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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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2
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Fan Q, Waldburger S, Neubauer P, Riedel SL, Gimpel M. Implementation of a high cell density fed-batch for heterologous production of active [NiFe]-hydrogenase in Escherichia coli bioreactor cultivations. Microb Cell Fact 2022; 21:193. [PMID: 36123684 PMCID: PMC9484157 DOI: 10.1186/s12934-022-01919-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background O2-tolerant [NiFe]-hydrogenases offer tremendous potential for applications in H2-based technology. As these metalloenzymes undergo a complicated maturation process that requires a dedicated set of multiple accessory proteins, their heterologous production is challenging, thus hindering their fundamental understanding and the development of related applications. Taking these challenges into account, we selected the comparably simple regulatory [NiFe]-hydrogenase (RH) from Cupriavidus necator as a model for the development of bioprocesses for heterologous [NiFe]-hydrogenase production. We already reported recently on the high-yield production of catalytically active RH in Escherichia coli by optimizing the culture conditions in shake flasks. Results In this study, we further increase the RH yield and ensure consistent product quality by a rationally designed high cell density fed-batch cultivation process. Overall, the bioreactor cultivations resulted in ˃130 mg L−1 of catalytically active RH which is a more than 100-fold increase compared to other RH laboratory bioreactor scale processes with C. necator. Furthermore, the process shows high reproducibility of the previously selected optimized conditions and high productivity. Conclusions This work provides a good opportunity to readily supply such difficult-to-express complex metalloproteins economically and at high concentrations to meet the demand in basic and applied studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01919-w.
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Affiliation(s)
- Qin Fan
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Saskia Waldburger
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Sebastian L Riedel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Ackerstr. 76, ACK24, D-13355, Berlin, Germany.
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3
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Lin L, Huang H, Zhang X, Dong L, Chen Y. Hydrogen-oxidizing bacteria and their applications in resource recovery and pollutant removal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155559. [PMID: 35483467 DOI: 10.1016/j.scitotenv.2022.155559] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/16/2022] [Accepted: 04/23/2022] [Indexed: 06/14/2023]
Abstract
Hydrogen oxidizing bacteria (HOB), a type of chemoautotroph, are a group of bacteria from different genera that share the ability to oxidize H2 and fix CO2 to provide energy and synthesize cellular material. Recently, HOB have received growing attention due to their potential for CO2 capture and waste recovery. This review provides a comprehensive overview of the biological characteristics of HOB and their application in resource recovery and pollutant removal. Firstly, the enzymes, genes and corresponding regulation systems responsible for the key metabolic processes of HOB are discussed in detail. Then, the enrichment and cultivation methods including the coupled water splitting-biosynthetic system cultivation, mixed cultivation and two-stage cultivation strategies for HOB are summarized, which is the critical prerequisite for their application. On the basis, recent advances of HOB application in the recovery of high-value products and the removal of pollutants are presented. Finally, the key points for future investigation are proposed that more attention should be paid to the main limitations in the large-scale industrial application of HOB, including the mass transfer rate of the gases, the safety of the production processes and products, and the commercial value of the products.
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Affiliation(s)
- Lin Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xin Zhang
- Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Rd, Shanghai 200092, China
| | - Lei Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Rd, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
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4
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Cavazza C, Collin-Faure V, Pérard J, Diemer H, Cianférani S, Rabilloud T, Darrouzet E. Proteomic analysis of Rhodospirillum rubrum after carbon monoxide exposure reveals an important effect on metallic cofactor biosynthesis. J Proteomics 2022; 250:104389. [PMID: 34601154 DOI: 10.1016/j.jprot.2021.104389] [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] [Received: 04/20/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/14/2022]
Abstract
Some carboxydotrophs like Rhodospirillum rubrum are able to grow with CO as their sole source of energy using a Carbone monoxide dehydrogenase (CODH) and an Energy conserving hydrogenase (ECH) to perform anaerobically the so called water-gas shift reaction (WGSR) (CO + H2O → CO2 + H2). Several studies have focused at the biochemical and biophysical level on this enzymatic system and a few OMICS studies on CO metabolism. Knowing that CO is toxic in particular due to its binding to heme iron atoms, and is even considered as a potential antibacterial agent, we decided to use a proteomic approach in order to analyze R. rubrum adaptation in term of metabolism and management of the toxic effect. In particular, this study allowed highlighting a set of proteins likely implicated in ECH maturation, and important perturbations in term of cofactor biosynthesis, especially metallic cofactors. This shows that even this CO tolerant microorganism cannot avoid completely CO toxic effects associated with its interaction with metallic ions. SIGNIFICANCE: This proteomic study highlights the fact that even in a microorganism able to handle carbon monoxide and in some way detoxifying it via the intrinsic action of the carbon monoxide dehydrogenase (CODH), CO has important effects on metal homeostasis, metal cofactors and metalloproteins. These effects are direct or indirect via transcription regulation, and amplified by the high interdependency of cofactors biosynthesis.
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Affiliation(s)
- Christine Cavazza
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
| | | | - Julien Pérard
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 (CNRS-CEA), 67087 Strasbourg, France.
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 (CNRS-CEA), 67087 Strasbourg, France.
| | - Thierry Rabilloud
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
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5
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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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6
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Fuji R, Umezawa K, Mizuguchi M, Ihara M. Protein Engineering of the Soluble Metal-dependent Formate Dehydrogenase from Escherichia coli. ANAL SCI 2021; 37:733-739. [PMID: 33455969 DOI: 10.2116/analsci.20scp15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Formate is the most targeted C1 building block and electron carrier in the post-petroleum era. Formate dehydrogenase (FDH), which catalyzes the production or degradation of formate, has acquired considerable attention. Among FDHs, a metal-dependent FDH that carries a complex active center, molybdenum-pterin cofactor, can directly transfer electrons from formate to other redox proteins without generating NAD(P)H. Previously, we reported an expression system for membrane-bound metal-dependent FDH from E. coli (encoded by the fdoG-fdoH-fdoI operon) and succeeded in its conversion to a soluble protein. However, this protein exhibited a too low stability to be purified and analyzed biochemically. In this study, we tried to improve the stability of heterologously expressed FDH through rational and irrational approaches. As a result, a mutant with the highest specific activity was obtained through a rational approach. This study not only yielded a promising FDH enzyme with enhanced activity and stability for industrial applications, but also offered relevant insights for the handling of recombinant large proteins.
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Affiliation(s)
- Rintaro Fuji
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University
| | - Koji Umezawa
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University.,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University
| | - Manami Mizuguchi
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University
| | - Masaki Ihara
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University.,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University
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7
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Fan Q, Neubauer P, Lenz O, Gimpel M. Heterologous Hydrogenase Overproduction Systems for Biotechnology-An Overview. Int J Mol Sci 2020; 21:E5890. [PMID: 32824336 PMCID: PMC7460606 DOI: 10.3390/ijms21165890] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/06/2020] [Accepted: 08/14/2020] [Indexed: 01/16/2023] Open
Abstract
Hydrogenases are complex metalloenzymes, showing tremendous potential as H2-converting redox catalysts for application in light-driven H2 production, enzymatic fuel cells and H2-driven cofactor regeneration. They catalyze the reversible oxidation of hydrogen into protons and electrons. The apo-enzymes are not active unless they are modified by a complicated post-translational maturation process that is responsible for the assembly and incorporation of the complex metal center. The catalytic center is usually easily inactivated by oxidation, and the separation and purification of the active protein is challenging. The understanding of the catalytic mechanisms progresses slowly, since the purification of the enzymes from their native hosts is often difficult, and in some case impossible. Over the past decades, only a limited number of studies report the homologous or heterologous production of high yields of hydrogenase. In this review, we emphasize recent discoveries that have greatly improved our understanding of microbial hydrogenases. We compare various heterologous hydrogenase production systems as well as in vitro hydrogenase maturation systems and discuss their perspectives for enhanced biohydrogen production. Additionally, activities of hydrogenases isolated from either recombinant organisms or in vivo/in vitro maturation approaches were systematically compared, and future perspectives for this research area are discussed.
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Affiliation(s)
- Qin Fan
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Peter Neubauer
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
| | - Oliver Lenz
- Department of Chemistry, Technical University of Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany;
| | - Matthias Gimpel
- Institute of Biotechnology, Technical University of Berlin, Ackerstraße 76, 13355 Berlin, Germany; (Q.F.); (P.N.)
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8
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Schiffels J, Selmer T. Combinatorial assembly of ferredoxin‐linked modules in
Escherichia coli
yields a testing platform for Rnf‐complexes. Biotechnol Bioeng 2019; 116:2316-2329. [DOI: 10.1002/bit.27079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/09/2019] [Accepted: 05/27/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Johannes Schiffels
- Enzyme TechnologyAachen University of Applied SciencesJuelich Germany
- RWTH Aachen University, Chair of BiotechnologyWorringerweg 3 Aachen Germany
| | - Thorsten Selmer
- Enzyme TechnologyAachen University of Applied SciencesJuelich Germany
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9
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Leister D. Genetic Engineering, Synthetic Biology and the Light Reactions of Photosynthesis. PLANT PHYSIOLOGY 2019; 179:778-793. [PMID: 29991483 PMCID: PMC6393809 DOI: 10.1104/pp.18.00360] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/14/2018] [Indexed: 05/21/2023]
Abstract
Applications of synthetic biology to photosynthesis currently range from exchanging photosynthetic proteins to the utilization of photosynthesis as a source of electrons for entirely unrelated reactions.
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Affiliation(s)
- Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152 Planegg-Martinsried, Germany
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10
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Budhraja R, Ding C, Walter P, Wagner S, Reemtsma T, Gary Sawers R, Adrian L. The impact of species, respiration type, growth phase and genetic inventory on absolute metal content of intact bacterial cells. Metallomics 2019; 11:925-935. [DOI: 10.1039/c9mt00009g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Absolute metal ion content was determined from whole cells of different microbial species and changes were related to growth conditions and change of encoded genes.
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Affiliation(s)
- Rohit Budhraja
- Helmholtz Centre for Environmental Research – UFZ
- Isotope Biogeochemistry
- 04318 Leipzig
- Germany
- Chair of Geobiotechnology
| | - Chang Ding
- Helmholtz Centre for Environmental Research – UFZ
- Isotope Biogeochemistry
- 04318 Leipzig
- Germany
| | - Philipp Walter
- Helmholtz Centre for Environmental Research – UFZ
- Isotope Biogeochemistry
- 04318 Leipzig
- Germany
| | - Stephan Wagner
- Helmholtz Centre for Environmental Research – UFZ
- Department of Analytical Chemistry
- Leipzig
- Germany
| | - Thorsten Reemtsma
- Helmholtz Centre for Environmental Research – UFZ
- Department of Analytical Chemistry
- Leipzig
- Germany
| | - R. Gary Sawers
- Institute of Biology/Microbiology
- Martin-Luther Universität
- Halle
- Germany
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research – UFZ
- Isotope Biogeochemistry
- 04318 Leipzig
- Germany
- Chair of Geobiotechnology
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11
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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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12
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Wu CH, Ponir CA, Haja DK, Adams MWW. Improved production of the NiFe-hydrogenase from Pyrococcus furiosus by increased expression of maturation genes. Protein Eng Des Sel 2018; 31:337-344. [DOI: 10.1093/protein/gzy025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 10/13/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chang-Hao Wu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Cynthia A Ponir
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Dominik K Haja
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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13
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The structure of hydrogenase-2 from Escherichia coli: implications for H 2-driven proton pumping. Biochem J 2018; 475:1353-1370. [PMID: 29555844 PMCID: PMC5902676 DOI: 10.1042/bcj20180053] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 01/19/2023]
Abstract
Under anaerobic conditions, Escherichia coli is able to metabolize molecular hydrogen via the action of several [NiFe]-hydrogenase enzymes. Hydrogenase-2, which is typically present in cells at low levels during anaerobic respiration, is a periplasmic-facing membrane-bound complex that functions as a proton pump to convert energy from hydrogen (H2) oxidation into a proton gradient; consequently, its structure is of great interest. Empirically, the complex consists of a tightly bound core catalytic module, comprising large (HybC) and small (HybO) subunits, which is attached to an Fe–S protein (HybA) and an integral membrane protein (HybB). To date, efforts to gain a more detailed picture have been thwarted by low native expression levels of Hydrogenase-2 and the labile interaction between HybOC and HybA/HybB subunits. In the present paper, we describe a new overexpression system that has facilitated the determination of high-resolution crystal structures of HybOC and, hence, a prediction of the quaternary structure of the HybOCAB complex.
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14
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Lamont CM, Sargent F. Design and characterisation of synthetic operons for biohydrogen technology. Arch Microbiol 2016; 199:495-503. [PMID: 27872947 PMCID: PMC5350229 DOI: 10.1007/s00203-016-1322-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 11/09/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022]
Abstract
Biohydrogen is produced by a number of microbial systems and the commonly used host bacterium Escherichia coli naturally produces hydrogen under fermentation conditions. One approach to engineering additional hydrogen production pathways is to introduce non-native hydrogenases into E. coli. An attractive candidate is the soluble [NiFe]-hydrogenase from Ralstonia eutropha, which has been shown to link NADH/NAD+ biochemistry directly to hydrogen metabolism, an activity that E. coli does not perform. In this work, three synthetic operons were designed that code for the soluble hydrogenase and two different enzyme maturase systems. Interestingly, using this system, the recombinant soluble hydrogenase was found to be assembled by the native E. coli [NiFe]-hydrogenase assembly machinery, and, vice versa, the synthetic maturase operons were able to complement E. coli mutants defective in hydrogenase biosynthesis. The heterologously expressed soluble hydrogenase was found to be active and was shown to produce biohydrogen in vivo.
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Affiliation(s)
- Ciaran M Lamont
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, MSI/WTB/JBC/DCTIR Research Complex, Dow Street, Dundee, DD1 5EH, Scotland, UK
| | - Frank Sargent
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, MSI/WTB/JBC/DCTIR Research Complex, Dow Street, Dundee, DD1 5EH, Scotland, UK.
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15
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Hartwig S, Thomas C, Krumova N, Quitzke V, Türkowsky D, Jehmlich N, Adrian L, Sawers RG. Heterologous complementation studies in Escherichia coli with the Hyp accessory protein machinery from Chloroflexi provide insight into [NiFe]-hydrogenase large subunit recognition by the HypC protein family. MICROBIOLOGY-SGM 2015; 161:2204-19. [PMID: 26364315 DOI: 10.1099/mic.0.000177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Six Hyp maturation proteins (HypABCDEF) are conserved in micro-organisms that synthesize [NiFe]-hydrogenases (Hyd). Of these, the HypC chaperones interact directly with the apo-form of the catalytically active large subunit of Hyd enzymes and are believed to transfer the Fe(CN)2CO moiety of the bimetallic cofactor from the Hyp machinery to this large subunit. In E. coli, HypC is specifically required for maturation of Hyd-3 while its paralogue, HybG, is specifically required for Hyd-2 maturation; either HypC or HybG can mature Hyd-1. In this study, we demonstrate that the products of the hypABFCDE operon from the deeply branching hydrogen-dependent and obligate organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 were capable of maturing and assembling active Hyd-1, Hyd-2 and Hyd-3 in an E. coli hyp mutant. Maturation of Hyd-1 was less efficient, presumably because HypB of E. coli was necessary to restore optimal enzyme activity. In a reciprocal maturation study, the highly O2-sensitive H2-uptake HupLS [NiFe]-hydrogenase from D. mccartyi CBDB1 was also synthesized in an active form in E. coli. Together, these findings indicated that HypC from D. mccartyi CBDB1 exhibits promiscuity in its large subunit interaction in E. coli. Based on these findings, we generated amino acid variants of E. coli HybG capable of partial recovery of Hyd-3-dependent H2 production in a hypC hybG double null mutant. Together, these findings identify amino acid regions in HypC accessory proteins that specify interaction with the large subunits of hydrogenase and demonstrate functional compatibility of Hyp accessory protein machineries.
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Affiliation(s)
- Stefanie Hartwig
- 1 Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale) 06120, Germany
| | - Claudia Thomas
- 1 Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale) 06120, Germany
| | - Nadya Krumova
- 1 Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale) 06120, Germany
| | - Vivien Quitzke
- 1 Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale) 06120, Germany
| | - Dominique Türkowsky
- 2 Department of Proteomics, Helmholz Centre for Environmental Research GmbH - UFZ, Permoserstraße 15, Leipzig 04318, Germany
| | - Nico Jehmlich
- 2 Department of Proteomics, Helmholz Centre for Environmental Research GmbH - UFZ, Permoserstraße 15, Leipzig 04318, Germany
| | - Lorenz Adrian
- 3 Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, Leipzig 04318, Germany
| | - R Gary Sawers
- 1 Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale) 06120, Germany
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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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Chandrayan SK, Wu CH, McTernan PM, Adams MWW. High yield purification of a tagged cytoplasmic [NiFe]-hydrogenase and a catalytically-active nickel-free intermediate form. Protein Expr Purif 2014; 107:90-4. [PMID: 25462812 DOI: 10.1016/j.pep.2014.10.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 11/30/2022]
Abstract
The cytoplasmic [NiFe]-hydrogenase I (SHI) of the hyperthermophile Pyrococcus furiosus evolves hydrogen gas (H2) from NADPH. It has been previously used for biohydrogen production from sugars using a mixture of enzymes in an in vitro cell-free synthetic pathway. The theoretical yield (12 H2/glucose) is three times greater than microbial fermentation (4 H2/glucose), making the in vitro approach very promising for large scale biohydrogen production. Further development of this process at an industrial scale is limited by the availability of the H2-producing SHI. To overcome the obstacles of the complex biosynthetic and maturation pathway for the [NiFe] site of SHI, the four gene operon encoding the enzyme was overexpressed in P. furiosus and included a polyhistidine affinity tag. The one-step purification resulted in a 50-fold increase in yield compared to the four-step purification procedure for the native enzyme. A trimeric form was also identified that lacked the [NiFe]-catalytic subunit but catalyzed NADPH oxidation with a specific activity similar to that of the tetrameric form. The presence of an active trimeric intermediate confirms the proposed maturation pathway where, in the terminal step, the NiFe-containing catalytic subunit assembles with NADPH-oxidizing trimeric form to give the active holoenzyme.
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Affiliation(s)
- Sanjeev K Chandrayan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Chang-Hao Wu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Patrick M McTernan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
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