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Kammel M, Erdmann C, Sawers RG. The formate-hydrogen axis and its impact on the physiology of enterobacterial fermentation. Adv Microb Physiol 2024; 84:51-82. [PMID: 38821634 DOI: 10.1016/bs.ampbs.2024.02.002] [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] [Indexed: 06/02/2024]
Abstract
Formic acid (HCOOH) and dihydrogen (H2) are characteristic products of enterobacterial mixed-acid fermentation, with H2 generation increasing in conjunction with a decrease in extracellular pH. Formate and acetyl-CoA are generated by radical-based and coenzyme A-dependent cleavage of pyruvate catalysed by pyruvate formate-lyase (PflB). Formate is also the source of H2, which is generated along with carbon dioxide through the action of the membrane-associated, cytoplasmically-oriented formate hydrogenlyase (FHL-1) complex. Synthesis of the FHL-1 complex is completely dependent on the cytoplasmic accumulation of formate. Consequently, formate determines its own disproportionation into H2 and CO2 by the FHL-1 complex. Cytoplasmic formate levels are controlled by FocA, a pentameric channel that translocates formic acid/formate bidirectionally between the cytoplasm and periplasm. Each protomer of FocA has a narrow hydrophobic pore through which neutral formic acid can pass. Two conserved amino acid residues, a histidine and a threonine, at the center of the pore control directionality of translocation. The histidine residue is essential for pH-dependent influx of formic acid. Studies with the formate analogue hypophosphite and amino acid variants of FocA suggest that the mechanisms of formic acid efflux and influx differ. Indeed, current data suggest, depending on extracellular formate levels, two separate uptake mechanisms exist, both likely contributing to maintain pH homeostasis. Bidirectional formate/formic acid translocation is dependent on PflB and influx requires an active FHL-1 complex. This review describes the coupling of formate and H2 production in enterobacteria.
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Affiliation(s)
- Michelle Kammel
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Saale, Germany
| | - Christopher Erdmann
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Saale, Germany
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Saale, Germany.
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2
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Mühlhofer M, Offensperger F, Reschke S, Wallmann G, Csaba G, Berchtold E, Riedl M, Blum H, Haslbeck M, Zimmer R, Buchner J. Deletion of the transcription factors Hsf1, Msn2 and Msn4 in yeast uncovers transcriptional reprogramming in response to proteotoxic stress. FEBS Lett 2024; 598:635-657. [PMID: 38366111 DOI: 10.1002/1873-3468.14821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
The response to proteotoxic stresses such as heat shock allows organisms to maintain protein homeostasis under changing environmental conditions. We asked what happens if an organism can no longer react to cytosolic proteotoxic stress. To test this, we deleted or depleted, either individually or in combination, the stress-responsive transcription factors Msn2, Msn4, and Hsf1 in Saccharomyces cerevisiae. Our study reveals a combination of survival strategies, which together protect essential proteins. Msn2 and 4 broadly reprogram transcription, triggering the response to oxidative stress, as well as biosynthesis of the protective sugar trehalose and glycolytic enzymes, while Hsf1 mainly induces the synthesis of molecular chaperones and reverses the transcriptional response upon prolonged mild heat stress (adaptation).
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Affiliation(s)
- Moritz Mühlhofer
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Felix Offensperger
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Sarah Reschke
- Laboratory for Functional Genome Analysis at the Gene Center, LMU München, München, Germany
| | - Georg Wallmann
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Gergely Csaba
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Evi Berchtold
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Maximilian Riedl
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis at the Gene Center, LMU München, München, Germany
| | - Martin Haslbeck
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Ralf Zimmer
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Johannes Buchner
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
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3
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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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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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5
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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: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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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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Fuji R, Umezawa K, Mizuguchi M, Ihara M. Protein Engineering of the Soluble Metal-dependent Formate Dehydrogenase from Escherichia coli. ANAL SCI 2021; 37:733-739. [PMID: 33455969 DOI: 10.2116/analsci.20scp15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Formate is the most targeted C1 building block and electron carrier in the post-petroleum era. Formate dehydrogenase (FDH), which catalyzes the production or degradation of formate, has acquired considerable attention. Among FDHs, a metal-dependent FDH that carries a complex active center, molybdenum-pterin cofactor, can directly transfer electrons from formate to other redox proteins without generating NAD(P)H. Previously, we reported an expression system for membrane-bound metal-dependent FDH from E. coli (encoded by the fdoG-fdoH-fdoI operon) and succeeded in its conversion to a soluble protein. However, this protein exhibited a too low stability to be purified and analyzed biochemically. In this study, we tried to improve the stability of heterologously expressed FDH through rational and irrational approaches. As a result, a mutant with the highest specific activity was obtained through a rational approach. This study not only yielded a promising FDH enzyme with enhanced activity and stability for industrial applications, but also offered relevant insights for the handling of recombinant large proteins.
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Affiliation(s)
- Rintaro Fuji
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University
| | - Koji Umezawa
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University.,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University
| | - Manami Mizuguchi
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University
| | - Masaki Ihara
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University.,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University
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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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Leimkühler S. The biosynthesis of the molybdenum cofactors in Escherichia coli. Environ Microbiol 2020; 22:2007-2026. [PMID: 32239579 DOI: 10.1111/1462-2920.15003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/29/2022]
Abstract
The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes containing Moco, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into four steps in in bacteria: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5'-GTP, (ii) in the second step the two sulfur atoms are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into MPT to form Moco and (iv) in the fourth step bis-Mo-MPT is formed and an additional modification of Moco is possible with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review presents an update on the well-characterized Moco biosynthesis in the model organism Escherichia coli including novel discoveries from the recent years.
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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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Zupok A, Iobbi-Nivol C, Méjean V, Leimkühler S. The regulation of Moco biosynthesis and molybdoenzyme gene expression by molybdenum and iron in bacteria. Metallomics 2019; 11:1602-1624. [DOI: 10.1039/c9mt00186g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The regulation of the operons involved in Moco biosynthesis is dependent on the availability of Fe–S clusters in the cell.
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Affiliation(s)
- Arkadiusz Zupok
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
| | - Chantal Iobbi-Nivol
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Vincent Méjean
- Aix-Marseille Université
- Institut de Microbiologie de la Méditerranée
- Laboratoire de Bioénergétique et Ingénierie des Protéines
- Centre National de la Recherche Scientifique
- Marseille
| | - Silke Leimkühler
- University of Potsdam
- Institute of Biochemistry and Biology
- Molecular Enzymology
- Potsdam-Golm
- Germany
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