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Schmider T, Hestnes AG, Brzykcy J, Schmidt H, Schintlmeister A, Roller BRK, Teran EJ, Söllinger A, Schmidt O, Polz MF, Richter A, Svenning MM, Tveit AT. Physiological basis for atmospheric methane oxidation and methanotrophic growth on air. Nat Commun 2024; 15:4151. [PMID: 38755154 DOI: 10.1038/s41467-024-48197-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Atmospheric methane oxidizing bacteria (atmMOB) constitute the sole biological sink for atmospheric methane. Still, the physiological basis allowing atmMOB to grow on air is not well understood. Here we assess the ability and strategies of seven methanotrophic species to grow with air as sole energy, carbon, and nitrogen source. Four species, including three outside the canonical atmMOB group USCα, enduringly oxidized atmospheric methane, carbon monoxide, and hydrogen during 12 months of growth on air. These four species exhibited distinct substrate preferences implying the existence of multiple metabolic strategies to grow on air. The estimated energy yields of the atmMOB were substantially lower than previously assumed necessary for cellular maintenance in atmMOB and other aerobic microorganisms. Moreover, the atmMOB also covered their nitrogen requirements from air. During growth on air, the atmMOB decreased investments in biosynthesis while increasing investments in trace gas oxidation. Furthermore, we confirm that a high apparent specific affinity for methane is a key characteristic of atmMOB. Our work shows that atmMOB grow on the trace concentrations of methane, carbon monoxide, and hydrogen present in air and outlines the metabolic strategies that enable atmMOB to mitigate greenhouse gases.
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Affiliation(s)
- Tilman Schmider
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway.
| | - Anne Grethe Hestnes
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Julia Brzykcy
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096, Warsaw, Poland
| | - Hannes Schmidt
- Department of Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1030, Vienna, Austria
| | - Arno Schintlmeister
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Benjamin R K Roller
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Ezequiel Jesús Teran
- Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires (CIFICEN-UNCPBA-CONICET-CICPBA), Pinto, 399, Tandil (7000), Argentina
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Facultad de Ciencias Exactas, Instituto de Física Arroyo Seco (IFAS), Pinto, 399, Tandil (7000), Argentina
| | - Andrea Söllinger
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Oliver Schmidt
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Martin F Polz
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Andreas Richter
- Department of Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1030, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway.
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2
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Abdeljelil N, Ben Miloud Yahia N, Landoulsi A, Chatti A, Wattiez R, Gillan D, Van Houdt R. Proteomic and morphological insights into the exposure of Cupriavidus metallidurans CH34 planktonic cells and biofilms to aluminium. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133403. [PMID: 38215523 DOI: 10.1016/j.jhazmat.2023.133403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/15/2023] [Accepted: 12/27/2023] [Indexed: 01/14/2024]
Abstract
Aluminium (Al) is one of the most popular materials for industrial and domestic use. Nevertheless, research has proven that this metal can be toxic to most organisms. This light metal has no known biological function and to date very few aluminium-specific biological pathways have been identified. In addition, information about the impact of this metal on microbial life is scarce. Here, we aimed to study the effect of aluminium on the metal-resistant soil bacterium Cupriavidus metallidurans CH34 in different growth modes, i.e. planktonic cells, adhered cells and mature biofilms. Our results indicated that despite a significant tolerance to aluminium (minimal inhibitory concentration of 6.25 mM Al₂(SO₄)₃.18H₂O), the exposure of C. metallidurans to a sub-inhibitory dose (0.78 mM) caused early oxidative stress and an increase in hydrolytic activity. Changes in the outer membrane surface of planktonic cells were observed, in addition to a rapid disruption of mature biofilms. On protein level, aluminium exposure increased the expression of proteins involved in metabolic activity such as pyruvate kinase, formate dehydrogenase and poly(3-hydroxybutyrate) polymerase, whereas proteins involved in chemotaxis, and the production and transport of iron scavenging siderophores were significantly downregulated.
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Affiliation(s)
- Nissem Abdeljelil
- Proteomics and Microbiology Lab, Research Institute for Biosciences, Mons University, Mons, Belgium; Microbiology Unit, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium; Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, University of Carthage, Jarzouna, Tunisia
| | | | - Ahmed Landoulsi
- Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Abdelwaheb Chatti
- Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Ruddy Wattiez
- Proteomics and Microbiology Lab, Research Institute for Biosciences, Mons University, Mons, Belgium
| | - David Gillan
- Proteomics and Microbiology Lab, Research Institute for Biosciences, Mons University, Mons, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium.
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3
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Ryu H, Nguyen CNM, Kuk Lee S, Park S. Development of Cupriavidus necator H16 as a host for heterologous production of formate dehydrogenase I of Methylorubrum extorquens: Possibilities and limitations. BIORESOURCE TECHNOLOGY 2024; 394:130187. [PMID: 38096999 DOI: 10.1016/j.biortech.2023.130187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
The discovery of formate dehydrogenase (Me-FDH1) from Methylorubrum extorquens has provided an avenue for sustainable CO2 fixation and utilization. However, the mass production of Me-FDH1 is challenging due to the presence of its unique tungsto-bis-metalopterin guanine dinucleotide (W-bis-MGD) cofactor, limiting its practical applications. In this study, C. necator H16 is proposed as a host for the large-scale production of Me-FDH1, utilizing fructose as a carbon source and its inherent machinery for cofactor synthesis. In a minimal salt medium, C. necator H16 could produce active Me-FDH1, which exhibited a specific activity of 80 to 100 U/mg for CO2 conversion to formate. In fed batch bioreactor experiments, approximately 50 g CDW/L (cell dry weight/L) and 10,000 U/L Me-FDH1 were achieved within 50 h. This study highlights C. necator H16 as the recombinant host for Me-FDH1, paving the way for the future development of efficient mass-production methods for this crucial enzyme.
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Affiliation(s)
- Huichang Ryu
- School of Energy and Chemical Engineering, UNIST, Ulsan 44919, Republic of Korea
| | | | - Sung Kuk Lee
- School of Energy and Chemical Engineering, UNIST, Ulsan 44919, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, UNIST, Ulsan 44919, Republic of Korea.
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4
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Boonkumkrong R, Chunthaboon P, Munkajohnpong P, Watthaisong P, Pimviriyakul P, Maenpuen S, Chaiyen P, Tinikul R. A high catalytic efficiency and chemotolerant formate dehydrogenase from Bacillus simplex. Biotechnol J 2024; 19:e2300330. [PMID: 38180313 DOI: 10.1002/biot.202300330] [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: 07/08/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 01/06/2024]
Abstract
NAD+ -dependent formate dehydrogenase (FDH) catalyzes the conversion of formate and NAD+ to produce carbon dioxide and NADH. The reaction is biotechnologically important because FDH is widely used for NADH regeneration in various enzymatic syntheses. However, major drawbacks of this versatile enzyme in industrial applications are its low activity, requiring its utilization in large amounts to achieve optimal process conditions. Here, FDH from Bacillus simplex (BsFDH) was characterized for its biochemical and catalytic properties in comparison to FDH from Pseudomonas sp. 101 (PsFDH), a commonly used FDH in various biocatalytic reactions. The data revealed that BsFDH possesses high formate oxidizing activity with a kcat value of 15.3 ± 1.9 s-1 at 25°C compared to 7.7 ± 1.0 s-1 for PsFDH. At the optimum temperature (60°C), BsFDH exhibited 6-fold greater activity than PsFDH. The BsFDH displayed higher pH stability and a superior tolerance toward sodium azide and H2 O2 inactivation, showing a 200-fold higher Ki value for azide inhibition and remaining stable in the presence of 0.5% H2 O2 compared to PsFDH. The application of BsFDH as a cofactor regeneration system for the detoxification of 4-nitrophenol by the reaction of HadA, which produced a H2 O2 byproduct was demonstrated. The biocatalytic cascades using BsFDH demonstrated a distinct superior conversion activity because the system tolerated H2 O2 well. Altogether, the data showed that BsFDH is a robust enzyme suitable for future application in industrial biotechnology.
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Affiliation(s)
- Rattima Boonkumkrong
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Paweenapon Chunthaboon
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pobthum Munkajohnpong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Pratchaya Watthaisong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
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5
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Oliveira AR, Mota C, Vilela-Alves G, Manuel RR, Pedrosa N, Fourmond V, Klymanska K, Léger C, Guigliarelli B, Romão MJ, Cardoso Pereira IA. An allosteric redox switch involved in oxygen protection in a CO 2 reductase. Nat Chem Biol 2024; 20:111-119. [PMID: 37985883 DOI: 10.1038/s41589-023-01484-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Metal-dependent formate dehydrogenases reduce CO2 with high efficiency and selectivity, but are usually very oxygen sensitive. An exception is Desulfovibrio vulgaris W/Sec-FdhAB, which can be handled aerobically, but the basis for this oxygen tolerance was unknown. Here we show that FdhAB activity is controlled by a redox switch based on an allosteric disulfide bond. When this bond is closed, the enzyme is in an oxygen-tolerant resting state presenting almost no catalytic activity and very low formate affinity. Opening this bond triggers large conformational changes that propagate to the active site, resulting in high activity and high formate affinity, but also higher oxygen sensitivity. We present the structure of activated FdhAB and show that activity loss is associated with partial loss of the metal sulfido ligand. The redox switch mechanism is reversible in vivo and prevents enzyme reduction by physiological formate levels, conferring a fitness advantage during O2 exposure.
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Affiliation(s)
- Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cristiano Mota
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Guilherme Vilela-Alves
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rita Rebelo Manuel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Neide Pedrosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Vincent Fourmond
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Kateryna Klymanska
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Christophe Léger
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Bruno Guigliarelli
- Laboratory of Bioenergetics and Protein Engineering, Aix Marseille University, CNRS, BIP, Marseille, France
| | - Maria João Romão
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
| | - Inês A Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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6
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Maia LB, Maiti BK, Moura I, Moura JJG. Selenium-More than Just a Fortuitous Sulfur Substitute in Redox Biology. Molecules 2023; 29:120. [PMID: 38202704 PMCID: PMC10779653 DOI: 10.3390/molecules29010120] [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: 11/30/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Living organisms use selenium mainly in the form of selenocysteine in the active site of oxidoreductases. Here, selenium's unique chemistry is believed to modulate the reaction mechanism and enhance the catalytic efficiency of specific enzymes in ways not achievable with a sulfur-containing cysteine. However, despite the fact that selenium/sulfur have different physicochemical properties, several selenoproteins have fully functional cysteine-containing homologues and some organisms do not use selenocysteine at all. In this review, selected selenocysteine-containing proteins will be discussed to showcase both situations: (i) selenium as an obligatory element for the protein's physiological function, and (ii) selenium presenting no clear advantage over sulfur (functional proteins with either selenium or sulfur). Selenium's physiological roles in antioxidant defence (to maintain cellular redox status/hinder oxidative stress), hormone metabolism, DNA synthesis, and repair (maintain genetic stability) will be also highlighted, as well as selenium's role in human health. Formate dehydrogenases, hydrogenases, glutathione peroxidases, thioredoxin reductases, and iodothyronine deiodinases will be herein featured.
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Affiliation(s)
- Luisa B. Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
| | - Biplab K. Maiti
- Department of Chemistry, School of Sciences, Cluster University of Jammu, Canal Road, Jammu 180001, India
| | - Isabel Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
| | - José J. G. Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
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7
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Harmer JR, Hakopian S, Niks D, Hille R, Bernhardt PV. Redox Characterization of the Complex Molybdenum Enzyme Formate Dehydrogenase from Cupriavidus necator. J Am Chem Soc 2023; 145:25850-25863. [PMID: 37967365 DOI: 10.1021/jacs.3c10199] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The oxygen-tolerant and molybdenum-dependent formate dehydrogenase FdsDABG from Cupriavidus necator is capable of catalyzing both formate oxidation to CO2 and the reverse reaction (CO2 reduction to formate) at neutral pH, which are both reactions of great importance to energy production and carbon capture. FdsDABG is replete with redox cofactors comprising seven Fe/S clusters, flavin mononucleotide, and a molybdenum ion coordinated by two pyranopterin dithiolene ligands. The redox potentials of these centers are described herein and assigned to specific cofactors using combinations of potential-dependent continuous wave and pulse EPR spectroscopy and UV/visible spectroelectrochemistry on both the FdsDABG holoenzyme and the FdsBG subcomplex. These data represent the first redox characterization of a complex metal dependent formate dehydrogenase and provide an understanding of the highly efficient catalytic formate oxidation and CO2 reduction activity that are associated with the enzyme.
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Affiliation(s)
- Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland, Brisbane 4072, Australia
| | - Sheron Hakopian
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Russ Hille
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
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8
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Sahin S, Lemaire ON, Belhamri M, Kurth JM, Welte CU, Wagner T, Milton RD. Bioelectrocatalytic CO 2 Reduction by Mo-Dependent Formylmethanofuran Dehydrogenase. Angew Chem Int Ed Engl 2023; 62:e202311981. [PMID: 37712590 DOI: 10.1002/anie.202311981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/16/2023]
Abstract
Massive efforts are invested in developing innovative CO2 -sequestration strategies to counter climate change and transform CO2 into higher-value products. CO2 -capture by reduction is a chemical challenge, and attention is turned toward biological systems that selectively and efficiently catalyse this reaction under mild conditions and in aqueous solvents. While a few reports have evaluated the effectiveness of isolated bacterial formate dehydrogenases as catalysts for the reversible electrochemical reduction of CO2 , it is imperative to explore other enzymes among the natural reservoir of potential models that might exhibit higher turnover rates or preferential directionality for the reductive reaction. Here, we present electroenzymatic catalysis of formylmethanofuran dehydrogenase, a CO2 -reducing-and-fixing biomachinery isolated from a thermophilic methanogen, which was deposited on a graphite rod electrode to enable direct electron transfer for electroenzymatic CO2 reduction. The gas is reduced with a high Faradaic efficiency (109±1 %), where a low affinity for formate prevents its electrochemical reoxidation and favours formate accumulation. These properties make the enzyme an excellent tool for electroenzymatic CO2 -fixation and inspiration for protein engineering that would be beneficial for biotechnological purposes to convert the greenhouse gas into stable formate that can subsequently be safely stored, transported, and used for power generation without energy loss.
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Affiliation(s)
- Selmihan Sahin
- University of Geneva, Department of Inorganic and Analytical Chemistry, Sciences II, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
- Department of Chemistry, Faculty of Arts and Sciences, Suleyman Demirel University, Cunur, 32260, Isparta, Turkiye
| | - Olivier N Lemaire
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Mélissa Belhamri
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Julia M Kurth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
- Microcosm Earth Center - Philipps-Universität Marburg & Max Planck Institute for Terrestrial Microbiology, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Ross D Milton
- University of Geneva, Department of Inorganic and Analytical Chemistry, Sciences II, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
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9
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Zhong W, Li H, Wang Y. Design and Construction of Artificial Biological Systems for One-Carbon Utilization. BIODESIGN RESEARCH 2023; 5:0021. [PMID: 37915992 PMCID: PMC10616972 DOI: 10.34133/bdr.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/05/2023] [Indexed: 11/03/2023] Open
Abstract
The third-generation (3G) biorefinery aims to use microbial cell factories or enzymatic systems to synthesize value-added chemicals from one-carbon (C1) sources, such as CO2, formate, and methanol, fueled by renewable energies like light and electricity. This promising technology represents an important step toward sustainable development, which can help address some of the most pressing environmental challenges faced by modern society. However, to establish processes competitive with the petroleum industry, it is crucial to determine the most viable pathways for C1 utilization and productivity and yield of the target products. In this review, we discuss the progresses that have been made in constructing artificial biological systems for 3G biorefineries in the last 10 years. Specifically, we highlight the representative works on the engineering of artificial autotrophic microorganisms, tandem enzymatic systems, and chemo-bio hybrid systems for C1 utilization. We also prospect the revolutionary impact of these developments on biotechnology. By harnessing the power of 3G biorefinery, scientists are establishing a new frontier that could potentially revolutionize our approach to industrial production and pave the way for a more sustainable future.
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Affiliation(s)
- Wei Zhong
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
| | - Hailong Li
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
- School of Materials Science and Engineering,
Zhejiang University, Zhejiang Province, Hangzhou 310000, PR China
| | - Yajie Wang
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering,
Westlake University, Hangzhou 310000, PR China
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10
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Li J, Shi J, Wang Y, Yao H, Meng L, Liu H. An elaborate biomolecular keypad lock based on electrochromism of viologen derivatives and bioelectrocatalytic reduction of CO 2 at supramolecular hydrogel film electrodes. Biosens Bioelectron 2023; 238:115560. [PMID: 37542980 DOI: 10.1016/j.bios.2023.115560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/01/2023] [Accepted: 07/30/2023] [Indexed: 08/07/2023]
Abstract
Herein, the short peptide N-fluorenemethoxycarbonyl diphenylalanine (Fmoc-FF) was used to immobilize both diallyl viologen (DAV) and the enzyme formate dehydrogenase (FDH) to form Fmoc-FF/DAV/FDH supramolecular hydrogel films on an electrode surface by a simple solvent-controlled self-assembly method. The DAV component in the films exhibited multiple properties, such as electrochromism and electrofluorochromism, and acted as an electrochemical mediator. A high efficiency of bioelectrocatalytic reduction of CO2 to formate (HCOO-) was obtained by the natural FDH enzyme and the artificial coenzyme factor DAV both immobilized in the same films. The supramolecular hydrogel films with CO2, voltage and light as stimulating factors and current, fluorescence and UV-vis extinction as responsive signals, were further applied for the construction of complex biomolecular logic systems and information encryption. A 3-input/7-output biomolecular logic gate and several logic devices, including an encoder/decoder, a parity checker, and a keypad lock, were constructed. Especially, the biomolecular keypad lock with 3 types of signals as outputs significantly enhanced the security level of information encryption. In this work, a supramolecular self-assembly interface was simply fabricated with complex biomolecular computational functions using immobilized molecules as the computational core, greatly broadening the application range of supramolecular hydrogel films and providing an idea for new designs of bioinformation encryption through the use of a simple film system.
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Affiliation(s)
- Jiaxuan Li
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Jiaqi Shi
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Yizhu Wang
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Huiqin Yao
- School of Public Health, Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, Yinchuan, 750004, People's Republic of China
| | - Lingchen Meng
- School of Public Health, Key Laboratory of Environmental Factors and Chronic Disease Control, Ningxia Medical University, Yinchuan, 750004, People's Republic of China
| | - Hongyun Liu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China.
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11
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Kalimuthu P, Hakopian S, Niks D, Hille R, Bernhardt PV. The Reversible Electrochemical Interconversion of Formate and CO 2 by Formate Dehydrogenase from Cupriavidus necator. J Phys Chem B 2023; 127:8382-8392. [PMID: 37728992 DOI: 10.1021/acs.jpcb.3c04652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The bacterial molybdenum (Mo)-containing formate dehydrogenase (FdsDABG) from Cupriavidus necator is a soluble NAD+-dependent enzyme belonging to the DMSO reductase family. The holoenzyme is complex and possesses nine redox-active cofactors including a bis(molybdopterin guanine dinucleotide) (bis-MGD) active site, seven iron-sulfur clusters, and 1 equiv of flavin mononucleotide (FMN). FdsDABG catalyzes the two-electron oxidation of HCOO- (formate) to CO2 and reversibly reduces CO2 to HCOO- under physiological conditions close to its thermodynamic redox potential. Here we develop an electrocatalytically active formate oxidation/CO2 reduction system by immobilizing FdsDABG on a glassy carbon electrode in the presence of coadsorbents such as chitosan and glutaraldehyde. The reversible enzymatic interconversion between HCOO- and CO2 by FdsDABG has been realized with cyclic voltammetry using a range of artificial electron transfer mediators, with methylene blue (MB) and phenazine methosulfate (PMS) being particularly effective as electron acceptors for FdsDABG in formate oxidation. Methyl viologen (MV) acts as both an electron acceptor (MV2+) in formate oxidation and an electron donor (MV+•) for CO2 reduction. The catalytic voltammetry was reproduced by electrochemical simulation across a range of sweep rates and concentrations of formate and mediators to provide new insights into the kinetics of the FdsDABG catalytic mechanism.
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Affiliation(s)
- Palraj Kalimuthu
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| | - Sheron Hakopian
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Russ Hille
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
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12
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Sapountzaki E, Rova U, Christakopoulos P, Antonopoulou I. Renewable Hydrogen Production and Storage Via Enzymatic Interconversion of CO 2 and Formate with Electrochemical Cofactor Regeneration. CHEMSUSCHEM 2023; 16:e202202312. [PMID: 37165995 DOI: 10.1002/cssc.202202312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023]
Abstract
The urgent need to reduce CO2 emissions has motivated the development of CO2 capture and utilization technologies. An emerging application is CO2 transformation into storage chemicals for clean energy carriers. Formic acid (FA), a valuable product of CO2 reduction, is an excellent hydrogen carrier. CO2 conversion to FA, followed by H2 release from FA, are conventionally chemically catalyzed. Biocatalysts offer a highly specific and less energy-intensive alternative. CO2 conversion to formate is catalyzed by formate dehydrogenase (FDH), which usually requires a cofactor to function. Several FDHs have been incorporated in bioelectrochemical systems where formate is produced by the biocathode and the cofactor is electrochemically regenerated. H2 production from formate is also catalyzed by several microorganisms possessing either formate hydrogenlyase or hydrogen-dependent CO2 reductase complexes. Combination of these two processes can lead to a CO2 -recycling cycle for H2 production, storage, and release with potentially lower environmental impact than conventional methods.
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Affiliation(s)
- Eleftheria Sapountzaki
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187, Luleå, Sweden
| | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187, Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187, Luleå, Sweden
| | - Io Antonopoulou
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187, Luleå, Sweden
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13
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Kobayashi A, Taketa M, Sowa K, Kano K, Higuchi Y, Ogata H. Structure and function relationship of formate dehydrogenases: an overview of recent progress. IUCRJ 2023; 10:544-554. [PMID: 37668215 PMCID: PMC10478512 DOI: 10.1107/s2052252523006437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/24/2023] [Indexed: 09/06/2023]
Abstract
Formate dehydrogenases (FDHs) catalyze the two-electron oxidation of formate to carbon dioxide. FDHs can be divided into several groups depending on their subunit composition and active-site metal ions. Metal-dependent (Mo- or W-containing) FDHs from prokaryotic organisms belong to the superfamily of molybdenum enzymes and are members of the dimethylsulfoxide reductase family. In this short review, recent progress in the structural analysis of FDHs together with their potential biotechnological applications are summarized.
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Affiliation(s)
- Ami Kobayashi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Midori Taketa
- Graduate School of Science, University of Hyogo, Koto 3-2-1 Kamigori, Ako, Hyogo 678-1297, Japan
| | - Keisei Sowa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kenji Kano
- Office of Society Academia Collaboration for Innovation, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Yoshiki Higuchi
- Graduate School of Science, University of Hyogo, Koto 3-2-1 Kamigori, Ako, Hyogo 678-1297, Japan
| | - Hideaki Ogata
- Graduate School of Science, University of Hyogo, Koto 3-2-1 Kamigori, Ako, Hyogo 678-1297, Japan
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14
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Villa R, Nieto S, Donaire A, Lozano P. Direct Biocatalytic Processes for CO 2 Capture as a Green Tool to Produce Value-Added Chemicals. Molecules 2023; 28:5520. [PMID: 37513391 PMCID: PMC10383722 DOI: 10.3390/molecules28145520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Direct biocatalytic processes for CO2 capture and transformation in value-added chemicals may be considered a useful tool for reducing the concentration of this greenhouse gas in the atmosphere. Among the other enzymes, carbonic anhydrase (CA) and formate dehydrogenase (FDH) are two key biocatalysts suitable for this challenge, facilitating the uptake of carbon dioxide from the atmosphere in complementary ways. Carbonic anhydrases accelerate CO2 uptake by promoting its solubility in water in the form of hydrogen carbonate as the first step in converting the gas into a species widely used in carbon capture storage and its utilization processes (CCSU), particularly in carbonation and mineralization methods. On the other hand, formate dehydrogenases represent the biocatalytic machinery evolved by certain organisms to convert CO2 into enriched, reduced, and easily transportable hydrogen species, such as formic acid, via enzymatic cascade systems that obtain energy from chemical species, electrochemical sources, or light. Formic acid is the basis for fixing C1-carbon species to other, more reduced molecules. In this review, the state-of-the-art of both methods of CO2 uptake is assessed, highlighting the biotechnological approaches that have been developed using both enzymes.
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Affiliation(s)
- Rocio Villa
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, 30100 Murcia, Spain
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Susana Nieto
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, 30100 Murcia, Spain
| | - Antonio Donaire
- Departamento de Química Inorgánica, Facultad de Química, Universidad de Murcia, 30100 Murcia, Spain
| | - Pedro Lozano
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, 30100 Murcia, Spain
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15
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Phan UT, Jeon BW, Kim YH. Microbial engineering of Methylorubrum extorquens AM1 to enhance CO 2 conversion into formate. Enzyme Microb Technol 2023; 168:110264. [PMID: 37244213 DOI: 10.1016/j.enzmictec.2023.110264] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Methylorubrum extorquens AM1 has the potential to consume C1 feedstock to produce a wide range of biomaterials, from bioplastic to pharmaceutical. However, the synthetic biology tools for engineering M. extorquens AM1 need to be employed for precise control of recombinant enzyme expression. In this study, we presented an approach to improve the expression level of formate dehydrogenase 1 from M. extorquens AM1 (MeFDH1) using an efficient terminator and 5'-untranslated region (5'-UTR) design for enhanced carbon dioxide (CO2) conversion activity of whole-cell biocatalyst. The rrnB terminator significantly increased mRNA levels of MeFDH1 alpha and beta subunits by 8.2-fold and 11-fold, respectively, compared to the T7 terminator. Moreover, enzyme production was 1.6-fold higher with 2.1 mg/wet cell weight (WCW) using rrnB terminator. Homologous 5'-untranslated regions (5'-UTR) determined based on proteomics data and UTR designer also influenced the expression level of MeFDH1. The 5'-UTR of the formaldehyde activating enzyme (fae) was the strongest, with 2.5-fold higher expression than that of the control sequence (T7g-10L). Furthermore, the electrochemical reaction of recombinant strains as whole-cell biocatalysts was investigated for their applicability to CO2 conversion, showing enhanced formate productivity. The recombinant strain containing the 5'-UTR sequence of fae exhibited formate productivity of 5.0 mM/h, 2.3-fold higher than that of the control strain (T7). Overall, this study suggested practical applications for CO2 conversion into bioavailable formate and provided valuable insights for recombinant expression systems in methylotrophic strains.
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Affiliation(s)
- Uyen Thu Phan
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, the Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, the Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, the Republic of Korea.
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16
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Wang KY, Zhang J, Hsu YC, Lin H, Han Z, Pang J, Yang Z, Liang RR, Shi W, Zhou HC. Bioinspired Framework Catalysts: From Enzyme Immobilization to Biomimetic Catalysis. Chem Rev 2023; 123:5347-5420. [PMID: 37043332 PMCID: PMC10853941 DOI: 10.1021/acs.chemrev.2c00879] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Indexed: 04/13/2023]
Abstract
Enzymatic catalysis has fueled considerable interest from chemists due to its high efficiency and selectivity. However, the structural complexity and vulnerability hamper the application potentials of enzymes. Driven by the practical demand for chemical conversion, there is a long-sought quest for bioinspired catalysts reproducing and even surpassing the functions of natural enzymes. As nanoporous materials with high surface areas and crystallinity, metal-organic frameworks (MOFs) represent an exquisite case of how natural enzymes and their active sites are integrated into porous solids, affording bioinspired heterogeneous catalysts with superior stability and customizable structures. In this review, we comprehensively summarize the advances of bioinspired MOFs for catalysis, discuss the design principle of various MOF-based catalysts, such as MOF-enzyme composites and MOFs embedded with active sites, and explore the utility of these catalysts in different reactions. The advantages of MOFs as enzyme mimetics are also highlighted, including confinement, templating effects, and functionality, in comparison with homogeneous supramolecular catalysts. A perspective is provided to discuss potential solutions addressing current challenges in MOF catalysis.
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Affiliation(s)
- Kun-Yu Wang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiaqi Zhang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu-Chuan Hsu
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hengyu Lin
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zongsu Han
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiandong Pang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- School
of Materials Science and Engineering, Tianjin Key Laboratory of Metal
and Molecule-Based Material Chemistry, Nankai
University, Tianjin 300350, China
| | - Zhentao Yang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Rong-Ran Liang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wei Shi
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong-Cai Zhou
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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17
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Iliuta I, Larachi F. Direct-air capture conversion of CO2 in fixed-bed microreactors with immobilized formate dehydrogenase and glucose dehydrogenase: Concept feasibility. Chem Eng Res Des 2023. [DOI: 10.1016/j.cherd.2023.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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18
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Bruinsma L, Wenk S, Claassens NJ, Martins Dos Santos VAP. Paving the way for synthetic C1 - Metabolism in Pseudomonas putida through the reductive glycine pathway. Metab Eng 2023; 76:215-224. [PMID: 36804222 DOI: 10.1016/j.ymben.2023.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
One-carbon (C1) compounds such as methanol, formate, and CO2 are alternative, sustainable microbial feedstocks for the biobased production of chemicals and fuels. In this study, we engineered the carbon metabolism of the industrially important bacterium Pseudomonas putida to modularly assimilate these three substrates through the reductive glycine pathway. First, we demonstrated the functionality of the C1-assimilation module by coupling the growth of auxotrophic strains to formate assimilation. Next, we extended the module in the auxotrophic strains from formate to methanol-dependent growth using both NAD and PQQ-dependent methanol dehydrogenases. Finally, we demonstrated, for the first time, engineered CO2-dependent formation of part of the biomass through CO2 reduction to formate by the native formate dehydrogenase, which required short-term evolution to rebalance the cellular NADH/NAD + ratio. This research paves the way to further engineer P. putida towards full growth on formate, methanol, and CO2 as sole feedstocks, thereby substantially expanding its potential as a sustainable and versatile cell factory.
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Affiliation(s)
- Lyon Bruinsma
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708, WE, the Netherlands
| | - Sebastian Wenk
- Systems and Synthetic Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708, WE, the Netherlands.
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708, WE, the Netherlands; LifeGlimmer GmbH, Berlin, 12163, Germany; Bioprocess Engineering, Wageningen University & Research, Wageningen, 6708, WE, the Netherlands.
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19
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Efficient expression of heterologous protein by engineered Komagataella phaffii by harnessing a bioelectrical CO2 reduction system. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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Bio-inspired CO2 reduction reaction catalysis using soft-oxometalates. J Inorg Biochem 2022; 234:111903. [DOI: 10.1016/j.jinorgbio.2022.111903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022]
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21
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Graham JE, Niks D, Zane GM, Gui Q, Hom K, Hille R, Wall JD, Raman CS. How a Formate Dehydrogenase Responds to Oxygen: Unexpected O 2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel E. Graham
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Qin Gui
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - C. S. Raman
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
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22
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Optimized Operating Conditions for a Biological Treatment Process of Industrial Residual Process Brine Using a Halophilic Mixed Culture. FERMENTATION 2022. [DOI: 10.3390/fermentation8060246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Residual process brine is a sustainable raw material for chlor-alkali electrolysis processes. This study investigates the influence of critical process parameters on the performance of a continuous treatment process for residual process brine using halophilic microorganisms. The goal of the bioprocess is an efficient degradation of the organic impurities formate, aniline, phenol, and 4,4′-methylenedianline from this residual stream. It was shown that formate could be degraded with high efficiencies (89–98%) during the treatment process. It was observed that formate degradation was influenced by the co-substrate glycerol. The lowest residual formate concentrations were achieved with specific glycerol uptake rates of 8.0–16.0 × 10−3 g L−1 h−1 OD600−1. Moreover, a triple-nutrient limitation for glycerol, ammonium, and phosphate was successfully applied for continuous cultivations. Furthermore, it was shown that all aromatic impurities were degraded with an efficiency of 100%. Ultimately, this study proposed optimized operating conditions, allowing the efficient degradation of organics in the residual process brine under various process conditions. Future optimization steps will require a strategy to prevent the accumulation of potential intermediate degradation products formed at high aniline feed concentrations and increase the liquid dilution rates of the system to achieve a higher throughput of brines.
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23
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Mainka T, Herwig C, Pflügl S. Reducing Organic Load From Industrial Residual Process Brine With a Novel Halophilic Mixed Culture: Scale-Up and Long-Term Piloting of an Integrated Bioprocess. Front Bioeng Biotechnol 2022; 10:896576. [PMID: 35519624 PMCID: PMC9062027 DOI: 10.3389/fbioe.2022.896576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Integrating bioprocess solutions for treatment and subsequent reuse of saline residual process brine into industrial processes could increase the sustainability of production chains. However, such bioprocesses require large-scales and a robust operation over a prolonged period. Consequently, the aim of this study was to analyze scale-up equivalence as well as continuous and stable process performance of a previously established lab scale process for the degradation of organic contaminants (formate and aromatic compounds) in an industrial context. To that end, a pilot-scale bubble column bioreactor system equipped with a membrane-based cell retention system for process intensification was integrated at an industrial production site. The process was successfully scaled-up and continuously operated for more than 210 days. Overall, the process proved to be robust towards changing compositions of the residual process brine stream and degradation rates for organic contaminants were close to 100%. Interestingly, due to the unsterile process conditions, the original Haloferax mediterranei culture was replaced by a novel halophilic bacterial community consisting of three bacterial genera. To further improve process economics and productivity, an optimization of the co-substrate feeding strategy for glycerol is required, as results indicated a potential correlation between glycerol feeding and formate degradation rates. To that end, decoupling of the glycerol feeding from the residual process brine feed is a potential way to increase process control options and allow for easy adaptation of the process to changing residual process brine compositions. Ultimately, the process described here could be a promising alternative for chemical or physical methods of treating residual process brine and once more underlines the potential to exploit natural microbial diversity for industrial purposes.
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Affiliation(s)
- Thomas Mainka
- Institute for Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christoph Herwig
- Institute for Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria,Competence Center CHASE GmbH, Linz, Austria
| | - Stefan Pflügl
- Institute for Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria,*Correspondence: Stefan Pflügl,
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24
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Moon M, Park GW, Lee JP, Lee JS, Min K. Recombinant expression and characterization of formate dehydrogenase from Clostridium ljungdahlii (ClFDH) as CO2 reductase for converting CO2 to formate. J CO2 UTIL 2022. [DOI: 10.1016/j.jcou.2021.101876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Min K, Moon M, Park GW, Lee JP, Kim SJ, Lee JS. Newly explored formate dehydrogenases from Clostridium species catalyze carbon dioxide to formate. BIORESOURCE TECHNOLOGY 2022; 348:126832. [PMID: 35149183 DOI: 10.1016/j.biortech.2022.126832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
With concerns over global warming and climate change, many efforts have been devoted to mitigate atmospheric CO2 level. As a CO2 utilization strategy, formate dehydrogenase (FDH) from Clostridium species were explored to discover O2-tolerant and efficient FDHs that can catalyze CO2 to formate (i.e. CO2 reductase). With FDH from Clostridium ljungdahlii (ClFDH) that plays as a CO2 reductase previously reported as the reference, FDH from C.autoethanogenum (CaFDH), C. coskatii (CcFDH), and C. ragsdalei (CrFDH) were newly discovered via genome-mining. The FDHs were expressed in Escherichia coli and the recombinant FDHs successfully catalyzed CO2 reduction with a specific activity of 15 U g-1-CaFDH, 17 U g-1-CcFDH, and 8.7 U g-1-CrFDH. Interestingly, all FDHs newly discovered retain their catalytic activity under aerobic condition, although Clostridium species are strict anaerobe. The results discussed herein can contribute to biocatalytic CO2 utilization.
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Affiliation(s)
- Kyoungseon Min
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea.
| | - Myounghoon Moon
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Gwon Woo Park
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Joon-Pyo Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Seon Jeong Kim
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
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26
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Sharma K, Park YK, Nadda AK, Banerjee P, Singh P, Raizada P, Banat F, Bharath G, Jeong SM, Lam SS. Emerging chemo-biocatalytic routes for valorization of major greenhouse gases (GHG) into industrial products: A comprehensive review. J IND ENG CHEM 2022. [DOI: 10.1016/j.jiec.2022.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Understanding the local chemical environment of bioelectrocatalysis. Proc Natl Acad Sci U S A 2022; 119:2114097119. [PMID: 35058361 PMCID: PMC8795565 DOI: 10.1073/pnas.2114097119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2021] [Indexed: 11/18/2022] Open
Abstract
Bioelectrochemistry employs an array of high-surface-area meso- and macroporous electrode architectures to increase protein loading and the electrochemical current response. While the local chemical environment has been studied in small-molecule and heterogenous electrocatalysis, conditions in enzyme electrochemistry are still commonly established based on bulk solution assays, without appropriate consideration of the nonequilibrium conditions of the confined electrode space. Here, we apply electrochemical and computational techniques to explore the local environment of fuel-producing oxidoreductases within porous electrode architectures. This improved understanding of the local environment enabled simple manipulation of the electrolyte solution by adjusting the bulk pH and buffer pKa to achieve an optimum local pH for maximal activity of the immobilized enzyme. When applied to macroporous inverse opal electrodes, the benefits of higher loading and increased mass transport were employed, and, consequently, the electrolyte adjusted to reach −8.0 mA ⋅ cm−2 for the H2 evolution reaction and −3.6 mA ⋅ cm−2 for the CO2 reduction reaction (CO2RR), demonstrating an 18-fold improvement on previously reported enzymatic CO2RR systems. This research emphasizes the critical importance of understanding the confined enzymatic chemical environment, thus expanding the known capabilities of enzyme bioelectrocatalysis. These considerations and insights can be directly applied to both bio(photo)electrochemical fuel and chemical synthesis, as well as enzymatic fuel cells, to significantly improve the fundamental understanding of the enzyme–electrode interface as well as device performance.
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Ahmad Rizal Lim FN, Marpani F, Anak Dilol VE, Mohamad Pauzi S, Othman NH, Alias NH, Nik Him NR, Luo J, Abd Rahman N. A Review on the Design and Performance of Enzyme-Aided Catalysis of Carbon Dioxide in Membrane, Electrochemical Cell and Photocatalytic Reactors. MEMBRANES 2021; 12:membranes12010028. [PMID: 35054554 PMCID: PMC8778536 DOI: 10.3390/membranes12010028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/28/2021] [Accepted: 12/04/2021] [Indexed: 11/17/2022]
Abstract
Multi-enzyme cascade catalysis involved three types of dehydrogenase enzymes, namely, formate dehydrogenase (FDH), formaldehyde dehydrogenase (FaldDH), alcohol dehydrogenase (ADH), and an equimolar electron donor, nicotinamide adenine dinucleotide (NADH), assisting the reaction is an interesting pathway to reduce thermodynamically stable molecules of CO2 from the atmosphere. The biocatalytic sequence is interesting because it operates under mild reaction conditions (low temperature and pressure) and all the enzymes are highly selective, which allows the reaction to produce three basic chemicals (formic acid, formaldehyde, and methanol) in just one pot. There are various challenges, however, in applying the enzymatic conversion of CO2, namely, to obtain high productivity, increase reusability of the enzymes and cofactors, and to design a simple, facile, and efficient reactor setup that will sustain the multi-enzymatic cascade catalysis. This review reports on enzyme-aided reactor systems that support the reduction of CO2 to methanol. Such systems include enzyme membrane reactors, electrochemical cells, and photocatalytic reactor systems. Existing reactor setups are described, product yields and biocatalytic productivities are evaluated, and effective enzyme immobilization methods are discussed.
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Affiliation(s)
- Fatin Nasreen Ahmad Rizal Lim
- School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia; (F.N.A.R.L.); (V.E.A.D.); (S.M.P.); (N.H.O.); (N.H.A.); (N.R.N.H.); (N.A.R.)
| | - Fauziah Marpani
- School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia; (F.N.A.R.L.); (V.E.A.D.); (S.M.P.); (N.H.O.); (N.H.A.); (N.R.N.H.); (N.A.R.)
- Catalysis for Sustainable Water and Energy Nexus Research Group, School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia
- Correspondence: ; Tel.: +60-35543-6510; Fax: +60-35543-6300
| | - Victoria Eliz Anak Dilol
- School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia; (F.N.A.R.L.); (V.E.A.D.); (S.M.P.); (N.H.O.); (N.H.A.); (N.R.N.H.); (N.A.R.)
| | - Syazana Mohamad Pauzi
- School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia; (F.N.A.R.L.); (V.E.A.D.); (S.M.P.); (N.H.O.); (N.H.A.); (N.R.N.H.); (N.A.R.)
| | - Nur Hidayati Othman
- School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia; (F.N.A.R.L.); (V.E.A.D.); (S.M.P.); (N.H.O.); (N.H.A.); (N.R.N.H.); (N.A.R.)
- Catalysis for Sustainable Water and Energy Nexus Research Group, School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia
| | - Nur Hashimah Alias
- School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia; (F.N.A.R.L.); (V.E.A.D.); (S.M.P.); (N.H.O.); (N.H.A.); (N.R.N.H.); (N.A.R.)
- Catalysis for Sustainable Water and Energy Nexus Research Group, School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia
| | - Nik Raikhan Nik Him
- School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia; (F.N.A.R.L.); (V.E.A.D.); (S.M.P.); (N.H.O.); (N.H.A.); (N.R.N.H.); (N.A.R.)
| | - Jianquan Luo
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China;
| | - Norazah Abd Rahman
- School of Chemical Engineering, College of Engineering, Universiti Teknologi MARA, Shah Alam 40450, Malaysia; (F.N.A.R.L.); (V.E.A.D.); (S.M.P.); (N.H.O.); (N.H.A.); (N.R.N.H.); (N.A.R.)
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Maiti BK, Maia LB, Moura JJG. Sulfide and transition metals - A partnership for life. J Inorg Biochem 2021; 227:111687. [PMID: 34953313 DOI: 10.1016/j.jinorgbio.2021.111687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/13/2022]
Abstract
Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.
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Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Department of Chemistry, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India.
| | - Luisa B Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
| | - José J G Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
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30
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Singh P, Srivastava R. Utilization of bio-inspired catalyst for CO2 reduction into green fuels: Recent advancement and future perspectives. J CO2 UTIL 2021. [DOI: 10.1016/j.jcou.2021.101748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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31
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Alpdağtaş S, Turunen O, Valjakka J, Binay B. The challenges of using NAD +-dependent formate dehydrogenases for CO 2 conversion. Crit Rev Biotechnol 2021; 42:953-972. [PMID: 34632901 DOI: 10.1080/07388551.2021.1981820] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In recent years, CO2 reduction and utilization have been proposed as an innovative solution for global warming and the ever-growing energy and raw material demands. In contrast to various classical methods, including chemical, electrochemical, and photochemical methods, enzymatic methods offer a green and sustainable option for CO2 conversion. In addition, enzymatic hydrogenation of CO2 into platform chemicals could be used to produce economically useful hydrogen storage materials, making it a win-win strategy. The thermodynamic and kinetic stability of the CO2 molecule makes its utilization a challenging task. However, Nicotine adenine dinucleotide (NAD+)-dependent formate dehydrogenases (FDHs), which have high selectivity and specificity, are attractive catalysts to overcome this issue and convert CO2 into fuels and renewable chemicals. It is necessary to improve the stability, cofactor necessity, and CO2 conversion efficiency of these enzymes, such as by combining them with appropriate hybrid systems. However, metal-independent, NAD+-dependent FDHs, and their CO2 reduction activity have received limited attention to date. This review outlines the CO2 reduction ability of these enzymes as well as their properties, reaction mechanisms, immobilization strategies, and integration with electrochemical and photochemical systems for the production of formic acid or formate. The biotechnological applications of FDH, future perspectives, barriers to CO2 reduction with FDH, and aspects that must be further developed are briefly summarized. We propose that constructing hybrid systems that include NAD+-dependent FDHs is a promising approach to convert CO2 and strengthen the sustainable carbon bio-economy.
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Affiliation(s)
- Saadet Alpdağtaş
- Department of Biology, Van Yuzuncu Yil University, Tusba, Turkey
| | - Ossi Turunen
- School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | - Jarkko Valjakka
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Barış Binay
- Department of Bioengineering, Gebze Technical University, Gebze, Turkey
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32
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Intasian P, Prakinee K, Phintha A, Trisrivirat D, Weeranoppanant N, Wongnate T, Chaiyen P. Enzymes, In Vivo Biocatalysis, and Metabolic Engineering for Enabling a Circular Economy and Sustainability. Chem Rev 2021; 121:10367-10451. [PMID: 34228428 DOI: 10.1021/acs.chemrev.1c00121] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the industrial revolution, the rapid growth and development of global industries have depended largely upon the utilization of coal-derived chemicals, and more recently, the utilization of petroleum-based chemicals. These developments have followed a linear economy model (produce, consume, and dispose). As the world is facing a serious threat from the climate change crisis, a more sustainable solution for manufacturing, i.e., circular economy in which waste from the same or different industries can be used as feedstocks or resources for production offers an attractive industrial/business model. In nature, biological systems, i.e., microorganisms routinely use their enzymes and metabolic pathways to convert organic and inorganic wastes to synthesize biochemicals and energy required for their growth. Therefore, an understanding of how selected enzymes convert biobased feedstocks into special (bio)chemicals serves as an important basis from which to build on for applications in biocatalysis, metabolic engineering, and synthetic biology to enable biobased processes that are greener and cleaner for the environment. This review article highlights the current state of knowledge regarding the enzymatic reactions used in converting biobased wastes (lignocellulosic biomass, sugar, phenolic acid, triglyceride, fatty acid, and glycerol) and greenhouse gases (CO2 and CH4) into value-added products and discusses the current progress made in their metabolic engineering. The commercial aspects and life cycle assessment of products from enzymatic and metabolic engineering are also discussed. Continued development in the field of metabolic engineering would offer diversified solutions which are sustainable and renewable for manufacturing valuable chemicals.
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Affiliation(s)
- Pattarawan Intasian
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Nopphon Weeranoppanant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.,Department of Chemical Engineering, Faculty of Engineering, Burapha University, 169, Long-hard Bangsaen, Saensook, Muang, Chonburi 20131, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand
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33
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Löwe H, Kremling A. In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways. BIODESIGN RESEARCH 2021; 2021:9898316. [PMID: 37849946 PMCID: PMC10521678 DOI: 10.34133/2021/9898316] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/02/2021] [Indexed: 10/19/2023] Open
Abstract
In the recent years, engineering new-to-nature CO2- and C1-fixing metabolic pathways made a leap forward. New, artificial pathways promise higher yields and activity than natural ones like the Calvin-Benson-Bassham (CBB) cycle. The question remains how to best predict their in vivo performance and what actually makes one pathway "better" than another. In this context, we explore aerobic carbon fixation pathways by a computational approach and compare them based on their specific activity and yield on methanol, formate, and CO2/H2 considering the kinetics and thermodynamics of the reactions. Besides pathways found in nature or implemented in the laboratory, this included two completely new cycles with favorable features: the reductive citramalyl-CoA cycle and the 2-hydroxyglutarate-reverse tricarboxylic acid cycle. A comprehensive kinetic data set was collected for all enzymes of all pathways, and missing kinetic data were sampled with the Parameter Balancing algorithm. Kinetic and thermodynamic data were fed to the Enzyme Cost Minimization algorithm to check for respective inconsistencies and calculate pathway-specific activities. The specific activities of the reductive glycine pathway, the CETCH cycle, and the new reductive citramalyl-CoA cycle were predicted to match the best natural cycles with superior product-substrate yield. However, the CBB cycle performed better in terms of activity compared to the alternative pathways than previously thought. We make an argument that stoichiometric yield is likely not the most important design criterion of the CBB cycle. Still, alternative carbon fixation pathways were paretooptimal for specific activity and product-substrate yield in simulations with C1 substrates and CO2/H2 and therefore hold great potential for future applications in Industrial Biotechnology and Synthetic Biology.
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Affiliation(s)
- Hannes Löwe
- Systems Biotechnology, Technical University of Munich, Germany
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34
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Wells M, Basu P, Stolz JF. The physiology and evolution of microbial selenium metabolism. Metallomics 2021; 13:6261189. [PMID: 33930157 DOI: 10.1093/mtomcs/mfab024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/27/2022]
Abstract
Selenium is an essential trace element whose compounds are widely metabolized by organisms from all three domains of life. Moreover, phylogenetic evidence indicates that selenium species, along with iron, molybdenum, tungsten, and nickel, were metabolized by the last universal common ancestor of all cellular lineages, primarily for the synthesis of the 21st amino acid selenocysteine. Thus, selenium metabolism is both environmentally ubiquitous and a physiological adaptation of primordial life. Selenium metabolic reactions comprise reductive transformations both for assimilation into macromolecules and dissimilatory reduction of selenium oxyanions and elemental selenium during anaerobic respiration. This review offers a comprehensive overview of the physiology and evolution of both assimilatory and dissimilatory selenium metabolism in bacteria and archaea, highlighting mechanisms of selenium respiration. This includes a thorough discussion of our current knowledge of the physiology of selenocysteine synthesis and incorporation into proteins in bacteria obtained from structural biology. Additionally, this is the first comprehensive discussion in a review of the incorporation of selenium into the tRNA nucleoside 5-methylaminomethyl-2-selenouridine and as an inorganic cofactor in certain molybdenum hydroxylase enzymes. Throughout, conserved mechanisms and derived features of selenium metabolism in both domains are emphasized and discussed within the context of the global selenium biogeochemical cycle.
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Affiliation(s)
- Michael Wells
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - John F Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
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35
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Meneghello M, Oliveira AR, Jacq‐Bailly A, Pereira IAC, Léger C, Fourmond V. Formate Dehydrogenases Reduce CO
2
Rather than HCO
3
−
: An Electrochemical Demonstration. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marta Meneghello
- CNRS Aix-Marseille Université BIP IMM IM2B 31 Chemin J. Aiguier, CS70071 13402 Marseille Cedex 20 France
| | - Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA) Universidade Nova de Lisboa Oeiras Portugal
| | - Aurore Jacq‐Bailly
- CNRS Aix-Marseille Université BIP IMM IM2B 31 Chemin J. Aiguier, CS70071 13402 Marseille Cedex 20 France
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA) Universidade Nova de Lisboa Oeiras Portugal
| | - Christophe Léger
- CNRS Aix-Marseille Université BIP IMM IM2B 31 Chemin J. Aiguier, CS70071 13402 Marseille Cedex 20 France
| | - Vincent Fourmond
- CNRS Aix-Marseille Université BIP IMM IM2B 31 Chemin J. Aiguier, CS70071 13402 Marseille Cedex 20 France
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36
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Meneghello M, Oliveira AR, Jacq‐Bailly A, Pereira IAC, Léger C, Fourmond V. Formate Dehydrogenases Reduce CO
2
Rather than HCO
3
−
: An Electrochemical Demonstration. Angew Chem Int Ed Engl 2021; 60:9964-9967. [DOI: 10.1002/anie.202101167] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 11/10/2022]
Affiliation(s)
- Marta Meneghello
- CNRS Aix-Marseille Université BIP IMM IM2B 31 Chemin J. Aiguier, CS70071 13402 Marseille Cedex 20 France
| | - Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA) Universidade Nova de Lisboa Oeiras Portugal
| | - Aurore Jacq‐Bailly
- CNRS Aix-Marseille Université BIP IMM IM2B 31 Chemin J. Aiguier, CS70071 13402 Marseille Cedex 20 France
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA) Universidade Nova de Lisboa Oeiras Portugal
| | - Christophe Léger
- CNRS Aix-Marseille Université BIP IMM IM2B 31 Chemin J. Aiguier, CS70071 13402 Marseille Cedex 20 France
| | - Vincent Fourmond
- CNRS Aix-Marseille Université BIP IMM IM2B 31 Chemin J. Aiguier, CS70071 13402 Marseille Cedex 20 France
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37
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Rouf S, Greish YE, Al-Zuhair S. Immobilization of formate dehydrogenase in metal organic frameworks for enhanced conversion of carbon dioxide to formate. CHEMOSPHERE 2021; 267:128921. [PMID: 33190911 DOI: 10.1016/j.chemosphere.2020.128921] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/13/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
Hydrogenation of carbon dioxide (CO2) to formic acid by the enzyme formate dehydrogenase (FDH) is a promising technology for reducing CO2 concentrations in an environmentally friendly manner. However, the easy separation of FDH with enhanced stability and reusability is essential to the practical and economical implementation of the process. To achieve this, the enzyme must be used in an immobilized form. However, conventional immobilization by physical adsorption is prone to leaching, resulting in low stability. Although other immobilization methods (such as chemical adsorption) enhance stability, they generally result in low activity. In addition, mass transfer limitations are a major problem with most conventional immobilized enzymes. In this review paper, the effectiveness of metal organic frameworks (MOFs) is assessed as a promising alternative support for FDH immobilization. Kinetic mechanisms and stability of wild FDH from various sources were assessed and compared to those of cloned and genetically modified FDH. Various techniques for the synthesis of MOFs and different immobilization strategies are presented, with special emphasis on in situ and post synthetic immobilization of FDH in MOFs for CO2 hydrogenation.
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Affiliation(s)
- Shadeera Rouf
- Chemical and Petroleum Engineering Department, UAE University, 15551, Al Ain, United Arab Emirates
| | - Yasser E Greish
- Chemistry Department, UAE University, 15551, Al Ain, United Arab Emirates
| | - Sulaiman Al-Zuhair
- Chemical and Petroleum Engineering Department, UAE University, 15551, Al Ain, United Arab Emirates.
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38
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Zhang X, Shao W, Chen B, Wang M. Cross-linking of carbonic anhydrase and formate dehydrogenase based on amino acid specific recognition: Conversion of carbon dioxide to formic acid. Enzyme Microb Technol 2021; 146:109763. [PMID: 33812561 DOI: 10.1016/j.enzmictec.2021.109763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/15/2021] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
Inspired by the cascades performed in vivo, the assembly of multiple enzymes in vitro has strongly moved into the focus of researchers in the field of biocatalysis. In this study, a new, mild and accurate enzyme cross-linking method is revealed. Microbial transglutaminase (MTG) acts as a "cross-linking medium" by identifying the amide group of the glutamine and the primary amine group of lysine in the artificial peptide tags specifically to form an iso-peptide bond. Here, carbonic anhydrase (CA) and formate dehydrogenase (FDH) with different peptide tags that can be recognized by MTG were linked together to obtain different proportions of cross-linked enzymes for efficient conversion of greenhouse gas carbon dioxide to formic acid. After cross-linking, we obtained "one-to-one" and "one-to-more" cross-linked enzyme aggregates. There is a minor residual loss of the two enzymes, the remaining enzyme activity of CA is more than 93%, and the remaining enzyme activity of FDH is more than 84%. In particular, the overall catalytic efficiency of the cross-linked enzyme is increased by 5.8 times compared with free enzymes and the thermal stability of FDH at different temperatures is improved. The applied strategy demonstrates the potential application of MTG in multi-enzyme assembly and synthetic biology.
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Affiliation(s)
- Xiaonan Zhang
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Wenxuan Shao
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Biqiang Chen
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, PR China.
| | - Meng Wang
- National Energy R&D Center for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, PR China
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39
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Adamson C, Kanai M. Integrating abiotic chemical catalysis and enzymatic catalysis in living cells. Org Biomol Chem 2021; 19:37-45. [DOI: 10.1039/d0ob01898h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review hybrid systems of abiotic catalysis and enzymatic catalysis, which function in living cells. This research direction will stimulate multidisciplinary fields, including complex molecule synthesis, energy production, and life science.
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Affiliation(s)
- Christopher Adamson
- Graduate School of Pharmaceutical Sciences
- The University of Tokyo
- Tokyo 113-0033
- Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences
- The University of Tokyo
- Tokyo 113-0033
- Japan
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40
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Alpdagtas S, Binay B. Nadp+-dependent formate dehydrogenase: a review. BIOCATAL BIOTRANSFOR 2020. [DOI: 10.1080/10242422.2020.1865933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Saadet Alpdagtas
- Department of Biology, Faculty of Science, Van Yuzuncu Yil University, Tusba, Turkey
| | - Barış Binay
- Department of Bioengineering, Gebze Technical University, Gebze, Turkey
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41
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Moon M, Park GW, Lee JP, Lee JS, Min K. Recent progress in formate dehydrogenase (FDH) as a non-photosynthetic CO2 utilizing enzyme: A short review. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.101353] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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42
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A cyanobacterial photorespiratory bypass model to enhance photosynthesis by rerouting photorespiratory pathway in C 3 plants. Sci Rep 2020; 10:20879. [PMID: 33257792 PMCID: PMC7705653 DOI: 10.1038/s41598-020-77894-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/05/2020] [Indexed: 11/08/2022] Open
Abstract
Plants employ photosynthesis to produce sugars for supporting their growth. During photosynthesis, an enzyme Ribulose 1,5 bisphosphate carboxylase/oxygenase (Rubisco) combines its substrate Ribulose 1,5 bisphosphate (RuBP) with CO2 to produce phosphoglycerate (PGA). Alongside, Rubisco also takes up O2 and produce 2-phosphoglycolate (2-PG), a toxic compound broken down into PGA through photorespiration. Photorespiration is not only a resource-demanding process but also results in CO2 loss which affects photosynthetic efficiency in C3 plants. Here, we propose to circumvent photorespiration by adopting the cyanobacterial glycolate decarboxylation pathway into C3 plants. For that, we have integrated the cyanobacterial glycolate decarboxylation pathway into a kinetic model of C3 photosynthetic pathway to evaluate its impact on photosynthesis and photorespiration. Our results show that the cyanobacterial glycolate decarboxylation bypass model exhibits a 10% increase in net photosynthetic rate (A) in comparison with C3 model. Moreover, an increased supply of intercellular CO2 (Ci) from the bypass resulted in a 54.8% increase in PGA while reducing photorespiratory intermediates including glycolate (− 49%) and serine (− 32%). The bypass model, at default conditions, also elucidated a decline in phosphate-based metabolites including RuBP (− 61.3%). The C3 model at elevated level of inorganic phosphate (Pi), exhibited a significant change in RuBP (+ 355%) and PGA (− 98%) which is attributable to the low availability of Ci. Whereas, at elevated Pi, the bypass model exhibited an increase of 73.1% and 33.9% in PGA and RuBP, respectively. Therefore, we deduce a synergistic effect of elevation in CO2 and Pi pool on photosynthesis. We also evaluated the integrative action of CO2, Pi, and Rubisco carboxylation activity (Vcmax) on A and observed that their simultaneous increase raised A by 26%, in the bypass model. Taken together, the study potentiates engineering of cyanobacterial decarboxylation pathway in C3 plants to bypass photorespiration thereby increasing the overall efficiency of photosynthesis.
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Liang B, Zhao Y, Yang J. Recent Advances in Developing Artificial Autotrophic Microorganism for Reinforcing CO 2 Fixation. Front Microbiol 2020; 11:592631. [PMID: 33240247 PMCID: PMC7680860 DOI: 10.3389/fmicb.2020.592631] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/21/2020] [Indexed: 11/13/2022] Open
Abstract
With the goal of achieving carbon sequestration, emission reduction and cleaner production, biological methods have been employed to convert carbon dioxide (CO2) into fuels and chemicals. However, natural autotrophic organisms are not suitable cell factories due to their poor carbon fixation efficiency and poor growth rate. Heterotrophic microorganisms are promising candidates, since they have been proven to be efficient biofuel and chemical production chassis. This review first briefly summarizes six naturally occurring CO2 fixation pathways, and then focuses on recent advances in artificially designing efficient CO2 fixation pathways. Moreover, this review discusses the transformation of heterotrophic microorganisms into hemiautotrophic microorganisms and delves further into fully autotrophic microorganisms (artificial autotrophy) by use of synthetic biological tools and strategies. Rapid developments in artificial autotrophy have laid a solid foundation for the development of efficient carbon fixation cell factories. Finally, this review highlights future directions toward large-scale applications. Artificial autotrophic microbial cell factories need further improvements in terms of CO2 fixation pathways, reducing power supply, compartmentalization and host selection.
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Affiliation(s)
- Bo Liang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China.,Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yunkun Zhao
- Pony Testing International Group, Qingdao, China
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China.,Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
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Sánchez-Andrea I, Guedes IA, Hornung B, Boeren S, Lawson CE, Sousa DZ, Bar-Even A, Claassens NJ, Stams AJM. The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans. Nat Commun 2020; 11:5090. [PMID: 33037220 PMCID: PMC7547702 DOI: 10.1038/s41467-020-18906-7] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 09/14/2020] [Indexed: 12/30/2022] Open
Abstract
Six CO2 fixation pathways are known to operate in photoautotrophic and chemoautotrophic microorganisms. Here, we describe chemolithoautotrophic growth of the sulphate-reducing bacterium Desulfovibrio desulfuricans (strain G11) with hydrogen and sulphate as energy substrates. Genomic, transcriptomic, proteomic and metabolomic analyses reveal that D. desulfuricans assimilates CO2 via the reductive glycine pathway, a seventh CO2 fixation pathway. In this pathway, CO2 is first reduced to formate, which is reduced and condensed with a second CO2 to generate glycine. Glycine is further reduced in D. desulfuricans by glycine reductase to acetyl-P, and then to acetyl-CoA, which is condensed with another CO2 to form pyruvate. Ammonia is involved in the operation of the pathway, which is reflected in the dependence of the autotrophic growth rate on the ammonia concentration. Our study demonstrates microbial autotrophic growth fully supported by this highly ATP-efficient CO2 fixation pathway.
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Affiliation(s)
- Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Iame Alves Guedes
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Bastian Hornung
- Leids Universitair Medisch Centrum (LUMC), Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Robinson WE, Bassegoda A, Blaza JN, Reisner E, Hirst J. Understanding How the Rate of C-H Bond Cleavage Affects Formate Oxidation Catalysis by a Mo-Dependent Formate Dehydrogenase. J Am Chem Soc 2020; 142:12226-12236. [PMID: 32551568 PMCID: PMC7366381 DOI: 10.1021/jacs.0c03574] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal-dependent formate dehydrogenases (FDHs) catalyze the reversible conversion of formate into CO2, a proton, and two electrons. Kinetic studies of FDHs provide key insights into their mechanism of catalysis, relevant as a guide for the development of efficient electrocatalysts for formate oxidation as well as for CO2 capture and utilization. Here, we identify and explain the kinetic isotope effect (KIE) observed for the oxidation of formate and deuterioformate by the Mo-containing FDH from Escherichia coli using three different techniques: steady-state solution kinetic assays, protein film electrochemistry (PFE), and pre-steady-state stopped-flow methods. For each technique, the Mo center of FDH is reoxidized at a different rate following formate oxidation, significantly affecting the observed kinetic behavior and providing three different viewpoints on the KIE. Steady-state turnover in solution, using an artificial electron acceptor, is kinetically limited by diffusional intermolecular electron transfer, masking the KIE. In contrast, interfacial electron transfer in PFE is fast, lifting the electron-transfer rate limitation and manifesting a KIE of 2.44. Pre-steady-state analyses using stopped-flow spectroscopy revealed a KIE of 3 that can be assigned to the C-H bond cleavage step during formate oxidation. We formalize our understanding of FDH catalysis by fitting all the data to a single kinetic model, recreating the condition-dependent shift in rate-limitation of FDH catalysis between active-site chemical catalysis and regenerative electron transfer. Furthermore, our model predicts the steady-state and time-dependent concentrations of catalytic intermediates, providing a valuable framework for the design of future mechanistic experiments.
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Affiliation(s)
- William E Robinson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Arnau Bassegoda
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, U.K
| | - James N Blaza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, U.K
| | - Erwin Reisner
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, U.K
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Structure: Function Studies of the Cytosolic, Mo- and NAD+-Dependent Formate Dehydrogenase from Cupriavidus necator. INORGANICS 2020. [DOI: 10.3390/inorganics8070041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Here, we report recent progress our laboratories have made in understanding the maturation and reaction mechanism of the cytosolic and NAD+-dependent formate dehydrogenase from Cupriavidus necator. Our recent work has established that the enzyme is fully capable of catalyzing the reverse of the physiological reaction, namely, the reduction of CO2 to formate using NADH as a source of reducing equivalents. The steady-state kinetic parameters in the forward and reverse directions are consistent with the expected Haldane relationship. The addition of an NADH-regenerating system consisting of glucose and glucose dehydrogenase increases the yield of formate approximately 10-fold. This work points to possible ways of optimizing the reverse of the enzyme’s physiological reaction with commercial potential as an effective means of CO2 remediation. New insight into the maturation of the enzyme comes from the recently reported structure of the FdhD sulfurase. In E. coli, FdhD transfers a catalytically essential sulfur to the maturing molybdenum cofactor prior to insertion into the apoenzyme of formate dehydrogenase FdhF, which has high sequence similarity to the molybdenum-containing domain of the C. necator FdsA. The FdhD structure suggests that the molybdenum cofactor may first be transferred from the sulfurase to the C-terminal cap domain of apo formate dehydrogenase, rather than being transferred directly to the body of the apoenzyme. Closing of the cap domain over the body of the enzymes delivers the Mo-cofactor into the active site, completing the maturation of formate dehydrogenase. The structural and kinetic characterization of the NADH reduction of the FdsBG subcomplex of the enzyme provides further insights in reversing of the formate dehydrogenase reaction. Most notably, we observe the transient formation of a neutral semiquinone FMNH·, a species that has not been observed previously with holoenzyme. After initial reduction of the FMN of FdsB by NADH to the hydroquinone (with a kred of 680 s−1 and Kd of 190 µM), one electron is rapidly transferred to the Fe2S2 cluster of FdsG, leaving FMNH·. The Fe4S4 cluster of FdsB does not become reduced in the process. These results provide insight into the function not only of the C. necator formate dehydrogenase but also of other members of the NADH dehydrogenase superfamily of enzymes to which it belongs.
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Methane, arsenic, selenium and the origins of the DMSO reductase family. Sci Rep 2020; 10:10946. [PMID: 32616801 PMCID: PMC7331816 DOI: 10.1038/s41598-020-67892-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/16/2020] [Indexed: 11/16/2022] Open
Abstract
Mononuclear molybdoenzymes of the dimethyl sulfoxide reductase (DMSOR) family catalyze a number of reactions essential to the carbon, nitrogen, sulfur, arsenic, and selenium biogeochemical cycles. These enzymes are also ancient, with many lineages likely predating the divergence of the last universal common ancestor into the Bacteria and Archaea domains. We have constructed rooted phylogenies for over 1,550 representatives of the DMSOR family using maximum likelihood methods to investigate the evolution of the arsenic biogeochemical cycle. The phylogenetic analysis provides compelling evidence that formylmethanofuran dehydrogenase B subunits, which catalyze the reduction of CO2 to formate during hydrogenotrophic methanogenesis, constitutes the most ancient lineage. Our analysis also provides robust support for selenocysteine as the ancestral ligand for the Mo/W atom. Finally, we demonstrate that anaerobic arsenite oxidase and respiratory arsenate reductase catalytic subunits represent a more ancient lineage of DMSORs compared to aerobic arsenite oxidase catalytic subunits, which evolved from the assimilatory nitrate reductase lineage. This provides substantial support for an active arsenic biogeochemical cycle on the anoxic Archean Earth. Our work emphasizes that the use of chalcophilic elements as substrates as well as the Mo/W ligand in DMSORs has indelibly shaped the diversification of these enzymes through deep time.
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Min K, Park YS, Park GW, Lee JP, Moon M, Ko CH, Lee JS. Elevated conversion of CO 2 to versatile formate by a newly discovered formate dehydrogenase from Rhodobacter aestuarii. BIORESOURCE TECHNOLOGY 2020; 305:123155. [PMID: 32178996 DOI: 10.1016/j.biortech.2020.123155] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Due to climate change, recent research interests have increased towards CO2 utilization as a strategy to mitigate the atmospheric CO2 level. Herein, we aimed to explore formate dehydrogenases (FDHs) from chemoautotroph to discover an efficient and O2-tolerant biocatalyst for catalyzing the CO2 reduction to a versatile formate. Through genome-mining and phylogenetic analysis, the FDH from Rhodobacter aestuarii (RaFDH) was newly discovered as a promising O2-tolernat CO2 reductase and was successfully expressed in Escherichia coli. In this study, the optimum conditions and turnover rates of RaFDH were examined for CO2 reduction and formate oxidation. In particular, the RaFDH-driven CO2 reduction far surpassed the formate oxidation with a turnover rate of 48.3 and 15.6 min-1, respectively. The outstanding superiority of RaFDH towards CO2 reduction can be applicable for constructing a feasible electroenzymatic system that produce a versatile formate from CO2 as a cheap, abundant, and renewable resource.
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Affiliation(s)
- Kyoungseon Min
- Gwangju Bio/Energy Research Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Yong-Soo Park
- Gwangju Bio/Energy Research Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea; School of Chemical Engineering, Chonnam National University, Gwangju 61886, Republic of Korea
| | - Gwon Woo Park
- Gwangju Bio/Energy Research Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Joon-Pyo Lee
- Gwangju Bio/Energy Research Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Myounghoon Moon
- Gwangju Bio/Energy Research Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Chang Hyun Ko
- School of Chemical Engineering, Chonnam National University, Gwangju 61886, Republic of Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy Research Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea.
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Young T, Niks D, Hakopian S, Tam TK, Yu X, Hille R, Blaha GM. Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG from Cupriavidus necator. J Biol Chem 2020; 295:6570-6585. [PMID: 32249211 PMCID: PMC7212643 DOI: 10.1074/jbc.ra120.013264] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/30/2020] [Indexed: 01/07/2023] Open
Abstract
Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD+-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium Cupriavidus necator H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, Fe4S4 in FdsB and Fe2S2 in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH•, not previously observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH-, initially formed via NADH-mediated reduction, to the Fe2S2 cluster. This Fe2S2 cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the re-face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD+ binding in proper NADH dehydrogenases.
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Affiliation(s)
- Tynan Young
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Sheron Hakopian
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Timothy K. Tam
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Xuejun Yu
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California 92521, To whom correspondence may be addressed:
Dept. of Biochemistry, University of California, Riverside, 900 University Ave., Boyce Hall 2404, Riverside, CA 92521. Tel.:
951-827-6354; E-mail:
| | - Gregor M. Blaha
- Department of Biochemistry, University of California, Riverside, California 92521, To whom correspondence may be addressed:
Dept. of Biochemistry, University of California, Riverside, 900 University Ave., Boyce Hall 5489, Riverside, CA 92521. Tel.:
951-827-3832; Fax:
951-827-4294; E-mail:
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50
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Radon C, Mittelstädt G, Duffus BR, Bürger J, Hartmann T, Mielke T, Teutloff C, Leimkühler S, Wendler P. Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase. Nat Commun 2020; 11:1912. [PMID: 32313256 PMCID: PMC7171172 DOI: 10.1038/s41467-020-15614-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/19/2020] [Indexed: 11/09/2022] Open
Abstract
Metal-containing formate dehydrogenases (FDH) catalyse the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active site. They display a diverse subunit and cofactor composition, but structural information on these enzymes is limited. Here we report the cryo-electron microscopic structures of the soluble Rhodobacter capsulatus FDH (RcFDH) as isolated and in the presence of reduced nicotinamide adenine dinucleotide (NADH). RcFDH assembles into a 360 kDa dimer of heterotetramers revealing a putative interconnection of electron pathway chains. In the presence of NADH, the RcFDH structure shows charging of cofactors, indicative of an increased electron load. Rhodobacter capsulatus NAD+ dependent formate dehydrogenase (RcFDH) is a molybdoenzyme that catalyses the reversible oxidation of formate to carbon dioxide, and is of interest for biotechnological applications. Here the authors present the cryo-EM structures of RcFDH as isolated from R. capsulatus and in the reduced state with bound NADH, and discuss the enzyme mechanism.
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Affiliation(s)
- Christin Radon
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany
| | - Gerd Mittelstädt
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany.,Ferrier Research Institute, Victoria University of Wellington, Kelburn Parade, Wellington, 6012, New Zealand
| | - Benjamin R Duffus
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany
| | - Jörg Bürger
- Max-Planck Institute of Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany.,Charité, Institut für Medizinische Physik und Biophysik, Charitéplatz 1, 10117, Berlin, Germany
| | - Tobias Hartmann
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany
| | - Thorsten Mielke
- Max-Planck Institute of Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Christian Teutloff
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany
| | - Petra Wendler
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476, Potsdam-Golm, Germany.
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