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Kropp A, Gillett DL, Venugopal H, Gonzálvez MA, Lingford JP, Jain S, Barlow CK, Zhang J, Greening C, Grinter R. Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria. Nat Chem Biol 2025:10.1038/s41589-025-01836-0. [PMID: 39881213 DOI: 10.1038/s41589-025-01836-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 01/06/2025] [Indexed: 01/31/2025]
Abstract
Diverse bacteria and archaea use atmospheric CO as an energy source for long-term survival. Bacteria use [MoCu]-CO dehydrogenases (Mo-CODH) to convert atmospheric CO to carbon dioxide, transferring the obtained electrons to the aerobic respiratory chain. However, it is unknown how these enzymes oxidize CO at low concentrations and interact with the respiratory chain. Here, we use cryo-electron microscopy and structural modeling to show how Mo-CODHMs (CoxSML) from Mycobacterium smegmatis interacts with its partner, the membrane-bound menaquinone-binding protein CoxG. We provide electrochemical, biochemical and genetic evidence that Mo-CODH transfers CO-derived electrons to the aerobic respiratory chain through CoxG. Lastly, we show that Mo-CODH and CoxG genetically and structurally associate in diverse bacteria and archaea. These findings reveal the basis of the biogeochemically and ecologically important process of atmospheric CO oxidation, while demonstrating that long-range quinone transport is a general mechanism of energy conservation, which convergently evolved on multiple occasions.
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Affiliation(s)
- Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - David L Gillett
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hari Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | | | - James P Lingford
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Surbhi Jain
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Christopher K Barlow
- Department of Biochemistry, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Monash Proteomics & Metabolomics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jie Zhang
- School of Chemistry, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence for Green Electrochemical Transformation of Carbon Dioxide, Monash University, Clayton, Victoria, Australia
- ARC Research Hub for Carbon Utilisation and Recycling, Monash University, Clayton, Victoria, USA
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- ARC Research Hub for Carbon Utilisation and Recycling, Monash University, Clayton, Victoria, USA.
- Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, USA.
- Centre to Impact AMR, Monash University, Clayton, Victoria, USA.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
- Centre for Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia.
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Terholsen H, Huerta-Zerón HD, Möller C, Junge H, Beller M, Bornscheuer UT. Photocatalytic CO 2 Reduction Using CO 2-Binding Enzymes. Angew Chem Int Ed Engl 2024; 63:e202319313. [PMID: 38324458 DOI: 10.1002/anie.202319313] [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: 12/14/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024]
Abstract
Novel concepts to utilize carbon dioxide are required to reach a circular carbon economy and minimize environmental issues. To achieve these goals, photo-, electro-, thermal-, and biocatalysis are key tools to realize this, preferentially in aqueous solutions. Nevertheless, catalytic systems that operate efficiently in water are scarce. Here, we present a general strategy for the identification of enzymes suitable for CO2 reduction based on structural analysis for potential carbon dioxide binding sites and subsequent mutations. We discovered that the phenolic acid decarboxylase from Bacillus subtilis (BsPAD) promotes the aqueous photocatalytic CO2 reduction selectively to carbon monoxide in the presence of a ruthenium photosensitizer and sodium ascorbate. With engineered variants of BsPAD, TONs of up to 978 and selectivities of up to 93 % (favoring the desired CO over H2 generation) were achieved. Mutating the active site region of BsPAD further improved turnover numbers for CO generation. This also revealed that electron transfer is rate-limiting and occurs via multistep tunneling. The generality of this approach was proven by using eight other enzymes, all showing the desired activity underlining that a range of proteins is capable of photocatalytic CO2 reduction.
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Affiliation(s)
- Henrik Terholsen
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | | | - Christina Möller
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | - Henrik Junge
- Leibniz Institute for Catalysis e.V., Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Matthias Beller
- Leibniz Institute for Catalysis e.V., Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Uwe T Bornscheuer
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
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3
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O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas. Nat Catal 2022. [DOI: 10.1038/s41929-022-00834-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Yoon J, Oh MK. Strategies for Biosynthesis of C1 Gas-derived Polyhydroxyalkanoates: A review. BIORESOURCE TECHNOLOGY 2022; 344:126307. [PMID: 34767907 DOI: 10.1016/j.biortech.2021.126307] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Biosynthesis of polyhydroxyalkanoates (PHAs) from C1 gases is highly desirable in solving problems such as climate change and microplastic pollution. PHAs are biopolymers synthesized in microbial cells and can be used as alternatives to petroleum-based plastics because of their biodegradability. Because 50% of the cost of PHA production is due to organic carbon sources and salts, the utilization of costless C1 gases as carbon sources is expected to be a promising approach for PHA production. In this review, strategies for PHA production using C1 gases through fermentation and metabolic engineering are discussed. In particular, autotrophs, acetogens, and methanotrophs are strains that can produce PHA from CO2, CO, and CH4. In addition, integrated bioprocesses for the efficient utilization of C1 gases are introduced. Biorefinery processes from C1 gas into bioplastics are prospective strategies with promising potential and feasibility to alleviate environmental issues.
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Affiliation(s)
- Jihee Yoon
- Department of Chemical and Biological Engineering, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea.
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5
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Reginald SS, Etzerodt M, Fapyane D, Chang IS. Functional Expression of a Mo-Cu-Dependent Carbon Monoxide Dehydrogenase (CODH) and Its Use as a Dissolved CO Bio-microsensor. ACS Sens 2021; 6:2772-2782. [PMID: 34253013 DOI: 10.1021/acssensors.1c01243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, we report the heterologous expression in Escherichia coli of a Mo-Cu-containing carbon monoxide dehydrogenase (Mo-Cu CODH) from Hydrogenophaga pseudoflava, which resulted in an active protein catalyzing CO oxidation to CO2. By supplying the E. coli growth medium with Na2MoO4 (Mo) and CuSO4 (Cu), the Mo-Cu CODH metal cofactors precursors, the expressed L-subunit was found to have CO-oxidation activity even without the M- and S- subunits. This successful expression of CO-oxidizing-capable single L-subunit provides direct evidence of its role as the catalytic center of Mo-Cu CODH that has not been discovered and studied before. Subsequently, we used the expressed protein to construct a CO bio-microsensor based on a newly developed fast and sensitive Clark-type CO2 transducer using an aprotic solvent/ionic liquid electrolyte. The CO bio-microsensor exhibited a linear response to CO concentration in the 0-9 μM range, with a limit of detection (LOD) of 15 nM CO. The sensor uses a mixture of Mo-Cu CODH's L-subunit/Mo, Cu cofactors/methylene blue, confined in the enzyme chamber that is placed in front of a CO2 transducer. The optimized sensor's sensitivity and performance were retained to levels of at least 80% for 1 week of continuous polarization and operation in an aqueous medium. We have also demonstrated the use of an alkaline front-trap solution to make a completely O2/CO2 interference-free microsensor. The CO bio-microsensor developed in this study is potentially useful as an analytical tool for the detection of trace CO in dissolved form for monitoring dissolved CO concentration dynamics in natural or synthetic systems.
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Affiliation(s)
- Stacy Simai Reginald
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Michael Etzerodt
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark
| | - Deby Fapyane
- Aarhus University Centre of Water Technology (WATEC), Department of Bioscience, Aarhus University, Ny Munkegade 116, Aarhus 8000, Denmark
| | - In Seop Chang
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
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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: 3.0] [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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Rovaletti A, Bruschi M, Moro G, Cosentino U, Greco C. The Challenging in silico Description of Carbon Monoxide Oxidation as Catalyzed by Molybdenum-Copper CO Dehydrogenase. Front Chem 2019; 6:630. [PMID: 30687693 PMCID: PMC6334162 DOI: 10.3389/fchem.2018.00630] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/03/2018] [Indexed: 01/05/2023] Open
Abstract
Carbon monoxide (CO) is a highly toxic gas to many living organisms. However, some microorganisms are able to use this molecule as the sole source of carbon and energy. Soil bacteria such as the aerobic Oligotropha carboxidovorans are responsible for the annual removal of about 2x108 tons of CO from the atmosphere. Detoxification through oxidation of CO to CO2 is enabled by the MoCu-dependent CO-dehydrogenase enzyme (MoCu-CODH) which-differently from other enzyme classes with similar function-retains its catalytic activity in the presence of atmospheric O2. In the last few years, targeted advancements have been described in the field of bioengineering and biomimetics, which is functional for future technological exploitation of the catalytic properties of MoCu-CODH and for the reproduction of its reactivity in synthetic complexes. Notably, a growing interest for the quantum chemical investigation of this enzyme has recently also emerged. This mini-review compiles the current knowledge of the MoCu-CODH catalytic cycle, with a specific focus on the outcomes of theoretical studies on this enzyme class. Rather controversial aspects from different theoretical studies will be highlighted, thus illustrating the challenges posed by this system as far as the application of density functional theory and hybrid quantum-classical methods are concerned.
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Affiliation(s)
- Anna Rovaletti
- Dipartimento di Scienze dell'Ambiente e della Terra, Università Degli Studi di Milano-Bicocca, Milan, Italy
| | - Maurizio Bruschi
- Dipartimento di Scienze dell'Ambiente e della Terra, Università Degli Studi di Milano-Bicocca, Milan, Italy
| | - Giorgio Moro
- Dipartimento di Biotecnologie e Bioscienze, Università Degli Studi di Milano-Bicocca, Milan, Italy
| | - Ugo Cosentino
- Dipartimento di Scienze dell'Ambiente e della Terra, Università Degli Studi di Milano-Bicocca, Milan, Italy
| | - Claudio Greco
- Dipartimento di Scienze dell'Ambiente e della Terra, Università Degli Studi di Milano-Bicocca, Milan, Italy
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8
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Kaufmann P, Duffus BR, Teutloff C, Leimkühler S. Functional Studies on Oligotropha carboxidovorans Molybdenum–Copper CO Dehydrogenase Produced in Escherichia coli. Biochemistry 2018; 57:2889-2901. [DOI: 10.1021/acs.biochem.8b00128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul Kaufmann
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, 14476 Potsdam, Germany
| | - Benjamin R. Duffus
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, 14476 Potsdam, Germany
| | - Christian Teutloff
- Institute for Experimental Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Silke Leimkühler
- Institute of Biochemistry and Biology, Department of Molecular Enzymology, University of Potsdam, 14476 Potsdam, Germany
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9
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Roger M, Brown F, Gabrielli W, Sargent F. Efficient Hydrogen-Dependent Carbon Dioxide Reduction by Escherichia coli. Curr Biol 2017; 28:140-145.e2. [PMID: 29290558 PMCID: PMC5772173 DOI: 10.1016/j.cub.2017.11.050] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/06/2017] [Accepted: 11/21/2017] [Indexed: 02/02/2023]
Abstract
Hydrogen-dependent reduction of carbon dioxide to formic acid offers a promising route to greenhouse gas sequestration, carbon abatement technologies, hydrogen transport and storage, and the sustainable generation of renewable chemical feedstocks [1]. The most common approach to performing direct hydrogenation of CO2 to formate is to use chemical catalysts in homogeneous or heterogeneous reactions [2]. An alternative approach is to use the ability of living organisms to perform this reaction biologically. However, although CO2 fixation pathways are widely distributed in nature, only a few enzymes have been described that have the ability to perform the direct hydrogenation of CO2 [3, 4, 5]. The formate hydrogenlyase (FHL) enzyme from Escherichia coli normally oxidizes formic acid to carbon dioxide and couples that reaction directly to the reduction of protons to molecular hydrogen [6]. In this work, the reverse reaction of FHL is unlocked. It is established that FHL can operate as a highly efficient hydrogen-dependent carbon dioxide reductase when gaseous CO2 and H2 are placed under pressure (up to 10 bar). Using intact whole cells, the pressurized system was observed to rapidly convert 100% of gaseous CO2 to formic acid, and >500 mM formate was observed to accumulate in solution. Harnessing the reverse reaction has the potential to allow the versatile E. coli system to be employed as an exciting new carbon capture technology or as a cell factory dedicated to formic acid production, which is a commodity in itself as well as a feedstock for the synthesis of other valued chemicals. Escherichia coli produces a formate hydrogenlyase (FHL) enzyme FHL can function in two modes dependent on the prevailing environmental conditions Pressurized CO2 and H2 allow FHL to function as a hydrogen-dependent CO2 reductase The produced formic acid accumulates outside of the bacterial cells
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Affiliation(s)
- Magali Roger
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Fraser Brown
- Ingenza, Roslin Biocentre, Edinburgh EH25 9PP, Scotland
| | - William Gabrielli
- Sasol UK, St Andrews Laboratory, North Haugh, St Andrews KY16 9ST, Scotland
| | - Frank Sargent
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.
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