1
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Patra AK, Puchala R. Methane mitigation in ruminants with structural analogues and other chemical compounds targeting archaeal methanogenesis pathways. Biotechnol Adv 2023; 69:108268. [PMID: 37793598 DOI: 10.1016/j.biotechadv.2023.108268] [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: 05/11/2023] [Revised: 09/20/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
Ruminants are responsible for enteric methane production contributing significantly to the anthropogenic greenhouse gases in the atmosphere. Moreover, dietary energy is lost as methane gas without being available for animal use. Therefore, many mitigation strategies aiming at interventions at animals, diet, and microbiota have been explored by researchers. Specific chemical analogues targeting the enzymes of the methanogenic pathway appear to be more effective in specifically inhibiting the growth of methane-producing archaea without hampering another microbiome, particularly, cellulolytic microbiota. The targets of methanogenesis reactions that have been mainly investigated in ruminal fluid include methyl coenzyme M reductase (halogenated sulfonate and nitrooxy compounds), corrinoid enzymes (halogenated aliphatic compounds), formate dehydrogenase (nitro compounds, e.g., nitroethane and 2-nitroethanol), and deazaflavin (F420) (pterin and statin compounds). Many other potential metabolic reaction targets in methanogenic archaea have not been evaluated properly. The analogues are specifically effective inhibitors of methanogens, but their efficacy to lower methanogenesis over time reduces due to the metabolism of the compounds by other microbiota or the development of resistance mechanisms by methanogens. In this short review, methanogen populations inhabited in the rumen, methanogenesis pathways and methane analogues, and other chemical compounds specifically targeting the metabolic reactions in the pathways and methane production in ruminants have been discussed. Although many methane inhibitors have been evaluated in lowering methane emission in ruminants, advancement in unravelling the molecular mechanisms of specific methane inhibitors targeting the metabolic pathways in methanogens is very limited.
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Affiliation(s)
- Amlan Kumar Patra
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA.
| | - Ryszard Puchala
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA; Applied Physiology Unit, Military Institute of Hygiene and Epidemiology, Kozielska 4, Warsaw, Poland
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2
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Barata‐Vallejo S, Yerien DE, Postigo A. Bioinspired Photocatalyzed Organic Synthetic Transformations. The Use of Natural Pigments and Vitamins in Photocatalysis. ChemCatChem 2022. [DOI: 10.1002/cctc.202200623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sebastián Barata‐Vallejo
- Departamento de Ciencias Químicas Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Junin 954 CP 1113- Buenos Aires Argentina
- Istituto per la Sintesis Organica e la Fotorreattivita, ISOF Consiglio Nazionale delle Ricerche Via P. Gobetti 101 40129 Bologna Italy
| | - Damian E. Yerien
- Departamento de Ciencias Químicas Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Junin 954 CP 1113- Buenos Aires Argentina
| | - Al Postigo
- Departamento de Ciencias Químicas Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Junin 954 CP 1113- Buenos Aires Argentina
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3
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Aragón J, Sun S, Pascual D, Jaworski S, Lloret-Fillol J. Photoredox Activation of Inert Alkyl Chlorides for the Reductive Cross-Coupling with Aromatic Alkenes. Angew Chem Int Ed Engl 2022; 61:e202114365. [PMID: 35289039 DOI: 10.1002/anie.202114365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Indexed: 11/08/2022]
Abstract
The inertness of chloroalkanes has precluded them as coupling partners for cross-coupling reactions. Herein we disclose a general strategy for the activation of inert alkyl chlorides through photoredox catalysis and their use as coupling partners with alkenes. The catalytic system is formed by [Ni(OTf)(Py2 Ts tacn)](OTf) (1Ni ), which is responsible for the Csp3 -Cl bond activation, and [Ir(NMe2 bpy)(ppy)2 ]PF6, (PCIr NMe2 ), which is the photoredox catalyst. Combined experimental and theoretical studies show an in situ photogenerated NiI intermediate ([Ni(Py2 Ts tacn)]+ ) which is catalytically competent for the Csp3 -Cl bond cleavage via a SN 2 mechanism for primary alkyl chlorides, forming carbon-centered free radicals, which react with the olefin leading to the formation of the Csp3 -Csp3 bond. These results suggest inert alkyl chlorides can be electrophiles for developing new intermolecular strategies in which low-valent aminopyridine nickel complexes act as key catalytic species.
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Affiliation(s)
- Jordi Aragón
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology, Technology Avda. Països Catalans, 16, 43007, Tarragona, Spain.,Departament de Química Organica i Analítica, Universitat Rovira i Virgili, Carrer Marcel⋅lí Domingo s/n, 43007, Tarragona, Spain
| | - Suyun Sun
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology, Technology Avda. Països Catalans, 16, 43007, Tarragona, Spain.,Departament de Química Organica i Analítica, Universitat Rovira i Virgili, Carrer Marcel⋅lí Domingo s/n, 43007, Tarragona, Spain
| | - David Pascual
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology, Technology Avda. Països Catalans, 16, 43007, Tarragona, Spain.,Departament de Química Organica i Analítica, Universitat Rovira i Virgili, Carrer Marcel⋅lí Domingo s/n, 43007, Tarragona, Spain
| | - Sebastian Jaworski
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology, Technology Avda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Julio Lloret-Fillol
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology, Technology Avda. Països Catalans, 16, 43007, Tarragona, Spain.,Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys, 23, 08010, Barcelona, Spain
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4
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Gropp J, Jin Q, Halevy I. Controls on the isotopic composition of microbial methane. SCIENCE ADVANCES 2022; 8:eabm5713. [PMID: 35385305 PMCID: PMC8985922 DOI: 10.1126/sciadv.abm5713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Microbial methane production (methanogenesis) is responsible for more than half of the annual emissions of this major greenhouse gas to the atmosphere. Although the stable isotopic composition of methane is often used to characterize its sources and sinks, strictly empirical descriptions of the isotopic signature of methanogenesis currently limit these attempts. We developed a metabolic-isotopic model of methanogenesis by carbon dioxide reduction, which predicts carbon and hydrogen isotopic fractionations, and clumped isotopologue distributions, as functions of the cell's environment. We mechanistically explain multiple isotopic patterns in laboratory and natural settings and show that these patterns constrain the in situ energetics of methanogenesis. Combining our model with data from environments in which methanogenic activity is energy-limited, we provide predictions for the biomass-specific methanogenesis rates and the associated isotopic effects.
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Affiliation(s)
- Jonathan Gropp
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Qusheng Jin
- Department of Earth Sciences, University of Oregon, Eugene, OR, USA
| | - Itay Halevy
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
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5
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Aragón J, Sun S, Pascual D, Jaworski S, Lloret‐Fillol J. Photoredox Activation of Inert Alkyl Chlorides for the Reductive Cross‐Coupling with Aromatic Alkenes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jordi Aragón
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology Technology Avda. Països Catalans, 16 43007 Tarragona Spain
- Departament de Química Organica i Analítica Universitat Rovira i Virgili Carrer Marcel⋅lí Domingo s/n 43007 Tarragona Spain
| | - Suyun Sun
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology Technology Avda. Països Catalans, 16 43007 Tarragona Spain
- Departament de Química Organica i Analítica Universitat Rovira i Virgili Carrer Marcel⋅lí Domingo s/n 43007 Tarragona Spain
| | - David Pascual
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology Technology Avda. Països Catalans, 16 43007 Tarragona Spain
- Departament de Química Organica i Analítica Universitat Rovira i Virgili Carrer Marcel⋅lí Domingo s/n 43007 Tarragona Spain
| | - Sebastian Jaworski
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology Technology Avda. Països Catalans, 16 43007 Tarragona Spain
| | - Julio Lloret‐Fillol
- Institute of Chemical Research of Catalonia (ICIQ) Barcelona Institute of Science and Technology Technology Avda. Països Catalans, 16 43007 Tarragona Spain
- Institution for Research and Advanced Studies (ICREA) Passeig Lluís Companys, 23 08010 Barcelona Spain
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6
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Patwardhan A, Sarangi R, Ginovska B, Raugei S, Ragsdale SW. Nickel-Sulfonate Mode of Substrate Binding for Forward and Reverse Reactions of Methyl-SCoM Reductase Suggest a Radical Mechanism Involving Long-Range Electron Transfer. J Am Chem Soc 2021; 143:5481-5496. [PMID: 33761259 DOI: 10.1021/jacs.1c01086] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F430. The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C-S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni-thiol interaction between Ni(II)-MCR and inhibitor CoMSH, a Ni(I)-thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)-disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)-sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)-N/O complex, not Ni(I)-S. These studies rule out direct Ni(I)-sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)-sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively.
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Affiliation(s)
- Anjali Patwardhan
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48103, United States
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Bojana Ginovska
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Simone Raugei
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48103, United States
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7
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Kisgeropoulos EC, Manesis AC, Shafaat HS. Ligand Field Inversion as a Mechanism to Gate Bioorganometallic Reactivity: Investigating a Biochemical Model of Acetyl CoA Synthase Using Spectroscopy and Computation. J Am Chem Soc 2021; 143:849-867. [PMID: 33415980 DOI: 10.1021/jacs.0c10135] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biological global carbon cycle is largely regulated through microbial nickel enzymes, including carbon monoxide dehydrogenase (CODH), acetyl coenzyme A synthase (ACS), and methyl coenzyme M reductase (MCR). These systems are suggested to utilize organometallic intermediates during catalysis, though characterization of these species has remained challenging. We have established a mutant of nickel-substituted azurin as a scaffold upon which to develop protein-based models of enzymatic intermediates, including the organometallic states of ACS. In this work, we report the comprehensive investigation of the S = 1/2 Ni-CO and Ni-CH3 states using pulsed EPR spectroscopy and computational techniques. While the Ni-CO state shows conventional metal-ligand interactions and a classical ligand field, the Ni-CH3 hyperfine interactions between the methyl protons and the nickel indicate a closer distance than would be expected for an anionic methyl ligand. Structural analysis instead suggests a near-planar methyl ligand that can be best described as cationic. Consistent with this conclusion, the frontier molecular orbitals of the Ni-CH3 species indicate a ligand-centered LUMO, with a d9 population on the metal center, rather than the d7 population expected for a typical metal-alkyl species generated by oxidative addition. Collectively, these data support the presence of an inverted ligand field configuration for the Ni-CH3 Az species, in which the lowest unoccupied orbital is centered on the ligands rather than the more electropositive metal. These analyses provide the first evidence for an inverted ligand field within a biological system. The functional relevance of the electronic structures of both the Ni-CO and Ni-CH3 species are discussed in the context of native ACS, and an inverted ligand field is proposed as a mechanism by which to gate reactivity both within ACS and in other thiolate-containing metalloenzymes.
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Affiliation(s)
- Effie C Kisgeropoulos
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anastasia C Manesis
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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8
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Nickel(II)‐Mediated Reversible Thiolate/Disulfide Conversion as a Mimic for a Key Step of the Catalytic Cycle of Methyl‐Coenzyme M Reductase. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Bhandari A, Mishra S, Maji RC, Kumar A, Olmstead MM, Patra AK. Nickel(II)‐Mediated Reversible Thiolate/Disulfide Conversion as a Mimic for a Key Step of the Catalytic Cycle of Methyl‐Coenzyme M Reductase. Angew Chem Int Ed Engl 2020; 59:9177-9185. [DOI: 10.1002/anie.202001363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Indexed: 01/22/2023]
Affiliation(s)
- Anirban Bhandari
- Department of Chemistry National Institute of Technology Durgapur Mahatma Gandhi Avenue Durgapur 713 209 (WB) India
| | - Saikat Mishra
- Department of Chemistry National Institute of Technology Durgapur Mahatma Gandhi Avenue Durgapur 713 209 (WB) India
| | - Ram Chandra Maji
- Department of Chemistry National Institute of Technology Durgapur Mahatma Gandhi Avenue Durgapur 713 209 (WB) India
| | - Akhilesh Kumar
- Department of Chemistry Indian Institute of Technology Kanpur Kanpur 208016 India
| | | | - Apurba K. Patra
- Department of Chemistry National Institute of Technology Durgapur Mahatma Gandhi Avenue Durgapur 713 209 (WB) India
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10
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Claros M, Ungeheuer F, Franco F, Martin‐Diaconescu V, Casitas A, Lloret‐Fillol J. Reductive Cyclization of Unactivated Alkyl Chlorides with Tethered Alkenes under Visible-Light Photoredox Catalysis. Angew Chem Int Ed Engl 2019; 58:4869-4874. [PMID: 30707782 PMCID: PMC6519206 DOI: 10.1002/anie.201812702] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/26/2019] [Indexed: 01/09/2023]
Abstract
The chemical inertness of abundant and commercially available alkyl chlorides precludes their widespread use as reactants in chemical transformations. Presented in this work is a metallaphotoredox methodology to achieve the catalytic intramolecular reductive cyclization of unactivated alkyl chlorides with tethered alkenes. The cleavage of strong C(sp3 )-Cl bonds is mediated by a highly nucleophilic low-valent cobalt or nickel intermediate generated by visible-light photoredox reduction employing a copper photosensitizer. The high basicity and multidentate nature of the ligands are key to obtaining efficient metal catalysts for the functionalization of unactivated alkyl chlorides.
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Affiliation(s)
- Miguel Claros
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and TechnologyAvda. Països Catalans, 1643007TarragonaSpain
| | - Felix Ungeheuer
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and TechnologyAvda. Països Catalans, 1643007TarragonaSpain
| | - Federico Franco
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and TechnologyAvda. Països Catalans, 1643007TarragonaSpain
| | - Vlad Martin‐Diaconescu
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and TechnologyAvda. Països Catalans, 1643007TarragonaSpain
| | - Alicia Casitas
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and TechnologyAvda. Països Catalans, 1643007TarragonaSpain
| | - Julio Lloret‐Fillol
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and TechnologyAvda. Països Catalans, 1643007TarragonaSpain
- Catalan Institution for Research and Advanced Studies (ICREA)Passeig Lluïs Companys, 2308010BarcelonaSpain
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11
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Claros M, Ungeheuer F, Franco F, Martin‐Diaconescu V, Casitas A, Lloret‐Fillol J. Reductive Cyclization of Unactivated Alkyl Chlorides with Tethered Alkenes under Visible‐Light Photoredox Catalysis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Miguel Claros
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and Technology Avda. Països Catalans, 16 43007 Tarragona Spain
| | - Felix Ungeheuer
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and Technology Avda. Països Catalans, 16 43007 Tarragona Spain
| | - Federico Franco
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and Technology Avda. Països Catalans, 16 43007 Tarragona Spain
| | - Vlad Martin‐Diaconescu
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and Technology Avda. Països Catalans, 16 43007 Tarragona Spain
| | - Alicia Casitas
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and Technology Avda. Països Catalans, 16 43007 Tarragona Spain
| | - Julio Lloret‐Fillol
- Institute of Chemical Research of Catalonia (ICIQ)Barcelona Institute of Science and Technology Avda. Països Catalans, 16 43007 Tarragona Spain
- Catalan Institution for Research and Advanced Studies (ICREA) Passeig Lluïs Companys, 23 08010 Barcelona Spain
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12
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Wu M, Feng K, Li Q, Ma H, Zhu H, Xie Y, Yan G, Chen C, Yan K. Glutaraldehyde-polymerized hemoglobin and tempol (PolyHb-tempol) has superoxide dismutase activity that can attenuate oxidative stress on endothelial cells induced by superoxide anion. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2017; 46:47-55. [PMID: 28521553 DOI: 10.1080/21691401.2017.1328685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A Tempol compound with an amine group (4-amino-2,2,6,6-tetramethylpiperidine-1-oxyl, NH2-Tempol) was cross-linked to hemoglobin in a one-step polymerization reaction to produce a novel hemoglobin-based oxygen carrier (HBOC) designated PolyHb-Tempol. The reaction parameters, including the reaction time, pH, temperature, and ratio of reactants, were optimized, and the physiochemical properties of the resulting product were characterized. PolyHb-Tempol didn't show any toxicity towards endothelial cells. Furthermore, from observations of cell morphology and viability, PolyHb-Tempol showed a significant ability to inhibit or eliminate oxidative stress induced by superoxide free radicals. These results suggest that PolyHb-Tempol may potentially be suitable as an HBOC.
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Affiliation(s)
- Mengdi Wu
- a College of Life Science , Northwest University , Xi'an , P.R. China
| | - Kun Feng
- a College of Life Science , Northwest University , Xi'an , P.R. China
| | - Qiuhui Li
- a College of Life Science , Northwest University , Xi'an , P.R. China
| | - Huiya Ma
- a College of Life Science , Northwest University , Xi'an , P.R. China
| | - Hongli Zhu
- a College of Life Science , Northwest University , Xi'an , P.R. China.,b National Engineering Research Center for Miniaturized Detection System , Xi'an , P.R. China
| | - Yudou Xie
- c Shaanxi Lifegen Co., Ltd. , Xi'an , P.R. China
| | - Gaofei Yan
- c Shaanxi Lifegen Co., Ltd. , Xi'an , P.R. China
| | - Chao Chen
- a College of Life Science , Northwest University , Xi'an , P.R. China.,b National Engineering Research Center for Miniaturized Detection System , Xi'an , P.R. China
| | - Kunping Yan
- a College of Life Science , Northwest University , Xi'an , P.R. China.,b National Engineering Research Center for Miniaturized Detection System , Xi'an , P.R. China
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13
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Ragsdale SW, Raugei S, Ginovska B, Wongnate T. Biochemistry of Methyl-Coenzyme M Reductase. THE BIOLOGICAL CHEMISTRY OF NICKEL 2017. [DOI: 10.1039/9781788010580-00149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Methanogens are masters of CO2 reduction. They conserve energy by coupling H2 oxidation to the reduction of CO2 to CH4, the primary constituent of natural gas. They also generate methane by the reduction of acetic acid, methanol, methane thiol, and methylamines. Methanogens produce 109 tons of methane per year and are the major source of the earth’s atmospheric methane. Reverse methanogenesis or anaerobic methane oxidation, which is catalyzed by methanotrophic archaea living in consortia among bacteria that can act as an electron acceptor, is responsible for annual oxidation of 108 tons of methane to CO2. This chapter briefly describes the overall process of methanogenesis and then describes the enzymatic mechanism of the nickel enzyme, methyl-CoM reductase (MCR), the key enzyme in methane synthesis and oxidation. MCR catalyzes the formation of methane and the heterodisulfide (CoBSSCoM) from methyl-coenzyme M (methyl-CoM) and coenzyme B (HSCoB). Uncovering the mechanistic and molecular details of MCR catalysis is critical since methane is an abundant and important fuel and is the second (to CO2) most prevalent greenhouse gas.
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Affiliation(s)
- Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School 1150 W. Medical Center Dr., 5301 MSRB III Ann Arbor MI 48109-0606 USA
| | - Simone Raugei
- Physical Sciences Division, Pacific Northwest National Laboratory, Post Office Box 999 K1-83 Richland WA 99352 USA
| | - Bojana Ginovska
- Physical Sciences Division, Pacific Northwest National Laboratory, Post Office Box 999 K1-83 Richland WA 99352 USA
| | - Thanyaporn Wongnate
- School of Bioresources and Technology and Excellent Center of Waste Utilization and Management (ECoWaste), King Mongkut's University of Technology Thonburi Bangkhunthian, Bangkok 10140 Thailand
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14
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Wintsche B, Glaser K, Sträuber H, Centler F, Liebetrau J, Harms H, Kleinsteuber S. Trace Elements Induce Predominance among Methanogenic Activity in Anaerobic Digestion. Front Microbiol 2016; 7:2034. [PMID: 28018337 PMCID: PMC5160323 DOI: 10.3389/fmicb.2016.02034] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 12/02/2016] [Indexed: 11/30/2022] Open
Abstract
Trace elements (TE) play an essential role in all organisms due to their functions in enzyme complexes. In anaerobic digesters, control, and supplementation of TEs lead to stable and more efficient methane production processes while TE deficits cause process imbalances. However, the underlying metabolic mechanisms and the adaptation of the affected microbial communities to such deficits are not yet fully understood. Here, we investigated the microbial community dynamics and resulting process changes induced by TE deprivation. Two identical lab-scale continuous stirred tank reactors fed with distiller’s grains and supplemented with TEs (cobalt, molybdenum, nickel, tungsten) and a commercial iron additive were operated in parallel. After 72 weeks of identical operation, the feeding regime of one reactor was changed by omitting TE supplements and reducing the amount of iron additive. Both reactors were operated for further 21 weeks. Various process parameters (biogas production and composition, total solids and volatile solids, TE concentration, volatile fatty acids, total ammonium nitrogen, total organic acids/alkalinity ratio, and pH) and the composition and activity of the microbial communities were monitored over the total experimental time. While the methane yield remained stable, the concentrations of hydrogen sulfide, total ammonia nitrogen, and acetate increased in the TE-depleted reactor compared to the well-supplied control reactor. Methanosarcina and Methanoculleus dominated the methanogenic communities in both reactors. However, the activity ratio of these two genera was shown to depend on TE supplementation explainable by different TE requirements of their energy conservation systems. Methanosarcina dominated the well-supplied anaerobic digester, pointing to acetoclastic methanogenesis as the dominant methanogenic pathway. Under TE deprivation, Methanoculleus and thus hydrogenotrophic methanogenesis was favored although Methanosarcina was not overgrown by Methanoculleus. Multivariate statistics revealed that the decline of nickel, cobalt, molybdenum, tungsten, and manganese most strongly influenced the balance of mcrA transcripts from both genera. Hydrogenotrophic methanogens seem to be favored under nickel- and cobalt-deficient conditions as their metabolism requires less nickel-dependent enzymes and corrinoid cofactors than the acetoclastic and methylotrophic pathways. Thus, TE supply is critical to sustain the activity of the versatile high-performance methanogen Methanosarcina.
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Affiliation(s)
- Babett Wintsche
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| | - Karin Glaser
- Department of Applied Ecology and Phycology, University of Rostock Rostock, Germany
| | - Heike Sträuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| | - Jan Liebetrau
- Department of Biochemical Conversion, Deutsches Biomasseforschungszentrum - DBFZ Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZLeipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv)Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
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15
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Lawton TJ, Rosenzweig AC. Biocatalysts for methane conversion: big progress on breaking a small substrate. Curr Opin Chem Biol 2016; 35:142-149. [PMID: 27768948 PMCID: PMC5161620 DOI: 10.1016/j.cbpa.2016.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/08/2023]
Abstract
Nature utilizes two groups of enzymes to catalyze methane conversions, methyl-coenzyme M reductases (MCRs) and methane monooxygenases (MMOs). These enzymes have been difficult to incorporate into industrial processes due to their complexity, poor stability, and lack of recombinant tractability. Despite these issues, new ways of preparing and stabilizing these enzymes have recently been discovered, and new mechanistic insight into how MCRs and MMOs break the C-H bond in nature's most inert hydrocarbon have been obtained. This review focuses on recent findings in the methane biocatalysis field, and discusses the impact of these finding on designing MMO and MCR-based biotechnologies.
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Affiliation(s)
- Thomas J Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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16
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Affiliation(s)
- Thomas J Lawton
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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17
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Wongnate T, Sliwa D, Ginovska B, Smith D, Wolf MW, Lehnert N, Raugei S, Ragsdale SW. The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase. Science 2016; 352:953-8. [PMID: 27199421 DOI: 10.1126/science.aaf0616] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/05/2016] [Indexed: 12/16/2022]
Abstract
Methyl-coenzyme M reductase, the rate-limiting enzyme in methanogenesis and anaerobic methane oxidation, is responsible for the biological production of more than 1 billion tons of methane per year. The mechanism of methane synthesis is thought to involve either methyl-nickel(III) or methyl radical/Ni(II)-thiolate intermediates. We employed transient kinetic, spectroscopic, and computational approaches to study the reaction between the active Ni(I) enzyme and substrates. Consistent with the methyl radical-based mechanism, there was no evidence for a methyl-Ni(III) species; furthermore, magnetic circular dichroism spectroscopy identified the Ni(II)-thiolate intermediate. Temperature-dependent transient kinetics also closely matched density functional theory predictions of the methyl radical mechanism. Identifying the key intermediate in methanogenesis provides fundamental insights to develop better catalysts for producing and activating an important fuel and potent greenhouse gas.
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Affiliation(s)
- Thanyaporn Wongnate
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-0606, USA
| | - Dariusz Sliwa
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-0606, USA
| | - Bojana Ginovska
- Physical Sciences Division, Pacific Northwest National Laboratory, Post Office Box 999, K1-83, Richland, WA 99352, USA
| | - Dayle Smith
- Physical Sciences Division, Pacific Northwest National Laboratory, Post Office Box 999, K1-83, Richland, WA 99352, USA
| | - Matthew W Wolf
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Simone Raugei
- Physical Sciences Division, Pacific Northwest National Laboratory, Post Office Box 999, K1-83, Richland, WA 99352, USA
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-0606, USA.
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18
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Wongnate T, Ragsdale SW. The reaction mechanism of methyl-coenzyme M reductase: how an enzyme enforces strict binding order. J Biol Chem 2015; 290:9322-34. [PMID: 25691570 DOI: 10.1074/jbc.m115.636761] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Indexed: 01/03/2023] Open
Abstract
Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB7SH) to CH4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM) is productive whereas the other (MCR·CoB7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB7SH complex is highly disfavored (Kd = 56 mM). However, binding of CoB7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB7SH·MCR(Ni(I))·CH3SCoM) is highly favored (Kd = 79 μM). Only then can the chemical reaction occur (kobs = 20 s(-1) at 25 °C), leading to rapid formation and dissociation of CH4 leaving the binary product complex (MCR(Ni(II))·CoB7S(-)·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. This first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates.
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Affiliation(s)
- Thanyaporn Wongnate
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Stephen W Ragsdale
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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19
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Discovery of multiple modified F(430) coenzymes in methanogens and anaerobic methanotrophic archaea suggests possible new roles for F(430) in nature. Appl Environ Microbiol 2014; 80:6403-12. [PMID: 25107965 DOI: 10.1128/aem.02202-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methane is a potent greenhouse gas that is generated and consumed in anaerobic environments through the energy metabolism of methanogens and anaerobic methanotrophic archaea (ANME), respectively. Coenzyme F430 is essential for methanogenesis, and a structural variant of F430, 17(2)-methylthio-F430 (F430-2), is found in ANME and is presumably essential for the anaerobic oxidation of methane. Here we use liquid chromatography-high-resolution mass spectrometry to identify several new structural variants of F430 in the cell extracts of selected methanogens and ANME. Methanocaldococcus jannaschii and Methanococcus maripaludis contain an F430 variant (denoted F430-3) that has an M(+) of 1,009.2781. This mass increase of 103.9913 over that of F430 corresponds to C3H4O2S and is consistent with the addition of a 3-mercaptopropionate moiety bound as a thioether followed by a cyclization. The UV absorbance spectrum of F430-3 was different from that of F430 and instead matched that of an F430 derivative where the 17(3) keto moiety had been reduced. This is the first report of a modified F430 in methanogens. In a search for F430-2 and F430-3 in other methanogens and ANME, we have identified a total of nine modified F430 structures. One of these compounds may be an abiotic oxidative product of F430, but the others represent naturally modified versions of F430. This work indicates that F430-related molecules have additional functions in nature and will inspire further research to determine the biochemical role(s) of these variants and the pathways involved in their biosynthesis.
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20
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Boer JL, Mulrooney SB, Hausinger RP. Nickel-dependent metalloenzymes. Arch Biochem Biophys 2014; 544:142-52. [PMID: 24036122 PMCID: PMC3946514 DOI: 10.1016/j.abb.2013.09.002] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/31/2013] [Accepted: 09/03/2013] [Indexed: 11/29/2022]
Abstract
This review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase I, acireductone dioxygenase, urease, superoxide dismutase, [NiFe]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme A synthase/decarbonylase, methyl-coenzyme M reductase, and lactate racemase. These enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more complex nickel-containing clusters, and nickel-tetrapyrroles. Selected other enzymes are active with nickel, but the physiological relevance of this metal specificity is unclear. Additional nickel-containing proteins of undefined function have been identified.
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Affiliation(s)
- Jodi L Boer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Scott B Mulrooney
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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21
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Chen SL, Blomberg MRA, Siegbahn PEM. An investigation of possible competing mechanisms for Ni-containing methyl–coenzyme M reductase. Phys Chem Chem Phys 2014; 16:14029-35. [DOI: 10.1039/c4cp01483a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Biochemistry of methyl-coenzyme M reductase: the nickel metalloenzyme that catalyzes the final step in synthesis and the first step in anaerobic oxidation of the greenhouse gas methane. Met Ions Life Sci 2014; 14:125-45. [PMID: 25416393 DOI: 10.1007/978-94-017-9269-1_6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methane, the major component of natural gas, has been in use in human civilization since ancient times as a source of fuel and light. Methanogens are responsible for synthesis of most of the methane found on Earth. The enzyme responsible for catalyzing the chemical step of methanogenesis is methyl-coenzyme M reductase (MCR), a nickel enzyme that contains a tetrapyrrole cofactor called coenzyme F430, which can traverse the Ni(I), (II), and (III) oxidation states. MCR and methanogens are also involved in anaerobic methane oxidation. This review describes structural, kinetic, and computational studies aimed at elucidating the mechanism of MCR. Such studies are expected to impact the many ramifications of methane in our society and environment, including energy production and greenhouse gas warming.
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23
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Callaghan AV. Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins. Front Microbiol 2013; 4:89. [PMID: 23717304 PMCID: PMC3653055 DOI: 10.3389/fmicb.2013.00089] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/31/2013] [Indexed: 11/13/2022] Open
Abstract
Anaerobic microorganisms play key roles in the biogeochemical cycling of methane and non-methane alkanes. To date, there appear to be at least three proposed mechanisms of anaerobic methane oxidation (AOM). The first pathway is mediated by consortia of archaeal anaerobic methane oxidizers and sulfate-reducing bacteria (SRB) via “reverse methanogenesis” and is catalyzed by a homolog of methyl-coenzyme M reductase. The second pathway is also mediated by anaerobic methane oxidizers and SRB, wherein the archaeal members catalyze both methane oxidation and sulfate reduction and zero-valent sulfur is a key intermediate. The third AOM mechanism is a nitrite-dependent, “intra-aerobic” pathway described for the denitrifying bacterium, ‘Candidatus Methylomirabilis oxyfera.’ It is hypothesized that AOM proceeds via reduction of nitrite to nitric oxide, followed by the conversion of two nitric oxide molecules to dinitrogen and molecular oxygen. The latter can be used to functionalize the methane via a particulate methane monooxygenase. With respect to non-methane alkanes, there also appear to be novel mechanisms of activation. The most well-described pathway is the addition of non-methane alkanes across the double bond of fumarate to form alkyl-substituted succinates via the putative glycyl radical enzyme, alkylsuccinate synthase (also known as methylalkylsuccinate synthase). Other proposed mechanisms include anaerobic hydroxylation via ethylbenzene dehydrogenase-like enzymes and an “intra-aerobic” denitrification pathway similar to that described for ‘Methylomirabilis oxyfera.’
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Affiliation(s)
- Amy V Callaghan
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
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24
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Zhou Y, Dorchak AE, Ragsdale SW. In vivo activation of methyl-coenzyme M reductase by carbon monoxide. Front Microbiol 2013; 4:69. [PMID: 23554601 PMCID: PMC3612591 DOI: 10.3389/fmicb.2013.00069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/11/2013] [Indexed: 12/21/2022] Open
Abstract
Methyl-coenzyme M reductase (MCR) from methanogenic archaea catalyzes the rate-limiting and final step in methane biosynthesis. Using coenzyme B as the two-electron donor, MCR reduces methyl-coenzyme M (CH3-SCoM) to methane and the mixed disulfide, CoBS-SCoM. MCR contains an essential redox-active nickel tetrahydrocorphinoid cofactor, Coenzyme F430, at its active site. The active form of the enzyme (MCRred1) contains Ni(I)-F430. Rapid and efficient conversion of MCR to MCRred1 is important for elucidating the enzymatic mechanism, yet this reduction is difficult because the Ni(I) state is subject to oxidative inactivation. Furthermore, no in vitro methods have yet been described to convert Ni(II) forms into MCRred1. Since 1991, it has been known that MCRred1 from Methanothermobacter marburgensis can be generated in vivo when cells are purged with 100% H2. Here we show that purging cells or cell extracts with CO can also activate MCR. The rate of in vivo activation by CO is about 15 times faster than by H2 (130 and 8 min-1, respectively) and CO leads to twofold higher MCRred1 than H2. Unlike H2-dependent activation, which exhibits a 10-h lag time, there is no lag for CO-dependent activation. Based on cyanide inhibition experiments, carbon monoxide dehydrogenase is required for the CO-dependent activation. Formate, which also is a strong reductant, cannot activate MCR in M. marburgensis in vivo.
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Affiliation(s)
- Yuzhen Zhou
- Department of Biological Chemistry, University of Michigan Medical School, University of Michigan Ann Arbor, MI, USA
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25
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An Y, Cheng C, Pan B, Wang Z. Mechanistic Insight into the Nickel-Catalyzed Intermolecular [3+2+2] Cocyclization of Ethyl Cyclopropylideneacetate with Alkynes: DFT Calculations. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200363] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Chen SL, Blomberg MRA, Siegbahn PEM. How Is Methane Formed and Oxidized Reversibly When Catalyzed by Ni-Containing Methyl-Coenzyme M Reductase? Chemistry 2012; 18:6309-15. [DOI: 10.1002/chem.201200274] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Indexed: 11/07/2022]
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Shima S, Krueger M, Weinert T, Demmer U, Kahnt J, Thauer RK, Ermler U. Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically. Nature 2011; 481:98-101. [DOI: 10.1038/nature10663] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 10/19/2011] [Indexed: 11/09/2022]
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28
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Ferry JG. Fundamentals of methanogenic pathways that are key to the biomethanation of complex biomass. Curr Opin Biotechnol 2011; 22:351-7. [PMID: 21555213 DOI: 10.1016/j.copbio.2011.04.011] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 04/18/2011] [Indexed: 12/17/2022]
Abstract
The conversion of biomass to CH4 (biomethanation) involves an anaerobic microbial food chain composed of at least three metabolic groups of which the first two decompose the complex biomass primarily to acetate, formate, and H2. The thermodynamics of these conversions are unfavorable requiring a symbiosis with the CH4-producing group (methanogens) that metabolize the decomposition products to favorable concentrations. The methanogens produce CH4 by two major pathways, conversion of the methyl group of acetate and reduction of CO2 coupled to the oxidation of formate or H2. This review covers recent advances in the fundamental understanding of both methanogenic pathways with the view of stimulating research towards improving the rate and reliability of the overall biomethanation process.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16801, United States.
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Cedervall PE, Dey M, Li X, Sarangi R, Hedman B, Ragsdale SW, Wilmot CM. Structural analysis of a Ni-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis. J Am Chem Soc 2011; 133:5626-8. [PMID: 21438550 DOI: 10.1021/ja110492p] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present the 1.2 Å resolution X-ray crystal structure of a Ni-methyl species that is a proposed catalytic intermediate in methyl-coenzyme M reductase (MCR), the enzyme that catalyzes the biological formation of methane. The methyl group is situated 2.1 Å proximal of the Ni atom of the MCR coenzyme F(430). A rearrangement of the substrate channel has been posited to bring together substrate species, but Ni(III)-methyl formation alone does not lead to any observable structural changes in the channel.
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Affiliation(s)
- Peder E Cedervall
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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