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Decembrino D, Cannella D. The thin line between monooxygenases and peroxygenases. P450s, UPOs, MMOs, and LPMOs: A brick to bridge fields of expertise. Biotechnol Adv 2024; 72:108321. [PMID: 38336187 DOI: 10.1016/j.biotechadv.2024.108321] [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: 10/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Many scientific fields, although driven by similar purposes and dealing with similar technologies, often appear so isolated and far from each other that even the vocabularies to describe the very same phenomenon might differ. Concerning the vast field of biocatalysis, a special role is played by those redox enzymes that employ oxygen-based chemistry to unlock transformations otherwise possible only with metal-based catalysts. As such, greener chemical synthesis methods and environmentally-driven biotechnological approaches were enabled over the last decades by the use of several enzymes and ultimately resulted in the first industrial applications. Among what can be called today the environmental biorefinery sector, biomass transformation, greenhouse gas reduction, bio-gas/fuels production, bioremediation, as well as bulk or fine chemicals and even pharmaceuticals manufacturing are all examples of fields in which successful prototypes have been demonstrated employing redox enzymes. In this review we decided to focus on the most prominent enzymes (MMOs, LPMO, P450 and UPO) capable of overcoming the ∼100 kcal mol-1 barrier of inactivated CH bonds for the oxyfunctionalization of organic compounds. Harnessing the enormous potential that lies within these enzymes is of extreme value to develop sustainable industrial schemes and it is still deeply coveted by many within the aforementioned fields of application. Hence, the ambitious scope of this account is to bridge the current cutting-edge knowledge gathered upon each enzyme. By creating a broad comparison, scientists belonging to the different fields may find inspiration and might overcome obstacles already solved by the others. This work is organised in three major parts: a first section will be serving as an introduction to each one of the enzymes regarding their structural and activity diversity, whereas a second one will be encompassing the mechanistic aspects of their catalysis. In this regard, the machineries that lead to analogous catalytic outcomes are depicted, highlighting the major differences and similarities. Finally, a third section will be focusing on the elements that allow the oxyfunctionalization chemistry to occur by delivering redox equivalents to the enzyme by the action of diverse redox partners. Redox partners are often overlooked in comparison to the catalytic counterparts, yet they represent fundamental elements to better understand and further develop practical applications based on mono- and peroxygenases.
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Affiliation(s)
- Davide Decembrino
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
| | - David Cannella
- Photobiocatalysis Unit - Crop Production and Biostimulation Lab (CPBL), and Biomass Transformation Lab (BTL), École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Belgium.
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2
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Peng W, Lu J, Kuang J, Tang R, Guan F, Xie K, Zhou L, Yuan Y. Enhancement of hydrogenotrophic methanogenesis for methane production by nano zero-valent iron in soils. ENVIRONMENTAL RESEARCH 2024; 247:118232. [PMID: 38262517 DOI: 10.1016/j.envres.2024.118232] [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: 12/04/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Nanoscale zero-valent iron (nZVI) is attracting increasing attention as the most commonly used environmental remediation material. However, given the high surface area and strong reducing capabilities of nZVI, there is a lack of understanding regarding its effects on the complex anaerobic methane production process in flooded soils. To elucidate the mechanism of CH4 production in soil exposed to nZVI, paddy soil was collected and subjected to anaerobic culture under continuous flooding conditions, with various dosages of nZVI applied. The results showed that the introduction of nZVI into anaerobic flooded rice paddy systems promoted microbial utilization of acetate and carbon dioxide as carbon sources for methane production, ultimately leading to increased methane production. Following the introduction of nZVI into the soil, there was a rapid increase in hydrogen levels in the headspace, surpassing that of the control group. The hydrogen levels in both the experimental and control groups were depleted by the 29th day of culture. These findings suggest that nZVI exposure facilitates the enrichment of hydrogenotrophic methanogens, providing them with a favorable environment for growth. Additionally, it affected soil physicochemical properties by increasing pH and electrical conductivity. The metagenomic analysis further indicates that under exposure to nZVI, hydrogenotrophic methanogens, particularly Methanobacteriaceae and Methanocellaceae, were enriched. The relative abundance of genes such as mcrA and mcrB associated with methane production was increased. This study provides important theoretical insights into the response of key microbes, functional genes, and methane production pathways to nZVI during anaerobic methane production in rice paddy soils, offering fundamental insights into the long-term fate and risks associated with the introduction of nZVI into soils.
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Affiliation(s)
- Weijie Peng
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Jinrong Lu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Jiajie Kuang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Rong Tang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Fengyi Guan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Kunting Xie
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Lihua Zhou
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
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Rawal P, Gupta P. Unidentical Twins: Geometrically Similar but Chemically Distinct Metal-Free Sites in Boron Oxide for Methane Oxidation to HCHO, CO and CO 2. Chemistry 2024:e202401050. [PMID: 38606609 DOI: 10.1002/chem.202401050] [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: 03/14/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/13/2024]
Abstract
Metal-free boron-based catalysts such as boron oxide (B2O3) and boron nitride (h-BN) are promising catalysts for methane oxidation to HCHO and CO. The B2O3 catalyst contains various probable boron sites (B1 to B6), which may be responsible for methane oxidation. In this work, we utilized density functional theory to compare two relevant geometrically identical boron sites (B2 and B4) for their reactivities. The two sites are explored in-detail for the conversion of methane to formaldehyde (M2F), carbon monoxide and carbon dioxide. The B4 site activates the methane C-H bond easily as compared to the B2 site. In M2F conversion, the rate-determining step for the B2 site is the co-activation of dioxygen and methane, whereas over the B4 site, formaldehyde formation is the rate-determining step. The computationally-determined RDS for the B4 site coincides well with the reported experiments. It is further revealed that this site also prefers the formation of CO over CO2, which is in-line with the experiments in literature. It is also shown through orbital analysis that methanol formation does not occur during methane oxidation. We employed descriptors such as condensed Fukui functions and global electrophilicity index to chemically distinct these twin sites.
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Affiliation(s)
- Parveen Rawal
- Computational Catalysis Center, Department of Chemistry, Indian Institute of Technology Roorkee, 247667, Roorkee, Uttarakhand, India
| | - Puneet Gupta
- Computational Catalysis Center, Department of Chemistry, Indian Institute of Technology Roorkee, 247667, Roorkee, Uttarakhand, India
- Center for Sustainable Energy, Indian Institute of Technology Roorkee, 247667, Roorkee, Uttarakhand, India
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [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] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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Zheng L, Cao M, Du Y, Liu Q, Emran MY, Kotb A, Sun M, Ma CB, Zhou M. Artificial enzyme innovations in electrochemical devices: advancing wearable and portable sensing technologies. NANOSCALE 2023; 16:44-60. [PMID: 38053393 DOI: 10.1039/d3nr05728c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
With the rapid evolution of sensing technologies, the integration of nanoscale catalysts, particularly those mimicking enzymatic functions, into electrochemical devices has surfaced as a pivotal advancement. These catalysts, dubbed artificial enzymes, embody a blend of heightened sensitivity, selectivity, and durability, laying the groundwork for innovative applications in real-time health monitoring and environmental detection. This minireview penetrates into the fundamental principles of electrochemical sensing, elucidating the unique attributes that establish artificial enzymes as foundational elements in this field. We spotlight a range of innovations where these catalysts have been proficiently incorporated into wearable and portable platforms. Navigating the pathway of amalgamating these nanoscale wonders into consumer-appealing devices presents a multitude of challenges; nevertheless, the progress made thus far signals a promising trajectory. As the intersection of materials science, biochemistry, and electronics progressively intensifies, a flourishing future seems imminent for artificial enzyme-infused electrochemical devices, with the potential to redefine the landscapes of wearable health diagnostics and portable sensing solutions.
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Affiliation(s)
- Long Zheng
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Analysis and Testing Center, Department of Chemistry, Northeast Normal University, Changchun, Jilin Province 130024, China.
| | - Mengzhu Cao
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Analysis and Testing Center, Department of Chemistry, Northeast Normal University, Changchun, Jilin Province 130024, China.
| | - Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130000, China
| | - Quanyi Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130000, China
| | - Mohammed Y Emran
- Chemistry Department, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt
| | - Ahmed Kotb
- Chemistry Department, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt
| | - Mimi Sun
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Analysis and Testing Center, Department of Chemistry, Northeast Normal University, Changchun, Jilin Province 130024, China.
| | - Chong-Bo Ma
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Analysis and Testing Center, Department of Chemistry, Northeast Normal University, Changchun, Jilin Province 130024, China.
| | - Ming Zhou
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province, Analysis and Testing Center, Department of Chemistry, Northeast Normal University, Changchun, Jilin Province 130024, China.
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Tucci FJ, Jodts RJ, Hoffman BM, Rosenzweig AC. Product analog binding identifies the copper active site of particulate methane monooxygenase. Nat Catal 2023; 6:1194-1204. [PMID: 38187819 PMCID: PMC10766429 DOI: 10.1038/s41929-023-01051-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/22/2023] [Indexed: 01/09/2024]
Abstract
Nature's primary methane-oxidizing enzyme, the membrane-bound particulate methane monooxygenase (pMMO), catalyzes the oxidation of methane to methanol. pMMO activity requires copper, and decades of structural and spectroscopic studies have sought to identify the active site among three candidates: the CuB, CuC, and CuD sites. Challenges associated with the isolation of active pMMO have hindered progress toward locating its catalytic center. However, reconstituting pMMO into native lipid nanodiscs stabilizes its structure and recovers its activity. Here, these active samples were incubated with 2,2,2,-trifluoroethanol (TFE), a product analog that serves as a readily visualized active-site probe. Interactions of TFE with the CuD site were observed by both pulsed ENDOR spectroscopy and cryoEM, implicating CuD and the surrounding hydrophobic pocket as the likely site of methane oxidation. Use of these orthogonal techniques on parallel samples is a powerful approach that can circumvent difficulties in interpreting metalloenzyme cryoEM maps.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
- These authors contributed equally
| | - Richard J Jodts
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
- These authors contributed equally
| | - Brian M Hoffman
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
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Cárdenas-Moreno Y, González-Bacerio J, García Arellano H, Del Monte-Martínez A. Oxidoreductase enzymes: Characteristics, applications, and challenges as a biocatalyst. Biotechnol Appl Biochem 2023; 70:2108-2135. [PMID: 37753743 DOI: 10.1002/bab.2513] [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: 09/26/2022] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
Oxidoreductases are enzymes with distinctive characteristics that favor their use in different areas, such as agriculture, environmental management, medicine, and analytical chemistry. Among these enzymes, oxidases, dehydrogenases, peroxidases, and oxygenases are very interesting. Because their substrate diversity, they can be used in different biocatalytic processes by homogeneous and heterogeneous catalysis. Immobilization of these enzymes has favored their use in the solution of different biotechnological problems, with a notable increase in the study and optimization of this technology in the last years. In this review, the main structural and catalytical features of oxidoreductases, their substrate specificity, immobilization, and usage in biocatalytic processes, such as bioconversion, bioremediation, and biosensors obtainment, are presented.
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Affiliation(s)
- Yosberto Cárdenas-Moreno
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Jorge González-Bacerio
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
- Department of Biochemistry, Faculty of Biology, University of Havana, Havana, Cuba
| | - Humberto García Arellano
- Department of Environmental Sciences, Division of Health and Biological Sciences, Metropolitan Autonomous University, Lerma, Mexico, Mexico
| | - Alberto Del Monte-Martínez
- Laboratory for Enzyme Technology, Centre for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
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8
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Peng W, Wang Z, Zhang Q, Yan S, Wang B. Unraveling the Valence State and Reactivity of Copper Centers in Membrane-Bound Particulate Methane Monooxygenase. J Am Chem Soc 2023; 145:25304-25317. [PMID: 37955571 DOI: 10.1021/jacs.3c08834] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Particulate methane monooxygenase (pMMO) plays a critical role in catalyzing the conversion of methane to methanol, constituting the initial step in the C1 metabolic pathway within methanotrophic bacteria. However, the membrane-bound pMMO's structure and catalytic mechanism, notably the copper's valence state and genuine active site for methane oxidation, have remained elusive. Based on the recently characterized structure of membrane-bound pMMO, extensive computational studies were conducted to address these long-standing issues. A comprehensive analysis comparing the quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulated structures with cryo-EM data indicates that both the CuC and CuD sites tend to stay in the Cu(I) valence state within the membrane environment. Additionally, the concurrent presence of Cu(I) at both CuC and CuD sites leads to the significant reduction of the ligand-binding cavity situated between them, making it less likely to accommodate a reductant molecule such as durohydroquinone (DQH2). Subsequent QM/MM calculations reveal that the CuD(I) site is more reactive than the CuC(I) site in oxygen activation, en route to H2O2 formation and the generation of Cu(II)-O•- species. Finally, our simulations demonstrate that the natural reductant ubiquinol (CoQH2) assumes a productive binding conformation at the CuD(I) site but not at the CuC(I) site. This provides evidence that the true active site of membrane-bound pMMOs may be CuD rather than CuC. These findings clarify pMMO's catalytic mechanism and emphasize the membrane environment's pivotal role in modulating the coordination structure and the activity of copper centers within pMMO.
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Affiliation(s)
- Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
- Key Laboratory of Aerosol Chemistry and Physics, State Key Laboratory of Loess and Quaternary Geology (SKLLQG), Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, P. R. China
| | - Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Qiaoyu Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Shengheng Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
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9
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Sahil M, Singh T, Ghosh S, Mondal J. 3site Multisubstrate-Bound State of Cytochrome P450cam. J Am Chem Soc 2023; 145:23488-23502. [PMID: 37867463 DOI: 10.1021/jacs.3c06144] [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: 10/24/2023]
Abstract
We identified a multisubstrate-bound state, hereby referred as a 3site state, in cytochrome P450cam via integrating molecular dynamics simulation with nuclear magnetic resonance (NMR) pseudocontact shift measurements. The 3site state is a result of simultaneous binding of three camphor molecules in three locations around P450cam: (a) in a well-established "catalytic" site near heme, (b) in a kink-separated "waiting" site along channel-1, and (c) in a previously reported "allosteric" site at E, F, G, and H helical junctions. These three spatially distinct binding modes in the 3site state mutually communicate with each other via homotropic allostery and act cooperatively to render P450cam functional. The 3site state shows a significantly superior fit with NMR pseudo contact shift (PCS) data with a Q-score of 0.045 than previously known bound states and consists of D251 free of salt-bridges with K178 and R186, rendering the enzyme functionally primed. To date, none of the reported cocomplex of P450cam with its redox partner putidaredoxin (pdx) has been able to match solution NMR data and controversial pdx-induced opening of P450cam's channel-1 remains a matter of recurrent discourse. In this regard, inclusion of pdx to the 3site state is able to perfectly fit the NMR PCS measurement with a Q-score of 0.08 and disfavors the pdx-induced opening of channel-1, reconciling previously unexplained remarkably fast hydroxylation kinetics with a koff of 10.2 s-1. Together, our findings hint that previous experimental observations may have inadvertently captured the 3site state as an in vitro solution state, instead of the catalytic state alone, and provided a distinct departure from the conventional understanding of cytochrome P450.
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Affiliation(s)
- Mohammad Sahil
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Tejender Singh
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Soumya Ghosh
- Tata Institute of Fundamental Research, Hyderabad 500046, India
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10
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Bedekar AA, Deewan A, Jagtap SS, Parker DA, Liu P, Mackie RI, Rao CV. Transcriptional and metabolomic responses of Methylococcus capsulatus Bath to nitrogen source and temperature downshift. Front Microbiol 2023; 14:1259015. [PMID: 37928661 PMCID: PMC10623323 DOI: 10.3389/fmicb.2023.1259015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Methanotrophs play a significant role in methane oxidation, because they are the only biological methane sink present in nature. The methane monooxygenase enzyme oxidizes methane or ammonia into methanol or hydroxylamine, respectively. While much is known about central carbon metabolism in methanotrophs, far less is known about nitrogen metabolism. In this study, we investigated how Methylococcus capsulatus Bath, a methane-oxidizing bacterium, responds to nitrogen source and temperature. Batch culture experiments were conducted using nitrate or ammonium as nitrogen sources at both 37°C and 42°C. While growth rates with nitrate and ammonium were comparable at 42°C, a significant growth advantage was observed with ammonium at 37°C. Utilization of nitrate was higher at 42°C than at 37°C, especially in the first 24 h. Use of ammonium remained constant between 42°C and 37°C; however, nitrite buildup and conversion to ammonia were found to be temperature-dependent processes. We performed RNA-seq to understand the underlying molecular mechanisms, and the results revealed complex transcriptional changes in response to varying conditions. Different gene expression patterns connected to respiration, nitrate and ammonia metabolism, methane oxidation, and amino acid biosynthesis were identified using gene ontology analysis. Notably, key pathways with variable expression profiles included oxidative phosphorylation and methane and methanol oxidation. Additionally, there were transcription levels that varied for genes related to nitrogen metabolism, particularly for ammonia oxidation, nitrate reduction, and transporters. Quantitative PCR was used to validate these transcriptional changes. Analyses of intracellular metabolites revealed changes in fatty acids, amino acids, central carbon intermediates, and nitrogen bases in response to various nitrogen sources and temperatures. Overall, our results offer improved understanding of the intricate interactions between nitrogen availability, temperature, and gene expression in M. capsulatus Bath. This study enhances our understanding of microbial adaptation strategies, offering potential applications in biotechnological and environmental contexts.
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Affiliation(s)
- Ashwini Ashok Bedekar
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Anshu Deewan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Sujit S. Jagtap
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - David A. Parker
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Shell Exploration and Production Inc., Westhollow Technology Center, Houston, TX, United States
| | - Ping Liu
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Shell Exploration and Production Inc., Westhollow Technology Center, Houston, TX, United States
| | - Roderick I. Mackie
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Christopher V. Rao
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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11
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Spatola Rossi T, Tolmie AF, Nichol T, Pain C, Harrison P, Smith TJ, Fricker M, Kriechbaumer V. Recombinant expression and subcellular targeting of the particulate methane monooxygenase (pMMO) protein components in plants. Sci Rep 2023; 13:15337. [PMID: 37714899 PMCID: PMC10504283 DOI: 10.1038/s41598-023-42224-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023] Open
Abstract
Methane is a potent greenhouse gas, which has contributed to approximately a fifth of global warming since pre-industrial times. The agricultural sector produces significant methane emissions, especially from livestock, waste management and rice cultivation. Rice fields alone generate around 9% of total anthropogenic emissions. Methane is produced in waterlogged paddy fields by methanogenic archaea, and transported to the atmosphere through the aerenchyma tissue of rice plants. Thus, bioengineering rice with catalysts to detoxify methane en route could contribute to an efficient emission mitigation strategy. Particulate methane monooxygenase (pMMO) is the predominant methane catalyst found in nature, and is an enzyme complex expressed by methanotrophic bacteria. Recombinant expression of pMMO has been challenging, potentially due to its membrane localization, multimeric structure, and polycistronic operon. Here we show the first steps towards the engineering of plants for methane detoxification with the three pMMO subunits expressed in the model systems tobacco and Arabidopsis. Membrane topology and protein-protein interactions were consistent with correct folding and assembly of the pMMO subunits on the plant ER. Moreover, a synthetic self-cleaving polypeptide resulted in simultaneous expression of all three subunits, although low expression levels precluded more detailed structural investigation. The work presents plant cells as a novel heterologous system for pMMO allowing for protein expression and modification.
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Affiliation(s)
- Tatiana Spatola Rossi
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - A Frances Tolmie
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Tim Nichol
- Molecular Microbiology Research Group, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Charlotte Pain
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Patrick Harrison
- Department of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Thomas J Smith
- Molecular Microbiology Research Group, Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Mark Fricker
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
- Centre for Bioimaging, Oxford Brookes University, Oxford, UK.
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12
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Weng C, Peng X, Han Y. From methane to value-added bioproducts: microbial metabolism, enzymes, and metabolic engineering. ADVANCES IN APPLIED MICROBIOLOGY 2023; 124:119-146. [PMID: 37597946 DOI: 10.1016/bs.aambs.2023.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
Methane is abundant in nature, and excessive emissions will cause the greenhouse effect. Methane is also an ideal carbon and energy feedstock for biosynthesis. In the review, the microorganisms, metabolism, and enzymes for methane utilization, and the advances of conversion to value-added bioproducts were summarized. First, the physiological characteristics, classification, and methane oxidation process of methanotrophs were introduced. The metabolic pathways for methane utilization and key intermediate metabolites of native and synthetic methanotrophs were summarized. Second, the enzymatic properties, crystal structures, and catalytic mechanisms of methane-oxidizing and metabolizing enzymes in methanotrophs were described. Third, challenges and prospects in metabolic pathways and enzymatic catalysis for methane utilization and conversion to value-added bioproducts were discussed. Finally, metabolic engineering of microorganisms for methane biooxidation and bioproducts synthesis based on different pathways were summarized. Understanding the metabolism and challenges of microbial methane utilization will provide insights into possible strategies for efficient methane-based synthesis.
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Affiliation(s)
- Caihong Weng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, P.R. China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, P.R. China.
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13
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Arevalo Villa C, Marienhagen J, Noack S, Wahl SA. Achieving net zero CO 2 emission in the biobased production of reduced platform chemicals using defined co-feeding of methanol. Curr Opin Biotechnol 2023; 82:102967. [PMID: 37441841 DOI: 10.1016/j.copbio.2023.102967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023]
Abstract
Next-generation bioprocesses of a future bio-based economy will rely on a flexible mix of readily available feedstocks. Renewable energy can be used to generate sustainable CO2-derived substrates. Metabolic engineering already enables the functional implementation of different pathways for the assimilation of C1 substrates in various microorganisms. In addition to feedstocks, the benchmark for all future bioprocesses will be sustainability, including the avoidance of CO2 emissions. Here we review recent advances in the utilization of C1-compounds from different perspectives, considering both strain and bioprocess engineering technologies. In particular, we evaluate methanol as a co-feed for enabling the CO2 emission-free production of acetyl-CoA-derived compounds. The possible metabolic strategies are analyzed using stoichiometric modeling combined with thermodynamic analysis and prospects for industrial-scale implementation are discussed.
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Affiliation(s)
- Carlos Arevalo Villa
- Lehrstuhl für Bioverfahrenstechnik, Friedrich Alexander Universität Erlangen-Nürnberg, D-91052 Erlangen, Germany
| | - Jan Marienhagen
- Institute of Bio, and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; Institute of Biotechnology, RWTH Aachen University, D-52074 Aachen, Germany
| | - Stephan Noack
- Institute of Bio, and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Sebastian Aljoscha Wahl
- Lehrstuhl für Bioverfahrenstechnik, Friedrich Alexander Universität Erlangen-Nürnberg, D-91052 Erlangen, Germany.
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14
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Thi Quynh Le H, Yeol Lee E. Methanotrophs: Metabolic versatility from utilization of methane to multi-carbon sources and perspectives on current and future applications. BIORESOURCE TECHNOLOGY 2023:129296. [PMID: 37302766 DOI: 10.1016/j.biortech.2023.129296] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/29/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023]
Abstract
The development of biorefineries for a sustainable bioeconomy has been driven by the concept of utilizing environmentally friendly and cost-effective renewable energy sources. Methanotrophic bacteria with a unique capacity to utilize methane as a carbon and energy source can serve as outstanding biocatalysts to develop C1 bioconversion technology. By establishing the utilization of diverse multi-carbon sources, integrated biorefinery platforms can be created for the concept of the circular bioeconomy. An understanding of physiology and metabolism could help to overcome challenges for biomanufacturing. This review summaries fundamental gaps for methane oxidation and the capability to utilize multi-carbon sources in methanotrophic bacteria. Subsequently, breakthroughs and challenges in harnessing methanotrophs as robust microbial chassis for industrial biotechnology were compiled and overviewed. Finally, capabilities to exploit the inherent advantages of methanotrophs to synthesize various target products in higher titers are proposed.
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Affiliation(s)
- Hoa Thi Quynh Le
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin 17104, Republic of Korea.
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15
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Ali Eltayb W, Abdalla M, Ahmed EL-Arabey A, Boufissiou A, Azam M, Al-Resayes SI, Alam M. Exploring particulate methane monooxygenase (pMMO) proteins using experimentation and computational molecular docking. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2023; 35:102634. [DOI: https:/doi.org/10.1016/j.jksus.2023.102634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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16
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Hwangbo M, Shao Y, Hatzinger PB, Chu KH. Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 37041665 DOI: 10.1111/1758-2229.13156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH4 ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH4 , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH4 monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.
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Affiliation(s)
- Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| | - Yiru Shao
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| | - Paul B Hatzinger
- Aptim Federal Services, LLC, 17 Princess Road, Lawrenceville, New Jersey, USA
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
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17
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Ray S, Jin JO, Choi I, Kim M. Recent trends of biotechnological production of polyhydroxyalkanoates from C1 carbon sources. Front Bioeng Biotechnol 2023; 10:907500. [PMID: 36686222 PMCID: PMC9852868 DOI: 10.3389/fbioe.2022.907500] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 12/06/2022] [Indexed: 01/09/2023] Open
Abstract
Growing concerns over the use of limited fossil fuels and their negative impacts on the ecological niches have facilitated the exploration of alternative routes. The use of conventional plastic material also negatively impacts the environment. One such green alternative is polyhydroxyalkanoates, which are biodegradable, biocompatible, and environmentally friendly. Recently, researchers have focused on the utilization of waste gases particularly those belonging to C1 sources derived directly from industries and anthropogenic activities, such as carbon dioxide, methane, and methanol as the substrate for polyhydroxyalkanoates production. Consequently, several microorganisms have been exploited to utilize waste gases for their growth and biopolymer accumulation. Methylotrophs such as Methylobacterium organophilum produced highest amount of PHA up to 88% using CH4 as the sole carbon source and 52-56% with CH3OH. On the other hand Cupriavidus necator, produced 71-81% of PHA by utilizing CO and CO2 as a substrate. The present review shows the potential of waste gas valorization as a promising solution for the sustainable production of polyhydroxyalkanoates. Key bottlenecks towards the usage of gaseous substrates obstructing their realization on a large scale and the possible technological solutions were also highlighted. Several strategies for PHA production using C1 gases through fermentation and metabolic engineering approaches are discussed. Microbes such as autotrophs, acetogens, and methanotrophs can produce PHA from CO2, CO, and CH4. Therefore, this article presents a vision of C1 gas into bioplastics are prospective strategies with promising potential application, and aspects related to the sustainability of the system.
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Affiliation(s)
- Subhasree Ray
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea,Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, India,*Correspondence: Myunghee Kim, ; Subhasree Ray,
| | - Jun-O Jin
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea,Department of Food Science and Technology, Yeungnam University, Gyeongsan, South Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea,Department of Food Science and Technology, Yeungnam University, Gyeongsan, South Korea
| | - Myunghee Kim
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, South Korea,Department of Food Science and Technology, Yeungnam University, Gyeongsan, South Korea,*Correspondence: Myunghee Kim, ; Subhasree Ray,
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18
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Pirro F, La Gatta S, Arrigoni F, Famulari A, Maglio O, Del Vecchio P, Chiesa M, De Gioia L, Bertini L, Chino M, Nastri F, Lombardi A. A De Novo-Designed Type 3 Copper Protein Tunes Catechol Substrate Recognition and Reactivity. Angew Chem Int Ed Engl 2023; 62:e202211552. [PMID: 36334012 DOI: 10.1002/anie.202211552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Indexed: 11/07/2022]
Abstract
De novo metalloprotein design is a remarkable approach to shape protein scaffolds toward specific functions. Here, we report the design and characterization of Due Rame 1 (DR1), a de novo designed protein housing a di-copper site and mimicking the Type 3 (T3) copper-containing polyphenol oxidases (PPOs). To achieve this goal, we hierarchically designed the first and the second di-metal coordination spheres to engineer the di-copper site into a simple four-helix bundle scaffold. Spectroscopic, thermodynamic, and functional characterization revealed that DR1 recapitulates the T3 copper site, supporting different copper redox states, and being active in the O2 -dependent oxidation of catechols to o-quinones. Careful design of the residues lining the substrate access site endows DR1 with substrate recognition, as revealed by Hammet analysis and computational studies on substituted catechols. This study represents a premier example in the construction of a functional T3 copper site into a designed four-helix bundle protein.
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Affiliation(s)
- Fabio Pirro
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Salvatore La Gatta
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonino Famulari
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy.,Department of Condensed Matter Physics, University of of Zaragoza, Calle Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy.,Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), Via Pietro Castellino 111, 80131, Napoli, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Luca Bertini
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
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19
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Hamadi H, Shakerzadeh E, Esrafili MD. Exploring the potential use of Fe-decorated B40 borospherene as a prospective catalyst for oxidation of methane to methanol. J Mol Graph Model 2022; 118:108369. [DOI: 10.1016/j.jmgm.2022.108369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/19/2022] [Accepted: 10/31/2022] [Indexed: 11/12/2022]
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20
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Recent Insights into Cu-Based Catalytic Sites for the Direct Conversion of Methane to Methanol. Molecules 2022; 27:molecules27217146. [DOI: 10.3390/molecules27217146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/13/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
Direct conversion of methane to methanol is an effective and practical process to improve the efficiency of natural gas utilization. Copper (Cu)-based catalysts have attracted great research attention, due to their unique ability to selectively catalyze the partial oxidation of methane to methanol at relatively low temperatures. In recent decades, many different catalysts have been studied to achieve a high conversion of methane to methanol, including the Cu-based enzymes, Cu-zeolites, Cu-MOFs (metal-organic frameworks) and Cu-oxides. In this mini review, we will detail the obtained evidence on the exact state of the active Cu sites on these various catalysts, which have arisen from the most recently developed techniques and the results of DFT calculations. We aim to establish the structure–performance relationship in terms of the properties of these materials and their catalytic functionalities, and also discuss the unresolved questions in the direct conversion of methane to methanol reactions. Finally, we hope to offer some suggestions and strategies for guiding the practical applications regarding the catalyst design and engineering for a high methanol yield in the methane oxidation reaction.
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21
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Contreras JA, Valenzuela EI, Quijano G. Nitrate/nitrite-dependent anaerobic oxidation of methane (N-AOM) as a technology platform for greenhouse gas abatement in wastewater treatment plants: State-of-the-art and challenges. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115671. [PMID: 35816965 DOI: 10.1016/j.jenvman.2022.115671] [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: 04/15/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Nitrate/nitrite-dependent anaerobic oxidation of methane (N-AOM) is a metabolic process recently discovered and partially characterized in terms of the microorganisms and pathways involved. The N-AOM process can be a powerful tool for mitigating the impacts of greenhouse gas emissions from wastewater treatment plants by coupling the reduction of nitrate or nitrite with the oxidation of residual dissolved methane. Besides specific anaerobic methanotrophs such as bacteria members of the phylum NC10 and archaea belonging to the lineage ANME-2d, recent reports suggested that other methane-oxidizing bacteria in syntrophy with denitrifiers can also perform the N-AOM process, which facilitates the application of this metabolic process for the oxidation of residual methane under realistic scenarios. This work constitutes a state-of-art review that includes the fundamentals of the N-AOM process, new information on process microbiology, bioreactor configurations, and operating conditions for process implementation in WWTP. Potential advantages of the N-AOM process over aerobic methanotrophic biotechnologies are presented, including the potential interrelation of the N-AOM with other nitrogen removal processes within the WWTP, such as the anaerobic ammonium oxidation. This work also addressed the challenges of this biotechnology towards its application at full scale, identifying and discussing critical research niches.
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Affiliation(s)
- José A Contreras
- Laboratory for Research on Advanced Processes for Water Treatment, Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro, 76230, Mexico
| | - Edgardo I Valenzuela
- Laboratory for Research on Advanced Processes for Water Treatment, Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro, 76230, Mexico
| | - Guillermo Quijano
- Laboratory for Research on Advanced Processes for Water Treatment, Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro, 76230, Mexico.
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22
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Sader S, Miliordos E. Being negative can be positive: metal oxide anions promise more selective methane to methanol conversion. Phys Chem Chem Phys 2022; 24:21583-21587. [PMID: 36097864 DOI: 10.1039/d2cp02771b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational studies are performed to show that metal oxide anionic complexes promote the CH4 + N2O → CH3OH + N2 reaction with low activation barriers for the C-H activation and the formation of the CH3-OH bond. The energy for the release of the produced methanol is minimal, reducing the residence time of methanol around the catalytic center and preventing its overoxidation.
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Affiliation(s)
- Safaa Sader
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849, USA.
| | - Evangelos Miliordos
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849, USA.
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23
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Kumar P, Al-Attas TA, Hu J, Kibria MG. Single Atom Catalysts for Selective Methane Oxidation to Oxygenates. ACS NANO 2022; 16:8557-8618. [PMID: 35638813 DOI: 10.1021/acsnano.2c02464] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Direct conversion of methane (CH4) to C1-2 liquid oxygenates is a captivating approach to lock carbons in transportable value-added chemicals, while reducing global warming. Existing approaches utilizing the transformation of CH4 to liquid fuel via tandemized steam methane reforming and the Fischer-Tropsch synthesis are energy and capital intensive. Chemocatalytic partial oxidation of methane remains challenging due to the negligible electron affinity, poor C-H bond polarizability, and high activation energy barrier. Transition-metal and stoichiometric catalysts utilizing harsh oxidants and reaction conditions perform poorly with randomized product distribution. Paradoxically, the catalysts which are active enough to break C-H also promote overoxidation, resulting in CO2 generation and reduced carbon balance. Developing catalysts which can break C-H bonds of methane to selectively make useful chemicals at mild conditions is vital to commercialization. Single atom catalysts (SACs) with specifically coordinated metal centers on active support have displayed intrigued reactivity and selectivity for methane oxidation. SACs can significantly reduce the activation energy due to induced electrostatic polarization of the C-H bond to facilitate the accelerated reaction rate at the low reaction temperature. The distinct metal-support interaction can stabilize the intermediate and prevent the overoxidation of the reaction products. The present review accounts for recent progress in the field of SACs for the selective oxidation of CH4 to C1-2 oxygenates. The chemical nature of catalytic sites, effects of metal-support interaction, and stabilization of intermediate species on catalysts to minimize overoxidation are thoroughly discussed with a forward-looking perspective to improve the catalytic performance.
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Affiliation(s)
- Pawan Kumar
- Department of Chemical and Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Tareq A Al-Attas
- Department of Chemical and Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Jinguang Hu
- Department of Chemical and Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Md Golam Kibria
- Department of Chemical and Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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24
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Gendron A, Allen KD. Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression. Front Microbiol 2022; 13:867342. [PMID: 35547147 PMCID: PMC9081873 DOI: 10.3389/fmicb.2022.867342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/01/2022] [Indexed: 12/02/2022] Open
Abstract
Methyl-coenzyme M reductase (MCR) is an archaeal enzyme that catalyzes the final step of methanogenesis and the first step in the anaerobic oxidation of methane, the energy metabolisms of methanogens and anaerobic methanotrophs (ANME), respectively. Variants of MCR, known as alkyl-coenzyme M reductases, are involved in the anaerobic oxidation of short-chain alkanes including ethane, propane, and butane as well as the catabolism of long-chain alkanes from oil reservoirs. MCR is a dimer of heterotrimers (encoded by mcrABG) and requires the nickel-containing tetrapyrrole prosthetic group known as coenzyme F430. MCR houses a series of unusual post-translational modifications within its active site whose identities vary depending on the organism and whose functions remain unclear. Methanogenic MCRs are encoded in a highly conserved mcrBDCGA gene cluster, which encodes two accessory proteins, McrD and McrC, that are believed to be involved in the assembly and activation of MCR, respectively. The requirement of a unique and complex coenzyme, various unusual post-translational modifications, and many remaining questions surrounding assembly and activation of MCR largely limit in vitro experiments to native enzymes with recombinant methods only recently appearing. Production of MCRs in a heterologous host is an important step toward developing optimized biocatalytic systems for methane production as well as for bioconversion of methane and other alkanes into value-added compounds. This review will first summarize MCR catalysis and structure, followed by a discussion of advances and challenges related to the production of diverse MCRs in a heterologous host.
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Affiliation(s)
- Aleksei Gendron
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kylie D Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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25
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Koo CW, Tucci FJ, He Y, Rosenzweig AC. Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer. Science 2022; 375:1287-1291. [PMID: 35298269 PMCID: PMC9357287 DOI: 10.1126/science.abm3282] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using inactive, detergent-solubilized pMMO lack several conserved regions neighboring the proposed active site. We show that reconstituting pMMO in nanodiscs with lipids extracted from the native organism restores methane oxidation activity. Multiple nanodisc-embedded pMMO structures determined by cryo-electron microscopy to 2.14- to 2.46-angstrom resolution reveal the structure of pMMO in a lipid environment. The resulting model includes stabilizing lipids, regions of the PmoA and PmoC subunits not observed in prior structures, and a previously undetected copper-binding site in the PmoC subunit with an adjacent hydrophobic cavity. These structures provide a revised framework for understanding and engineering pMMO function.
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Affiliation(s)
- Christopher W. Koo
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Frank J. Tucci
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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26
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Microorganisms harbor keys to a circular bioeconomy making them useful tools in fighting plastic pollution and rising CO 2 levels. Extremophiles 2022; 26:10. [PMID: 35118556 PMCID: PMC8813813 DOI: 10.1007/s00792-022-01261-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/21/2022] [Indexed: 12/19/2022]
Abstract
The major global and man-made challenges of our time are the fossil fuel-driven climate change a global plastic pollution and rapidly emerging plant, human and animal infections. To meet the necessary global changes, a dramatic transformation must take place in science and society. This transformation will involve very intense and forward oriented industrial and basic research strongly focusing on (bio)technology and industrial bioprocesses developments towards engineering a zero-carbon sustainable bioeconomy. Within this transition microorganisms-and especially extremophiles-will play a significant and global role as technology drivers. They harbor the keys and blueprints to a sustainable biotechnology in their genomes. Within this article, we outline urgent and important areas of microbial research and technology advancements and that will ultimately make major contributions during the transition from a linear towards a circular bioeconomy.
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Jackson RB, Abernethy S, Canadell JG, Cargnello M, Davis SJ, Féron S, Fuss S, Heyer AJ, Hong C, Jones CD, Damon Matthews H, O'Connor FM, Pisciotta M, Rhoda HM, de Richter R, Solomon EI, Wilcox JL, Zickfeld K. Atmospheric methane removal: a research agenda. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200454. [PMID: 34565221 PMCID: PMC8473948 DOI: 10.1098/rsta.2020.0454] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Atmospheric methane removal (e.g. in situ methane oxidation to carbon dioxide) may be needed to offset continued methane release and limit the global warming contribution of this potent greenhouse gas. Because mitigating most anthropogenic emissions of methane is uncertain this century, and sudden methane releases from the Arctic or elsewhere cannot be excluded, technologies for methane removal or oxidation may be required. Carbon dioxide removal has an increasingly well-established research agenda and technological foundation. No similar framework exists for methane removal. We believe that a research agenda for negative methane emissions-'removal' or atmospheric methane oxidation-is needed. We outline some considerations for such an agenda here, including a proposed Methane Removal Model Intercomparison Project (MR-MIP). This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 1)'.
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Affiliation(s)
- Robert B. Jackson
- Department of Earth System Science, Stanford University, Stanford, CA 94305-2210, USA
- Woods Institute for the Environment, and Precourt Institute for Energy, Stanford University, Stanford, CA 94305-2210, USA
| | - Sam Abernethy
- Department of Earth System Science, Stanford University, Stanford, CA 94305-2210, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Josep G. Canadell
- Global Carbon Project, CSIRO Oceans and Atmosphere, Canberra, Australian Capital Territory 2601, Australia
| | - Matteo Cargnello
- Department of Chemical Engineering and SUNCAT Center for Interface Science and Catalysis, Stanford University, Stanford, CA, USA
| | - Steven J. Davis
- Department of Earth System Science, University of California at Irvine, Irvine, CA 92697, USA
| | - Sarah Féron
- Department of Earth System Science, Stanford University, Stanford, CA 94305-2210, USA
| | - Sabine Fuss
- Mercator Research Institute on Global Commons and Climate Change, Berlin, Germany
- Geographisches Institut, Humboldt Universität zu, Berlin, Germany
| | | | - Chaopeng Hong
- Department of Earth System Science, University of California at Irvine, Irvine, CA 92697, USA
| | - Chris D. Jones
- Met Office Hadley Centre, FitzRoy Road, Exeter EX1 3PB, UK
| | - H. Damon Matthews
- Department of Geography Planning and Environment, Concordia University, Montreal, Quebec, Canada
| | | | - Maxwell Pisciotta
- Chemical and Biomolecular Engineering Department, University of Pennsylvania, Pennsylvania, PA, USA
| | - Hannah M. Rhoda
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Renaud de Richter
- Ecole Nationale Supérieure de Chimie de Montpellier, Montpellier, Languedoc-Roussillon FR, USA
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA, USA
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Jennifer L. Wilcox
- Chemical and Biomolecular Engineering Department, University of Pennsylvania, Pennsylvania, PA, USA
| | - Kirsten Zickfeld
- Department of Geography, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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28
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Jodts RJ, Ross MO, Koo CW, Doan PE, Rosenzweig AC, Hoffman BM. Coordination of the Copper Centers in Particulate Methane Monooxygenase: Comparison between Methanotrophs and Characterization of the Cu C Site by EPR and ENDOR Spectroscopies. J Am Chem Soc 2021; 143:15358-15368. [PMID: 34498465 DOI: 10.1021/jacs.1c07018] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In nature, methane is oxidized to methanol by two enzymes, the iron-dependent soluble methane monooxygenase (sMMO) and the copper-dependent particulate MMO (pMMO). While sMMO's diiron metal active site is spectroscopically and structurally well-characterized, pMMO's copper sites are not. Recent EPR and ENDOR studies have established the presence of two monocopper sites, but the coordination environment of only one has been determined, that within the PmoB subunit and denoted CuB. Moreover, this recent work only focused on a type I methanotrophic pMMO, while previous observations of the type II enzyme were interpreted in terms of the presence of a dicopper site. First, this report shows that the type II Methylocystis species strain Rockwell pMMO, like the type I pMMOs, contains two monocopper sites and that its CuB site has a coordination environment identical to that of type I enzymes. As such, for the full range of pMMOs this report completes the refutation of prior and ongoing suggestions of multicopper sites. Second, and of primary importance, EPR/ENDOR measurements (a) for the first time establish the coordination environment of the spectroscopically observed site, provisionally denoted CuC, in both types of pMMO, thereby (b) establishing the assignment of this site observed by EPR to the crystallographically observed metal-binding site in the PmoC subunit. Finally, these results further indicate that CuC is the likely site of biological methane oxidation by pMMO, a conclusion that will serve as a foundation for proposals regarding the mechanism of this reaction.
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Affiliation(s)
- Richard J Jodts
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew O Ross
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher W Koo
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Peter E Doan
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Brian M Hoffman
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
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Meyet J, Ashuiev A, Noh G, Newton MA, Klose D, Searles K, Bavel AP, Horton AD, Jeschke G, Bokhoven JA, Copéret C. Methane‐to‐Methanol on Mononuclear Copper(II) Sites Supported on Al
2
O
3
: Structure of Active Sites from Electron Paramagnetic Resonance**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jordan Meyet
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1–5 8093 Zürich Switzerland
| | - Anton Ashuiev
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1–5 8093 Zürich Switzerland
| | - Gina Noh
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1–5 8093 Zürich Switzerland
| | - Mark A. Newton
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1–5 8093 Zürich Switzerland
| | - Daniel Klose
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1–5 8093 Zürich Switzerland
| | - Keith Searles
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1–5 8093 Zürich Switzerland
| | - Alexander P. Bavel
- Shell Global Solutions International B.V. Grasweg 31 1031 HW Amsterdam The Netherlands
| | - Andrew D. Horton
- Shell Global Solutions International B.V. Grasweg 31 1031 HW Amsterdam The Netherlands
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1–5 8093 Zürich Switzerland
| | - Jeroen A. Bokhoven
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1–5 8093 Zürich Switzerland
- Laboratory for Catalysis and Sustainable Chemistry Paul Scherrer Institute 5232 Villigen Switzerland
| | - Christophe Copéret
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1–5 8093 Zürich Switzerland
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30
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Meyet J, Ashuiev A, Noh G, Newton MA, Klose D, Searles K, van Bavel AP, Horton AD, Jeschke G, van Bokhoven JA, Copéret C. Methane-to-Methanol on Mononuclear Copper(II) Sites Supported on Al 2 O 3 : Structure of Active Sites from Electron Paramagnetic Resonance*. Angew Chem Int Ed Engl 2021; 60:16200-16207. [PMID: 34132453 PMCID: PMC8361669 DOI: 10.1002/anie.202105307] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 01/28/2023]
Abstract
The selective conversion of methane to methanol remains one of the holy grails of chemistry, where Cu‐exchanged zeolites have been shown promote this reaction under stepwise conditions. Over the years, several active sites have been proposed, ranging from mono‐, di‐ to trimeric CuII. Herein, we report the formation of well‐dispersed monomeric CuII species supported on alumina using surface organometallic chemistry and their reactivity towards the selective and stepwise conversion of methane to methanol. Extensive studies using various transition alumina supports combined with spectroscopic characterization, in particular electron paramagnetic resonance (EPR), show that the active sites are associated with specific facets, which are typically found in γ‐ and η‐alumina phase, and that their EPR signature can be attributed to species having a tri‐coordinated [(Al2O)CuIIO(OH)]− T‐shape geometry. Overall, the selective conversion of methane to methanol, a two‐electron process, involves two monomeric CuII sites that play in concert.
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Affiliation(s)
- Jordan Meyet
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Anton Ashuiev
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Gina Noh
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Mark A Newton
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Daniel Klose
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Keith Searles
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Alexander P van Bavel
- Shell Global Solutions International B.V., Grasweg 31, 1031, HW, Amsterdam, The Netherlands
| | - Andrew D Horton
- Shell Global Solutions International B.V., Grasweg 31, 1031, HW, Amsterdam, The Netherlands
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Jeroen A van Bokhoven
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland.,Laboratory for Catalysis and Sustainable Chemistry, Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Christophe Copéret
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
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31
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Methylotrophic bacterium-based molecular sensor for the detection of low concentrations of methanol. J Biosci Bioeng 2021; 132:247-252. [PMID: 34092492 DOI: 10.1016/j.jbiosc.2021.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 11/21/2022]
Abstract
Methylotrophic bacterium Methylorubrum extorquens is a promising microorganism for the production of value-added compounds from methanol. This study focused on the development of a single-cell level biosensor system that detects methanol by using the intrinsic regulatory machinery which responds to the presence of methanol in this bacterium. A green fluorescent protein (GFP) gene located downstream of the promoter region of the serine glyoxylate aminotransferase gene (Psga) or the methanol dehydrogenase subunit 1 precursor gene (PmxaF) was inserted into the chromosome of M. extorquens wild-type strain AM1. The expression of GFP upon methanol exposure was measured by spectrofluorometer and fluorescence-activated cell sorting (FACS). The strain harboring Psga-gfp emitted fluorescence only when methanol was supplied to the culture medium, while the other strain harboring PmxaF-gfp showed high basal fluorescence even in the absence of methanol. The fluorescence intensity of the Psga-gfp strain depended on a methanol concentration higher than 25 μM, and the sensitivity and dose-dependency of this strain were much higher than previous systems using Escherichia coli. The methanol-sensing properties of the engineered M. extorquens strain were comparable to those of a methylotrophic yeast-based biosensor, suggesting the usefulness of methylotrophic microorganisms as platforms for single-cell sensing of C1 compounds. The constructed methanol sensor strain, coupled with flow cytometry techniques, provides a high-throughput and highly sensitive screening method for the selection of functional methanol-producing enzymes.
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Chou JCC, Stafford VE, Kenney GE, Dassama LMK. The enzymology of oxazolone and thioamide synthesis in methanobactin. Methods Enzymol 2021; 656:341-373. [PMID: 34325792 DOI: 10.1016/bs.mie.2021.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Methanobactins are ribosomally synthesized and post-translationally modified peptidic (RiPP) natural products that are known for their ability to chelate copper ions. Crucial for their high copper affinity is a pair of bidentate ligands comprising a nitrogen-containing heterocycle and an adjacent thioamide or enethiol group. The previously uncharacterized proteins MbnB and MbnC were recently shown to synthesize these groups. In this chapter, we describe the methods that were used to determine that MbnB and MbnC are the core biosynthetic enzymes in methanobactin biosynthesis. The two proteins form a heterodimeric complex (MbnBC) which, through a dioxygen-dependent four-electron oxidation of the precursor peptide (MbnA), modifies a cysteine residue in order to install the oxazolone and thioamide moieties. This overview covers the heterologous expression and purification of MbnBC, characterization of the iron cluster found in MbnB, and characterization of the modification installed on MbnA. While this chapter is specific to MbnBC, the methods outlined here can be broadly applied to the enzymology of other proteins that install similar groups as well as enzyme pairs related to MbnB and MbnC.
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Affiliation(s)
| | | | - Grace E Kenney
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States.
| | - Laura M K Dassama
- Department of Chemistry, Stanford University, Stanford, CA, United States; ChEM-H Institute, Stanford University, Stanford, CA, United States.
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33
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Bartosiewicz M, Rzepka P, Lehmann MF. Tapping Freshwaters for Methane and Energy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:4183-4189. [PMID: 33666422 DOI: 10.1021/acs.est.0c06210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Energy supply limits development through fuel constraints and climatic effects. Production of renewable energy is a central pillar of sustainability but will need to play an increasingly important role in energy generation in order to mitigate fossil-fuel based greenhouse-gas emissions. Global freshwaters represent a vast reservoir of biomass and biogenic CH4. Here we demonstrate the great potential for the optimized use of this nonfossil carbon as a source of energy that is replenishable within a human lifetime. The feasibility of up-scaled adsorption-driven technologies to capture and refine aqueous CH4 still awaits verification, yet recent estimates of global freshwater CH4 production imply that the worldwide energy demand could be satisfied by using the "biofuel" building up in lakes and wetlands. Biogenic CH4 is mostly generated from biomass produced through atmospheric CO2 uptake. Its exploitation in freshwaters can thus secure large amounts of carbon-neutral energy, helping to sustain the planetary equilibrium.
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Affiliation(s)
- Maciej Bartosiewicz
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Przemyslaw Rzepka
- Institute for Chemistry and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Moritz F Lehmann
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
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Khider MLK, Brautaset T, Irla M. Methane monooxygenases: central enzymes in methanotrophy with promising biotechnological applications. World J Microbiol Biotechnol 2021; 37:72. [PMID: 33765207 PMCID: PMC7994243 DOI: 10.1007/s11274-021-03038-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/09/2021] [Indexed: 12/02/2022]
Abstract
Worldwide, the use of methane is limited to generating power, electricity, heating, and for production of chemicals. We believe this valuable gas can be employed more widely. Here we review the possibility of using methane as a feedstock for biotechnological processes based on the application of synthetic methanotrophs. Methane monooxygenase (MMO) enables aerobic methanotrophs to utilize methane as a sole carbon and energy source, in contrast to industrial microorganisms that grow on carbon sources, such as sugar cane, which directly compete with the food market. However, naturally occurring methanotrophs have proven to be difficult to manipulate genetically and their current industrial use is limited to generating animal feed biomass. Shifting the focus from genetic engineering of methanotrophs, towards introducing metabolic pathways for methane utilization in familiar industrial microorganisms, may lead to construction of efficient and economically feasible microbial cell factories. The applications of a technology for MMO production are not limited to methane-based industrial synthesis of fuels and value-added products, but are also of interest in bioremediation where mitigating anthropogenic pollution is an increasingly relevant issue. Published research on successful functional expression of MMO does not exist, but several attempts provide promising future perspectives and a few recent patents indicate that there is an ongoing research in this field. Combining the knowledge on genetics and metabolism of methanotrophy with tools for functional heterologous expression of MMO-encoding genes in non-methanotrophic bacterial species, is a key step for construction of synthetic methanotrophs that holds a great biotechnological potential.
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Affiliation(s)
- May L K Khider
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Marta Irla
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
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Abstract
The isomorphous substitution of Si with metals other than Al in zeotype frameworks allows for tuning the acidity of the zeotype and, therefore, to tailor the catalyst’s properties as a function of the desired catalytic reaction. In this study, B, Ga, and Ti are incorporated in the MFI framework of silicalite samples and the following series of increasing acidity is observed: Ti-silicalite < B-silicalite < Ga-silicalite. It is also observed that the lower the acidity of the sample, the easier the methanol desorption from the zeotype surface. In the target reaction, namely the direct conversion of methane to methanol, methanol extraction is affected by the zeotype acidity. Therefore, the results shown in this study contribute to a more enriched knowledge of this reaction.
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Sher Shah MSA, Oh C, Park H, Hwang YJ, Ma M, Park JH. Catalytic Oxidation of Methane to Oxygenated Products: Recent Advancements and Prospects for Electrocatalytic and Photocatalytic Conversion at Low Temperatures. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001946. [PMID: 33304753 PMCID: PMC7709990 DOI: 10.1002/advs.202001946] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/22/2020] [Indexed: 05/24/2023]
Abstract
Methane is an important fossil fuel and widely available on the earth's crust. It is a greenhouse gas that has more severe warming effect than CO2. Unfortunately, the emission of methane into the atmosphere has long been ignored and considered as a trivial matter. Therefore, emphatic effort must be put into decreasing the concentration of methane in the atmosphere of the earth. At the same time, the conversion of less valuable methane into value-added chemicals is of significant importance in the chemical and pharmaceutical industries. Although, the transformation of methane to valuable chemicals and fuels is considered the "holy grail," the low intrinsic reactivity of its C-H bonds is still a major challenge. This review discusses the advancements in the electrocatalytic and photocatalytic oxidation of methane at low temperatures with products containing oxygen atom(s). Additionally, the future research direction is noted that may be adopted for methane oxidation via electrocatalysis and photocatalysis at low temperatures.
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Affiliation(s)
- Md. Selim Arif Sher Shah
- Department of Chemical and Biomolecular EngineeringYonsei University50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Cheoulwoo Oh
- Department of Chemical and Biomolecular EngineeringYonsei University50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Hyesung Park
- Department of Energy EngineeringSchool of Energy and Chemical EngineeringLow Dimensional Carbon Materials CenterPerovtronics Research CenterUlsan National Institute of Science and Technology (UNIST)Ulsan44919Republic of Korea
| | - Yun Jeong Hwang
- Department of Chemical and Biomolecular EngineeringYonsei University50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
- Clean Energy Research CenterKorea Institute of Science and Technology (KIST)Seoul02792Republic of Korea
| | - Ming Ma
- Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong518055China
| | - Jong Hyeok Park
- Department of Chemical and Biomolecular EngineeringYonsei University50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
- Clean Energy Research CenterKorea Institute of Science and Technology (KIST)Seoul02792Republic of Korea
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37
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NC10 bacteria promoted methane oxidation coupled to chlorate reduction. Biodegradation 2020; 31:319-329. [PMID: 32915337 DOI: 10.1007/s10532-020-09912-z] [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] [Received: 07/31/2020] [Accepted: 09/05/2020] [Indexed: 10/23/2022]
Abstract
The strictly anaerobic serum bottles were applied to investigate methane oxidation coupled to chlorate (ClO3-) reduction (MO-CR) without exogenous oxygen. 0.35 mM ClO3- was consumed within 20 days at the reduction rate of 17.50 μM/d, over three times than that of ClO4-. Chlorite (ClO2-) was not detected throughout the experiment and the mass recovery of Cl- was over 89%. Isotope tracing results showed most of 13CH4 was oxided to CO2, and the electrons recovery reached to 77.6%. Small amounts of 13CH4 was consumed for DOC production probably through aerobic methane oxidation process, with oxygen generated from disproportionation reaction. In pMMO (key enzyme in aerobic oxidation of methane) inhibition tests, ClO3- reduction rate was slowed to 7. 0 μmol/d by 2 mM C2H2, real-time quantitative PCR also showed the transcript abundance of pMMO and Cld were significantly dropped at the later period of experiment, indicating that the O2 disproportionated from ClO2- was utilized to active CH4. NC10 bacteria Candidatus Methylomirabilis, related closely to oxygenic denitrifiers M. oxyfera, was detected in the system, and got enriched along with chlorate reduction. Several pieces of evidence supported that NC10 bacteria promoted CH4 oxidation coupled to ClO3- reduction, these oxygenic denitrifiers may perform ClO2- disproportionation to produce O2, and then oxidized methane intracellularly.
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38
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Yin H, Dou Y, Chen S, Zhu Z, Liu P, Zhao H. 2D Electrocatalysts for Converting Earth-Abundant Simple Molecules into Value-Added Commodity Chemicals: Recent Progress and Perspectives. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1904870. [PMID: 31573704 DOI: 10.1002/adma.201904870] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/05/2019] [Indexed: 06/10/2023]
Abstract
The electrocatalytic conversion of earth-abundant simple molecules into value-added commodity chemicals can transform current chemical production regimes with enormous socioeconomic and environmental benefits. For these applications, 2D electrocatalysts have emerged as a new class of high-performance electrocatalyst with massive forward-looking potential. Recent advances in 2D electrocatalysts are reviewed for emerging applications that utilize naturally existing H2 O, N2 , O2 , Cl- (seawater) and CH4 (natural gas) as reactants for nitrogen reduction (N2 → NH3 ), two-electron oxygen reduction (O2 → H2 O2 ), chlorine evolution (Cl- → Cl2 ), and methane partial oxidation (CH4 → CH3 OH) reactions to generate NH3 , H2 O2 , Cl2 , and CH3 OH. The unique 2D features and effective approaches that take advantage of such features to create high-performance 2D electrocatalysts are articulated with emphasis. To benefit the readers and expedite future progress, the challenges facing the future development of 2D electrocatalysts for each of the above reactions and the related perspectives are provided.
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Affiliation(s)
- Huajie Yin
- Centre for Clean Environment and Energy, Griffith University, Southport, Queensland, 4222, Australia
| | - Yuhai Dou
- Centre for Clean Environment and Energy, Griffith University, Southport, Queensland, 4222, Australia
| | - Shan Chen
- Centre for Clean Environment and Energy, Griffith University, Southport, Queensland, 4222, Australia
| | - Zhengju Zhu
- Centre for Clean Environment and Energy, Griffith University, Southport, Queensland, 4222, Australia
| | - Porun Liu
- Centre for Clean Environment and Energy, Griffith University, Southport, Queensland, 4222, Australia
| | - Huijun Zhao
- Centre for Clean Environment and Energy, Griffith University, Southport, Queensland, 4222, Australia
- Centre for Environmental and Energy Nanomaterials, CAS Center for Excellence in Nanoscience, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei, 230031, P. R. China
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Lee H, Baek JI, Kim SJ, Kwon KK, Rha E, Yeom SJ, Kim H, Lee DH, Kim DM, Lee SG. Sensitive and Rapid Phenotyping of Microbes With Soluble Methane Monooxygenase Using a Droplet-Based Assay. Front Bioeng Biotechnol 2020; 8:358. [PMID: 32391352 PMCID: PMC7193049 DOI: 10.3389/fbioe.2020.00358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/31/2020] [Indexed: 12/22/2022] Open
Abstract
Methanotrophs with soluble methane monooxygenase (sMMO) show high potential for various ecological and biotechnological applications. Here, we developed a high throughput method to identify sMMO-producing microbes by integrating droplet microfluidics and a genetic circuit-based biosensor system. sMMO-producers and sensor cells were encapsulated in monodispersed droplets with benzene as the substrate and incubated for 5 h. The sensor cells were analyzed as the reporter for phenol-sensitive transcription activation of fluorescence. Various combinations of methanotrophs and biosensor cells were investigated to optimize the performance of our droplet-integrated transcriptional factor biosensor system. As a result, the conditions to ensure sMMO activity to convert the starting material, benzene, into phenol, were determined. The biosensor signals were sensitive and quantitative under optimal conditions, showing that phenol is metabolically stable within both cell species and accumulates in picoliter-sized droplets, and the biosensor cells are healthy enough to respond quantitatively to the phenol produced. These results show that our system would be useful for rapid evaluation of phenotypes of methanotrophs showing sMMO activity, while minimizing the necessity of time-consuming cultivation and enzyme preparation, which are required for conventional analysis of sMMO activity.
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Affiliation(s)
- Hyewon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Ji In Baek
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, South Korea
| | - Su Jin Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Kil Koang Kwon
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Eugene Rha
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Soo-Jin Yeom
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, South Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, South Korea
| | - Dong-Myung Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, South Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, South Korea
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40
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Park H, Lee D. Ligand Taxonomy for Bioinorganic Modeling of Dioxygen-Activating Non-Heme Iron Enzymes. Chemistry 2020; 26:5916-5926. [PMID: 31909506 DOI: 10.1002/chem.201904975] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/04/2020] [Indexed: 12/15/2022]
Abstract
Novel functions emerge from novel structures. To develop efficient catalytic systems for challenging chemical transformations, chemists often seek inspirations from enzymatic catalysis. A large number of iron complexes supported by nitrogen-rich multidentate ligands have thus been developed to mimic oxo-transfer reactivity of dioxygen-activating metalloenzymes. Such efforts have significantly advanced our understanding of the reaction mechanisms by trapping key intermediates and elucidating their geometric and electronic properties. Critical to the success of this biomimetic approach is the design and synthesis of elaborate ligand systems to balance the thermodynamic stability, structural adaptability, and chemical reactivity. In this Concept article, representative design strategies for biomimetic atom-transfer chemistry are discussed from the perspectives of "ligand builders". Emphasis is placed on how the primary coordination sphere is constructed, and how it can be elaborated further by rational design for desired functions.
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Affiliation(s)
- Hyunchang Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Dongwhan Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
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41
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Nayak DD, Liu A, Agrawal N, Rodriguez-Carerro R, Dong SH, Mitchell DA, Nair SK, Metcalf WW. Functional interactions between posttranslationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans. PLoS Biol 2020; 18:e3000507. [PMID: 32092071 PMCID: PMC7058361 DOI: 10.1371/journal.pbio.3000507] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/05/2020] [Accepted: 02/04/2020] [Indexed: 01/27/2023] Open
Abstract
The enzyme methyl-coenzyme M reductase (MCR) plays an important role in mediating global levels of methane by catalyzing a reversible reaction that leads to the production or consumption of this potent greenhouse gas in methanogenic and methanotrophic archaea. In methanogenic archaea, the alpha subunit of MCR (McrA) typically contains four to six posttranslationally modified amino acids near the active site. Recent studies have identified enzymes performing two of these modifications (thioglycine and 5-[S]-methylarginine), yet little is known about the formation and function of the remaining posttranslationally modified residues. Here, we provide in vivo evidence that a dedicated S-adenosylmethionine-dependent methyltransferase encoded by a gene we designated methylcysteine modification (mcmA) is responsible for formation of S-methylcysteine in Methanosarcina acetivorans McrA. Phenotypic analysis of mutants incapable of cysteine methylation suggests that the S-methylcysteine residue might play a role in adaption to mesophilic conditions. To examine the interactions between the S-methylcysteine residue and the previously characterized thioglycine, 5-(S)-methylarginine modifications, we generated M. acetivorans mutants lacking the three known modification genes in all possible combinations. Phenotypic analyses revealed complex, physiologically relevant interactions between the modified residues, which alter the thermal stability of MCR in a combinatorial fashion that is not readily predictable from the phenotypes of single mutants. High-resolution crystal structures of inactive MCR lacking the modified amino acids were indistinguishable from the fully modified enzyme, suggesting that interactions between the posttranslationally modified residues do not exert a major influence on the static structure of the enzyme but rather serve to fine-tune the activity and efficiency of MCR.
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Affiliation(s)
- Dipti D. Nayak
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Andi Liu
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Neha Agrawal
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Roy Rodriguez-Carerro
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Shi-Hui Dong
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Douglas A. Mitchell
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
- Center for Biophysics & Quantitative Biology, University of Illinois, Urbana, Illinois, United States of America
| | - William W. Metcalf
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
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42
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Fungal Peroxygenases: A Phylogenetically Old Superfamily of Heme Enzymes with Promiscuity for Oxygen Transfer Reactions. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-3-030-29541-7_14] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Fukatsu A, Morimoto Y, Sugimoto H, Itoh S. Modelling a ‘histidine brace’ motif in mononuclear copper monooxygenases. Chem Commun (Camb) 2020; 56:5123-5126. [DOI: 10.1039/d0cc01392g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A mononuclear copper complex bearing a ‘histidine brace’ is synthesised and characterised as an active-site model of mononuclear copper monooxygenases such as lytic polysaccharide monooxygenases (LPMOs) and particulate methane monooxygenase (pMMO).
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Affiliation(s)
- Arisa Fukatsu
- Department of Material and Life Science
- Division of Advanced Science and Biotechnology
- Graduate School of Engineering
- Osaka University
- Osaka 565-0871
| | - Yuma Morimoto
- Department of Material and Life Science
- Division of Advanced Science and Biotechnology
- Graduate School of Engineering
- Osaka University
- Osaka 565-0871
| | - Hideki Sugimoto
- Department of Material and Life Science
- Division of Advanced Science and Biotechnology
- Graduate School of Engineering
- Osaka University
- Osaka 565-0871
| | - Shinobu Itoh
- Department of Material and Life Science
- Division of Advanced Science and Biotechnology
- Graduate School of Engineering
- Osaka University
- Osaka 565-0871
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44
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Liu Y, You T, Wang HX, Tang Z, Zhou CY, Che CM. Iron- and cobalt-catalyzed C(sp3)–H bond functionalization reactions and their application in organic synthesis. Chem Soc Rev 2020; 49:5310-5358. [DOI: 10.1039/d0cs00340a] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review highlights the developments in iron and cobalt catalyzed C(sp3)–H bond functionalization reactions with emphasis on their applications in organic synthesis, i.e. natural products and pharmaceuticals synthesis and/or modification.
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Affiliation(s)
- Yungen Liu
- Department of Chemistry
- Southern University of Science and Technology
- Shenzhen
- P. R. China
| | - Tingjie You
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Hai-Xu Wang
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Zhou Tang
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Cong-Ying Zhou
- Department of Chemistry
- State Key Laboratory of Synthetic Chemistry
- The University of Hong Kong
- Hong Kong
- P. R. China
| | - Chi-Ming Che
- Department of Chemistry
- Southern University of Science and Technology
- Shenzhen
- P. R. China
- Department of Chemistry
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45
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Schuelke-Sanchez AE, Stone AA, Liptak MD. CfbA promotes insertion of cobalt and nickel into ruffled tetrapyrroles in vitro. Dalton Trans 2019; 49:1065-1076. [PMID: 31868194 DOI: 10.1039/c9dt03601f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The nickel chelatase CfbA is the smallest member of the chelatase family, but the mechanism by which this enzyme inserts nickel into sirohydrochlorin is unknown. In order to gain mechanistic insight, metal binding, tetrapyrrole binding, and enzyme activity were characterized for a variety of substrates using several spectroscopic and computational approaches. Mass spectrometery and magnetic circular dichroism experiments revealed that CfbA binds an octahedral, high-spin metal substrate. UV/Vis absorption spectroscopy demonstrated that the enzyme binds a wide range of tetrapyrrole substrates and perturbs their electronic structures. Based upon activity assays, CfbA promotes insertion of cobalt and nickel into several tetrapyrroles, including cobalt insertion into protopophyrin IX. Finally, density functional theory models were developed which strongly suggest that observed spectral changes upon binding to the enzyme can be explained by tetrapyrrole ruffling, but not deprotonation or saddling. The observation of an octahedral, high-spin metal bound to CfbA leads to a generalization for all class II chelatases: these enzymes bind labile metal substrates and metal desolvation is not a rate-limiting step. The conclusion that CfbA ruffles its tetrapyrrole substrate reveals that the CfbA mechanism is different from that currently proposed for ferrochelatase, and identifies an intriguing correlation between metal substrate specificity and tetrapyrrole distortion mode in chelatases.
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Affiliation(s)
| | - Alissa A Stone
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA.
| | - Matthew D Liptak
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA.
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46
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Shi Y, Liu S, Liu Y, Huang W, Guan G, Zuo Z. Quasicatalytic and catalytic selective oxidation of methane to methanol over solid materials: a review on the roles of water. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2019. [DOI: 10.1080/01614940.2019.1674475] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Yayun Shi
- Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan, Shanxi, China
| | - Shizhong Liu
- Department of Chemistry, Stony Brook University, New York, NY, USA
| | - Yiming Liu
- Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan, Shanxi, China
| | - Wei Huang
- Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan, Shanxi, China
| | - Guoqing Guan
- Institute of Regional Innovation (IRI), Hirosaki University, Aomori, Japan
| | - Zhijun Zuo
- Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan, Shanxi, China
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47
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Fukuzumi S, Lee YM, Nam W. Photocatalytic Oxygenation Reactions Using Water and Dioxygen. CHEMSUSCHEM 2019; 12:3931-3940. [PMID: 31250964 DOI: 10.1002/cssc.201901276] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/25/2019] [Indexed: 06/09/2023]
Abstract
Water (H2 O) is the most environmentally benign reductant and is oxidized to evolve dioxygen (O2 )-the greenest oxidant-in photosystem II. This Minireview focuses on photocatalytic oxygenation of substrates with H2 O as an oxygen source and O2 as an oxidant. Metal complexes can be oxidized by two molecules of one-electron oxidants with H2 O to produce high-valent metal-oxo complexes, which act as active oxidants for oxygenating organic substrates. When an appropriate oxidant is employed for the substrate oxidation, the reduced oxidant can be oxidized by dioxygen to regenerate the oxidant when water and dioxygen are used as an oxygen source and an oxidant, respectively. Photoinduced electron transfer from a substrate (S) to the excited state of complex [(L)MIII ]+ produces a substrate radical cation (S.+ ), accompanied by the regeneration of [(L)MII ]. S.+ then reacts with H2 O to produce an OH adduct radical that is oxidized by [(L)MIII ]+ to yield an oxygenated product (SO), in which the oxygen atom originates from H2 O, accompanied by regeneration of [(L)MII ]. Photocatalytic oxidation of H2 O by O2 to produce H2 O2 is combined with the catalytic oxygenation of substrates with H2 O2 to produce the oxygenated products, in which the oxygen atom originates from O2 at the beginning but later from water. This Minireview provides a promising strategy for oxygenation of substrates by using H2 O as an oxygen source and O2 as the greenest oxidant.
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Affiliation(s)
- Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 03760, Korea
- Graduate School of Science and Engineering, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 03760, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 03760, Korea
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48
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Whiddon KT, Gudneppanavar R, Hammer TJ, West DA, Konopka MC. Fluorescence-based analysis of the intracytoplasmic membranes of type I methanotrophs. Microb Biotechnol 2019; 12:1024-1033. [PMID: 31264365 PMCID: PMC6680624 DOI: 10.1111/1751-7915.13458] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/16/2019] [Indexed: 12/15/2022] Open
Abstract
Most methanotrophic bacteria maintain intracytoplasmic membranes which house the methane-oxidizing enzyme, particulate methane monooxygenase. Previous studies have primarily used transmission electron microscopy or cryo-electron microscopy to look at the structure of these membranes or lipid extraction methods to determine the per cent of cell dry weight composed of lipids. We show an alternative approach using lipophilic membrane probes and other fluorescent dyes to assess the extent of intracytoplasmic membrane formation in living cells. This fluorescence method is sensitive enough to show not only the characteristic shift in intracytoplasmic membrane formation that is present when methanotrophs are grown with or without copper, but also differences in intracytoplasmic membrane levels at intermediate copper concentrations. This technique can also be employed to monitor dynamic intracytoplasmic membrane changes in the same cell in real time under changing growth conditions. We anticipate that this approach will be of use to researchers wishing to visualize intracytoplasmic membranes who may not have access to electron microscopes. It will also have the capability to relate membrane changes in individual living cells to other measurements by fluorescence labelling or other single-cell analysis methods.
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Affiliation(s)
| | | | - Theodore J. Hammer
- Department of ChemistryThe University of AkronAkronOHUSA
- Department of Polymer ScienceThe University of AkronAkronOHUSA
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49
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Chen J, Kong F, Ma N, Zhao P, Liu C, Wang X, Cong Z. Peroxide-Driven Hydroxylation of Small Alkanes Catalyzed by an Artificial P450BM3 Peroxygenase System. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02507] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jie Chen
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanhui Kong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Nana Ma
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Panxia Zhao
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanfei Liu
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Xiling Wang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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50
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Guo C, Duan D, Tang Q, Pei H, Guo F. Experimental investigation of coalescence behaviour of bubble pairs forming at capillary orifices submerged in bacterial suspension. CAN J CHEM ENG 2019. [DOI: 10.1002/cjce.23460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Cheng‐Long Guo
- School of Electrical and Power EngineeringChina University of Mining and TechnologyXuzhou221116China
| | - Dan‐Ru Duan
- School of Electrical and Power EngineeringChina University of Mining and TechnologyXuzhou221116China
| | - Qin‐Yuan Tang
- School of Electrical and Power EngineeringChina University of Mining and TechnologyXuzhou221116China
| | - Hong‐Shan Pei
- School of Electrical and Power EngineeringChina University of Mining and TechnologyXuzhou221116China
| | - Fei‐Qiang Guo
- School of Electrical and Power EngineeringChina University of Mining and TechnologyXuzhou221116China
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