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Deng Y, Wang JX, Ghosh B, Lu Y. Enzymatic CO 2 reduction catalyzed by natural and artificial Metalloenzymes. J Inorg Biochem 2024; 259:112669. [PMID: 39059175 DOI: 10.1016/j.jinorgbio.2024.112669] [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: 05/21/2024] [Revised: 07/04/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
The continuously increasing level of atmospheric CO2 in the atmosphere has led to global warming. Converting CO2 into other carbon compounds could mitigate its atmospheric levels and produce valuable products, as CO2 also serves as a plentiful and inexpensive carbon feedstock. However, the inert nature of CO2 poses a major challenge for its reduction. To meet the challenge, nature has evolved metalloenzymes using transition metal ions like Fe, Ni, Mo, and W, as well as electron-transfer partners for their functions. Mimicking these enzymes, artificial metalloenzymes (ArMs) have been designed using alternative protein scaffolds and various metallocofactors like Ni, Co, Re, Rh, and FeS clusters. Both the catalytic efficiency and the scope of CO2-reduction product of these ArMs have been improved over the past decade. This review first focuses on the natural metalloenzymes that directly reduce CO2 by discussing their structures and active sites, as well as the proposed reaction mechanisms. It then introduces the common strategies for electrochemical, photochemical, or photoelectrochemical utilization of these native enzymes for CO2 reduction and highlights the most recent advancements from the past five years. We also summarize principles of protein design for bio-inspired ArMs, comparing them with native enzymatic systems and outlining challenges and opportunities in enzymatic CO2 reduction.
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Affiliation(s)
- Yunling Deng
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Jing-Xiang Wang
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Barshali Ghosh
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America.
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2
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Mrnjavac N, Schwander L, Brabender M, Martin WF. Chemical Antiquity in Metabolism. Acc Chem Res 2024. [PMID: 39083571 DOI: 10.1021/acs.accounts.4c00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
ConspectusLife is an exergonic chemical reaction. The same was true when the very first cells emerged at life's origin. In order to live, all cells need a source of carbon, energy, and electrons to drive their overall reaction network (metabolism). In most cells, these are separate pathways. There is only one biochemical pathway that serves all three needs simultaneously: the acetyl-CoA pathway of CO2 fixation. In the acetyl-CoA pathway, electrons from H2 reduce CO2 to pyruvate for carbon supply, while methane or acetate synthesis are coupled to energy conservation as ATP. This simplicity and thermodynamic favorability prompted Georg Fuchs and Erhard Stupperich to propose in 1985 that the acetyl-CoA pathway might mark the origin of metabolism, at the same time that Steve Ragsdale and Harland Wood were uncovering catalytic roles for Fe, Co, and Ni in the enzymes of the pathway. Subsequent work has provided strong support for those proposals.In the presence of Fe, Co, and Ni in their native metallic state as catalysts, aqueous H2 and CO2 react specifically to formate, acetate, methane, and pyruvate overnight at 100 °C. These metals (and their alloys) thus replace the function of over 120 enzymes required for the conversion of H2 and CO2 to pyruvate via the pathway and its cofactors, an unprecedented set of findings in the study of biochemical evolution. The reactions require alkaline conditions, which promote hydrogen oxidation by proton removal and are naturally generated in serpentinizing (H2-producing) hydrothermal vents. Serpentinizing hydrothermal vents furthermore produce natural deposits of native Fe, Co, Ni, and their alloys. These are precisely the metals that reduce CO2 with H2 in the laboratory; they are also the metals found at the active sites of enzymes in the acetyl-CoA pathway. Iron, cobalt and nickel are relicts of the environments in which metabolism arose, environments that still harbor ancient methane- and acetate-producing autotrophs today. This convergence indicates bedrock-level antiquity for the acetyl-CoA pathway. In acetogens and methanogens growing on H2 as reductant, the acetyl-CoA pathway requires flavin-based electron bifurcation as a source of reduced ferredoxin (a 4Fe4S cluster-containing protein) in order to function. Recent findings show that H2 can reduce the 4Fe4S clusters of ferredoxin in the presence of native iron, uncovering an evolutionary precursor of flavin-based electron bifurcation and suggesting an origin of FeS-dependent electron transfer in proteins. Traditionally discussed as catalysts in early evolution, the most common function of FeS clusters in metabolism is one-electron transfer, also in radical SAM enzymes, a large and ancient enzyme family. The cofactors and active sites in enzymes of the acetyl-CoA pathway uncover chemical antiquity in metabolism involving metals, methyl groups, methyl transfer reactions, cobamides, pterins, GTP, S-adenosylmethionine, radical SAM enzymes, and carbon-metal bonds. The reaction sequence from H2 and CO2 to pyruvate on naturally deposited native metals is maximally simple. It requires neither nitrogen, sulfur, phosphorus, RNA, ion gradients, nor light. Solid-state metal catalysts tether the origin of metabolism to a H2-producing, serpentinizing hydrothermal vent.
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Affiliation(s)
- Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Loraine Schwander
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Max Brabender
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - William F Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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Ma Y, Qu Y, Yao X, Xia C, Lv M, Lin X, Zhang L, Zhang M, Hu B. Unveiling the unique role of iron in the metabolism of methanogens: A review. ENVIRONMENTAL RESEARCH 2024; 250:118495. [PMID: 38367837 DOI: 10.1016/j.envres.2024.118495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Methanogens are the main participants in the carbon cycle, catalyzing five methanogenic pathways. Methanogens utilize different iron-containing functional enzymes in different methanogenic processes. Iron is a vital element in methanogens, which can serve as a carrier or reactant in electron transfer. Therefore, iron plays an important role in the growth and metabolism of methanogens. In this paper, we cast light on the types and functions of iron-containing functional enzymes involved in different methanogenic pathways, and the roles iron play in energy/substance metabolism of methanogenesis. Furthermore, this review provides certain guiding significance for lowering CH4 emissions, boosting the carbon sink capacity of ecosystems and promoting green and low-carbon development in the future.
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Affiliation(s)
- Yuxin Ma
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ying Qu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangwu Yao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chujun Xia
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengjie Lv
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiao Lin
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lili Zhang
- Beijing Enterprises Water Group Limited, Beijing, China
| | - Meng Zhang
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Baolan Hu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China.
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Nomura S, Paczia N, Kahnt J, Shima S. Isolation of an H 2-dependent electron-bifurcating CO 2-reducing megacomplex with MvhB polyferredoxin from Methanothermobacter marburgensis. FEBS J 2024; 291:2449-2460. [PMID: 38468562 DOI: 10.1111/febs.17115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/29/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
In the hydrogenotrophic methanogenic pathway, formylmethanofuran dehydrogenase (Fmd) catalyzes the formation of formylmethanofuran through reducing CO2. Heterodisulfide reductase (Hdr) provides two low potential electrons for the Fmd reaction using a flavin-based electron-bifurcating mechanism. [NiFe]-hydrogenase (Mvh) or formate dehydrogenase (Fdh) complexes with Hdr and provides electrons to Hdr from H2 and formate, or the reduced form of F420, respectively. Recently, an Fdh-Hdr complex was purified as a 3-MDa megacomplex that contained Fmd, and its three-dimensional structure was elucidated by cryo-electron microscopy. In contrast, the Mvh-Hdr complex has been characterized only as a complex without Fmd. Here, we report the isolation and characterization of a 1-MDa Mvh-Hdr-Fmd megacomplex from Methanothermobacter marburgensis. After anion-exchange and hydrophobic chromatography was performed, the proteins with Hdr activity eluted in the 1- and 0.5-MDa fractions during size exclusion chromatography. Considering the apparent molecular mass and the protein profile in the fractions, the 1-MDa megacomplex was determined to be a dimeric Mvh-Hdr-Fmd complex. The megacomplex fraction contained a polyferredoxin subunit MvhB, which contains 12 [4Fe-4S]-clusters. MvhB polyferredoxin has never been identified in the previously purified Mvh-Hdr and Fmd preparations, suggesting that MvhB polyferredoxin is stabilized by the binding between Mvh-Hdr and Fmd in the Mvh-Hdr-Fmd complex. The purified Mvh-Hdr-Fmd megacomplex catalyzed electron-bifurcating reduction of [13C]-CO2 to form [13C]-formylmethanofuran in the absence of extrinsic ferredoxin. These results demonstrated that the subunits in the Mvh-Hdr-Fmd megacomplex are electronically connected for the reduction of CO2, which likely involves MvhB polyferredoxin as an electron relay.
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Affiliation(s)
- Shunsuke Nomura
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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5
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Aziz I, Kayastha K, Kaltwasser S, Vonck J, Welsch S, Murphy BJ, Kahnt J, Wu D, Wagner T, Shima S, Ermler U. Structural and mechanistic basis of the central energy-converting methyltransferase complex of methanogenesis. Proc Natl Acad Sci U S A 2024; 121:e2315568121. [PMID: 38530900 PMCID: PMC10998594 DOI: 10.1073/pnas.2315568121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/24/2024] [Indexed: 03/28/2024] Open
Abstract
Methanogenic archaea inhabiting anaerobic environments play a crucial role in the global biogeochemical material cycle. The most universal electrogenic reaction of their methane-producing energy metabolism is catalyzed by N 5-methyl-tetrahydromethanopterin: coenzyme M methyltransferase (MtrABCDEFGH), which couples the vectorial Na+ transport with a methyl transfer between the one-carbon carriers tetrahydromethanopterin and coenzyme M via a vitamin B12 derivative (cobamide) as prosthetic group. We present the 2.08 Å cryo-EM structure of Mtr(ABCDEFG)3 composed of the central Mtr(ABFG)3 stalk symmetrically flanked by three membrane-spanning MtrCDE globes. Tetraether glycolipids visible in the map fill gaps inside the multisubunit complex. Putative coenzyme M and Na+ were identified inside or in a side-pocket of a cytoplasmic cavity formed within MtrCDE. Its bottom marks the gate of the transmembrane pore occluded in the cryo-EM map. By integrating Alphafold2 information, functionally competent MtrA-MtrH and MtrA-MtrCDE subcomplexes could be modeled and thus the methyl-tetrahydromethanopterin demethylation and coenzyme M methylation half-reactions structurally described. Methyl-transfer-driven Na+ transport is proposed to be based on a strong and weak complex between MtrCDE and MtrA carrying vitamin B12, the latter being placed at the entrance of the cytoplasmic MtrCDE cavity. Hypothetically, strongly attached methyl-cob(III)amide (His-on) carrying MtrA induces an inward-facing conformation, Na+ flux into the membrane protein center and finally coenzyme M methylation while the generated loosely attached (or detached) MtrA carrying cob(I)amide (His-off) induces an outward-facing conformation and an extracellular Na+ outflux. Methyl-cob(III)amide (His-on) is regenerated in the distant active site of the methyl-tetrahydromethanopterin binding MtrH implicating a large-scale shuttling movement of the vitamin B12-carrying domain.
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Affiliation(s)
- Iram Aziz
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Kanwal Kayastha
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Susann Kaltwasser
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Janet Vonck
- Structural Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Bonnie J. Murphy
- Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, MarburgD-35043, Germany
| | - Di Wu
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, BremenD-28359, Germany
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, MarburgD-35043, Germany
| | - Ulrich Ermler
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
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6
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Duffus BR, Gauglitz M, Teutloff C, Leimkühler S. Redox potentials elucidate the electron transfer pathway of NAD +-dependent formate dehydrogenases. J Inorg Biochem 2024; 253:112487. [PMID: 38306887 DOI: 10.1016/j.jinorgbio.2024.112487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/04/2024]
Abstract
Metal-dependent, nicotine adenine dinucleotide (NAD+)-dependent formate dehydrogenases (FDHs) are complex metalloenzymes coupling biochemical transformations through intricate electron transfer pathways. Rhodobacter capsulatus FDH is a model enzyme for understanding coupled catalysis, in that reversible CO2 reduction and formate oxidation are linked to a flavin mononuclotide (FMN)-bound diaphorase module via seven iron-sulfur (FeS) clusters as a dimer of heterotetramers. Catalysis occurs at a bis-metal-binding pterin (Mo) binding two molybdopterin guanine dinucleotides (bis-MGD), a protein-based Cys residue and a participatory sulfido ligand. Insights regarding the proposed electron transfer mechanism between the bis-MGD and the FMN have been complicated by the discovery that an alternative pathway might occur via intersubunit electron transfer between two [4Fe4S] clusters within electron transfer distance. To clarify this difference, the redox potentials of the bis-MGD and the FeS clusters were determined via redox titration by EPR spectroscopy. Redox potentials for the bis-MGD cofactor and five of the seven FeS clusters could be assigned. Furthermore, substitution of the active site residue Lys295 with Ala resulted in altered enzyme kinetics, primarily due to a more negative redox potential of the A1 [4Fe4S] cluster. Finally, characterization of the monomeric FdsGBAD heterotetramer exhibited slightly decreased formate oxidation activity and similar iron-sulfur clusters reduced relative to the dimeric heterotetramer. Comparison of the measured redox potentials relative to structurally defined FeS clusters support a mechanism by which electron transfer occurs within a heterotetrameric unit, with the interfacial [4Fe4S] cluster serving as a structural component toward the integrity of the heterodimeric structure to drive efficient catalysis.
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Affiliation(s)
- Benjamin R Duffus
- Institute for Biochemistry and Biology, Molecular Enzymology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Marcel Gauglitz
- Institute for Experimental Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Christian Teutloff
- Institute for Experimental Physics, Free University of Berlin, Arnimallee 14, 14195 Berlin, Germany.
| | - Silke Leimkühler
- Institute for Biochemistry and Biology, Molecular Enzymology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
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7
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Brabender M, Henriques Pereira DP, Mrnjavac N, Schlikker ML, Kimura ZI, Sucharitakul J, Kleinermanns K, Tüysüz H, Buckel W, Preiner M, Martin WF. Ferredoxin reduction by hydrogen with iron functions as an evolutionary precursor of flavin-based electron bifurcation. Proc Natl Acad Sci U S A 2024; 121:e2318969121. [PMID: 38513105 PMCID: PMC7615787 DOI: 10.1073/pnas.2318969121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/14/2024] [Indexed: 03/23/2024] Open
Abstract
Autotrophic theories for the origin of metabolism posit that the first cells satisfied their carbon needs from CO2 and were chemolithoautotrophs that obtained their energy and electrons from H2. The acetyl-CoA pathway of CO2 fixation is central to that view because of its antiquity: Among known CO2 fixing pathways it is the only one that is i) exergonic, ii) occurs in both bacteria and archaea, and iii) can be functionally replaced in full by single transition metal catalysts in vitro. In order to operate in cells at a pH close to 7, however, the acetyl-CoA pathway requires complex multi-enzyme systems capable of flavin-based electron bifurcation that reduce low potential ferredoxin-the physiological donor of electrons in the acetyl-CoA pathway-with electrons from H2. How can the acetyl-CoA pathway be primordial if it requires flavin-based electron bifurcation? Here, we show that native iron (Fe0), but not Ni0, Co0, Mo0, NiFe, Ni2Fe, Ni3Fe, or Fe3O4, promotes the H2-dependent reduction of aqueous Clostridium pasteurianum ferredoxin at pH 8.5 or higher within a few hours at 40 °C, providing the physiological function of flavin-based electron bifurcation, but without the help of enzymes or organic redox cofactors. H2-dependent ferredoxin reduction by iron ties primordial ferredoxin reduction and early metabolic evolution to a chemical process in the Earth's crust promoted by solid-state iron, a metal that is still deposited in serpentinizing hydrothermal vents today.
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Affiliation(s)
- Max Brabender
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Delfina P. Henriques Pereira
- Microcosm Earth Center, Research Group for Geochemical Protozymes, Max Planck Institute for Terrestrial Microbiology and Philipps University, Marburg35032, Germany
| | - Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Manon Laura Schlikker
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Zen-Ichiro Kimura
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, Kure, Hiroshima737-8506, Japan
| | - Jeerus Sucharitakul
- Department of Biochemistry, Chulalongkorn University, Patumwan, Bangkok10330, Thailand
| | - Karl Kleinermanns
- Institute for Physical Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Harun Tüysüz
- Max Planck Institute for Coal Research, Department of Heterogeneous Catalysis, Mülheim an der Ruhr45470, Germany
| | - Wolfgang Buckel
- Max Planck Institute for Terrestrial Microbiology, Marburg35043, Germany
- Laboratory for Microbiology, Department of Biology, Philipps University, Marburg35043, Germany
- Center for Synthetic Microbiology SYNMIKRO, Philipps University, Marburg35043, Germany
| | - Martina Preiner
- Microcosm Earth Center, Research Group for Geochemical Protozymes, Max Planck Institute for Terrestrial Microbiology and Philipps University, Marburg35032, Germany
| | - William F. Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
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Kim SM, Kang SH, Jeon BW, Kim YH. Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration. BIORESOURCE TECHNOLOGY 2024; 394:130248. [PMID: 38158090 DOI: 10.1016/j.biortech.2023.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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9
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Jiang Z, Tang Y, Chen X, Chen X, Wang H, Zhang H, Zheng C, Chen J. Enhancing electricity-driven methanogenesis by assembling biotic-abiotic hybrid system in anaerobic membrane bioreactor. BIORESOURCE TECHNOLOGY 2024; 391:129945. [PMID: 37914054 DOI: 10.1016/j.biortech.2023.129945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/17/2023] [Accepted: 10/28/2023] [Indexed: 11/03/2023]
Abstract
Biotic-abiotic hybrid systems are promising technologies to enhance methane production in anaerobic wastewater treatment. However, the dense structure of the extracellular polymeric substances (EPS) present in anaerobic granular sludge (AGS) poses challenges with respect to the implementation of hybrid systems and efficient interspecies electron transfer. In this study, the use of AGS with a Ni/Fe layered double hydroxide@activated carbon (Ni/Fe LDH@C-AGS) was investigated in an anaerobic membrane bioreactor (AnMBR). The hybrid system showed a significant increase of 82% in methane production. Further research revealed that Ni/Fe LDH@C regulated the dense structure of EPS, stimulated the production of cytochromes, and facilitated the decomposition of nonconductive substances. Surprisingly, the hybrid system also promoted resistance to membrane fouling and extended membrane life by 81%. This study provides insights into the operation of a biotic-abiotic hybrid system by regulating the dense structure of EPS ultimately resulting in an enhanced methane production.
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Affiliation(s)
- Zhuwu Jiang
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, Fujian 350118, China.
| | - Yi Tang
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, Fujian 350118, China
| | - Xinyan Chen
- Fujian Provincial Engineering Research Center of Rural Waste Recycling Technology, College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Xueming Chen
- Fujian Provincial Engineering Research Center of Rural Waste Recycling Technology, College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Haoshuai Wang
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, Fujian 350118, China
| | - Hongyu Zhang
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, Fujian 350118, China
| | - Chaoqun Zheng
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, Fujian 350118, China
| | - Jinfeng Chen
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou, Fujian 350118, China.
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10
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Maia LB, Maiti BK, Moura I, Moura JJG. Selenium-More than Just a Fortuitous Sulfur Substitute in Redox Biology. Molecules 2023; 29:120. [PMID: 38202704 PMCID: PMC10779653 DOI: 10.3390/molecules29010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Living organisms use selenium mainly in the form of selenocysteine in the active site of oxidoreductases. Here, selenium's unique chemistry is believed to modulate the reaction mechanism and enhance the catalytic efficiency of specific enzymes in ways not achievable with a sulfur-containing cysteine. However, despite the fact that selenium/sulfur have different physicochemical properties, several selenoproteins have fully functional cysteine-containing homologues and some organisms do not use selenocysteine at all. In this review, selected selenocysteine-containing proteins will be discussed to showcase both situations: (i) selenium as an obligatory element for the protein's physiological function, and (ii) selenium presenting no clear advantage over sulfur (functional proteins with either selenium or sulfur). Selenium's physiological roles in antioxidant defence (to maintain cellular redox status/hinder oxidative stress), hormone metabolism, DNA synthesis, and repair (maintain genetic stability) will be also highlighted, as well as selenium's role in human health. Formate dehydrogenases, hydrogenases, glutathione peroxidases, thioredoxin reductases, and iodothyronine deiodinases will be herein featured.
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Affiliation(s)
- Luisa B. Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
| | - Biplab K. Maiti
- Department of Chemistry, School of Sciences, Cluster University of Jammu, Canal Road, Jammu 180001, India
| | - Isabel Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
| | - José J. G. Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
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11
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Zhu C, D'Agostino C, de Visser SP. Mechanism of CO 2 Reduction to Methanol with H 2 on an Iron(II)-scorpionate Catalyst. Chemistry 2023; 29:e202302832. [PMID: 37694535 DOI: 10.1002/chem.202302832] [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: 09/07/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/12/2023]
Abstract
CO2 utilization is an important process in the chemical industry with great environmental power. In this work we show how CO2 and H2 can be reacted to form methanol on an iron(II) center and highlight the bottlenecks for the reaction and what structural features of the catalyst are essential for efficient turnover. The calculations predict the reactions to proceed through three successive reaction cycles that start with heterolytic cleavage of H2 followed by sequential hydride and proton transfer processes. The H2 splitting process is an endergonic process and hence high pressures will be needed to overcome this step and trigger the hydrogenation reaction. Moreover, H2 cleavage into a hydride and proton requires a metal to bind hydride and a nearby source to bind the proton, such as an amide or pyrazolyl group, which the scorpionate ligand used here facilitates. As such the computations highlight the non-innocence of the ligand scaffold through proton shuttle from H2 to substrate as an important step in the reaction mechanism.
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Affiliation(s)
- Chengxu Zhu
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Carmine D'Agostino
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Dipartimento di Ingegneria Civile, Chimica, Ambientale e dei Materiali (DICAM), Alma Mater Studiorum, Università di Bologna, Via Terracini, 28, 40131, Bologna, Italy
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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12
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Sahin S, Lemaire ON, Belhamri M, Kurth JM, Welte CU, Wagner T, Milton RD. Bioelectrocatalytic CO 2 Reduction by Mo-Dependent Formylmethanofuran Dehydrogenase. Angew Chem Int Ed Engl 2023; 62:e202311981. [PMID: 37712590 DOI: 10.1002/anie.202311981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/16/2023]
Abstract
Massive efforts are invested in developing innovative CO2 -sequestration strategies to counter climate change and transform CO2 into higher-value products. CO2 -capture by reduction is a chemical challenge, and attention is turned toward biological systems that selectively and efficiently catalyse this reaction under mild conditions and in aqueous solvents. While a few reports have evaluated the effectiveness of isolated bacterial formate dehydrogenases as catalysts for the reversible electrochemical reduction of CO2 , it is imperative to explore other enzymes among the natural reservoir of potential models that might exhibit higher turnover rates or preferential directionality for the reductive reaction. Here, we present electroenzymatic catalysis of formylmethanofuran dehydrogenase, a CO2 -reducing-and-fixing biomachinery isolated from a thermophilic methanogen, which was deposited on a graphite rod electrode to enable direct electron transfer for electroenzymatic CO2 reduction. The gas is reduced with a high Faradaic efficiency (109±1 %), where a low affinity for formate prevents its electrochemical reoxidation and favours formate accumulation. These properties make the enzyme an excellent tool for electroenzymatic CO2 -fixation and inspiration for protein engineering that would be beneficial for biotechnological purposes to convert the greenhouse gas into stable formate that can subsequently be safely stored, transported, and used for power generation without energy loss.
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Affiliation(s)
- Selmihan Sahin
- University of Geneva, Department of Inorganic and Analytical Chemistry, Sciences II, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
- Department of Chemistry, Faculty of Arts and Sciences, Suleyman Demirel University, Cunur, 32260, Isparta, Turkiye
| | - Olivier N Lemaire
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Mélissa Belhamri
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Julia M Kurth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
- Microcosm Earth Center - Philipps-Universität Marburg & Max Planck Institute for Terrestrial Microbiology, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Ross D Milton
- University of Geneva, Department of Inorganic and Analytical Chemistry, Sciences II, Quai Ernest-Ansermet 30, 1211, Geneva 4, Switzerland
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13
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Li X, Mitchell S, Fang Y, Li J, Perez-Ramirez J, Lu J. Advances in heterogeneous single-cluster catalysis. Nat Rev Chem 2023; 7:754-767. [PMID: 37814032 DOI: 10.1038/s41570-023-00540-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/11/2023]
Abstract
Heterogeneous single-cluster catalysts (SCCs) comprising atomically precise and isolated metal clusters stabilized on appropriately chosen supports offer exciting prospects for enabling novel chemical reactions owing to their broad structural diversity with unparalled opportunities for engineering their properties. Although the pioneering work revealed intriguing performance trends of size-selected metal clusters deposited on supports, synthetic and analytical challenges hindered a thorough understanding of surface chemistry under realistic conditions. This Review underscores the importance of considering the cluster environment in SCCs, encompassing the development of robust metal-support interactions, precise control over the ligand sphere, the influence of reaction media and dynamic behaviour, to uncover new reactivities. Through examples, we illustrate the criticality of tailoring the entire catalytic ensemble in SCCs to achieve stable and selective performance with practically relevant metal coverages. This expansion in application scope transcends from model reactions to complex and technically relevant reactions. Furthermore, we provide a perspective on the opportunities and future directions for SCC design within this rapidly evolving field.
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Affiliation(s)
- Xinzhe Li
- Department of Environmental Science and Engineering, School of Energy and Power Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Sharon Mitchell
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Yiyun Fang
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Jun Li
- Department of Chemistry and Engineering Research Center of Advanced Rare-Earth Materials of Ministry of Education, Tsinghua University, Beijing, China.
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen, China.
| | - Javier Perez-Ramirez
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
| | - Jiong Lu
- Department of Chemistry, National University of Singapore, Singapore, Singapore.
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14
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Magalon A. History of Maturation of Prokaryotic Molybdoenzymes-A Personal View. Molecules 2023; 28:7195. [PMID: 37894674 PMCID: PMC10609526 DOI: 10.3390/molecules28207195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
In prokaryotes, the role of Mo/W enzymes in physiology and bioenergetics is widely recognized. It is worth noting that the most diverse family of Mo/W enzymes is exclusive to prokaryotes, with the probable existence of several of them from the earliest forms of life on Earth. The structural organization of these enzymes, which often include additional redox centers, is as diverse as ever, as is their cellular localization. The most notable observation is the involvement of dedicated chaperones assisting with the assembly and acquisition of the metal centers, including Mo/W-bisPGD, one of the largest organic cofactors in nature. This review seeks to provide a new understanding and a unified model of Mo/W enzyme maturation.
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Affiliation(s)
- Axel Magalon
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13402 Marseille, France
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15
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Arriaza-Gallardo FJ, Zheng YC, Gehl M, Nomura S, Fernandes-Queiroz JP, Shima S. [Fe]-Hydrogenase, Cofactor Biosynthesis and Engineering. Chembiochem 2023; 24:e202300330. [PMID: 37671838 DOI: 10.1002/cbic.202300330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/07/2023]
Abstract
[Fe]-hydrogenase catalyzes the heterolytic cleavage of H2 and reversible hydride transfer to methenyl-tetrahydromethanopterin. The iron-guanylylpyridinol (FeGP) cofactor is the prosthetic group of this enzyme, in which mononuclear Fe(II) is ligated with a pyridinol and two CO ligands. The pyridinol ligand fixes the iron by an acyl carbon and a pyridinol nitrogen. Biosynthetic proteins for this cofactor are encoded in the hmd co-occurring (hcg) genes. The function of HcgB, HcgC, HcgD, HcgE, and HcgF was studied by using structure-to-function analysis, which is based on the crystal structure of the proteins and subsequent enzyme assays. Recently, we reported the catalytic properties of HcgA and HcgG, novel radical S-adenosyl methionine enzymes, by using an in vitro biosynthesis assay. Here, we review the properties of [Fe]-hydrogenase and the FeGP cofactor, and the biosynthesis of the FeGP cofactor. Finally, we discuss the expected engineering of [Fe]-hydrogenase and the FeGP cofactor.
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Affiliation(s)
| | - Yu-Cong Zheng
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Manuel Gehl
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Shunsuke Nomura
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - J Pedro Fernandes-Queiroz
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany
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16
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Schwander L, Brabender M, Mrnjavac N, Wimmer JLE, Preiner M, Martin WF. Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life. Front Microbiol 2023; 14:1257597. [PMID: 37854333 PMCID: PMC10581274 DOI: 10.3389/fmicb.2023.1257597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/04/2023] [Indexed: 10/20/2023] Open
Abstract
Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During the process of serpentinization, water circulates through hydrothermal systems in the crust where it oxidizes Fe (II) in ultramafic minerals to generate Fe (III) minerals and H2. Molecular hydrogen can, in turn, serve as a freely diffusible source of electrons for the reduction of CO2 to organic compounds, provided that suitable catalysts are present. Using catalysts that are naturally synthesized in hydrothermal vents during serpentinization H2 reduces CO2 to formate, acetate, pyruvate, and methane. These compounds represent the backbone of microbial carbon and energy metabolism in acetogens and methanogens, strictly anaerobic chemolithoautotrophs that use the acetyl-CoA pathway of CO2 fixation and that inhabit serpentinizing environments today. Serpentinization generates reduced carbon, nitrogen and - as newer findings suggest - reduced phosphorous compounds that were likely conducive to the origins process. In addition, it gives rise to inorganic microcompartments and proton gradients of the right polarity and of sufficient magnitude to support chemiosmotic ATP synthesis by the rotor-stator ATP synthase. This would help to explain why the principle of chemiosmotic energy harnessing is more conserved (older) than the machinery to generate ion gradients via pumping coupled to exergonic chemical reactions, which in the case of acetogens and methanogens involve H2-dependent CO2 reduction. Serpentinizing systems exist in terrestrial and deep ocean environments. On the early Earth they were probably more abundant than today. There is evidence that serpentinization once occurred on Mars and is likely still occurring on Saturn's icy moon Enceladus, providing a perspective on serpentinization as a source of reductants, catalysts and chemical disequilibrium for life on other worlds.
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Affiliation(s)
- Loraine Schwander
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Max Brabender
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Natalia Mrnjavac
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jessica L. E. Wimmer
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Martina Preiner
- Microcosm Earth Center, Max Planck Institute for Terrestrial Microbiology and Philipps-Universität, Marburg, Germany
| | - William F. Martin
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
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17
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Saini J, Deere TM, Lessner DJ. The minimal SUF system is not required for Fe-S cluster biogenesis in the methanogenic archaeon Methanosarcina acetivorans. Sci Rep 2023; 13:15120. [PMID: 37704679 PMCID: PMC10500019 DOI: 10.1038/s41598-023-42400-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023] Open
Abstract
Iron-sulfur (Fe-S) proteins are essential for the ability of methanogens to carry out methanogenesis and biological nitrogen fixation (diazotrophy). Nonetheless, the factors involved in Fe-S cluster biogenesis in methanogens remain largely unknown. The minimal SUF Fe-S cluster biogenesis system (i.e., SufBC) is postulated to serve as the primary system in methanogens. Here, the role of SufBC in Methanosarcina acetivorans, which contains two sufCB gene clusters, was investigated. The CRISPRi-dCas9 and CRISPR-Cas9 systems were utilized to repress or delete sufC1B1 and sufC2B2, respectively. Neither the dual repression of sufC1B1 and sufC2B2 nor the deletion of both sufC1B1 and sufC2B2 affected the growth of M. acetivorans under any conditions tested, including diazotrophy. Interestingly, deletion of only sufC1B1 led to a delayed-growth phenotype under all growth conditions, suggesting that the deletion of sufC2B2 acts as a suppressor mutation in the absence of sufC1B1. In addition, the deletion of sufC1B1 and/or sufC2B2 did not affect the total Fe-S cluster content in M. acetivorans cells. Overall, these results reveal that the minimal SUF system is not required for Fe-S cluster biogenesis in M. acetivorans and challenge the universal role of SufBC in Fe-S cluster biogenesis in methanogens.
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Affiliation(s)
- Jasleen Saini
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA
| | - Thomas M Deere
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA
| | - Daniel J Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, USA.
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18
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Leimkühler S. Metal-Containing Formate Dehydrogenases, a Personal View. Molecules 2023; 28:5338. [PMID: 37513211 PMCID: PMC10385643 DOI: 10.3390/molecules28145338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/04/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Mo/W-containing formate dehydrogenases (FDH) catalyzes the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active sites. The metal-containing FDHs are members of the dimethylsulfoxide reductase family of mononuclear molybdenum cofactor (Moco)- or tungsten cofactor (Wco)-containing enzymes. In these enzymes, the active site in the oxidized state comprises a Mo or W atom present in the bis-Moco, which is coordinated by the two dithiolene groups from the two MGD moieties, a protein-derived SeCys or Cys, and a sixth ligand that is now accepted as being a sulfido group. SeCys-containing enzymes have a generally higher turnover number than Cys-containing enzymes. The analogous chemical properties of W and Mo, the similar active sites of W- and Mo-containing enzymes, and the fact that W can replace Mo in some enzymes have led to the conclusion that Mo- and W-containing FDHs have the same reaction mechanism. Details of the catalytic mechanism of metal-containing formate dehydrogenases are still not completely understood and have been discussed here.
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Affiliation(s)
- Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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19
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Wells M, Kim M, Akob DM, Basu P, Stolz JF. Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles. Microbiol Spectr 2023; 11:e0414522. [PMID: 36951557 PMCID: PMC10100899 DOI: 10.1128/spectrum.04145-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/01/2023] [Indexed: 03/24/2023] Open
Abstract
The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO2 reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere. IMPORTANCE The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have coevolved over deep time to how anaerobic life adapted to increasing concentrations of O2 during the transition from an anoxic to an oxic world. Our work emphasizes that phylogenetic analyses can reveal how domain gain or loss events, the acquisition of novel partner subunits, and the loss of metal cofactors can stimulate novel radiations of enzymes that dramatically increase the catalytic versatility of superfamilies. We also contend that the superfamily concept in protein evolution can uncover surprising kinships between enzymes that have remarkably different catalytic and physiological functions.
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Affiliation(s)
- Michael Wells
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado, USA
| | - Minjae Kim
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado, USA
| | - Denise M. Akob
- United States Geological Survey, Geology, Energy, and Minerals Science Center, Reston, Virginia, USA
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, Indiana, USA
| | - John F. Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
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20
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Aithal A, Dagar S, Rajamani S. Metals in Prebiotic Catalysis: A Possible Evolutionary Pathway for the Emergence of Metalloproteins. ACS OMEGA 2023; 8:5197-5208. [PMID: 36816708 PMCID: PMC9933472 DOI: 10.1021/acsomega.2c07635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/12/2023] [Indexed: 06/07/2023]
Abstract
Proteinaceous catalysts found in extant biology are products of life that were potentially derived through prolonged periods of evolution. Given their complexity, it is reasonable to assume that they were not accessible to prebiotic chemistry as such. Nevertheless, the dependence of many enzymes on metal ions or metal-ligand cores suggests that catalysis relevant to biology could also be possible with just the metal centers. Given their availability on the Hadean/Archean Earth, it is fair to conjecture that metal ions could have constituted the first forms of catalysts. A slow increase of complexity that was facilitated through the provision of organic ligands and amino acids/peptides possibly allowed for further evolution and diversification, eventually demarcating them into specific functions. Herein, we summarize some key experimental developments and observations that support the possible roles of metal catalysts in shaping the origins of life. Further, we also discuss how they could have evolved into modern-day enzymes, with some suggestions for what could be the imminent next steps that researchers can pursue, to delineate the putative sequence of catalyst evolution during the early stages of life.
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Affiliation(s)
- Anuraag Aithal
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
| | - Shikha Dagar
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
| | - Sudha Rajamani
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
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21
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The Mechanism of Metal-Containing Formate Dehydrogenases Revisited: The Formation of Bicarbonate as Product Intermediate Provides Evidence for an Oxygen Atom Transfer Mechanism. Molecules 2023; 28:molecules28041537. [PMID: 36838526 PMCID: PMC9962302 DOI: 10.3390/molecules28041537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Mo/W-containing formate dehydrogenases (FDH) catalyzed the reversible oxidation of formate to carbon dioxide at their molybdenum or tungsten active sites. While in the reaction of formate oxidation, the product is CO2, which exits the active site via a hydrophobic channel; bicarbonate is formed as the first intermediate during the reaction at the active site. Other than what has been previously reported, bicarbonate is formed after an oxygen atom transfer reaction, transferring the oxygen from water to formate and a subsequent proton-coupled electron transfer or hydride transfer reaction involving the sulfido ligand as acceptor.
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22
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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23
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Diversity of gut methanogens and functional enzymes associated with methane metabolism in smallholder dairy cattle. Arch Microbiol 2022; 204:608. [PMID: 36075991 DOI: 10.1007/s00203-022-03187-z] [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: 11/27/2021] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/02/2022]
Abstract
Methane is a greenhouse gas with disastrous consequences when released to intolerable levels. Ruminants produce methane during gut fermentation releasing it through belching and/or flatulence. To better understand the diversity of methanogens and functional enzymes associated with methane metabolism in dairy cows, 48 samples; 6 rumen fluid and 42 dung samples were collected from Kenyan and Tanzanian farms and were analyzed using shotgun metagenomic approach. Statistical analysis for species frequency, relative abundance, percentages, and P values were undertaken using MS Excel and IBM SPSS statistics 20. The results showed archaea from 5 phyla, 9 classes, 16 orders, 25 families, 59 genera, and 87 species. Gut sites significantly contributed to the presence and distribution of various methanogens (P < 0.01). The class Methanomicrobia was abundant in the rumen samples (~ 39%) and dung (~ 44%). The most abundant (~ 17%) methanogen species identified was Methanocorpusculum labreanum. However, some taxonomic class data were unclassified (~ 6% in the rumen and ~ 4% in the dung). Five functional enzymes: Glycine/Serine hydroxymethyltransferase, Formylmethanofuran-tetrahydromethanopterin N-formyltransferase, Formate dehydrogenase, anaerobic carbon monoxide dehydrogenase, and catalase-peroxidase associated with methane metabolism were identified. KEGG functional metabolic analysis for the enzymes identified during this study was significant (P < 0.05) for five metabolism processes. The methanogen species abundances from this study in numbers/kind can be utilized exclusively or jointly as indirect selection criteria for methane mitigation. When targeting functional genes of the microbes/animal for better performance, the concern not to affect the host animal's functionality should be undertaken. Future studies should consider taxonomically categorizing unclassified species.
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan.,Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan.,Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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25
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Jia M, Luo Z, Chen H, Ma B, Qiao L, Xiao Q, Zhang P, Wang A. Programmable Polyproteams of Tyrosine Ammonia Lyases as Cross-Linked Enzymes for Synthesizing p-Coumaric Acid. Biomolecules 2022; 12:biom12070997. [PMID: 35883553 PMCID: PMC9313006 DOI: 10.3390/biom12070997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 12/20/2022] Open
Abstract
Ideal immobilization with enhanced biocatalyst activity and thermostability enables natural enzymes to serve as a powerful tool to yield synthetically useful chemicals in industry. Such an enzymatic method strategy becomes easier and more convenient with the use of genetic and protein engineering. Here, we developed a covalent programmable polyproteam of tyrosine ammonia lyases (TAL-CLEs) by fusing SpyTag and SpyCatcher peptides into the N-terminal and C-terminal of the TAL, respectively. The resulting circular enzymes were clear after the spontaneous isopeptide bonds formed between the SpyTag and SpyCatcher. Furthermore, the catalytic performance of the TAL-CLEs was measured via a synthesis sample of p-Coumaric acid. Our TAL-CLEs showed excellent catalytic efficiency, with 98.31 ± 1.14% yield of the target product—which is 4.15 ± 0.08 times higher than that of traditional glutaraldehyde-mediated enzyme aggregates. They also showed over four times as much enzyme-activity as wild-type TAL does and demonstrated good reusability, and so may become a good candidate for industrial enzymes.
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Affiliation(s)
| | | | | | | | - Li Qiao
- Correspondence: (L.Q.); (A.W.)
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26
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Garcia PS, Gribaldo S, Borrel G. Diversity and Evolution of Methane-Related Pathways in Archaea. Annu Rev Microbiol 2022; 76:727-755. [PMID: 35759872 DOI: 10.1146/annurev-micro-041020-024935] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase (Mcr) complex. Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pierre Simon Garcia
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
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27
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Kanda T, Saito K, Ishikita H. Mechanism of Mixed-Valence Fe 2.5+···Fe 2.5+ Formation in Fe 4S 4 Clusters in the Ferredoxin Binding Motif. J Phys Chem B 2022; 126:3059-3066. [PMID: 35435680 PMCID: PMC9059760 DOI: 10.1021/acs.jpcb.2c01320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most low-potential Fe4S4 clusters exist in the conserved binding sequence CxxCxxC (CnCn+3Cn+6). Fe(II) and Fe(III) at the first (Cn) and third (Cn+6) cysteine ligand sites form a mixed-valence Fe2.5+···Fe2.5+ pair in the reduced Fe(II)3Fe(III) cluster. Here, we investigate the mechanism of how the conserved protein environment induces mixed-valence pair formation in the Fe4S4 clusters, FX, FA, and FB in photosystem I, using a quantum mechanical/molecular mechanical approach. Exchange coupling between Fe sites is predominantly determined by the shape of the Fe4S4 cluster, which is stabilized by the preorganized protein electrostatic environment. The backbone NH and CO groups in the conserved CxxCxxC and adjacent helix regions orient along the FeCn···FeC(n+6) axis, generating an electric field and stabilizing the FeCn(II)FeC(n+6)(III) state in FA and FB. The overlap of the d orbitals via -S- (superexchange) is observed for the single FeCn(II)···FeC(n+6)(III) pair, leading to the formation of the mixed-valence Fe2.5+···Fe2.5+ pair. In contrast, several superexchange Fe(II)···Fe(III) pairs are observed in FX due to the highly symmetric pair of the CDGPGRGGTC sequences. This is likely the origin of FX serving as an electron acceptor in the two electron transfer branches.
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Affiliation(s)
- Tomoki Kanda
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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28
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Wu J, Chen SL. Key Piece in the Wolfe Cycle of Methanogenesis: The S–S Bond Dissociation Conducted by Noncubane [Fe4S4] Cluster-Dependent Heterodisulfide Reductase. ACS Catal 2022. [DOI: 10.1021/acscatal.1c06036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jue Wu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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29
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Mostafa A, Im S, Kim J, Lim KH, Kim I, Kim DH. Electron bifurcation reactions in dark fermentation: An overview for better understanding and improvement. BIORESOURCE TECHNOLOGY 2022; 344:126327. [PMID: 34785332 DOI: 10.1016/j.biortech.2021.126327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Electron bifurcation (EB) is the most recently found mode of energy conservation, which involves both exergonic and endergonic electron transfer reactions to minimize energy loss. Several works have been devoted on EB reactions (EBRs) in anaerobic digestion but limited in dark fermentative hydrogen production (DF). Two main electron carriers in DF are ferredoxin (Fd) and reduced nicotinamide adenine dinucleotide (NADH), complicatedly involved in EB. Here, i) the importance of EB involvement in DF, ii) all EBRs possible to present in DF, as well as iii) the limitation of previous studies that tried incorporating any of EBRs in DF metabolic model, were highlighted. In addition, the concept of using metagenomic analysis for estimating the share of each EB reaction in the metabolic model, was proposed. This review is expected to initiate a new wave for studying EB, as a tool for explaining and predicting DF products.
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Affiliation(s)
- Alsayed Mostafa
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Seongwon Im
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Jimin Kim
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Kyeong-Ho Lim
- Department of Civil and Environmental Engineering, Kongju National University, Cheonan, Chungnam 31080, Republic of Korea
| | - Ijung Kim
- Department of Civil and Environmental Engineering, Hongik University, 94 Wausan-ro, Mapo-gu, Seoul 04066, Republic of Korea
| | - Dong-Hoon Kim
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea.
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30
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Maiti BK, Maia LB, Moura JJG. Sulfide and transition metals - A partnership for life. J Inorg Biochem 2021; 227:111687. [PMID: 34953313 DOI: 10.1016/j.jinorgbio.2021.111687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/13/2022]
Abstract
Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.
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Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Department of Chemistry, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India.
| | - Luisa B Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
| | - José J G Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
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31
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Al-Attar S, Rendon J, Sidore M, Duneau JP, Seduk F, Biaso F, Grimaldi S, Guigliarelli B, Magalon A. Gating of Substrate Access and Long-Range Proton Transfer in Escherichia coli Nitrate Reductase A: The Essential Role of a Remote Glutamate Residue. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sinan Al-Attar
- Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Julia Rendon
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Marlon Sidore
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (UMR7255), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Jean-Pierre Duneau
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (UMR7255), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Farida Seduk
- Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Frédéric Biaso
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Stéphane Grimaldi
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Bruno Guigliarelli
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
| | - Axel Magalon
- Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, Aix Marseille Université, CNRS, 13402 Marseille, France
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32
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Arias-Cartin R, Uzel A, Seduk F, Gerbaud G, Pierrel F, Broc M, Lebrun R, Guigliarelli B, Magalon A, Grimaldi S, Walburger A. Identification and characterization of a non-canonical menaquinone-linked formate dehydrogenase. J Biol Chem 2021; 298:101384. [PMID: 34748728 PMCID: PMC8808070 DOI: 10.1016/j.jbc.2021.101384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 10/25/2022] Open
Abstract
The Molybdenum/Tungsten-bispyranopterin guanine dinucleotides (Mo/W-bisPGD) family of Formate Dehydrogenases (FDHs) plays roles in several metabolic pathways ranging from carbon fixation to energy harvesting owing to their reaction with a wide variety of redox partners. Indeed, this metabolic plasticity results from the diverse structures, cofactor content, and substrates employed by partner subunits interacting with the catalytic hub. Here, we unveiled two non-canonical FDHs in Bacillus subtilis which are organized into two-subunit complexes with unique features, ForCE1 and ForCE2. We show that the ForC catalytic subunit interacts with an unprecedented partner subunit, ForE, and that its amino acid sequence within the active site deviates from the consensus residues typically associated with FDH activity, as a histidine residue is naturally substituted with a glutamine. The ForE essential subunit mediates the utilization of menaquinone as an electron acceptor as shown by the formate:menadione oxidoreductase activity of both enzymes, their copurification with menaquinone, and the distinctive detection of a protein-bound neutral menasemiquinone radical by multifrequency electron paramagnetic resonance (EPR) experiments on the purified enzymes. Moreover, EPR characterization of both FDHs reveals the presence of several [Fe-S] clusters with distinct relaxation properties and a weakly anisotropic Mo(V) EPR signature, consistent with the characteristic Mo/bisPGD cofactor of this enzyme family. Altogether, this work enlarges our knowledge of the FDH family by identifying a non-canonical FDH, which differs in terms of architecture, amino acid conservation around the Mo cofactor, and reactivity.
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Affiliation(s)
- Rodrigo Arias-Cartin
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13009 Marseille, France; Aix Marseille Université, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, 13009 Marseille, France.
| | - Alexandre Uzel
- Aix Marseille Université, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, 13009 Marseille, France
| | - Farida Seduk
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13009 Marseille, France
| | - Guillaume Gerbaud
- Aix Marseille Université, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, 13009 Marseille, France
| | - Fabien Pierrel
- Grenoble Alpes Université, CNRS, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Marianne Broc
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13009 Marseille, France
| | - Régine Lebrun
- Aix Marseille Université, CNRS, Plateforme Protéomique de l'IMM, IM2B Marseille Protéomique (MaP), 13009 Marseille, France
| | - Bruno Guigliarelli
- Aix Marseille Université, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, 13009 Marseille, France
| | - Axel Magalon
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13009 Marseille, France
| | - Stéphane Grimaldi
- Aix Marseille Université, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR7281), IMM, IM2B, 13009 Marseille, France.
| | - Anne Walburger
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13009 Marseille, France.
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33
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Jagilinki BP, Paluy I, Tyryshkin AM, Nanda V, Noy D. Biophysical Characterization of Iron-Sulfur Proteins. Bio Protoc 2021; 11:e4202. [PMID: 34761074 DOI: 10.21769/bioprotoc.4202] [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: 03/01/2021] [Revised: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 11/02/2022] Open
Abstract
Iron-sulfur proteins are primordial catalysts and biological electron carriers that today drive major metabolic pathways across all forms of life. They can access a diversity of oxidation states and can mediate electron transfer over an extended range of reduction potentials spanning more than 1 V. Depending on the protein micro-environment and geometry of ligand, co-ordination the iron-sulfur clusters can occur in different forms [2Fe-2S], [3Fe-4S], HiPIP [4Fe-4S], and [4Fe-4S]. There are several spectroscopic methods available to characterize the composition and electronic configuration of the iron-sulfur clusters, such as optical methods and electron paramagnetic resonance. This paper presents the protocols used to characterize the metal center of Coiled-Coil Iron-Sulfur (CCIS), an artificial metalloprotein containing one [4Fe-4S] cluster. It is expected that these protocols will be of general utility for other iron-sulfur proteins.
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Affiliation(s)
- Bhanu P Jagilinki
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel.,Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Irina Paluy
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Alexei M Tyryshkin
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Dror Noy
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
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34
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Watanabe T, Pfeil-Gardiner O, Kahnt J, Koch J, Shima S, Murphy BJ. Three-megadalton complex of methanogenic electron-bifurcating and CO 2-fixing enzymes. Science 2021; 373:1151-1156. [PMID: 34516836 DOI: 10.1126/science.abg5550] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Tomohiro Watanabe
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Olivia Pfeil-Gardiner
- Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Jörg Kahnt
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Jürgen Koch
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Seigo Shima
- Microbial Protein Structure Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Bonnie J Murphy
- Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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35
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Methods to Screen for Radical SAM Enzyme Crystallization Conditions. Methods Mol Biol 2021. [PMID: 34292557 DOI: 10.1007/978-1-0716-1605-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Radical S-adenosyl-L-methionine proteins most probably belong to the widest superfamily of metalloenzymes. Thanks to their ability to catalyze difficult reactions, combined with their involvement in the biosynthesis of numbers of natural products, they sound promising for various biotechnological applications. Their structural study is often limited because they are usually challenging to crystallize. This chapter presents protocols and equipment developed to quickly screen for crystallization conditions under anaerobic conditions, as exemplified by our recent study of the nitrogenase maturase NifB.
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36
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Examining pathways of iron and sulfur acquisition, trafficking, deployment, and storage in mineral-grown methanogen cells. J Bacteriol 2021; 203:e0014621. [PMID: 34251867 PMCID: PMC8516115 DOI: 10.1128/jb.00146-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanogens have a high demand for iron (Fe) and sulfur (S); however, little is known of how they acquire, deploy, and store these elements and how this, in turn, affects their physiology. Methanogens were recently shown to reduce pyrite (FeS2) generating aqueous iron-sulfide (FeS(aq)) clusters that are likely assimilated as a source of Fe and S. Here, we compare the phenotype of Methanococcus voltae when grown with FeS2 or ferrous iron (Fe(II)) and sulfide (HS-). FeS2-grown cells are 33% smaller yet have 193% more Fe than Fe(II)/HS--grown cells. Whole cell EPR revealed similar distributions of paramagnetic Fe, although FeS2-grown cells showed a broad spectral feature attributed to intracellular thioferrate-like nanoparticles. Differential proteomic analyses showed similar expression of core methanogenesis enzymes, indicating that Fe and S source does not substantively alter the energy metabolism of cells. However, a homolog of the Fe(II) transporter FeoB and its putative transcriptional regulator DtxR were up-expressed in FeS2-grown cells, suggesting that cells sense Fe(II) limitation. Two homologs of IssA, a protein putatively involved in coordinating thioferrate nanoparticles, were also up-expressed in FeS2-grown cells. We interpret these data to indicate that, in FeS2-grown cells, DtxR cannot sense Fe(II) and therefore cannot down-regulate FeoB. We suggest this is due to the transport of Fe(II) complexed with sulfide (FeS(aq)) leading to excess Fe that is sequestered by IssA as a thioferrate-like species. This model provides a framework for the design of targeted experiments aimed at further characterizing Fe acquisition and homeostasis in M. voltae and other methanogens. IMPORTANCE FeS2 is the most abundant sulfide mineral in the Earth's crust and is common in environments inhabited by methanogenic archaea. FeS2 can be reduced by methanogens, yielding aqueous FeS(aq) clusters that are thought to be a source of Fe and S. Here, we show that growth of Methanococcus voltae on FeS2 results in smaller cell size and higher Fe content per cell, with Fe likely stored intracellularly as thioferrate-like nanoparticles. Fe(II) transporters and storage proteins were up-regulated in FeS2-grown cells. These responses are interpreted to result from cells incorrectly sensing Fe(II) limitation due to assimilation of Fe(II) as FeS(aq). These findings have implications for our understanding of how Fe/S availability influences methanogen physiology and the biogeochemical cycling of these elements.
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Dietrich HM, Kremp F, Öppinger C, Ribaric L, Müller V. Biochemistry of methanol-dependent acetogenesis in Eubacterium callanderi KIST612. Environ Microbiol 2021; 23:4505-4517. [PMID: 34125457 DOI: 10.1111/1462-2920.15643] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/13/2021] [Indexed: 11/26/2022]
Abstract
Methanol is the simplest of all alcohols, is universally distributed in anoxic sediments as a result of plant material decomposition and is constantly attracting attention as an interesting substrate for anaerobes like acetogens that can convert bio-renewable methanol into value-added chemicals. A major drawback in the development of environmentally friendly but economically attractive biotechnological processes is the present lack of information on biochemistry and bioenergetics during methanol conversion in these bacteria. The mesophilic acetogen Eubacterium callanderi KIST612 is naturally able to consume methanol and produce acetate as well as butyrate. To grasp the full potential of methanol-based production of chemicals, we analysed the genes and enzymes involved in methanol conversion to acetate and identified the redox carriers involved. We will display a complete model for methanol-derived acetogenesis and butyrogenesis in Eubacterium callanderi KIST612, tracing the electron transfer routes and shed light on the bioenergetics during the process.
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Affiliation(s)
- Helge M Dietrich
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Florian Kremp
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Christian Öppinger
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Luna Ribaric
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
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38
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Sproules S. Oxo versus Sulfido Coordination at Tungsten: A Spectroscopic and Correlated Ab Initio Electronic Structure Study. Inorg Chem 2021; 60:9057-9063. [PMID: 34096284 DOI: 10.1021/acs.inorgchem.1c01055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tungsten ion that resides at the active site of a unique class of enzymes only found in esoteric hyperthermophilic archaea bacteria is known to possess at least one terminal chalcogenide ligand. The identity of this as either an oxo or sulfido (or both) is difficult to ascertain from structural studies; therefore, small-molecule analogues are developed to calibrate and substantiate spectroscopic signatures obtained from native proteins. The electronic structures of Tp*WECl2 (E = O, S; Tp* = hydrotris(3,5-dimethylpyrazol-1-yl)borate) have been scrutinized using electronic, electron paramagnetic resonance (EPR), and X-ray absorption spectroscopy to assess the impact of terminal chalcogen on the adjacent cis chloride ligands. Examination at the Cl K-edge provides a direct probe of the bonding and therein lability of these chloride ligands, and in conjunction with density functional theoretical and multireference calculations reveals greater bond covalency in Tp*WOCl2 compared to Tp*WSCl2. The computational model and electronic structure assignment are corroborated by the reproduction of spin-Hamiltonian parameters, whose magnitude is dominated by the sizeable spin-orbit coupling of tungsten.
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Affiliation(s)
- Stephen Sproules
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
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Han C, Li Y, Li J, Qi M, Tang Z, Xu Y. Cooperative Syngas Production and C−N Bond Formation in One Photoredox Cycle. Angew Chem Int Ed Engl 2021; 60:7962-7970. [DOI: 10.1002/anie.202015756] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/12/2020] [Indexed: 01/02/2023]
Affiliation(s)
- Chuang Han
- State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350116 China
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
| | - Yue‐Hua Li
- State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350116 China
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
| | - Jing‐Yu Li
- State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350116 China
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
| | - Ming‐Yu Qi
- State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350116 China
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
| | - Zi‐Rong Tang
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
| | - Yi‐Jun Xu
- State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350116 China
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
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40
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Han C, Li Y, Li J, Qi M, Tang Z, Xu Y. Cooperative Syngas Production and C−N Bond Formation in One Photoredox Cycle. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015756] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Chuang Han
- State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350116 China
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
| | - Yue‐Hua Li
- State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350116 China
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
| | - Jing‐Yu Li
- State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350116 China
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
| | - Ming‐Yu Qi
- State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350116 China
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
| | - Zi‐Rong Tang
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
| | - Yi‐Jun Xu
- State Key Laboratory of Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350116 China
- College of Chemistry New Campus Fuzhou University Fuzhou 350116 China
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41
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Kayastha K, Vitt S, Buckel W, Ermler U. Flavins in the electron bifurcation process. Arch Biochem Biophys 2021; 701:108796. [PMID: 33609536 DOI: 10.1016/j.abb.2021.108796] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 11/18/2022]
Abstract
The discovery of a new energy-coupling mechanism termed flavin-based electron bifurcation (FBEB) in 2008 revealed a novel field of application for flavins in biology. The key component is the bifurcating flavin endowed with strongly inverted one-electron reduction potentials (FAD/FAD•- ≪ FAD•-/FADH-) that cooperatively transfers in its reduced state one low and one high-energy electron into different directions and thereby drives an endergonic with an exergonic reduction reaction. As energy splitting at the bifurcating flavin apparently implicates one-electron chemistry, the FBEB machinery has to incorporate prior to and behind the central bifurcating flavin 2e-to-1e and 1e-to-2e switches, frequently also flavins, for oxidizing variable medium-potential two-electron donating substrates and for reducing high-potential two-electron accepting substrates. The one-electron carriers ferredoxin or flavodoxin serve as low-potential (high-energy) electron acceptors, which power endergonic processes almost exclusively in obligate anaerobic microorganisms to increase the efficiency of their energy metabolism. In this review, we outline the global organization of FBEB enzymes, the functions of the flavins therein and the surrounding of the isoalloxazine rings by which their reduction potentials are specifically adjusted in a finely tuned energy landscape.
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Affiliation(s)
- Kanwal Kayastha
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Stella Vitt
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany; Laboratorium für Mikrobiologie, Fachbereich Biologie and SYNMIKRO, Philipps-Universität, 35032, Marburg, Germany
| | - Wolfgang Buckel
- Laboratorium für Mikrobiologie, Fachbereich Biologie and SYNMIKRO, Philipps-Universität, 35032, Marburg, Germany; Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
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Watanabe T, Shima S. MvhB-type Polyferredoxin as an Electron-transfer Chain in Putative Redox-enzyme Complexes. CHEM LETT 2021. [DOI: 10.1246/cl.200774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomohiro Watanabe
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0819, Japan
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
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Deere TM, Prakash D, Lessner FH, Duin EC, Lessner DJ. Methanosarcina acetivorans contains a functional ISC system for iron-sulfur cluster biogenesis. BMC Microbiol 2020; 20:323. [PMID: 33096982 PMCID: PMC7585200 DOI: 10.1186/s12866-020-02014-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The production of methane by methanogens is dependent on numerous iron-sulfur (Fe-S) cluster proteins; yet, the machinery involved in Fe-S cluster biogenesis in methanogens remains largely unknown. Methanogen genomes encode uncharacterized homologs of the core components of the ISC (IscS and IscU) and SUF (SufBC) Fe-S cluster biogenesis systems found in bacteria and eukaryotes. Methanosarcina acetivorans contains three iscSU and two sufCB gene clusters. Here, we report genetic and biochemical characterization of M. acetivorans iscSU2. RESULTS Purified IscS2 exhibited pyridoxal 5'- phosphate-dependent release of sulfur from L-cysteine. Incubation of purified IscU2 with IscS2, cysteine, and iron (Fe2+) resulted in the formation of [4Fe-4S] clusters in IscU2. IscU2 transferred a [4Fe-4S] cluster to purified M. acetivorans apo-aconitase. IscU2 also restored the aconitase activity in air-exposed M. acetivorans cell lysate. These biochemical results demonstrate that IscS2 is a cysteine desulfurase and that IscU2 is a Fe-S cluster scaffold. M. acetivorans strain DJL60 deleted of iscSU2 was generated to ascertain the in vivo importance of IscSU2. Strain DJL60 had Fe-S cluster content and growth similar to the parent strain but lower cysteine desulfurase activity. Strain DJL60 also had lower intracellular persulfide content compared to the parent strain when cysteine was an exogenous sulfur source, linking IscSU2 to sulfur metabolism. CONCLUSIONS This study establishes that M. acetivorans contains functional IscS and IscU, the core components of the ISC Fe-S cluster biogenesis system and provides the first evidence that ISC operates in methanogens.
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Affiliation(s)
- Thomas M Deere
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, 72701, USA
| | - Divya Prakash
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Faith H Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, 72701, USA
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849, USA
| | - Daniel J Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, 72701, USA.
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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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Methanothermobacter thermautotrophicus strain ΔH as a potential microorganism for bioconversion of CO2 to methane. J CO2 UTIL 2020. [DOI: 10.1016/j.jcou.2020.101210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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46
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Qiu M, Li Y, Zhang Y. The mechanism for CO 2 reduction over Fe-modified Cu(100) surfaces with thermodynamics and kinetics: a DFT study. RSC Adv 2020; 10:32569-32580. [PMID: 35516500 PMCID: PMC9056627 DOI: 10.1039/d0ra06319c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 08/24/2020] [Indexed: 11/23/2022] Open
Abstract
The adsorption, activation and reduction of CO2 over Fex/Cu(100) (x = 1–9) surfaces were examined by density functional theory. The most stable structure of CO2 adsorption on the Fex/Cu(100) surface was realized. The electronic structure analysis showed that the doped Fe improved the adsorption, activation and reduction of CO2 on the pure Cu(100) surface. From the perspective of thermodynamics and kinetics, the Fe4/Cu(100) surface acted as a potential catalyst to decompose CO2 into CO with a barrier of 32.8 kJ mol−1. Meanwhile, the first principle molecular dynamics (FPMD) analysis indicated that the decomposition of the C–O1 bond of CO2 on the Fe4/Cu(100) surface was only observed from 350 K to 450 K under a CO2 partial pressure from 0 atm to 10 atm. Furthermore, the results of FPMD analysis revealed that CO2 would rather decompose than hydrogenate when CO2 and H co-adsorbed on the Fe4/Cu(100) surface. The adsorption, activation and reduction of CO2 over Fex/Cu(100) (x = 1–9) surfaces were examined by density functional theory.![]()
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Affiliation(s)
- Mei Qiu
- Department of Chemistry, College of Science, Jiangxi Agricultural University Nanchang Jiangxi 330045 China .,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences 350002 Fuzhou Fujian 350002 China
| | - Yi Li
- College of Chemistry, Fuzhou University Fuzhou Fujian 350116 China
| | - Yongfan Zhang
- College of Chemistry, Fuzhou University Fuzhou Fujian 350116 China
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47
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Abstract
Tungsten is the heaviest element used in biological systems. It occurs in the active sites of several bacterial or archaeal enzymes and is ligated to an organic cofactor (metallopterin or metal binding pterin; MPT) which is referred to as tungsten cofactor (Wco). Wco-containing enzymes are found in the dimethyl sulfoxide reductase (DMSOR) and the aldehyde:ferredoxin oxidoreductase (AOR) families of MPT-containing enzymes. Some depend on Wco, such as aldehyde oxidoreductases (AORs), class II benzoyl-CoA reductases (BCRs) and acetylene hydratases (AHs), whereas others may incorporate either Wco or molybdenum cofactor (Moco), such as formate dehydrogenases, formylmethanofuran dehydrogenases or nitrate reductases. The obligately tungsten-dependent enzymes catalyze rather unusual reactions such as ones with extremely low-potential electron transfers (AOR, BCR) or an unusual hydration reaction (AH). In recent years, insights into the structure and function of many tungstoenzymes have been obtained. Though specific and unspecific ABC transporter uptake systems have been described for tungstate and molybdate, only little is known about further discriminative steps in Moco and Wco biosynthesis. In bacteria producing Moco- and Wco-containing enzymes simultaneously, paralogous isoforms of the metal insertase MoeA may be specifically involved in the molybdenum- and tungsten-insertion into MPT, and in targeting Moco or Wco to their respective apo-enzymes. Wco-containing enzymes are of emerging biotechnological interest for a number of applications such as the biocatalytic reduction of CO2, carboxylic acids and aromatic compounds, or the conversion of acetylene to acetaldehyde.
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Robinson WE, Bassegoda A, Blaza JN, Reisner E, Hirst J. Understanding How the Rate of C-H Bond Cleavage Affects Formate Oxidation Catalysis by a Mo-Dependent Formate Dehydrogenase. J Am Chem Soc 2020; 142:12226-12236. [PMID: 32551568 PMCID: PMC7366381 DOI: 10.1021/jacs.0c03574] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metal-dependent formate dehydrogenases (FDHs) catalyze the reversible conversion of formate into CO2, a proton, and two electrons. Kinetic studies of FDHs provide key insights into their mechanism of catalysis, relevant as a guide for the development of efficient electrocatalysts for formate oxidation as well as for CO2 capture and utilization. Here, we identify and explain the kinetic isotope effect (KIE) observed for the oxidation of formate and deuterioformate by the Mo-containing FDH from Escherichia coli using three different techniques: steady-state solution kinetic assays, protein film electrochemistry (PFE), and pre-steady-state stopped-flow methods. For each technique, the Mo center of FDH is reoxidized at a different rate following formate oxidation, significantly affecting the observed kinetic behavior and providing three different viewpoints on the KIE. Steady-state turnover in solution, using an artificial electron acceptor, is kinetically limited by diffusional intermolecular electron transfer, masking the KIE. In contrast, interfacial electron transfer in PFE is fast, lifting the electron-transfer rate limitation and manifesting a KIE of 2.44. Pre-steady-state analyses using stopped-flow spectroscopy revealed a KIE of 3 that can be assigned to the C-H bond cleavage step during formate oxidation. We formalize our understanding of FDH catalysis by fitting all the data to a single kinetic model, recreating the condition-dependent shift in rate-limitation of FDH catalysis between active-site chemical catalysis and regenerative electron transfer. Furthermore, our model predicts the steady-state and time-dependent concentrations of catalytic intermediates, providing a valuable framework for the design of future mechanistic experiments.
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Affiliation(s)
- William E Robinson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Arnau Bassegoda
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, U.K
| | - James N Blaza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, U.K
| | - Erwin Reisner
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, U.K
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Chen B, Dong M, Liu S, Xie Z, Yang J, Li S, Wang Y, Du J, Liu H, Han B. CO2 Hydrogenation to Formate Catalyzed by Ru Coordinated with a N,P-Containing Polymer. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01678] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Bingfeng Chen
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Minghua Dong
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Shulin Liu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhenbing Xie
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Junjuan Yang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Shaopeng Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yanyan Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Du
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Huizhen Liu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Buxing Han
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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50
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Structure: Function Studies of the Cytosolic, Mo- and NAD+-Dependent Formate Dehydrogenase from Cupriavidus necator. INORGANICS 2020. [DOI: 10.3390/inorganics8070041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Here, we report recent progress our laboratories have made in understanding the maturation and reaction mechanism of the cytosolic and NAD+-dependent formate dehydrogenase from Cupriavidus necator. Our recent work has established that the enzyme is fully capable of catalyzing the reverse of the physiological reaction, namely, the reduction of CO2 to formate using NADH as a source of reducing equivalents. The steady-state kinetic parameters in the forward and reverse directions are consistent with the expected Haldane relationship. The addition of an NADH-regenerating system consisting of glucose and glucose dehydrogenase increases the yield of formate approximately 10-fold. This work points to possible ways of optimizing the reverse of the enzyme’s physiological reaction with commercial potential as an effective means of CO2 remediation. New insight into the maturation of the enzyme comes from the recently reported structure of the FdhD sulfurase. In E. coli, FdhD transfers a catalytically essential sulfur to the maturing molybdenum cofactor prior to insertion into the apoenzyme of formate dehydrogenase FdhF, which has high sequence similarity to the molybdenum-containing domain of the C. necator FdsA. The FdhD structure suggests that the molybdenum cofactor may first be transferred from the sulfurase to the C-terminal cap domain of apo formate dehydrogenase, rather than being transferred directly to the body of the apoenzyme. Closing of the cap domain over the body of the enzymes delivers the Mo-cofactor into the active site, completing the maturation of formate dehydrogenase. The structural and kinetic characterization of the NADH reduction of the FdsBG subcomplex of the enzyme provides further insights in reversing of the formate dehydrogenase reaction. Most notably, we observe the transient formation of a neutral semiquinone FMNH·, a species that has not been observed previously with holoenzyme. After initial reduction of the FMN of FdsB by NADH to the hydroquinone (with a kred of 680 s−1 and Kd of 190 µM), one electron is rapidly transferred to the Fe2S2 cluster of FdsG, leaving FMNH·. The Fe4S4 cluster of FdsB does not become reduced in the process. These results provide insight into the function not only of the C. necator formate dehydrogenase but also of other members of the NADH dehydrogenase superfamily of enzymes to which it belongs.
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