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Wilkens D, Simon J. Biosynthesis and function of microbial methylmenaquinones. Adv Microb Physiol 2023; 83:1-58. [PMID: 37507157 DOI: 10.1016/bs.ampbs.2023.05.002] [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: 07/30/2023]
Abstract
The membranous quinone/quinol pool is essential for the majority of life forms and its composition has been widely used as a biomarker in microbial taxonomy. The most abundant quinone is menaquinone (MK), which serves as an essential redox mediator in various electron transport chains of aerobic and anaerobic respiration. Several methylated derivatives of MK, designated methylmenaquinones (MMKs), have been reported to be present in members of various microbial phyla possessing either the classical MK biosynthesis pathway (Men) or the futalosine pathway (Mqn). Due to their low redox midpoint potentials, MMKs have been proposed to be specifically involved in appropriate electron transport chains of anaerobic respiration. The class C radical SAM methyltransferases MqnK, MenK and MenK2 have recently been shown to catalyse specific MK methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesise 8-MMK, 7-MMK and 7,8-dimethylmenaquinone (DMMK). MqnK, MenK and MenK2 from organisms such as Wolinella succinogenes, Adlercreutzia equolifaciens, Collinsella tanakaei, Ferrimonas marina and Syntrophus aciditrophicus have been functionally produced in Escherichia coli, enabling extensive quinone/quinol pool engineering of the native MK and 2-demethylmenaquinone (DMK). Cluster and phylogenetic analyses of available MK and MMK methyltransferase sequences revealed signature motifs that allowed the discrimination of MenK/MqnK/MenK2 family enzymes from other radical SAM enzymes and the identification of C-7-specific menaquinone methyltransferases of the MenK2 subfamily. It is envisaged that this knowledge will help to predict the methylation status of the menaquinone/menaquinol pool of any microbial species (or even a microbial community) from its (meta)genome.
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Affiliation(s)
- Dennis Wilkens
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, Germany; Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany.
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2
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Liang J, Huang H, Wang Y, Li L, Yi J, Wang S. A Cytoplasmic NAD(P)H-Dependent Polysulfide Reductase with Thiosulfate Reductase Activity from the Hyperthermophilic Bacterium Thermotoga maritima. Microbiol Spectr 2022; 10:e0043622. [PMID: 35762779 PMCID: PMC9431562 DOI: 10.1128/spectrum.00436-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/05/2022] [Indexed: 11/22/2022] Open
Abstract
Thermotoga maritima is an anaerobic hyperthermophilic bacterium that efficiently produces H2 by fermenting carbohydrates. High concentration of H2 inhibits the growth of T. maritima, and S0 could eliminate the inhibition and stimulate the growth through its reduction. The mechanism of T. maritima sulfur reduction, however, has not been fully understood. Herein, based on its similarity with archaeal NAD(P)H-dependent sulfur reductases (NSR), the ORF THEMA_RS02810 was identified and expressed in Escherichia coli, and the recombinant protein was characterized. The purified flavoprotein possessed NAD(P)H-dependent S0 reductase activity (1.3 U/mg for NADH and 0.8 U/mg for NADPH), polysulfide reductase activity (0.32 U/mg for NADH and 0.35 U/mg for NADPH), and thiosulfate reductase activity (2.3 U/mg for NADH and 2.5 U/mg for NADPH), which increased 3~4-folds by coenzyme A stimulation. Quantitative RT-PCR analysis showed that nsr was upregulated together with the mbx, yeeE, and rnf genes when the strain grew in S0- or thiosulfate-containing medium. The mechanism for sulfur reduction in T. maritima was discussed, which may affect the redox balance and energy metabolism of T. maritima. Genome search revealed that NSR homolog is widely distributed in thermophilic bacteria and archaea, implying its important role in the sulfur cycle of geothermal environments. IMPORTANCE The reduction of S0 and thiosulfate is essential in the sulfur cycle of geothermal environments, in which thermophiles play an important role. Despite previous research on some sulfur reductases of thermophilic archaea, the mechanism of sulfur reduction in thermophilic bacteria is still not clearly understood. Herein, we confirmed the presence of a cytoplasmic NAD(P)H-dependent polysulfide reductase (NSR) from the hyperthermophile T. maritima, with S0, polysulfide, and thiosulfate reduction activities, in contrast to other sulfur reductases. When grown in S0- or thiosulfate-containing medium, its expression was upregulated. And the putative membrane-bound MBX and Rnf may also play a role in the metabolism, which might influence the redox balance and energy metabolism of T. maritima. This is distinct from the mechanism of sulfur reduction in mesophiles such as Wolinella succinogenes. NSR homologs are widely distributed among heterotrophic thermophiles, suggesting that they may be vital in the sulfur cycle in geothermal environments.
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Affiliation(s)
- Jiyu Liang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Haiyan Huang
- Department of Pathogen Biology, School of Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Yubo Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Lexin Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Jihong Yi
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, People’s Republic of China
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3
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Pätsch S, Correia JV, Elvers BJ, Steuer M, Schulzke C. Inspired by Nature-Functional Analogues of Molybdenum and Tungsten-Dependent Oxidoreductases. Molecules 2022; 27:molecules27123695. [PMID: 35744820 PMCID: PMC9227248 DOI: 10.3390/molecules27123695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Throughout the previous ten years many scientists took inspiration from natural molybdenum and tungsten-dependent oxidoreductases to build functional active site analogues. These studies not only led to an ever more detailed mechanistic understanding of the biological template, but also paved the way to atypical selectivity and activity, such as catalytic hydrogen evolution. This review is aimed at representing the last decade’s progress in the research of and with molybdenum and tungsten functional model compounds. The portrayed systems, organized according to their ability to facilitate typical and artificial enzyme reactions, comprise complexes with non-innocent dithiolene ligands, resembling molybdopterin, as well as entirely non-natural nitrogen, oxygen, and/or sulfur bearing chelating donor ligands. All model compounds receive individual attention, highlighting the specific novelty that each provides for our understanding of the enzymatic mechanisms, such as oxygen atom transfer and proton-coupled electron transfer, or that each presents for exploiting new and useful catalytic capability. Overall, a shift in the application of these model compounds towards uncommon reactions is noted, the latter are comprehensively discussed.
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Spring S, Rohde M, Bunk B, Spröer C, Will SE, Neumann-Schaal M. New insights into the energy metabolism and taxonomy of Deferribacteres revealed by the characterization of a new isolate from a hypersaline microbial mat. Environ Microbiol 2022; 24:2543-2575. [PMID: 35415868 DOI: 10.1111/1462-2920.15999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022]
Abstract
Strain L21-Ace-BEST , isolated from a lithifying cyanobacterial mat, could be assigned to a novel species and genus within the Deferribacteres. It is an important model organism for the study of anaerobic acetate degradation under hypersaline conditions. The metabolism of strain L21-Ace-BEST was characterized by biochemical studies, comparative genome analyses, and the evaluation of gene expression patterns. The central metabolic pathway is the citric acid cycle, which is mainly controlled by the enzyme succinyl-CoA:acetate-CoA transferase. The potential use of a reversed oxidative citric acid cycle to fix CO2 has been revealed through genome analysis. However, no autotrophic growth was detected in this strain, whereas sulfide and H2 can be used mixotrophically. Preferred electron acceptors for the anaerobic oxidation of acetate are nitrate, fumarate and DMSO, while oxygen can be utilized only under microoxic conditions. Aerotolerant growth by fermentation was observed at higher oxygen concentrations. The redox cycling of sulfur/sulfide enables the generation of reducing power for the assimilation of acetate during growth and could prevent the over-reduction of cells in stationary phase. Extracellular electron transfer appears to be an essential component of the respiratory metabolism in this clade of Deferribacteres and may be involved in the reduction of nitrite to ammonium. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Boyke Bunk
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Eva Will
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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5
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Modularity of membrane-bound charge-translocating protein complexes. Biochem Soc Trans 2021; 49:2669-2685. [PMID: 34854900 DOI: 10.1042/bst20210462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 02/05/2023]
Abstract
Energy transduction is the conversion of one form of energy into another; this makes life possible as we know it. Organisms have developed different systems for acquiring energy and storing it in useable forms: the so-called energy currencies. A universal energy currency is the transmembrane difference of electrochemical potential (Δμ~). This results from the translocation of charges across a membrane, powered by exergonic reactions. Different reactions may be coupled to charge-translocation and, in the majority of cases, these reactions are catalyzed by modular enzymes that always include a transmembrane subunit. The modular arrangement of these enzymes allows for different catalytic and charge-translocating modules to be combined. Thus, a transmembrane charge-translocating module can be associated with different catalytic subunits to form an energy-transducing complex. Likewise, the same catalytic subunit may be combined with a different membrane charge-translocating module. In this work, we analyze the modular arrangement of energy-transducing membrane complexes and discuss their different combinations, focusing on the charge-translocating module.
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6
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Wu B, Liu F, Fang W, Yang T, Chen GH, He Z, Wang S. Microbial sulfur metabolism and environmental implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146085. [PMID: 33714092 DOI: 10.1016/j.scitotenv.2021.146085] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.
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Affiliation(s)
- Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Feifei Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Wenwen Fang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Tony Yang
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.
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Murphy CL, Biggerstaff J, Eichhorn A, Ewing E, Shahan R, Soriano D, Stewart S, VanMol K, Walker R, Walters P, Elshahed MS, Youssef NH. Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the phylum. Environ Microbiol 2021; 23:4326-4343. [PMID: 34056821 DOI: 10.1111/1462-2920.15614] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 12/01/2022]
Abstract
We report on the genomic characterization of three novel classes in the phylum Desulfobacterota. One class (proposed name Candidatus 'Anaeroferrophillalia') was characterized by heterotrophic growth capacity, either fermentatively or utilizing polysulfide, tetrathionate or thiosulfate as electron acceptors. In the absence of organic carbon sources, autotrophic growth via the Wood-Ljungdahl (WL) pathway and using hydrogen or Fe(II) as an electron donor is also inferred for members of the 'Anaeroferrophillalia'. The second class (proposed name Candidatus 'Anaeropigmentia') was characterized by its capacity for growth at low oxygen concentration, and the capacity to synthesize the methyl/alkyl carrier CoM, an ability that is prevalent in the archaeal but rare in the bacterial domain. Pigmentation is inferred from the capacity for carotenoid (lycopene) production. The third class (proposed name Candidatus 'Zymogenia') was characterized by fermentative heterotrophic growth capacity, broad substrate range and the adaptation of some of its members to hypersaline habitats. Analysis of the distribution pattern of all three classes showed their occurrence as rare community members in multiple habitats, with preferences for anaerobic terrestrial, freshwater and marine environments over oxygenated (e.g. pelagic ocean and agricultural land) settings. Special preference for some members of the class Candidatus 'Zymogenia' for hypersaline environments such as hypersaline microbial mats and lagoons was observed.
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Affiliation(s)
- Chelsea L Murphy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - James Biggerstaff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Alexis Eichhorn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Essences Ewing
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Ryan Shahan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Diana Soriano
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Sydney Stewart
- Department of Animal Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Kaitlynn VanMol
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Ross Walker
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Payton Walters
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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8
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Calisto F, Pereira MM. The Ion-Translocating NrfD-Like Subunit of Energy-Transducing Membrane Complexes. Front Chem 2021; 9:663706. [PMID: 33928068 PMCID: PMC8076601 DOI: 10.3389/fchem.2021.663706] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/19/2021] [Indexed: 11/23/2022] Open
Abstract
Several energy-transducing microbial enzymes have their peripheral subunits connected to the membrane through an integral membrane protein, that interacts with quinones but does not have redox cofactors, the so-called NrfD-like subunit. The periplasmic nitrite reductase (NrfABCD) was the first complex recognized to have a membrane subunit with these characteristics and consequently provided the family's name: NrfD. Sequence analyses indicate that NrfD homologs are present in many diverse enzymes, such as polysulfide reductase (PsrABC), respiratory alternative complex III (ACIII), dimethyl sulfoxide (DMSO) reductase (DmsABC), tetrathionate reductase (TtrABC), sulfur reductase complex (SreABC), sulfite dehydrogenase (SoeABC), quinone reductase complex (QrcABCD), nine-heme cytochrome complex (NhcABCD), group-2 [NiFe] hydrogenase (Hyd-2), dissimilatory sulfite-reductase complex (DsrMKJOP), arsenate reductase (ArrC) and multiheme cytochrome c sulfite reductase (MccACD). The molecular structure of ACIII subunit C (ActC) and Psr subunit C (PsrC), NrfD-like subunits, revealed the existence of ion-conducting pathways. We performed thorough primary structural analyses and built structural models of the NrfD-like subunits. We observed that all these subunits are constituted by two structural repeats composed of four-helix bundles, possibly harboring ion-conducting pathways and containing a quinone/quinol binding site. NrfD-like subunits may be the ion-pumping module of several enzymes. Our data impact on the discussion of functional implications of the NrfD-like subunit-containing complexes, namely in their ability to transduce energy.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universdade de Lisboa, Lisboa, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universdade de Lisboa, Lisboa, Portugal
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9
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Duarte AG, Barbosa ACC, Ferreira D, Manteigas G, Domingos RM, Pereira IAC. Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148416. [PMID: 33753023 DOI: 10.1016/j.bbabio.2021.148416] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/25/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023]
Abstract
In prokaryotes, the proton or sodium motive force required for ATP synthesis is produced by respiratory complexes that present an ion-pumping mechanism or are involved in redox loops performed by membrane proteins that usually have substrate and quinone-binding sites on opposite sides of the membrane. Some respiratory complexes include a dimeric redox module composed of a quinone-interacting membrane protein of the NrfD family and an iron‑sulfur protein of the NrfC family. The QrcABCD complex of sulfate reducers, which includes the QrcCD module homologous to NrfCD, was recently shown to perform electrogenic quinone reduction providing the first conclusive evidence for energy conservation among this family. Similar redox modules are present in multiple respiratory complexes, which can be associated with electroneutral, energy-driven or electrogenic reactions. This work discusses the presence of the NrfCD/PsrBC dimeric redox module in different bioenergetics contexts and its role in prokaryotic energy conservation mechanisms.
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Affiliation(s)
- Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal.
| | - Ana C C Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Delfim Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Gonçalo Manteigas
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Renato M Domingos
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal.
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10
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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11
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Wilkens D, Meusinger R, Hein S, Simon J. Sequence analysis and specificity of distinct types of menaquinone methyltransferases indicate the widespread potential of methylmenaquinone production in bacteria and archaea. Environ Microbiol 2020; 23:1407-1421. [PMID: 33264482 DOI: 10.1111/1462-2920.15344] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/30/2020] [Indexed: 01/06/2023]
Abstract
Menaquinone (MK) serves as an essential membranous redox mediator in various electron transport chains of aerobic and anaerobic respiration. In addition, the composition of the quinone/quinol pool has been widely used as a biomarker in microbial taxonomy. The HemN-like class C radical SAM methyltransferases (RSMTs) MqnK, MenK and MenK2 have recently been shown to facilitate specific menaquinone methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesize 8-methylmenaquinone, 7-methylmenaquinone and 7,8-dimethylmenaquinone. However, the vast majority of protein sequences from the MqnK/MenK/MenK2 family belong to organisms, whose capacity to produce methylated menaquinones has not been investigated biochemically. Here, representative putative menK and menK2 genes from Collinsella tanakaei and Ferrimonas marina were individually expressed in Escherichia coli (wild-type or ubiE deletion mutant) and the corresponding cells were found to produce methylated derivatives of the endogenous MK and 2-demethylmenaquinone. Cluster and phylogenetic analyses of 828 (methyl)menaquinone methyltransferase sequences revealed signature motifs that allowed to discriminate enzymes of the MqnK/MenK/MenK2 family from other radical SAM enzymes and to identify C-7-specific menaquinone methyltransferases of the MenK2 subfamily. This study will help to predict the methylation status of the quinone/quinol pool of a microbial species (or even a microbial community) from its (meta)genome and contribute to the future design of microbial quinone/quinol pools in a Synthetic Biology approach.
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Affiliation(s)
- Dennis Wilkens
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, 64287, Germany
| | - Reinhard Meusinger
- Department of Chemistry, Macromolecular Chemistry, Technical University of Darmstadt, Alarich-Weiss-Str. 4, Darmstadt, 64287, Germany
| | - Sascha Hein
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, 64287, Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt, 64287, Germany.,Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, 64283, Germany
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12
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Sulfite oxidation by the quinone-reducing molybdenum sulfite dehydrogenase SoeABC from the bacterium Aquifex aeolicus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148279. [DOI: 10.1016/j.bbabio.2020.148279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/03/2020] [Accepted: 07/10/2020] [Indexed: 01/26/2023]
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13
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Wang S, Jiang L, Hu Q, Liu X, Yang S, Shao Z. Elemental sulfur reduction by a deep-sea hydrothermal vent Campylobacterium Sulfurimonas sp. NW10. Environ Microbiol 2020; 23:965-979. [PMID: 32974951 DOI: 10.1111/1462-2920.15247] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/22/2020] [Indexed: 01/10/2023]
Abstract
Sulfurimonas species (class Campylobacteria, phylum Campylobacterota) were globally distributed and especially predominant in deep-sea hydrothermal environments. They were previously identified as chemolithoautotrophic sulfur-oxidizing bacteria (SOB), whereas little is known about their potential in sulfur reduction. In this report, we found that the elemental sulfur reduction is quite common in different species of genus Sulfurimonas. To gain insights into the sulfur reduction mechanism, growth tests, morphology observation, as well as genomic and transcriptomic analyses were performed on a deep-sea hydrothermal vent bacterium Sulfurimonas sp. NW10. Scanning electron micrographs and dialysis tubing tests confirmed that elemental sulfur reduction occurred without direct contact of cells with sulfur particles while direct access strongly promoted bacterial growth. Furthermore, we demonstrated that most species of Sulfurimonas probably employ both periplasmic and cytoplasmic polysulfide reductases, encoded by genes psrA1 B1 CDE and psrA2 B2 , respectively, to accomplish cyclooctasulfur reduction. This is the first report showing two different sulfur reduction pathways coupled to different energy conservations could coexist in one sulfur-reducing microorganism, and demonstrates that most bacteria of Sulfurimonas could employ both periplasmic and cytoplasmic polysulfide reductases to perform cyclooctasulfur reduction. The capability of sulfur reduction coupling with hydrogen oxidation may partially explain the prevalenceof Sulfurimonas in deep-sea hydrothermal vent environments.
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Affiliation(s)
- Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China.,Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Qitao Hu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Xuewen Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
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14
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Szyttenholm J, Chaspoul F, Bauzan M, Ducluzeau AL, Chehade MH, Pierrel F, Denis Y, Nitschke W, Schoepp-Cothenet B. The controversy on the ancestral arsenite oxidizing enzyme; deducing evolutionary histories with phylogeny and thermodynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148252. [PMID: 32569664 DOI: 10.1016/j.bbabio.2020.148252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 06/07/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022]
Abstract
The three presently known enzymes responsible for arsenic-using bioenergetic processes are arsenite oxidase (Aio), arsenate reductase (Arr) and alternative arsenite oxidase (Arx), all of which are molybdoenzymes from the vast group referred to as the Mo/W-bisPGD enzyme superfamily. Since arsenite is present in substantial amounts in hydrothermal environments, frequently considered as vestiges of primordial biochemistry, arsenite-based bioenergetics has long been predicted to be ancient. Conflicting scenarios, however, have been put forward proposing either Arr/Arx or Aio as operating in the ancestral metabolism. Phylogenetic data argue in favor of Aio whereas biochemical and physiological data led several authors to propose Arx/Arr as the most ancient anaerobic arsenite metabolizing enzymes. Here we combine phylogenetic approaches with physiological and biochemical experiments to demonstrate that the Arx/Arr enzymes could not have been functional in the Archaean geological eon. We propose that Arr reacts with menaquinones to reduce arsenate whereas Arx reacts with ubiquinone to oxidize arsenite, in line with thermodynamic considerations. The distribution of the quinone biosynthesis pathways, however, clearly indicates that the ubiquinone pathway is recent. An updated phylogeny of Arx furthermore reinforces the hypothesis of a recent emergence of this enzyme. We therefore conclude that anaerobic arsenite redox conversion in the Archaean must have been performed in a metabolism involving Aio.
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Affiliation(s)
- Julie Szyttenholm
- Aix-Marseille Univ., CNRS, BIP UMR 7281, FR 3479, IMM, 13402 Marseille Cedex 20, France
| | - Florence Chaspoul
- Aix Marseille Univ., CNRS, IRD, IMBE UMR 7263, Faculté de Pharmacie, 13005 Marseille, France
| | - Marielle Bauzan
- Aix-Marseille Univ., CNRS, Plateforme Fermentation, FR3479, IMM, 13402 Marseille Cedex 20, France
| | - Anne-Lise Ducluzeau
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775-7220, USA
| | | | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38000 Grenoble, France
| | - Yann Denis
- Aix-Marseille Univ., CNRS, Plateforme Transcriptomique, FR3479, IMM, 13402 Marseille Cedex 20, France
| | - Wolfgang Nitschke
- Aix-Marseille Univ., CNRS, BIP UMR 7281, FR 3479, IMM, 13402 Marseille Cedex 20, France
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15
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Shi Y, Xin Y, Wang C, Blankenship RE, Sun F, Xu X. Cryo-EM structures of the air-oxidized and dithionite-reduced photosynthetic alternative complex III from Roseiflexus castenholzii. SCIENCE ADVANCES 2020; 6:eaba2739. [PMID: 32832681 PMCID: PMC7439408 DOI: 10.1126/sciadv.aba2739] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/11/2020] [Indexed: 05/27/2023]
Abstract
Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation in both the respiratory and photosynthetic electron transport chains of bacteria. The coupling mechanism, however, is poorly understood. Here, we report the cryo-EM structures of air-oxidized and dithionite-reduced ACIII from the photosynthetic bacterium Roseiflexus castenholzii at 3.3- and 3.5-Å resolution, respectively. We identified a menaquinol binding pocket and an electron transfer wire comprising six hemes and four iron-sulfur clusters that is capable of transferring electrons to periplasmic acceptors. We detected a proton translocation passage in which three strictly conserved, mid-passage residues are likely essential for coupling the redox-driven proton translocation across the membrane. These results allow us to propose a previously unrecognized coupling mechanism that links the respiratory and photosynthetic functions of ACIII. This study provides a structural basis for further investigation of the energy transformation mechanisms in bacterial photosynthesis and respiration.
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Affiliation(s)
- Yang Shi
- National Laboratory of Biomacromolecules, National Center of Protein Science-Beijing, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yueyong Xin
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou 311121, Zhejiang Province, China
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
| | - Chao Wang
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou 311121, Zhejiang Province, China
| | - Robert E. Blankenship
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Fei Sun
- National Laboratory of Biomacromolecules, National Center of Protein Science-Beijing, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoling Xu
- Hangzhou Normal University, 2318 Yuhangtang Road, Cangqian, Yuhang District, Hangzhou 311121, Zhejiang Province, China
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Medicine and The Affiliated Hospital, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
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16
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Ntagia E, Chatzigiannidou I, Williamson AJ, Arends JBA, Rabaey K. Homoacetogenesis and microbial community composition are shaped by pH and total sulfide concentration. Microb Biotechnol 2020; 13:1026-1038. [PMID: 32126162 PMCID: PMC7264883 DOI: 10.1111/1751-7915.13546] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 12/27/2022] Open
Abstract
Biological CO2 sequestration through acetogenesis with H2 as electron donor is a promising technology to reduce greenhouse gas emissions. Today, a major issue is the presence of impurities such as hydrogen sulfide (H2 S) in CO2 containing gases, as they are known to inhibit acetogenesis in CO2 -based fermentations. However, exact values of toxicity and inhibition are not well-defined. To tackle this uncertainty, a series of toxicity experiments were conducted, with a mixed homoacetogenic culture, total dissolved sulfide concentrations ([TDS]) varied between 0 and 5 mM and pH between 5 and 7. The extent of inhibition was evaluated based on acetate production rates and microbial growth. Maximum acetate production rates of 0.12, 0.09 and 0.04 mM h-1 were achieved in the controls without sulfide at pH 7, pH 6 and pH 5. The half-maximal inhibitory concentration (IC50 qAc ) was 0.86, 1.16 and 1.36 mM [TDS] for pH 7, pH 6 and pH 5. At [TDS] above 3.33 mM, acetate production and microbial growth were completely inhibited at all pHs. 16S rRNA gene amplicon sequencing revealed major community composition transitions that could be attributed to both pH and [TDS]. Based on the observed toxicity levels, treatment approaches for incoming industrial CO2 streams can be determined.
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Affiliation(s)
- Eleftheria Ntagia
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653Ghent9000Belgium
| | - Ioanna Chatzigiannidou
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653Ghent9000Belgium
| | - Adam J. Williamson
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653Ghent9000Belgium
| | - Jan B. A. Arends
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653Ghent9000Belgium
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653Ghent9000Belgium
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17
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van der Stel AX, Wösten MMSM. Regulation of Respiratory Pathways in Campylobacterota: A Review. Front Microbiol 2019; 10:1719. [PMID: 31417516 PMCID: PMC6682613 DOI: 10.3389/fmicb.2019.01719] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 07/11/2019] [Indexed: 12/19/2022] Open
Abstract
The Campylobacterota, previously known as Epsilonproteobacteria, are a large group of Gram-negative mainly, spiral-shaped motile bacteria. Some members like the Sulfurospirillum spp. are free-living, while others such as Helicobacter spp. can only persist in strict association with a host organism as commensal or as pathogen. Species of this phylum colonize diverse habitats ranging from deep-sea thermal vents to the human stomach wall. Despite their divergent environments, they share common energy conservation mechanisms. The Campylobacterota have a large and remarkable repertoire of electron transport chain enzymes, given their small genomes. Although members of recognized families of transcriptional regulators are found in these genomes, sofar no orthologs known to be important for energy or redox metabolism such as ArcA, FNR or NarP are encoded in the genomes of the Campylobacterota. In this review, we discuss the strategies that members of Campylobacterota utilize to conserve energy and the corresponding regulatory mechanisms that regulate the branched electron transport chains in these bacteria.
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Affiliation(s)
| | - Marc M. S. M. Wösten
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands
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18
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Characterization of thiosulfate reductase from Pyrobaculum aerophilum heterologously produced in Pyrococcus furiosus. Extremophiles 2019; 24:53-62. [PMID: 31278423 DOI: 10.1007/s00792-019-01112-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022]
Abstract
The genome of the archaeon Pyrobaculum aerophilum (Topt ~ 100 °C) contains an operon (PAE2859-2861) encoding a putative pyranopterin-containing oxidoreductase of unknown function and metal content. These genes (with one gene modified to encode a His-affinity tag) were inserted into the fermentative anaerobic archaeon, Pyrococcus furiosus (Topt ~ 100 °C). Dye-linked assays of cytoplasmic extracts from recombinant P. furiosus show that the P. aerophilum enzyme is a thiosulfate reductase (Tsr) and reduces thiosulfate but not polysulfide. The enzyme (Tsr-Mo) from molybdenum-grown cells contains Mo (Mo:W = 9:1) while the enzyme (Tsr-W) from tungsten-grown cells contains mainly W (Mo:W = 1:6). Purified Tsr-Mo has over ten times the activity (Vmax = 1580 vs. 141 µmol min-1 mg-1) and twice the affinity for thiosulfate (Km = ~ 100 vs. ~ 200 μM) than Tsr-W and is reduced at a lower potential (Epeak = - 255 vs - 402 mV). Tsr-Mo and Tsr-W proteins are heterodimers lacking the membrane anchor subunit (PAE2861). Recombinant P. furiosus expressing P. aerophilum Tsr could not use thiosulfate as a terminal electron acceptor. P. furiosus contains five pyranopterin-containing enzymes, all of which utilize W. P. aerophilum Tsr-Mo is the first example of an active Mo-containing enzyme produced in P. furiosus.
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19
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Respiratory Selenite Reductase from Bacillus selenitireducens Strain MLS10. J Bacteriol 2019; 201:JB.00614-18. [PMID: 30642986 DOI: 10.1128/jb.00614-18] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/03/2019] [Indexed: 11/20/2022] Open
Abstract
The putative respiratory selenite [Se(IV)] reductase (Srr) from Bacillus selenitireducens MLS10 has been identified through a polyphasic approach involving genomics, proteomics, and enzymology. Nondenaturing gel assays were used to identify Srr in cell fractions, and the active band was shown to contain a single protein of 80 kDa. The protein was identified through liquid chromatography-tandem mass spectrometry (LC-MS/MS) as a homolog of the catalytic subunit of polysulfide reductase (PsrA). It was found to be encoded as part of an operon that contains six genes that we designated srrE, srrA, srrB, srrC, srrD, and srrF SrrA is the catalytic subunit (80 kDa), with a twin-arginine translocation (TAT) leader sequence indicative of a periplasmic protein and one putative 4Fe-4S binding site. SrrB is a small subunit (17 kDa) with four putative 4Fe-4S binding sites, SrrC (43 kDa) is an anchoring subunit, and SrrD (24 kDa) is a chaperon protein. Both SrrE (38 kDa) and SrrF (45 kDa) were annotated as rhodanese domain-containing proteins. Phylogenetic analysis revealed that SrrA belonged to the PsrA/PhsA clade but that it did not define a distinct subgroup, based on the putative homologs that were subsequently identified from other known selenite-respiring bacteria (e.g., Desulfurispirillum indicum and Pyrobaculum aerophilum). The enzyme appeared to be specific for Se(IV), showing no activity with selenate, arsenate, or thiosulfate, with a Km of 145 ± 53 μM, a V max of 23 ± 2.5 μM min-1, and a k cat of 23 ± 2.68 s-1 These results further our understanding of the mechanisms of selenium biotransformation and its biogeochemical cycle.IMPORTANCE Selenium is an essential element for life, with Se(IV) reduction a key step in its biogeochemical cycle. This report identifies for the first time a dissimilatory Se(IV) reductase, Srr, from a known selenite-respiring bacterium, the haloalkalophilic Bacillus selenitireducens strain MLS10. The work extends the versatility of the complex iron-sulfur molybdoenzyme (CISM) superfamily in electron transfer involving chalcogen substrates with different redox potentials. Further, it underscores the importance of biochemical and enzymological approaches in establishing the functionality of these enzymes.
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20
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Significance of MccR, MccC, MccD, MccL and 8-methylmenaquinone in sulfite respiration of Wolinella succinogenes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:12-21. [DOI: 10.1016/j.bbabio.2018.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/26/2018] [Accepted: 10/13/2018] [Indexed: 11/17/2022]
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21
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Duarte AG, Catarino T, White GF, Lousa D, Neukirchen S, Soares CM, Sousa FL, Clarke TA, Pereira IAC. An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation. Nat Commun 2018; 9:5448. [PMID: 30575735 PMCID: PMC6303296 DOI: 10.1038/s41467-018-07839-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/27/2018] [Indexed: 02/02/2023] Open
Abstract
The bioenergetics of anaerobic metabolism frequently relies on redox loops performed by membrane complexes with substrate- and quinone-binding sites on opposite sides of the membrane. However, in sulfate respiration (a key process in the biogeochemical sulfur cycle), the substrate- and quinone-binding sites of the QrcABCD complex are periplasmic, and their role in energy conservation has not been elucidated. Here we show that the QrcABCD complex of Desulfovibrio vulgaris is electrogenic, as protons and electrons required for quinone reduction are extracted from opposite sides of the membrane, with a H+/e− ratio of 1. Although the complex does not act as a H+-pump, QrcD may include a conserved proton channel leading from the N-side to the P-side menaquinone pocket. Our work provides evidence of how energy is conserved during dissimilatory sulfate reduction, and suggests mechanisms behind the functions of related bacterial respiratory complexes in other bioenergetic contexts. The bacterial complex QrcABCD plays a key role in the bioenergetics of sulfate respiration. Here, Duarte et al. show that this complex is electrogenic, with protons and electrons required for quinone reduction being extracted from opposite sides of the membrane.
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Affiliation(s)
- Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.,Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Gaye F White
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Sinje Neukirchen
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14 UZA I, 1090, Vienna, Austria
| | - Cláudio M Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipa L Sousa
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14 UZA I, 1090, Vienna, Austria
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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22
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Insight into Energy Conservation via Alternative Carbon Monoxide Metabolism in Carboxydothermus pertinax Revealed by Comparative Genome Analysis. Appl Environ Microbiol 2018; 84:AEM.00458-18. [PMID: 29728389 DOI: 10.1128/aem.00458-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/28/2018] [Indexed: 11/20/2022] Open
Abstract
Carboxydothermus species are some of the most studied thermophilic carboxydotrophs. Their varied carboxydotrophic growth properties suggest distinct strategies for energy conservation via carbon monoxide (CO) metabolism. In this study, we used comparative genome analysis of the genus Carboxydothermus to show variations in the CO dehydrogenase-energy-converting hydrogenase gene cluster, which is responsible for CO metabolism with H2 production (hydrogenogenic CO metabolism). Indeed, the ability or inability to produce H2 with CO oxidation is explained by the presence or absence of this gene cluster in Carboxydothermus hydrogenoformans, Carboxydothermus islandicus, and Carboxydothermus ferrireducens Interestingly, despite its hydrogenogenic CO metabolism, Carboxydothermus pertinax lacks the Ni-CO dehydrogenase catalytic subunit (CooS-I) and its transcriptional regulator-encoding genes in this gene cluster, probably due to inversion. Transcriptional analysis in C. pertinax showed that the Ni-CO dehydrogenase gene (cooS-II) and distantly encoded energy-converting-hydrogenase-related genes were remarkably upregulated with 100% CO. In addition, when thiosulfate was available as a terminal electron acceptor in 100% CO, the maximum cell density and maximum specific growth rate of C. pertinax were 3.1-fold and 1.5-fold higher, respectively, than when thiosulfate was absent. The amount of H2 produced was only 62% of the amount of CO consumed, less than expected according to hydrogenogenic CO oxidation (CO + H2O → CO2 + H2). Accordingly, C. pertinax would couple CO oxidation by Ni-CO dehydrogenase II with simultaneous reduction of not only H2O but also thiosulfate when grown in 100% CO.IMPORTANCE Anaerobic hydrogenogenic carboxydotrophs are thought to fill a vital niche by scavenging potentially toxic CO and producing H2 as an available energy source for thermophilic microbes. This hydrogenogenic carboxydotrophy relies on a Ni-CO dehydrogenase-energy-converting hydrogenase gene cluster. This feature is thought to be common to these organisms. However, the hydrogenogenic carboxydotroph Carboxydothermus pertinax lacks the gene for the Ni-CO dehydrogenase catalytic subunit encoded in the gene cluster. Here, we performed a comparative genome analysis of the genus Carboxydothermus, a transcriptional analysis, and a cultivation study in 100% CO to prove the hydrogenogenic CO metabolism. Results revealed that C. pertinax could couple Ni-CO dehydrogenase II alternatively to the distal energy-converting hydrogenase. Furthermore, C. pertinax represents an example of the functioning of Ni-CO dehydrogenase that does not always correspond to its genomic context, owing to the versatility of CO metabolism and the low redox potential of CO.
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23
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Structure of the alternative complex III in a supercomplex with cytochrome oxidase. Nature 2018; 557:123-126. [PMID: 29695868 PMCID: PMC6004266 DOI: 10.1038/s41586-018-0061-y] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 03/20/2018] [Indexed: 12/31/2022]
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Two dedicated class C radical S-adenosylmethionine methyltransferases concertedly catalyse the synthesis of 7,8-dimethylmenaquinone. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:300-308. [DOI: 10.1016/j.bbabio.2018.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/24/2018] [Accepted: 01/28/2018] [Indexed: 12/24/2022]
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25
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Hein S, Witt S, Simon J. Clade II nitrous oxide respiration of Wolinella succinogenes depends on the NosG, -C1, -C2, -H electron transport module, NosB and a Rieske/cytochrome bc complex. Environ Microbiol 2017; 19:4913-4925. [PMID: 28925551 DOI: 10.1111/1462-2920.13935] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/14/2017] [Accepted: 09/16/2017] [Indexed: 01/20/2023]
Abstract
Microbial reduction of nitrous oxide (N2 O) is an environmentally significant process in the biogeochemical nitrogen cycle. However, it has been recognized only recently that the gene encoding N2 O reductase (nosZ) is organized in varying genetic contexts, thereby defining clade I (or 'typical') and clade II (or 'atypical') N2 O reductases and nos gene clusters. This study addresses the enzymology of the clade II Nos system from Wolinella succinogenes, a nitrate-ammonifying and N2 O-respiring Epsilonproteobacterium that contains a cytochrome c N2 O reductase (cNosZ). The characterization of single non-polar nos gene deletion mutants demonstrated that the NosG, -C1, -C2, -H and -B proteins were essential for N2 O respiration. Moreover, cells of a W. succinogenes mutant lacking a putative menaquinol-oxidizing Rieske/cytochrome bc complex (QcrABC) were found to be incapable of N2 O (and also nitrate) respiration. Proton motive menaquinol oxidation by N2 O is suggested, supported by the finding that the molar yield for W. succinogenes cells grown by N2 O respiration using formate as electron donor exceeded that of fumarate respiration by about 30%. The results demand revision of the electron transport chain model of clade II N2 O respiration and challenge the assumption that NosGH(NapGH)-type iron-sulfur proteins are menaquinol-reactive.
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Affiliation(s)
- Sascha Hein
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Samantha Witt
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
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van der Stel AX, Boogerd FC, Huynh S, Parker CT, van Dijk L, van Putten JPM, Wösten MMSM. Generation of the membrane potential and its impact on the motility, ATP production and growth in Campylobacter jejuni. Mol Microbiol 2017; 105:637-651. [PMID: 28586527 DOI: 10.1111/mmi.13723] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/29/2017] [Accepted: 06/04/2017] [Indexed: 02/06/2023]
Abstract
The generation of a membrane potential (Δψ), the major constituent of the proton motive force (pmf), is crucial for ATP synthesis, transport of nutrients and flagellar rotation. Campylobacter jejuni harbors a branched electron transport chain, enabling respiration with different electron donors and acceptors. Here, we demonstrate that a relatively high Δψ is only generated in the presence of either formate as electron donor or oxygen as electron acceptor, in combination with an acceptor/donor respectively. We show the necessity of the pmf for motility and growth of C. jejuni. ATP generation is not only accomplished by oxidative phosphorylation via the pmf, but also by substrate-level phosphorylation via the enzyme AckA. In response to a low oxygen tension, C. jejuni increases the transcription and activity of the donor complexes formate dehydrogenase (FdhABC) and hydrogenase (HydABCD) as well as the transcription of the alternative respiratory acceptor complexes. Our findings suggest that in the gut of warm-blooded animals, C. jejuni depends on at least formate or hydrogen as donor (in the anaerobic lumen) or oxygen as acceptor (near the epithelial cells) to generate a pmf that sustains efficient motility and growth for colonization and pathogenesis.
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Affiliation(s)
| | - Fred C Boogerd
- Department of Molecular Cell Biology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Craig T Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Linda van Dijk
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Jos P M van Putten
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Marc M S M Wösten
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
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Hein S, Klimmek O, Polly M, Kern M, Simon J. A class C radicalS-adenosylmethionine methyltransferase synthesizes 8-methylmenaquinone. Mol Microbiol 2017; 104:449-462. [DOI: 10.1111/mmi.13638] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sascha Hein
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Oliver Klimmek
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Markus Polly
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Melanie Kern
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
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Choi AR, Kim MS, Kang SG, Lee HS. Dimethyl sulfoxide reduction by a hyperhermophilic archaeon Thermococcus onnurineus NA1 via a cysteine-cystine redox shuttle. J Microbiol 2016; 54:31-38. [DOI: 10.1007/s12275-016-5574-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 12/03/2015] [Indexed: 10/22/2022]
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Florentino AP, Weijma J, Stams AJM, Sánchez-Andrea I. Ecophysiology and Application of Acidophilic Sulfur-Reducing Microorganisms. BIOTECHNOLOGY OF EXTREMOPHILES: 2016. [DOI: 10.1007/978-3-319-13521-2_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Keller AH, Schleinitz KM, Starke R, Bertilsson S, Vogt C, Kleinsteuber S. Metagenome-Based Metabolic Reconstruction Reveals the Ecophysiological Function of Epsilonproteobacteria in a Hydrocarbon-Contaminated Sulfidic Aquifer. Front Microbiol 2015; 6:1396. [PMID: 26696999 PMCID: PMC4674564 DOI: 10.3389/fmicb.2015.01396] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/23/2015] [Indexed: 11/13/2022] Open
Abstract
The population genome of an uncultured bacterium assigned to the Campylobacterales (Epsilonproteobacteria) was reconstructed from a metagenome dataset obtained by whole-genome shotgun pyrosequencing. Genomic DNA was extracted from a sulfate-reducing, m-xylene-mineralizing enrichment culture isolated from groundwater of a benzene-contaminated sulfidic aquifer. The identical epsilonproteobacterial phylotype has previously been detected in toluene- or benzene-mineralizing, sulfate-reducing consortia enriched from the same site. Previous stable isotope probing (SIP) experiments with 13C6-labeled benzene suggested that this phylotype assimilates benzene-derived carbon in a syntrophic benzene-mineralizing consortium that uses sulfate as terminal electron acceptor. However, the type of energy metabolism and the ecophysiological function of this epsilonproteobacterium within aromatic hydrocarbon-degrading consortia and in the sulfidic aquifer are poorly understood. Annotation of the epsilonproteobacterial population genome suggests that the bacterium plays a key role in sulfur cycling as indicated by the presence of an sqr gene encoding a sulfide quinone oxidoreductase and psr genes encoding a polysulfide reductase. It may gain energy by using sulfide or hydrogen/formate as electron donors. Polysulfide, fumarate, as well as oxygen are potential electron acceptors. Auto- or mixotrophic carbon metabolism seems plausible since a complete reductive citric acid cycle was detected. Thus the bacterium can thrive in pristine groundwater as well as in hydrocarbon-contaminated aquifers. In hydrocarbon-contaminated sulfidic habitats, the epsilonproteobacterium may generate energy by coupling the oxidation of hydrogen or formate and highly abundant sulfide with the reduction of fumarate and/or polysulfide, accompanied by efficient assimilation of acetate produced during fermentation or incomplete oxidation of hydrocarbons. The highly efficient assimilation of acetate was recently demonstrated by a pulsed 13C2-acetate protein SIP experiment. The capability of nitrogen fixation as indicated by the presence of nif genes may provide a selective advantage in nitrogen-depleted habitats. Based on this metabolic reconstruction, we propose acetate capture and sulfur cycling as key functions of Epsilonproteobacteria within the intermediary ecosystem metabolism of hydrocarbon-rich sulfidic sediments.
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Affiliation(s)
- Andreas H Keller
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany ; Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| | - Kathleen M Schleinitz
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| | - Robert Starke
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University Uppsala, Sweden
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany
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Abstract
Nitrate reduction to ammonia via nitrite occurs widely as an anabolic process through which bacteria, archaea, and plants can assimilate nitrate into cellular biomass. Escherichia coli and related enteric bacteria can couple the eight-electron reduction of nitrate to ammonium to growth by coupling the nitrate and nitrite reductases involved to energy-conserving respiratory electron transport systems. In global terms, the respiratory reduction of nitrate to ammonium dominates nitrate and nitrite reduction in many electron-rich environments such as anoxic marine sediments and sulfide-rich thermal vents, the human gastrointestinal tract, and the bodies of warm-blooded animals. This review reviews the regulation and enzymology of this process in E. coli and, where relevant detail is available, also in Salmonella and draws comparisons with and implications for the process in other bacteria where it is pertinent to do so. Fatty acids may be present in high levels in many of the natural environments of E. coli and Salmonella in which oxygen is limited but nitrate is available to support respiration. In E. coli, nitrate reduction in the periplasm involves the products of two seven-gene operons, napFDAGHBC, encoding the periplasmic nitrate reductase, and nrfABCDEFG, encoding the periplasmic nitrite reductase. No bacterium has yet been shown to couple a periplasmic nitrate reductase solely to the cytoplasmic nitrite reductase NirB. The cytoplasmic pathway for nitrate reduction to ammonia is restricted almost exclusively to a few groups of facultative anaerobic bacteria that encounter high concentrations of environmental nitrate.
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Tengölics R, Mészáros L, Győri E, Doffkay Z, Kovács KL, Rákhely G. Connection between the membrane electron transport system and Hyn hydrogenase in the purple sulfur bacterium, Thiocapsa roseopersicina BBS. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1691-8. [DOI: 10.1016/j.bbabio.2014.07.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 07/26/2014] [Accepted: 07/29/2014] [Indexed: 10/24/2022]
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - James Hall
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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Abstract
Despite its reactivity and hence toxicity to living cells, sulfite is readily converted by various microorganisms using distinct assimilatory and dissimilatory metabolic routes. In respiratory pathways, sulfite either serves as a primary electron donor or terminal electron acceptor (yielding sulfate or sulfide, respectively), and its conversion drives electron transport chains that are coupled to chemiosmotic ATP synthesis. Notably, such processes are also seen to play a general role in sulfite detoxification, which is assumed to have an evolutionary ancient origin. The diversity of sulfite conversion is reflected by the fact that the range of microbial sulfite-converting enzymes displays different cofactors such as siroheme, heme c, or molybdopterin. This chapter aims to summarize the current knowledge of microbial sulfite metabolism and focuses on sulfite catabolism. The structure and function of sulfite-converting enzymes and the emerging picture of the modular architecture of the corresponding respiratory/detoxifying electron transport chains is emphasized.
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Affiliation(s)
- Jörg Simon
- Department of Biology, Microbial Energy Conversion and Biotechnology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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Guiral M, Prunetti L, Aussignargues C, Ciaccafava A, Infossi P, Ilbert M, Lojou E, Giudici-Orticoni MT. The hyperthermophilic bacterium Aquifex aeolicus: from respiratory pathways to extremely resistant enzymes and biotechnological applications. Adv Microb Physiol 2013; 61:125-94. [PMID: 23046953 DOI: 10.1016/b978-0-12-394423-8.00004-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aquifex aeolicus isolated from a shallow submarine hydrothermal system belongs to the order Aquificales which constitute an important component of the microbial communities at elevated temperatures. This hyperthermophilic chemolithoautotrophic bacterium, which utilizes molecular hydrogen, molecular oxygen, and inorganic sulfur compounds to flourish, uses the reductive TCA cycle for CO(2) fixation. In this review, the intricate energy metabolism of A. aeolicus is described. As the chemistry of sulfur is complex and multiple sulfur species can be generated, A. aeolicus possesses a multitude of different enzymes related to the energy sulfur metabolism. It contains also membrane-embedded [NiFe] hydrogenases as well as oxidases enzymes involved in hydrogen and oxygen utilization. We have focused on some of these proteins that have been extensively studied and characterized as super-resistant enzymes with outstanding properties. We discuss the potential use of hydrogenases in an attractive H(2)/O(2) biofuel cell in replacement of chemical catalysts. Using complete genomic sequence and biochemical data, we present here a global view of the energy-generating mechanisms of A. aeolicus including sulfur compounds reduction and oxidation pathways as well as hydrogen and oxygen utilization.
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Affiliation(s)
- Marianne Guiral
- Unité de Bioénergétique et Ingénierie des Protéines, UMR7281-FR3479, CNRS, Aix-Marseille Université, Marseille, France.
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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van Lis R, Nitschke W, Duval S, Schoepp-Cothenet B. Arsenics as bioenergetic substrates. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:176-88. [PMID: 22982475 DOI: 10.1016/j.bbabio.2012.08.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/28/2012] [Accepted: 08/31/2012] [Indexed: 01/24/2023]
Abstract
Although at low concentrations, arsenic commonly occurs naturally as a local geological constituent. Whereas both arsenate and arsenite are strongly toxic to life, a number of prokaryotes use these compounds as electron acceptors or donors, respectively, for bioenergetic purposes via respiratory arsenate reductase, arsenite oxidase and alternative arsenite oxidase. The recent burst in discovered arsenite oxidizing and arsenate respiring microbes suggests the arsenic bioenergetic metabolisms to be anything but exotic. The first goal of the present review is to bring to light the widespread distribution and diversity of these metabolizing pathways. The second goal is to present an evolutionary analysis of these diverse energetic pathways. Taking into account not only the available data on the arsenic metabolizing enzymes and their phylogenetical relatives but also the palaeogeochemical records, we propose a crucial role of arsenite oxidation via arsenite oxidase in primordial life. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Robert van Lis
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, FR3479, F-13402 Marseille Cedex 20, France
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Stoffels L, Krehenbrink M, Berks BC, Unden G. Thiosulfate reduction in Salmonella enterica is driven by the proton motive force. J Bacteriol 2012; 194:475-85. [PMID: 22081391 PMCID: PMC3256639 DOI: 10.1128/jb.06014-11] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 11/01/2011] [Indexed: 11/20/2022] Open
Abstract
Thiosulfate respiration in Salmonella enterica serovar Typhimurium is catalyzed by the membrane-bound enzyme thiosulfate reductase. Experiments with quinone biosynthesis mutants show that menaquinol is the sole electron donor to thiosulfate reductase. However, the reduction of thiosulfate by menaquinol is highly endergonic under standard conditions (ΔE°' = -328 mV). Thiosulfate reductase activity was found to depend on the proton motive force (PMF) across the cytoplasmic membrane. A structural model for thiosulfate reductase suggests that the PMF drives endergonic electron flow within the enzyme by a reverse loop mechanism. Thiosulfate reductase was able to catalyze the combined oxidation of sulfide and sulfite to thiosulfate in a reverse of the physiological reaction. In contrast to the forward reaction the exergonic thiosulfate-forming reaction was PMF independent. Electron transfer from formate to thiosulfate in whole cells occurs predominantly by intraspecies hydrogen transfer.
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Affiliation(s)
- Laura Stoffels
- Institute for Microbiology and Wine Research, Johannes Gutenberg-University of Mainz, Mainz, Germany
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Martin Krehenbrink
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ben C. Berks
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Gottfried Unden
- Institute for Microbiology and Wine Research, Johannes Gutenberg-University of Mainz, Mainz, Germany
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Kern M, Klotz MG, Simon J. The Wolinella succinogenes mcc gene cluster encodes an unconventional respiratory sulphite reduction system. Mol Microbiol 2011; 82:1515-30. [DOI: 10.1111/j.1365-2958.2011.07906.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Majumdar A, Sarkar S. Bioinorganic chemistry of molybdenum and tungsten enzymes: A structural–functional modeling approach. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2010.11.027] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Magalon A, Fedor JG, Walburger A, Weiner JH. Molybdenum enzymes in bacteria and their maturation. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2010.12.031] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Sorokin DY, Detkova EN, Muyzer G. Sulfur-dependent respiration under extremely haloalkaline conditions in soda lake 'acetogens' and the description of Natroniella sulfidigena sp. nov. FEMS Microbiol Lett 2011; 319:88-95. [PMID: 21438913 DOI: 10.1111/j.1574-6968.2011.02272.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Microbial sulfidogenesis is the main dissimilatory anaerobic process in anoxic sediments of extremely haloalkaline soda lakes. In soda lakes with a salinity >2 M of the total Na(+) sulfate reduction is depressed, while thiosulfate- and sulfur-dependent sulfidogenesis may still be very active. Anaerobic enrichments at pH 10 and a salinity of 2-4 M total Na(+) from sediments of hypersaline soda lakes with thiosulfate and elemental sulfur as electron acceptors and simple nonfermentable electron donors resulted in the isolation of two groups of haloalkaliphilic bacteria capable of dissimilatory sulfidogenesis. Both were closely related to obligately heterotrophic fermentative homoacetogens from soda lakes. The salt-tolerant alkaliphilic thiosulfate-reducing isolates were identified as representatives of Tindallia magadiensis, while the extremely natronophilic obligate sulfur/polysulfide-respiring strains belonged to the genus Natroniella and are proposed here as a novel species Natroniella sulfidigena. Despite the close phylogenetic relation to Natroniella acetigena, it drastically differed from the type strain phenotypically (chemolithoautotrophic and acetate-dependent sulfur respiration, absence of acetate as the final metabolic product). Apparently, in the absence of specialized respiratory sulfidogens, primarily fermentative bacteria that are well adapted to extreme salinity may take over an uncharacteristic ecological function. This finding, once again, exemplifies the importance of isolation and phenotypic investigation of pure cultures.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.
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Biochemical characterization of individual components of the Allochromatium vinosum DsrMKJOP transmembrane complex aids understanding of complex function in vivo. J Bacteriol 2010; 192:6369-77. [PMID: 20952577 DOI: 10.1128/jb.00849-10] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The DsrMKJOP transmembrane complex has a most important function in dissimilatory sulfur metabolism and consists of cytoplasmic, periplasmic, and membrane integral proteins carrying FeS centers and b- and c-type cytochromes as cofactors. In this study, the complex was isolated from the purple sulfur bacterium Allochromatium vinosum and individual components were characterized as recombinant proteins. The two integral membrane proteins DsrM and DsrP were successfully produced in Escherichia coli C43(DE3) and C41(DE3), respectively. DsrM was identified as a diheme cytochrome b, and the two hemes were found to be in low-spin state. Their midpoint redox potentials were determined to be +60 and +110 mV. Although no hemes were predicted for DsrP, it was also clearly identified as a b-type cytochrome. To the best of our knowledge, this is the first time that heme binding has been experimentally proven for a member of the NrfD protein family. Both cytochromes were partly reduced after addition of a menaquinol analogue, suggesting interaction with quinones in vivo. DsrO and DsrK were both experimentally proven to be FeS-containing proteins. In addition, DsrK was shown to be membrane associated, and we propose a monotopic membrane anchoring for this protein. Coelution assays provide support for the proposed interaction of DsrK with the soluble cytoplasmic protein DsrC, which might be its substrate. A model for the function of DsrMKJOP in the purple sulfur bacterium A. vinosum is presented.
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Shirodkar S, Reed S, Romine M, Saffarini D. The octahaem SirA catalyses dissimilatory sulfite reduction inShewanella oneidensisMR-1. Environ Microbiol 2010; 13:108-115. [DOI: 10.1111/j.1462-2920.2010.02313.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Characterization of NADH oxidase/NADPH polysulfide oxidoreductase and its unexpected participation in oxygen sensitivity in an anaerobic hyperthermophilic archaeon. J Bacteriol 2010; 192:5192-202. [PMID: 20675490 DOI: 10.1128/jb.00235-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many genomes of anaerobic hyperthermophiles encode multiple homologs of NAD(P)H oxidase that are thought to function in response to oxidative stress. We investigated one of the seven NAD(P)H oxidase homologs (TK1481) in the sulfur-reducing hyperthermophilic archaeon Thermococcus kodakarensis, focusing on the catalytic properties and roles in oxidative-stress defense and sulfur-dependent energy conservation. The recombinant form of TK1481 exhibited both NAD(P)H oxidase and NAD(P)H:polysulfide oxidoreductase activities. The enzyme also possessed low NAD(P)H peroxidase and NAD(P)H:elemental sulfur oxidoreductase activities under anaerobic conditions. A mutant form of the enzyme, in which the putative redox-active residue Cys43 was replaced by Ala, still showed NADH-dependent flavin adenine dinucleotide (FAD) reduction activity. Although it also retained successive oxidase and anaerobic peroxidase activities, the ability to reduce polysulfide and sulfur was completely lost, suggesting the specific reactivity of the Cys43 residue for sulfur. To evaluate the physiological function of TK1481, we constructed a gene deletant, ΔTK1481, and mutant KUTK1481C43A, into which two base mutations altering Cys43 of TK1481 to Ala were introduced. ΔTK1481 exhibited growth properties nearly identical to those of the parent strain, KU216, in sulfur-containing media. Interestingly, in the absence of elemental sulfur, the growth of ΔTK1481 was not affected by dissolved oxygen, whereas the growth of KU216 and KUTK1481C43A was significantly impaired. These results indicate that although TK1481 does not play a critical role in either sulfur reduction or the response to oxidative stress, the NAD(P)H oxidase activity of TK1481 unexpectedly participates in the oxygen sensitivity of the hyperthermophilic archaeon T. kodakarensis in the absence of sulfur.
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Nowicka B, Kruk J. Occurrence, biosynthesis and function of isoprenoid quinones. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1587-605. [PMID: 20599680 DOI: 10.1016/j.bbabio.2010.06.007] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 06/09/2010] [Accepted: 06/14/2010] [Indexed: 12/23/2022]
Abstract
Isoprenoid quinones are one of the most important groups of compounds occurring in membranes of living organisms. These compounds are composed of a hydrophilic head group and an apolar isoprenoid side chain, giving the molecules a lipid-soluble character. Isoprenoid quinones function mainly as electron and proton carriers in photosynthetic and respiratory electron transport chains and these compounds show also additional functions, such as antioxidant function. Most of naturally occurring isoprenoid quinones belong to naphthoquinones or evolutionary younger benzoquinones. Among benzoquinones, the most widespread and important are ubiquinones and plastoquinones. Menaquinones, belonging to naphthoquinones, function in respiratory and photosynthetic electron transport chains of bacteria. Phylloquinone K(1), a phytyl naphthoquinone, functions in the photosynthetic electron transport in photosystem I. Ubiquinones participate in respiratory chains of eukaryotic mitochondria and some bacteria. Plastoquinones are components of photosynthetic electron transport chains of cyanobacteria and plant chloroplasts. Biosynthetic pathway of isoprenoid quinones has been described, as well as their additional, recently recognized, diverse functions in bacterial, plant and animal metabolism.
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Affiliation(s)
- Beatrycze Nowicka
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
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Anaerobic respiration of elemental sulfur and thiosulfate by Shewanella oneidensis MR-1 requires psrA, a homolog of the phsA gene of Salmonella enterica serovar typhimurium LT2. Appl Environ Microbiol 2009; 75:5209-17. [PMID: 19542325 DOI: 10.1128/aem.00888-09] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shewanella oneidensis MR-1, a facultatively anaerobic gammaproteobacterium, respires a variety of anaerobic terminal electron acceptors, including the inorganic sulfur compounds sulfite (SO3(2-)), thiosulfate (S2O3(2-)), tetrathionate (S4O6(2-)), and elemental sulfur (S(0)). The molecular mechanism of anaerobic respiration of inorganic sulfur compounds by S. oneidensis, however, is poorly understood. In the present study, we identified a three-gene cluster in the S. oneidensis genome whose translated products displayed 59 to 73% amino acid similarity to the products of phsABC, a gene cluster required for S(0) and S2O3(2-) respiration by Salmonella enterica serovar Typhimurium LT2. Homologs of phsA (annotated as psrA) were identified in the genomes of Shewanella strains that reduce S(0) and S2O3(2-) yet were missing from the genomes of Shewanella strains unable to reduce these electron acceptors. A new suicide vector was constructed and used to generate a markerless, in-frame deletion of psrA, the gene encoding the putative thiosulfate reductase. The psrA deletion mutant (PSRA1) retained expression of downstream genes psrB and psrC but was unable to respire S(0) or S2O3(2-) as the terminal electron acceptor. Based on these results, we postulate that PsrA functions as the main subunit of the S. oneidensis S2O3(2-) terminal reductase whose end products (sulfide [HS-] or SO3(2-)) participate in an intraspecies sulfur cycle that drives S(0) respiration.
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A molybdopterin oxidoreductase is involved in H2 oxidation in Desulfovibrio desulfuricans G20. J Bacteriol 2009; 191:2675-82. [PMID: 19233927 DOI: 10.1128/jb.01814-08] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three mutants deficient in hydrogen/formate uptake were obtained through screening of a transposon mutant library containing 5,760 mutants of Desulfovibrio desulfuricans G20. Mutations were in the genes encoding the type I tetraheme cytochrome c(3) (cycA), Fe hydrogenase (hydB), and molybdopterin oxidoreductase (mopB). Mutations did not decrease the ability of cells to produce H(2) or formate during growth. Complementation of the cycA and mopB mutants with a plasmid carrying the intact cycA and/or mopB gene and the putative promoter from the parental strain allowed the recovery of H(2) uptake ability, showing that these specific genes are involved in H(2) oxidation. The mop operon encodes a periplasm-facing transmembrane protein complex which may shuttle electrons from periplasmic cytochrome c(3) to the menaquinone pool. Electrons can then be used for sulfate reduction in the cytoplasm.
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Juhnke HD, Hiltscher H, Nasiri HR, Schwalbe H, Lancaster CRD. Production, characterization and determination of the real catalytic properties of the putative 'succinate dehydrogenase' from Wolinella succinogenes. Mol Microbiol 2008; 71:1088-101. [PMID: 19170876 PMCID: PMC2680327 DOI: 10.1111/j.1365-2958.2008.06581.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Both the genomes of the epsilonproteobacteria Wolinella succinogenes and Campylobacter jejuni contain operons (sdhABE) that encode for so far uncharacterized enzyme complexes annotated as ‘non-classical’ succinate:quinone reductases (SQRs). However, the role of such an enzyme ostensibly involved in aerobic respiration in an anaerobic organism such as W. succinogenes has hitherto been unknown. We have established the first genetic system for the manipulation and production of a member of the non-classical succinate:quinone oxidoreductase family. Biochemical characterization of the W. succinogenes enzyme reveals that the putative SQR is in fact a novel methylmenaquinol:fumarate reductase (MFR) with no detectable succinate oxidation activity, clearly indicative of its involvement in anaerobic metabolism. We demonstrate that the hydrophilic subunits of the MFR complex are, in contrast to all other previously characterized members of the superfamily, exported into the periplasm via the twin-arginine translocation (tat)-pathway. Furthermore we show that a single amino acid exchange (Ala86→His) in the flavoprotein of that enzyme complex is the only additional requirement for the covalent binding of the otherwise non-covalently bound FAD. Our results provide an explanation for the previously published puzzling observation that the C. jejuni sdhABE operon is upregulated in an oxygen-limited environment as compared with microaerophilic laboratory conditions.
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Affiliation(s)
- Hanno D Juhnke
- Cluster of Excellence 'Macromolecular Complexes', Max Planck Institute of Biophysics, Department of Molecular Membrane Biology, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
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Simon J, van Spanning RJ, Richardson DJ. The organisation of proton motive and non-proton motive redox loops in prokaryotic respiratory systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1480-90. [DOI: 10.1016/j.bbabio.2008.09.008] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 09/08/2008] [Accepted: 09/09/2008] [Indexed: 10/21/2022]
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