases. FEBS J 2013; 280:3058-68. [PMID: 23497170 DOI: 10.1111/febs.12245] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/05/2013] [Accepted: 03/08/2013] [Indexed: 12/15/2022]
Abstract
A large number of industrially relevant enzymes depend upon nicotinamide cofactors, which are too expensive to be added in stoichiometric amounts. Existing NAD(P)H-recycling systems suffer from low activity, or the generation of side products. H₂-driven cofactor regeneration has the advantage of 100% atom efficiency and the use of H₂ as a cheap reducing agent, in a world where sustainable energy carriers are increasingly attractive. The state of development of H₂-driven cofactor-recycling systems and examples of their integration with enzyme reactions are summarized in this article. The O₂-tolerant NAD⁺-reducing hydrogenase from Ralstonia eutropha is a particularly attractive candidate for this approach, and we therefore discuss its catalytic properties that are relevant for technical applications.
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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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Horch M, Rippers Y, Mroginski MA, Hildebrandt P, Zebger I. Combining Spectroscopy and Theory to Evaluate Structural Models of Metalloenzymes: A Case Study on the Soluble [NiFe] Hydrogenase fromRalstonia eutropha. Chemphyschem 2012; 14:185-91. [DOI: 10.1002/cphc.201200853] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Indexed: 11/09/2022]
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Ratzka J, Lauterbach L, Lenz O, Ansorge-Schumacher MB. Stabilisation of the NAD+-reducing soluble [NiFe]-hydrogenase from Ralstonia eutropha H16 through modification with methoxy-poly(ethylene) glycol. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2011.10.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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46
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Horch M, Lauterbach L, Lenz O, Hildebrandt P, Zebger I. NAD(H)-coupled hydrogen cycling - structure-function relationships of bidirectional [NiFe] hydrogenases. FEBS Lett 2011; 586:545-56. [PMID: 22056977 DOI: 10.1016/j.febslet.2011.10.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/05/2011] [Accepted: 10/06/2011] [Indexed: 10/15/2022]
Abstract
Hydrogenases catalyze the activation or production of molecular hydrogen. Due to their potential importance for future biotechnological applications, these enzymes have been in the focus of intense research for the past decades. Bidirectional [NiFe] hydrogenases are of particular interest as they couple the reversible cleavage of hydrogen to the redox conversion of NAD(H). In this account, we review the current state of knowledge about mechanistic aspects and structural determinants of these complex multi-cofactor enzymes. Special emphasis is laid on the oxygen-tolerant NAD(H)-linked bidirectional [NiFe] hydrogenase from Ralstonia eutropha.
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Affiliation(s)
- M Horch
- Technische Universität Berlin, Institut für Chemie, Sekr. PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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Lauterbach L, Idris Z, Vincent KA, Lenz O. Catalytic properties of the isolated diaphorase fragment of the NAD-reducing [NiFe]-hydrogenase from Ralstonia eutropha. PLoS One 2011; 6:e25939. [PMID: 22016788 PMCID: PMC3189943 DOI: 10.1371/journal.pone.0025939] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 09/14/2011] [Indexed: 11/19/2022] Open
Abstract
The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha H16 catalyzes the H2-driven reduction of NAD+, as well as reverse electron transfer from NADH to H+, in the presence of O2. It comprises six subunits, HoxHYFUI2, and incorporates a [NiFe] H+/H2 cycling catalytic centre, two non-covalently bound flavin mononucleotide (FMN) groups and an iron-sulfur cluster relay for electron transfer. This study provides the first characterization of the diaphorase sub-complex made up of HoxF and HoxU. Sequence comparisons with the closely related peripheral subunits of Complex I in combination with UV/Vis spectroscopy and the quantification of the metal and FMN content revealed that HoxFU accommodates a [2Fe2S] cluster, FMN and a series of [4Fe4S] clusters. Protein film electrochemistry (PFE) experiments show clear electrocatalytic activity for both NAD+ reduction and NADH oxidation with minimal overpotential relative to the potential of the NAD+/NADH couple. Michaelis-Menten constants of 56 µM and 197 µM were determined for NADH and NAD+, respectively. Catalysis in both directions is product inhibited with KI values of around 0.2 mM. In PFE experiments, the electrocatalytic current was unaffected by O2, however in aerobic solution assays, a moderate superoxide production rate of 54 nmol per mg of protein was observed, meaning that the formation of reactive oxygen species (ROS) observed for the native SH can be attributed mainly to HoxFU. The results are discussed in terms of their implications for aerobic functioning of the SH and possible control mechanism for the direction of catalysis.
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Affiliation(s)
- Lars Lauterbach
- Institute of Biology, Department of Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Zulkifli Idris
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Kylie A. Vincent
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
- * E-mail: (KAV); (OL)
| | - Oliver Lenz
- Institute of Biology, Department of Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
- * E-mail: (KAV); (OL)
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Reeve HA, Lauterbach L, Ash PA, Lenz O, Vincent KA. A modular system for regeneration of NAD cofactors using graphite particles modified with hydrogenase and diaphorase moieties. Chem Commun (Camb) 2011; 48:1589-91. [PMID: 21986817 DOI: 10.1039/c1cc14826e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyrolytic graphite particles modified with hydrogenase and an NAD(+)/NADH cycling enzyme provide a modular heterogeneous catalyst system for regeneration of oxidised or reduced nicotinamide cofactors using H(2) and H(+) as electron source or sink. Particles can be tuned for cofactor supply under different conditions by appropriate choice of hydrogenase.
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Affiliation(s)
- Holly A Reeve
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
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Ratzka J, Lauterbach L, Lenz O, Ansorge-Schumacher MB. Systematic evaluation of the dihydrogen-oxidising and NAD+-reducing soluble [NiFe]-hydrogenase from Ralstonia eutropha H16 as a cofactor regeneration catalyst. BIOCATAL BIOTRANSFOR 2011. [DOI: 10.3109/10242422.2011.615393] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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50
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Lauterbach L, Liu J, Horch M, Hummel P, Schwarze A, Haumann M, Vincent KA, Lenz O, Zebger I. The Hydrogenase Subcomplex of the NAD+-Reducing [NiFe] Hydrogenase from Ralstonia eutropha - Insights into Catalysis and Redox Interconversions. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201001053] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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