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Runda ME, de Kok NAW, Schmidt S. Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities. Chembiochem 2023; 24:e202300078. [PMID: 36964978 DOI: 10.1002/cbic.202300078] [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: 01/31/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or exploited for synthetic applications. This review aims to provide a general overview of the most important Fd-dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non-heme iron-dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure-function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.
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Affiliation(s)
- Michael E Runda
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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2
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Xuan J, He L, Wen W, Feng Y. Hydrogenase and Nitrogenase: Key Catalysts in Biohydrogen Production. Molecules 2023; 28:molecules28031392. [PMID: 36771068 PMCID: PMC9919214 DOI: 10.3390/molecules28031392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Hydrogen with high energy content is considered to be a promising alternative clean energy source. Biohydrogen production through microbes provides a renewable and immense hydrogen supply by utilizing raw materials such as inexhaustible natural sunlight, water, and even organic waste, which is supposed to solve the two problems of "energy supply and environment protection" at the same time. Hydrogenases and nitrogenases are two classes of key enzymes involved in biohydrogen production and can be applied under different biological conditions. Both the research on enzymatic catalytic mechanisms and the innovations of enzymatic techniques are important and necessary for the application of biohydrogen production. In this review, we introduce the enzymatic structures related to biohydrogen production, summarize recent enzymatic and genetic engineering works to enhance hydrogen production, and describe the chemical efforts of novel synthetic artificial enzymes inspired by the two biocatalysts. Continual studies on the two types of enzymes in the future will further improve the efficiency of biohydrogen production and contribute to the economic feasibility of biohydrogen as an energy source.
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Affiliation(s)
- Jinsong Xuan
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
- Correspondence: (J.X.); (Y.F.)
| | - Lingling He
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Wen Wen
- Department of Bioscience and Bioengineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing 100083, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
- Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.X.); (Y.F.)
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3
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Arriaza‐Gallardo FJ, Schaupp S, Zheng Y, Abdul‐Halim MF, Pan H, Kahnt J, Angelidou G, Paczia N, Hu X, Costa K, Shima S. The Function of Two Radical-SAM Enzymes, HcgA and HcgG, in the Biosynthesis of the [Fe]-Hydrogenase Cofactor. Angew Chem Int Ed Engl 2022; 61:e202213239. [PMID: 36264001 PMCID: PMC10100467 DOI: 10.1002/anie.202213239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Indexed: 11/05/2022]
Abstract
In the biosynthesis of the iron-guanylylpyridinol (FeGP) cofactor, 6-carboxymethyl-5-methyl-4-hydroxy-2-pyridinol (1) is 3-methylated to form 2, then 4-guanylylated to form 3, and converted into the full cofactor. HcgA-G proteins catalyze the biosynthetic reactions. Herein, we report the function of two radical S-adenosyl methionine enzymes, HcgA and HcgG, as uncovered by in vitro complementation experiments and the use of purified enzymes. In vitro biosynthesis using the cell extract from the Methanococcus maripaludis ΔhcgA strain was complemented with HcgA or precursors 1, 2 or 3. The results suggested that HcgA catalyzes the biosynthetic reaction that forms 1. We demonstrated the formation of 1 by HcgA using the 3 kDa cell extract filtrate as the substrate. Biosynthesis in the ΔhcgG system was recovered by HcgG but not by 3, which indicated that HcgG catalyzes the reactions after the biosynthesis of 3. The data indicated that HcgG contributes to the formation of CO and completes biosynthesis of the FeGP cofactor.
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Affiliation(s)
| | - Sebastian Schaupp
- Max Planck Institute for Terrestrial MicrobiologyKarl-von-Frisch-Straße 1035043MarburgGermany
| | - Yu‐Cong Zheng
- Max Planck Institute for Terrestrial MicrobiologyKarl-von-Frisch-Straße 1035043MarburgGermany
| | - Mohd Farid Abdul‐Halim
- Department of Plant and Microbial BiologyUniversity of MinnesotaTwin Cities, St. PaulMinnesotaUSA
| | - Hui‐Jie Pan
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringEcole Polytechnique Fédérale de Lausanne (EPFL)ISIC-LSCI, BCH3305Lausanne1015Switzerland
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial MicrobiologyKarl-von-Frisch-Straße 1035043MarburgGermany
| | - Georgia Angelidou
- Max Planck Institute for Terrestrial MicrobiologyKarl-von-Frisch-Straße 1035043MarburgGermany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial MicrobiologyKarl-von-Frisch-Straße 1035043MarburgGermany
| | - Xile Hu
- Laboratory of Inorganic Synthesis and CatalysisInstitute of Chemical Sciences and EngineeringEcole Polytechnique Fédérale de Lausanne (EPFL)ISIC-LSCI, BCH3305Lausanne1015Switzerland
| | - Kyle Costa
- Department of Plant and Microbial BiologyUniversity of MinnesotaTwin Cities, St. PaulMinnesotaUSA
| | - Seigo Shima
- Max Planck Institute for Terrestrial MicrobiologyKarl-von-Frisch-Straße 1035043MarburgGermany
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4
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Peltier JL, Tomás-Mendivil E, Tolentino DR, Hansmann MM, Jazzar R, Bertrand G. Realizing Metal-Free Carbene-Catalyzed Carbonylation Reactions with CO. J Am Chem Soc 2020; 142:18336-18340. [DOI: 10.1021/jacs.0c09938] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jesse L. Peltier
- UCSD−CNRS Joint Research Chemistry Laboratory (UMI 3555), Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
| | - Eder Tomás-Mendivil
- UCSD−CNRS Joint Research Chemistry Laboratory (UMI 3555), Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
- Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country (UPV-EHU), Donostia-San Sebastián, 20018 Gipuzkoa, Spain
| | - Daniel R. Tolentino
- UCSD−CNRS Joint Research Chemistry Laboratory (UMI 3555), Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
| | - Max M. Hansmann
- UCSD−CNRS Joint Research Chemistry Laboratory (UMI 3555), Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
| | - Rodolphe Jazzar
- UCSD−CNRS Joint Research Chemistry Laboratory (UMI 3555), Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
| | - Guy Bertrand
- UCSD−CNRS Joint Research Chemistry Laboratory (UMI 3555), Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
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5
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Crystal Structures of [Fe]-Hydrogenase from Methanolacinia paynteri Suggest a Path of the FeGP-Cofactor Incorporation Process. INORGANICS 2020. [DOI: 10.3390/inorganics8090050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
[Fe]-hydrogenase (Hmd) catalyzes the reversible heterolytic cleavage of H2, and hydride transfer to methenyl-tetrahydromethanopterin (methenyl-H4MPT+). The iron-guanylylpyridinol (FeGP) cofactor, the prosthetic group of Hmd, can be extracted from the holoenzyme and inserted back into the protein. Here, we report the crystal structure of an asymmetric homodimer of Hmd from Methanolacinia paynteri (pHmd), which was composed of one monomer in the open conformation with the FeGP cofactor (holo-form) and a second monomer in the closed conformation without the cofactor (apo-form). In addition, we report the symmetric pHmd-homodimer structure in complex with guanosine monophosphate (GMP) or guanylylpyridinol (GP), in which each ligand was bound to the protein, where the GMP moiety of the FeGP-cofactor is bound in the holo-form. Binding of GMP and GP modified the local protein structure but did not induce the open conformation. The amino-group of the Lys150 appears to interact with the 2-hydroxy group of pyridinol ring in the pHmd–GP complex, which is not the case in the structure of the pHmd–FeGP complex. Lys150Ala mutation decreased the reconstitution rate of the active enzyme with the FeGP cofactor at the physiological pH. These results suggest that Lys150 might be involved in the FeGP-cofactor incorporation into the Hmd protein in vivo.
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6
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Shima S, Huang G, Wagner T, Ermler U. Structural Basis of Hydrogenotrophic Methanogenesis. Annu Rev Microbiol 2020; 74:713-733. [DOI: 10.1146/annurev-micro-011720-122807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most methanogenic archaea use the rudimentary hydrogenotrophic pathway—from CO2and H2to methane—as the terminal step of microbial biomass degradation in anoxic habitats. The barely exergonic process that just conserves sufficient energy for a modest lifestyle involves chemically challenging reactions catalyzed by complex enzyme machineries with unique metal-containing cofactors. The basic strategy of the methanogenic energy metabolism is to covalently bind C1species to the C1carriers methanofuran, tetrahydromethanopterin, and coenzyme M at different oxidation states. The four reduction reactions from CO2to methane involve one molybdopterin-based two-electron reduction, two coenzyme F420–based hydride transfers, and one coenzyme F430–based radical process. For energy conservation, one ion-gradient-forming methyl transfer reaction is sufficient, albeit supported by a sophisticated energy-coupling process termed flavin-based electron bifurcation for driving the endergonic CO2reduction and fixation. Here, we review the knowledge about the structure-based catalytic mechanism of each enzyme of hydrogenotrophic methanogenesis.
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Affiliation(s)
- Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Gangfeng Huang
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Ulrich Ermler
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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8
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Abstract
Hydrogenases catalyze the simple yet important interconversion between H2 and protons and electrons. Found throughout prokaryotes, lower eukaryotes, and archaea, hydrogenases are used for a variety of redox and signaling purposes and are found in many different forms. This diverse group of metalloenzymes is divided into [NiFe], [FeFe], and [Fe] variants, based on the transition metal contents of their active sites. A wide array of biochemical and spectroscopic methods has been used to elucidate hydrogenases, and this along with a general description of the main enzyme types and catalytic mechanisms is discussed in this chapter.
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9
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Wagner T, Huang G, Ermler U, Shima S. How [Fe]-Hydrogenase from Methanothermobacter is Protected Against Light and Oxidative Stress. Angew Chem Int Ed Engl 2018; 57:15056-15059. [PMID: 30207625 DOI: 10.1002/anie.201807203] [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: 06/22/2018] [Revised: 08/24/2018] [Indexed: 11/09/2022]
Abstract
[Fe]-hydrogenase (Hmd) catalyzes the reversible hydrogenation of methenyltetrahydromethanopterin (methenyl-H4 MPT+ ) with H2 . Hmd contains the iron-guanylylpyridinol (FeGP) cofactor, which is sensitive to light and oxidative stress. A natural protection mechanism is reported for Hmd based on structural and biophysical data. Hmd from Methanothermobacter marburgensis (mHmd) was found in a hexameric state, where an expanded oligomerization loop is detached from the dimer core and intrudes into the active site of a neighboring dimer. An aspartic acid residue from the loop ligates to FeII of the FeGP cofactor and thus blocks the postulated H2 -binding site. In solution, this enzyme is in a hexamer-to-dimer equilibrium. Lower enzyme concentrations, and the presence of methenyl-H4 MPT+ , shift the equilibrium toward the active dimer side. At higher enzyme concentrations-as present in the cell-the enzyme is predominantly in the inactive hexameric state and is thereby protected against light and oxidative stress.
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Affiliation(s)
- Tristan Wagner
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
| | - Gangfeng Huang
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438, Frankfurt/Main, Germany
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
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10
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Wagner T, Huang G, Ermler U, Shima S. How [Fe]‐Hydrogenase from
Methanothermobacter
is Protected Against Light and Oxidative Stress. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tristan Wagner
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Straße 10 35043 Marburg Germany
| | - Gangfeng Huang
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Straße 10 35043 Marburg Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik Max-von-Laue-Straße 3 60438 Frankfurt/Main Germany
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Straße 10 35043 Marburg Germany
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11
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Bharadwaz P, Dewhurst RD, Phukan AK. Metal-Free Activation of Enthalpically Strong Bonds: Unraveling the Potential of Hitherto Unexplored Singlet Carbenes. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800873] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Priyam Bharadwaz
- Department of Chemical Sciences; Tezpur University, Napam -; 784 028 Assam India
| | - Rian D. Dewhurst
- Institut für Anorganische Chemie and Institute for Sustainable Chemistry & Catalysis with Boron; Julius-Maximilians-Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Ashwini K. Phukan
- Department of Chemical Sciences; Tezpur University, Napam -; 784 028 Assam India
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12
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Rigid scaffolds for the design of molecular catalysts and biomimetic active sites: A case study of anthracene-based ligands for modeling mono-iron hydrogenase (Hmd). Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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13
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Bharadwaz P, Chetia P, Phukan AK. Electronic and Ligand Properties of Skeletally Substituted Cyclic (Alkyl)(Amino)Carbenes (CAACs) and Their Reactivity towards Small Molecule Activation: A Theoretical Study. Chemistry 2017; 23:9926-9936. [DOI: 10.1002/chem.201701645] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Priyam Bharadwaz
- Department of Chemical Sciences; Tezpur University, Napam; 784 028 Assam India
| | - Pubali Chetia
- Department of Chemical Sciences; Tezpur University, Napam; 784 028 Assam India
| | - Ashwini K. Phukan
- Department of Chemical Sciences; Tezpur University, Napam; 784 028 Assam India
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14
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Wang M, Zhao Q, Li L, Niu K, Li Y, Wang F, Jiang B, Liu K, Jiang Y, Fang X. Contributing factors in the improvement of cellulosic H2 production in Clostridium thermocellum/Thermoanaerobacterium co-cultures. Appl Microbiol Biotechnol 2016; 100:8607-20. [PMID: 27538932 DOI: 10.1007/s00253-016-7776-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/17/2016] [Accepted: 08/01/2016] [Indexed: 02/04/2023]
Abstract
Lignocellulosic biohydrogen is a promising renewable energy source that could be a potential alternative to the unsustainable fossil fuel-based energy. Biohydrogen production could be performed by Clostridium thermocellum that is the fastest known cellulose-degrading bacterium. Previous investigations have shown that the co-culture of C. thermocellum JN4 and a non-cellulolytic bacterium Thermoanaerobacterium thermosaccharolyticum GD17 produces more hydrogen than the C. thermocellum JN4 mono-culture, but the mechanism of this improvement is unknown. In this work, we carried out genomic and evolutionary analysis of hydrogenase-coding genes in C. thermocellum and T. thermosaccharolyticum, identifying one Ech-type [NiFe] hydrogenase complex in each species, and, respectively, five and four monomeric or multimeric [FeFe] hydrogenases in the two species. Further transcriptional analysis showed hydrogenase-coding genes in C. thermocellum are regulated by carbon sources, while hydrogenase-coding genes in T. thermosaccharolyticum are not. However, comparison between transcriptional abundance of hydrogenase-coding genes in mono- and co-cultures showed the co-culturing condition leads to transcriptional changes of hydrogenase-coding genes in T. thermosaccharolyticum but not C. thermocellum. Further metabolic analysis showed T. thermosaccharolyticum produces H2 at a rate 4-12-fold higher than C. thermocellum. These findings lead to the suggestion that the improvement of H2 production in the co-culture over mono-culture should be attributed to changes in T. thermosaccharolyticum but not C. thermocellum. Further suggestions can be made that C. thermocellum and T. thermosaccharolyticum perform highly specialized tasks in the co-culture, and optimization of the co-culture for more lignocellulosic biohydrogen production should be focused on the improvement of the non-cellulolytic bacterium.
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Affiliation(s)
- Mingyu Wang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Qi Zhao
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Ling Li
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Yi Li
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China.,Taishan College, Shandong University, Jinan, 250100, China
| | - Fangzhong Wang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Baojie Jiang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Kuimei Liu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Yi Jiang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China.
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15
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Lal S, Levin DB. Comparative Genomics of Core Metabolism Genes of Cellulolytic and Non-cellulolytic Clostridium Species. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:79-112. [PMID: 26907553 DOI: 10.1007/10_2015_5007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Microbial production of fuels such as ethanol, butanol, hydrogen (H2), and methane (CH4) from waste biomass has the potential to provide sustainable energy systems that can displace fossil fuel consumption. Screening for microbial diversity and genome sequencing of a wide-range of microorganisms can identify organisms with natural abilities to synthesize these alternative fuels and/or other biotechnological applications. Clostridium species are the most widely studied strict anaerobes capable of fermentative synthesis of ethanol, butanol, or hydrogen directly from waste biomass. Clostridium termitidis CT1112 is a mesophilic, cellulolytic species capable of direct cellulose fermentation to ethanol and organic acids, with concomitant synthesis of H2 and CO2. On the basis of 16S ribosomal RNA (rRNA) and chaperonin 60 (cpn60) gene sequence data, phylogenetic analyses revealed a close relationship between C. termitidis and C. cellobioparum. Comparative bioinformatic analyses of the C. termitidis genome with 18 cellulolytic and 10 non-cellulolytic Clostridium species confirmed this relationship, and further revealed that the majority of core metabolic pathway genes in C. termitidis and C. cellobioparum share more than 90% amino acid sequence identity. The gene loci and corresponding amino acid sequences of the encoded enzymes for each pathway were correlated by percentage identity, higher score (better alignment), and lowest e-value (most significant "hit"). In addition, the function of each enzyme was proposed by conserved domain analysis. In this chapter we discuss the comparative analysis of metabolic pathways involved in synthesis of various useful products by cellulolytic and non-cellulolytic biofuel and solvent producing Clostridium species. This study has generated valuable information concerning the core metabolism genes and pathways of C. termitidis CT1112, which is helpful in developing metabolic engineering strategies to enhance its natural capacity for better industrial applications.
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Affiliation(s)
- Sadhana Lal
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada, R3T 5V6
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada, R3T 5V6.
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16
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Li C, Fu Z, Zhang X, Liu Y, Wang Y. Theoretical study of iron acyl complexes modeling the active site of [Fe]-hydrogenase: Solvation effects play a significant role. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Fujishiro T, Ataka K, Ermler U, Shima S. Towards a functional identification of catalytically inactive [Fe]-hydrogenase paralogs. FEBS J 2015; 282:3412-23. [PMID: 26094576 DOI: 10.1111/febs.13351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 11/29/2022]
Abstract
UNLABELLED [Fe]-hydrogenase (Hmd), an enzyme of the methanogenic energy metabolism, harbors an iron-guanylylpyridinol (FeGP) cofactor used for H2 cleavage. The generated hydride is transferred to methenyl-tetrahydromethanopterin (methenyl-H4MPT(+)). Most hydrogenotrophic methanogens contain the hmd-related genes hmdII and hmdIII. Their function is still elusive. We were able to reconstitute the HmdII holoenzyme of Methanocaldococcus jannaschii with recombinantly produced apoenzyme and the FeGP cofactor, which is a prerequisite for in vitro functional analysis. Infrared spectroscopic and X-ray structural data clearly indicated binding of the FeGP cofactor. Methylene-H4MPT binding was detectable in the significantly altered infrared spectra of the HmdII holoenzyme and in the HmdII apoenzyme-methylene-H4 MPT complex structure. The related binding mode of the FeGP cofactor and methenyl-H4MPT(+) compared with Hmd and their multiple contacts to the polypeptide highly suggest a biological role in HmdII. However, holo-HmdII did not catalyze the Hmd reaction, not even in a single turnover process, as demonstrated by kinetic measurements. The found inactivity can be rationalized by an increased contact area between the C- and N-terminal folding units in HmdII compared with in Hmd, which impairs the catalytically necessary open-to-close transition, and by an exchange of a crucial histidine to a tyrosine. Mainly based on the presented data, a function of HmdII as Hmd isoenzyme, H2 sensor, FeGP-cofactor storage protein and scaffold protein for FeGP-cofactor biosynthesis could be excluded. Inspired by the recently found binding of HmdII to aminoacyl-tRNA synthetases and tRNA, we tentatively consider HmdII as a regulatory protein for protein synthesis that senses the intracellular methylene-H4 MPT concentration. DATABASE Structural data are available in the Protein Data Bank under the accession numbers 4YT8; 4YT2; 4YT4 and 4YT5.
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Affiliation(s)
- Takashi Fujishiro
- Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Frankfurt/Main, Germany
| | - Seigo Shima
- Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany.,PRESTO, Japan Science and Technology Agency (JST), Saitama, Japan
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18
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Hedegård ED, Kongsted J, Ryde U. Multiscale Modeling of the Active Site of [Fe] Hydrogenase: The H 2Binding Site in Open and Closed Protein Conformations. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Hedegård ED, Kongsted J, Ryde U. Multiscale Modeling of the Active Site of [Fe] Hydrogenase: The H2Binding Site in Open and Closed Protein Conformations. Angew Chem Int Ed Engl 2015; 54:6246-50. [DOI: 10.1002/anie.201501737] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Indexed: 11/07/2022]
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20
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Murray KA, Wodrich MD, Hu X, Corminboeuf C. Toward functional type III [Fe]-hydrogenase biomimics for H2 activation: insights from computation. Chemistry 2015; 21:3987-96. [PMID: 25649221 DOI: 10.1002/chem.201405619] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Indexed: 11/06/2022]
Abstract
The chemistry of [Fe]-hydrogenase has attracted significant interest due to its ability to activate molecular hydrogen. The intriguing properties of this enzyme have prompted the synthesis of numerous small molecule mimics aimed at activating H2. Despite considerable effort, a majority of these compounds remain nonfunctional for hydrogenation reactions. By using a recently synthesized model as an entry point, seven biomimetic complexes have been examined through DFT computations to probe the influence of ligand environment on the ability of a mimic to bind and split H2. One mimic, featuring a bidentate diphosphine group incorporating an internal nitrogen base, was found to have particularly attractive energetics, prompting a study of the role played by the proton/hydride acceptor necessary to complete the catalytic cycle. Computations revealed an experimentally accessible energetic pathway involving a benzaldehyde proton/hydride acceptor and the most promising catalyst.
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Affiliation(s)
- Kevin A Murray
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne (Switzerland)
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21
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Byer AS, Shepard EM, Peters JW, Broderick JB. Radical S-adenosyl-L-methionine chemistry in the synthesis of hydrogenase and nitrogenase metal cofactors. J Biol Chem 2014; 290:3987-94. [PMID: 25477518 DOI: 10.1074/jbc.r114.578161] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitrogenase, [FeFe]-hydrogenase, and [Fe]-hydrogenase enzymes perform catalysis at metal cofactors with biologically unusual non-protein ligands. The FeMo cofactor of nitrogenase has a MoFe7S9 cluster with a central carbon, whereas the H-cluster of [FeFe]-hydrogenase contains a 2Fe subcluster coordinated by cyanide and CO ligands as well as dithiomethylamine; the [Fe]-hydrogenase cofactor has CO and guanylylpyridinol ligands at a mononuclear iron site. Intriguingly, radical S-adenosyl-L-methionine enzymes are vital for the assembly of all three of these diverse cofactors. This minireview presents and discusses the current state of knowledge of the radical S-adenosylmethionine enzymes required for synthesis of these remarkable metal cofactors.
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Affiliation(s)
- Amanda S Byer
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Eric M Shepard
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - John W Peters
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Joan B Broderick
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
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22
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Affiliation(s)
- Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Edward Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
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23
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Paradies J. Metallfreie Hydrierung von ungesättigten Kohlenwasserstoffen mit molekularem Wasserstoff. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309253] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Paradies J. Metal-Free Hydrogenation of Unsaturated Hydrocarbons Employing Molecular Hydrogen. Angew Chem Int Ed Engl 2014; 53:3552-7. [DOI: 10.1002/anie.201309253] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Indexed: 11/06/2022]
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25
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Finkelmann AR, Senn HM, Reiher M. Hydrogen-activation mechanism of [Fe] hydrogenase revealed by multi-scale modeling. Chem Sci 2014. [DOI: 10.1039/c4sc01605j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A complete atomistic model of [Fe] hydrogenase reveals important details of its mechanism.
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Affiliation(s)
| | - Hans Martin Senn
- WestCHEM and School of Chemistry
- University of Glasgow
- Glasgow G12 8QQ
- UK
| | - Markus Reiher
- Laboratory of Physical Chemistry
- ETH Zürich
- Zürich
- Switzerland
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26
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Gubler J, Finkelmann AR, Reiher M. Theoretical 57Fe Mössbauer Spectroscopy for Structure Elucidation of [Fe] Hydrogenase Active Site Intermediates. Inorg Chem 2013; 52:14205-15. [DOI: 10.1021/ic4021349] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Joël Gubler
- Laboratorium
für Physikalische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Arndt R. Finkelmann
- Laboratorium
für Physikalische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium
für Physikalische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10 8093 Zürich, Switzerland
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27
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Tamura H, Salomone-Stagni M, Fujishiro T, Warkentin E, Meyer-Klaucke W, Ermler U, Shima S. Crystal Structures of [Fe]-Hydrogenase in Complex with Inhibitory Isocyanides: Implications for the H2-Activation Site. Angew Chem Int Ed Engl 2013; 52:9656-9. [DOI: 10.1002/anie.201305089] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Indexed: 01/08/2023]
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28
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Crystal Structures of [Fe]-Hydrogenase in Complex with Inhibitory Isocyanides: Implications for the H2-Activation Site. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305089] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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30
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31
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Praneeth VKK, Ringenberg MR, Ward TR. Redox-Active Ligands in Catalysis. Angew Chem Int Ed Engl 2012; 51:10228-34. [DOI: 10.1002/anie.201204100] [Citation(s) in RCA: 277] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Indexed: 11/10/2022]
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32
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Oza JP, Sowers KR, Perona JJ. Linking energy production and protein synthesis in hydrogenotrophic methanogens. Biochemistry 2012; 51:2378-89. [PMID: 22401293 DOI: 10.1021/bi300106p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogenotrophic methanogens possessing the hydrogen-dependent dehydrogenase Hmd also encode paralogs of this protein whose function is poorly understood. Here we present biochemical evidence that the two inactive Hmd paralogs of Methanocaldococcus jannaschii, HmdII and HmdIII, form binary and ternary complexes with several components of the protein translation apparatus. HmdII and HmdIII, but not the active dehydrogenase Hmd, bind with micromolar binding affinities to a number of tRNAs and form ternary complexes with tRNA(Pro) and prolyl-tRNA synthetase (ProRS). Fluorescence spectroscopy experiments also suggest that binding of HmdII and ProRS involves distinct binding determinants on the tRNA. These biochemical data suggest the possibility of a regulatory link between energy production and protein translation pathways that may allow a rapid cellular response to altered environmental conditions.
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Affiliation(s)
- Javin P Oza
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, California 93106-9510, United States
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33
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Chen D, Scopelliti R, Hu X. Reversible Protonation of a Thiolate Ligand in an [Fe]-Hydrogenase Model Complex. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107634] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Chen D, Scopelliti R, Hu X. Reversible Protonation of a Thiolate Ligand in an [Fe]-Hydrogenase Model Complex. Angew Chem Int Ed Engl 2012; 51:1919-21. [DOI: 10.1002/anie.201107634] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Indexed: 11/07/2022]
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35
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36
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Chen D, Scopelliti R, Hu X. A Five-Coordinate Iron Center in the Active Site of [Fe]-Hydrogenase: Hints from a Model Study. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100201] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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37
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Chen D, Scopelliti R, Hu X. A Five-Coordinate Iron Center in the Active Site of [Fe]-Hydrogenase: Hints from a Model Study. Angew Chem Int Ed Engl 2011; 50:5671-3. [DOI: 10.1002/anie.201100201] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 03/24/2011] [Indexed: 11/07/2022]
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38
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Vardar-Schara G, Maeda T, Wood TK. Metabolically engineered bacteria for producing hydrogen via fermentation. Microb Biotechnol 2011; 1:107-25. [PMID: 21261829 PMCID: PMC3864445 DOI: 10.1111/j.1751-7915.2007.00009.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Hydrogen, the most abundant and lightest element in the universe, has much potential as a future energy source. Hydrogenases catalyse one of the simplest chemical reactions, 2H+ + 2e‐ ↔ H2, yet their structure is very complex. Biologically, hydrogen can be produced via photosynthetic or fermentative routes. This review provides an overview of microbial production of hydrogen by fermentation (currently the more favourable route) and focuses on biochemical pathways, theoretical hydrogen yields and hydrogenase structure. In addition, several examples of metabolic engineering to enhance fermentative hydrogen production are presented along with some examples of expression of heterologous hydrogenases for enhanced hydrogen production.
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Affiliation(s)
- Gönül Vardar-Schara
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Agricultural Sciences 218, Honolulu, HI 96822, USA.
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39
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Abstract
Hydrogenases catalyse redox reactions with molecular hydrogen, either as substrate or product. The enzymes harness hydrogen as a reductant using metals that are abundant and economical, namely, nickel and iron, and should provide new pointers for the economic use of hydrogen in manmade devices. The most recently discovered and perhaps the most enigmatic of the hydrogenases is the [Fe]-hydrogenase, used by certain microorganisms in the pathway that reduces carbon dioxide to methane. Since its discovery some twenty years ago, [Fe]-hydrogenase has consistently provided structural and mechanistic surprises, often requiring complete re-evaluation of its mechanism of action. This tutorial review combines recent advances in X-ray crystallography and other analytical techniques, as well as in computational studies and in chemical synthesis to provide a platform for understanding this remarkable enzyme type.
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Affiliation(s)
- Michael J Corr
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
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40
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Harb MK, Apfel U, Sakamoto T, El‐khateeb M, Weigand W. Diiron Dichalcogenolato (Se and Te) Complexes: Models for the Active Site of [FeFe] Hydrogenase. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201001112] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mohammad K. Harb
- Institut für Anorganische und Analytische Chemie, Friedrich‐Schiller‐Universität Jena, August‐Bebel‐Straße 2, 07743 Jena, Germany
| | - Ulf‐Peter Apfel
- Institut für Anorganische und Analytische Chemie, Friedrich‐Schiller‐Universität Jena, August‐Bebel‐Straße 2, 07743 Jena, Germany
| | - Takahiro Sakamoto
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721, U.S.A
| | - Mohammad El‐khateeb
- Chemistry Department, Jordan University of Science and Technology, 22110 Irbid, Jordan
| | - Wolfgang Weigand
- Institut für Anorganische und Analytische Chemie, Friedrich‐Schiller‐Universität Jena, August‐Bebel‐Straße 2, 07743 Jena, Germany
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41
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Swanson KD, Duffus BR, Beard TE, Peters JW, Broderick JB. Cyanide and Carbon Monoxide Ligand Formation in Hydrogenase Biosynthesis. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201001056] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kevin D. Swanson
- Department of Chemistry & Biochemistry, AstrobiologyBiogeocatalysis Research Center, Montana State University Bozeman, MT 59717, USA, Fax: +1‐406‐994‐7470
| | - Benjamin R. Duffus
- Department of Chemistry & Biochemistry, AstrobiologyBiogeocatalysis Research Center, Montana State University Bozeman, MT 59717, USA, Fax: +1‐406‐994‐7470
| | - Trevor E. Beard
- Department of Chemistry & Biochemistry, AstrobiologyBiogeocatalysis Research Center, Montana State University Bozeman, MT 59717, USA, Fax: +1‐406‐994‐7470
| | - John W. Peters
- Department of Chemistry & Biochemistry, AstrobiologyBiogeocatalysis Research Center, Montana State University Bozeman, MT 59717, USA, Fax: +1‐406‐994‐7470
| | - Joan B. Broderick
- Department of Chemistry & Biochemistry, AstrobiologyBiogeocatalysis Research Center, Montana State University Bozeman, MT 59717, USA, Fax: +1‐406‐994‐7470
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42
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Martin D, Soleilhavoup M, Bertrand G. Stable singlet carbenes as mimics for transition metal centers. Chem Sci 2011; 2:389-399. [PMID: 21743834 PMCID: PMC3129870 DOI: 10.1039/c0sc00388c] [Citation(s) in RCA: 545] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This perspective summarizes recent results, which demonstrate that stable carbenes can activate small molecules (CO, H(2), NH(3) and P(4)) and stabilize highly reactive intermediates (main group elements in the zero oxidation state and paramagnetic species). These two tasks were previously exclusive for transition metal complexes.
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Affiliation(s)
- David Martin
- UCR-CNRS Joint Research Chemistry Laboratory (UMI 2957), Department of Chemistry, University of California, Riverside, California, 92521-0403, USA; Tel: +1 951 827 2719
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43
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Abstract
[Fe]-hydrogenase is one of the three types of hydrogenases. This enzyme is found in many hydrogenotrophic methanogenic archaea and catalyzes the reversible hydride transfer from H(2) to methenyl-H(4)MPT(+) in methanogenesis from H(2) and CO(2). The enzyme harbors a unique iron-guanylyl pyridinol (FeGP) cofactor as a prosthetic group. Here, we describe the purification of [Fe]-hydrogenase from Methanothermobacter marburgensis, the isolation of the FeGP cofactor from the native holoenzyme, and the reconstitution of [Fe]-hydrogenase from the isolated FeGP cofactor and the heterologously produced apoenzyme.
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Affiliation(s)
- Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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44
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Shima S, Ermler U. Structure and Function of [Fe]‐Hydrogenase and its Iron–Guanylylpyridinol (FeGP) Cofactor. Eur J Inorg Chem 2010. [DOI: 10.1002/ejic.201000955] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl‐von‐Frisch‐Straße, 35043 Marburg, Germany, Fax: +49‐6421‐178109
- PRESTO, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332‐0012, Japan
| | - Ulrich Ermler
- Max Planck Institute for Biophysics, Max‐von‐Laue‐Straße 3, 60438 Frankfurt/Main, Germany
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45
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Shima S, Vogt S, Göbels A, Bill E. Iron-Chromophore Circular Dichroism of [Fe]-Hydrogenase: The Conformational Change Required for H2 Activation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201006255] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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46
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Shima S, Vogt S, Göbels A, Bill E. Iron-Chromophore Circular Dichroism of [Fe]-Hydrogenase: The Conformational Change Required for H2 Activation. Angew Chem Int Ed Engl 2010; 49:9917-21. [DOI: 10.1002/anie.201006255] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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Wright JA, Turrell PJ, Pickett CJ. The Third Hydrogenase: More Natural Organometallics. Organometallics 2010. [DOI: 10.1021/om1008567] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph A. Wright
- Energy Materials Laboratory, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Peter J. Turrell
- Energy Materials Laboratory, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Christopher J. Pickett
- Energy Materials Laboratory, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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48
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Chen D, Scopelliti R, Hu X. [Fe]-Hydrogenase Models Featuring Acylmethylpyridinyl Ligands. Angew Chem Int Ed Engl 2010; 49:7512-5. [DOI: 10.1002/anie.201004579] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Chen D, Scopelliti R, Hu X. [Fe]-Hydrogenase Models Featuring Acylmethylpyridinyl Ligands. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004579] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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50
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Ogata H, Kellers P, Lubitz W. The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state). J Mol Biol 2010; 402:428-44. [PMID: 20673834 DOI: 10.1016/j.jmb.2010.07.041] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 11/18/2022]
Abstract
The crystal structure of the membrane-associated [NiFe] hydrogenase from Allochromatium vinosum has been determined to 2.1 Å resolution. Electron paramagnetic resonance (EPR) and Fourier transform infrared spectroscopy on dissolved crystals showed that it is present in the Ni-A state (>90%). The structure of the A. vinosum [NiFe] hydrogenase shows significant similarities with [NiFe] hydrogenase structures derived from Desulfovibrio species. The amino acid sequence identity is ∼ 50%. The bimetallic [NiFe] active site is located in the large subunit of the heterodimer and possesses three diatomic non-protein ligands coordinated to the Fe (two CN(-) , one CO). Ni is bound to the protein backbone via four cysteine thiolates; two of them also bridge the two metals. One of the bridging cysteines (Cys64) exhibits a modified thiolate in part of the sample. A mono-oxo bridging ligand was assigned between the metal ions of the catalytic center. This is in contrast to a proposal for Desulfovibrio sp. hydrogenases that show a di-oxo species in this position for the Ni-A state. The additional metal site located in the large subunit appears to be a Mg(2+) ion. Three iron-sulfur clusters were found in the small subunit that forms the electron transfer chain connecting the catalytic site with the molecular surface. The calculated anomalous Fourier map indicates a distorted proximal iron-sulfur cluster in part of the crystals. This altered proximal cluster is supposed to be paramagnetic and is exchange coupled to the Ni(3+) ion and the medial [Fe(3)S(4)](+) cluster that are both EPR active (S=1/2 species). This finding of a modified proximal cluster in the [NiFe] hydrogenase might explain the observation of split EPR signals that are occasionally detected in the oxidized state of membrane-bound [NiFe] hydrogenases as from A. vinosum.
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Affiliation(s)
- Hideaki Ogata
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.
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