1
|
Noori MT, Rossi R, Logan BE, Min B. Hydrogen production in microbial electrolysis cells with biocathodes. Trends Biotechnol 2024; 42:815-828. [PMID: 38360421 DOI: 10.1016/j.tibtech.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/17/2023] [Accepted: 12/29/2023] [Indexed: 02/17/2024]
Abstract
Electroautotrophic microbes at biocathodes in microbial electrolysis cells (MECs) can catalyze the hydrogen evolution reaction with low energy demand, facilitating long-term stable performance through specific and renewable biocatalysts. However, MECs have not yet reached commercialization due to a lack of understanding of the optimal microbial strains and reactor configurations for achieving high performance. Here, we critically analyze the criteria for the inocula selection, with a focus on the effect of hydrogenase activity and microbe-electrode interactions. We also evaluate the impact of the reactor design and key parameters, such as membrane type, composition, and electrode surface area on internal resistance, mass transport, and pH imbalances within MECs. This analysis paves the way for advancements that could propel biocathode-assisted MECs toward scalable hydrogen gas production.
Collapse
Affiliation(s)
- Md Tabish Noori
- Department of Environmental Science and Engineering, Kyung Hee University - Global Campus, Yongin-Si, South Korea
| | - Ruggero Rossi
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bruce E Logan
- Department of Civil and Environmental Engineering, Penn State University, Pennsylvania, PA 16801, USA
| | - Booki Min
- Department of Environmental Science and Engineering, Kyung Hee University - Global Campus, Yongin-Si, South Korea.
| |
Collapse
|
2
|
Gasteazoro F, Catucci G, Barbieri L, De Angelis M, Dalla Costa A, Sadeghi SJ, Gilardi G, Valetti F. Cascade reactions with two non-physiological partners for NAD(P)H regeneration via renewable hydrogen. Biotechnol J 2024; 19:e2300567. [PMID: 38581100 DOI: 10.1002/biot.202300567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024]
Abstract
An attractive application of hydrogenases, combined with the availability of cheap and renewable hydrogen (i.e., from solar and wind powered electrolysis or from recycled wastes), is the production of high-value electron-rich intermediates such as reduced nicotinamide adenine dinucleotides. Here, the capability of a very robust and oxygen-resilient [FeFe]-hydrogenase (CbA5H) from Clostridium beijerinckii SM10, previously identified in our group, combined with a reductase (BMR) from Bacillus megaterium (now reclassified as Priestia megaterium) was tested. The system shows a good stability and it was demonstrated to reach up to 28 ± 2 nmol NADPH regenerated s-1 mg of hydrogenase-1 (i.e., 1.68 ± 0.12 U mg-1, TOF: 126 ± 9 min-1) and 0.46 ± 0.04 nmol NADH regenerated s-1 mg of hydrogenase-1 (i.e., 0.028 ± 0.002 U mg-1, TOF: 2.1 ± 0.2 min-1), meaning up to 74 mg of NADPH and 1.23 mg of NADH produced per hour by a system involving 1 mg of CbA5H. The TOF is comparable with similar systems based on hydrogen as regenerating molecule for NADPH, but the system is first of its kind as for the [FeFe]-hydrogenase and the non-physiological partners used. As a proof of concept a cascade reaction involving CbA5H, BMR and a mutant BVMO from Acinetobacter radioresistens able to oxidize indole is presented. The data show how the cascade can be exploited for indigo production and multiple reaction cycles can be sustained using the regenerated NADPH.
Collapse
Affiliation(s)
- Francisco Gasteazoro
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
- CICATA Unidad Morelos, Instituto Politécnico Nacional, Mexico D. F., Mexico
| | - Gianluca Catucci
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Lisa Barbieri
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
- University School for Advanced Studies IUSS Pavia, Pavia, Italy
| | - Melissa De Angelis
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | | | - Sheila J Sadeghi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| |
Collapse
|
3
|
DeCola AC, Toppen LC, Brown KP, Dadkhah A, Rizzo DM, Ziels RM, Scarborough MJ. Microbiome assembly and stability during start-up of a full-scale, two-phase anaerobic digester fed cow manure and mixed organic feedstocks. BIORESOURCE TECHNOLOGY 2024; 394:130247. [PMID: 38158092 DOI: 10.1016/j.biortech.2023.130247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Carbon transformations during anaerobic digestion are mediated by complex microbiomes, but their assembly is poorly understood, especially in full-scale digesters. Gene-centric metagenomics combining functional and taxonomic classification was performed for an on-farm digester during start-up. Cow manure and organic waste pre-treated in a hydrolysis tank were fed to the methane-producing digester and the volatile solids loading rate was slowly increased from 0 to 3.5 kg volatile solids m-3 d-1 over one year. The microbial community in the anaerobic digester exhibited a high ratio of archaea, which were dominated by hydrogenotrophic methanogens. Bacteria in the anaerobic digester had a high abundance of genes for ferredoxin cycling, H2 generation, and more metabolically complex fermentations than in the hydrolysis tank. In total, the results show that a functionally stable microbiome was achieved quickly during start-up and that the microbiome created in the low-pH hydrolysis tank did not persist in the downstream anaerobic digester.
Collapse
Affiliation(s)
- Amy C DeCola
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Lucinda C Toppen
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Kennedy P Brown
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Ali Dadkhah
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Donna M Rizzo
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States; Gund Institute for Environment, University of Vermont, Burlington, VT, United States
| | - Ryan M Ziels
- Department of Civil Engineering, University of British Columbia, Vancouver, Canada
| | - Matthew J Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States; Gund Institute for Environment, University of Vermont, Burlington, VT, United States.
| |
Collapse
|
4
|
Hassa J, Tubbesing TJ, Maus I, Heyer R, Benndorf D, Effenberger M, Henke C, Osterholz B, Beckstette M, Pühler A, Sczyrba A, Schlüter A. Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics. Microorganisms 2023; 11:2412. [PMID: 37894070 PMCID: PMC10608942 DOI: 10.3390/microorganisms11102412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.
Collapse
Affiliation(s)
- Julia Hassa
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Tom Jonas Tubbesing
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Irena Maus
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Robert Heyer
- Multidimensional Omics Data Analyses Group, Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, Dortmund 44139, Germany
- Multidimensional Omics Data Analyses Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Dirk Benndorf
- Biosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Straße 55, Postfach 1458, 06366 Köthen, Germany
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Mathias Effenberger
- Bavarian State Research Center for Agriculture, Institute for Agricultural Engineering and Animal Husbandry, Vöttinger Straße 36, 85354 Freising, Germany
| | - Christian Henke
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Benedikt Osterholz
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Michael Beckstette
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Alexander Sczyrba
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Andreas Schlüter
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| |
Collapse
|
5
|
Kpebe A, Guendon C, Payne N, Ros J, Khelil Berbar M, Lebrun R, Baffert C, Shintu L, Brugna M. An essential role of the reversible electron-bifurcating hydrogenase Hnd for ethanol oxidation in Solidesulfovibrio fructosivorans. Front Microbiol 2023; 14:1139276. [PMID: 37051519 PMCID: PMC10084766 DOI: 10.3389/fmicb.2023.1139276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
The tetrameric cytoplasmic FeFe hydrogenase Hnd from Solidesulfovibrio fructosivorans (formely Desulfovibrio fructosovorans) catalyses H2 oxidation and couples the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin by using a flavin-based electron-bifurcating mechanism. Regarding its implication in the bacterial physiology, we previously showed that Hnd, which is non-essential when bacteria grow fermentatively on pyruvate, is involved in ethanol metabolism. Under these conditions, it consumes H2 to produce reducing equivalents for ethanol production as a fermentative product. In this study, the approach implemented was to compare the two S. fructosivorans WT and the hndD deletion mutant strains when grown on ethanol as the sole carbon and energy source. Based on the determination of bacterial growth, metabolite consumption and production, gene expression followed by RT-q-PCR, and Hnd protein level followed by mass spectrometry, our results confirm the role of Hnd hydrogenase in the ethanol metabolism and furthermore uncover for the first time an essential function for a Desulfovibrio hydrogenase. Hnd is unequivocally required for S. fructosivorans growth on ethanol, and we propose that it produces H2 from NADH and reduced ferredoxin generated by an alcohol dehydrogenase and an aldehyde ferredoxin oxidoreductase catalyzing the conversion of ethanol into acetate. The produced H2 could then be recycled and used for sulfate reduction. Hnd is thus a reversible hydrogenase that operates in H2-consumption by an electron-bifurcating mechanism during pyruvate fermentation and in H2-production by an electron-confurcating mechanism when the bacterium uses ethanol as electron donor.
Collapse
Affiliation(s)
| | | | - Natalie Payne
- CNRS, Aix-Marseille Univ, BIP, Marseille, France
- CNRS, Aix-Marseille Univ, Centrale Marseille, ISM2, Marseille, France
| | - Julien Ros
- CNRS, Aix-Marseille Univ, BIP, Marseille, France
| | - Manel Khelil Berbar
- CNRS, Aix-Marseille Univ, Plate-forme Protéomique de l’IMM, FR 3479, Marseille Protéomique (MaP), Marseille, France
| | - Régine Lebrun
- CNRS, Aix-Marseille Univ, Plate-forme Protéomique de l’IMM, FR 3479, Marseille Protéomique (MaP), Marseille, France
| | | | - Laetitia Shintu
- CNRS, Aix-Marseille Univ, Centrale Marseille, ISM2, Marseille, France
| | - Myriam Brugna
- CNRS, Aix-Marseille Univ, BIP, Marseille, France
- *Correspondence: Myriam Brugna,
| |
Collapse
|
6
|
Payne N, Kpebe A, Guendon C, Baffert C, Maillot M, Haurogné T, Tranchida F, Brugna M, Shintu L. NMR-based metabolomic analysis of the physiological role of the electron-bifurcating FeFe-hydrogenase Hnd in Solidesulfovibrio fructosivorans under pyruvate fermentation. Microbiol Res 2023; 268:127279. [PMID: 36592576 DOI: 10.1016/j.micres.2022.127279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Solidesulfovibrio fructosivorans (formely Desulfovibrio fructosovorans), an anaerobic sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases catalyzing the reversible oxidation of hydrogen gas (H2) into protons and electrons. One of these, named Hnd, was demonstrated to be an electron-bifurcating hydrogenase Hnd (Kpebe et al., 2018). It couples the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin with electrons derived from H2 and whose function has been recently shown to be involved in ethanol production under pyruvate fermentation (Payne 2022). To understand further the physiological role of Hnd in S. fructosivorans, we compared the mutant deleted of part of the hnd gene with the wild-type strain grown on pyruvate without sulfate using NMR-based metabolomics. Our results confirm that Hnd is profoundly involved in ethanol metabolism, but also indirectly intervenes in global carbon metabolism and additional metabolic processes such as the biosynthesis of branched-chain amino acids. We also highlight the metabolic reprogramming induced by the deletion of hndD that leads to the upregulation of several NADP-dependent pathways.
Collapse
Affiliation(s)
- Natalie Payne
- Aix Marseille Univ, CNRS, BIP, Marseille, France; Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France
| | | | | | | | | | | | - Fabrice Tranchida
- Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France
| | | | - Laetitia Shintu
- Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France.
| |
Collapse
|
7
|
Prioretti L, D’Ermo G, Infossi P, Kpebe A, Lebrun R, Bauzan M, Lojou E, Guigliarelli B, Giudici-Orticoni MT, Guiral M. Carbon Fixation in the Chemolithoautotrophic Bacterium Aquifex aeolicus Involves Two Low-Potential Ferredoxins as Partners of the PFOR and OGOR Enzymes. Life (Basel) 2023; 13:life13030627. [PMID: 36983784 PMCID: PMC10052474 DOI: 10.3390/life13030627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
Aquifex aeolicus is a microaerophilic hydrogen- and sulfur -oxidizing bacterium that assimilates CO2 via the reverse tricarboxylic acid cycle (rTCA). Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR), which are responsible, respectively, for the reductive carboxylation of acetyl-CoA to pyruvate and of succinyl-CoA to 2-oxoglutarate, two energetically unfavorable reactions that require a strong reduction potential. We have confirmed, by biochemistry and proteomics, that A. aeolicus possesses a pentameric version of these enzyme complexes ((αβγδε)2) and that they are highly abundant in the cell. In addition, we have purified and characterized, from the soluble fraction of A. aeolicus, two low redox potential and oxygen-stable [4Fe-4S] ferredoxins (Fd6 and Fd7, E0 = −440 and −460 mV, respectively) and shown that they can physically interact and exchange electrons with both PFOR and OGOR, suggesting that they could be the physiological electron donors of the system in vivo. Shotgun proteomics indicated that all the enzymes assumed to be involved in the rTCA cycle are produced in the A. aeolicus cells. A number of additional enzymes, previously suggested to be part of a putative partial Wood-Ljungdahl pathway used for the synthesis of serine and glycine from CO2 were identified by mass spectrometry, but their abundance in the cell seems to be much lower than that of the rTCA cycle. Their possible involvement in carbon assimilation is discussed.
Collapse
Affiliation(s)
- Laura Prioretti
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Giulia D’Ermo
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Pascale Infossi
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Arlette Kpebe
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Régine Lebrun
- CNRS, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Marielle Bauzan
- CNRS, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Elisabeth Lojou
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Bruno Guigliarelli
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | | | - Marianne Guiral
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
- Correspondence:
| |
Collapse
|
8
|
Willemin MS, Hamelin R, Armand F, Holliger C, Maillard J. Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms. Front Microbiol 2023; 14:1058127. [PMID: 36733918 PMCID: PMC9888536 DOI: 10.3389/fmicb.2023.1058127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023] Open
Abstract
Introduction Desulfitobacterium hafniense was isolated for its ability to use organohalogens as terminal electron acceptors via organohalide respiration (OHR). In contrast to obligate OHR bacteria, Desulfitobacterium spp. show a highly versatile energy metabolism with the capacity to use different electron donors and acceptors and to grow fermentatively. Desulfitobacterium genomes display numerous and apparently redundant members of redox enzyme families which confirm their metabolic potential. Nonetheless, the enzymes responsible for many metabolic traits are not yet identified. Methods In the present work, we conducted an extended proteomic study by comparing the proteomes of Desulfitobacterium hafniense strain DCB-2 cultivated in combinations of electron donors and acceptors, triggering five alternative respiratory metabolisms that include OHR, as well as fermentation. Tandem Mass Tag labelling proteomics allowed us to identify and quantify almost 60% of the predicted proteome of strain DCB-2 (2,796 proteins) in all six growth conditions. Raw data are available via ProteomeXchange with identifier PXD030393. Results and discussion This dataset was analyzed in order to highlight the proteins that were significantly up-regulated in one or a subset of growth conditions and to identify possible key players in the different energy metabolisms. The addition of sodium sulfide as reducing agent in the medium - a very widespread practice in the cultivation of strictly anaerobic bacteria - triggered the expression of the dissimilatory sulfite reduction pathway in relatively less favorable conditions such as fermentative growth on pyruvate, respiration with H2 as electron donor and OHR conditions. The presence of H2, CO2 and acetate in the medium induced several metabolic pathways involved in carbon metabolism including the Wood-Ljungdahl pathway and two pathways related to the fermentation of butyrate that rely on electron-bifurcating enzymes. While the predicted fumarate reductase appears to be constitutively expressed, a new lactate dehydrogenase and lactate transporters were identified. Finally, the OHR metabolism with 3-chloro-4-hydroxyphenylacetate as electron acceptor strongly induced proteins encoded in several reductive dehalogenase gene clusters, as well as four new proteins related to corrinoid metabolism. We believe that this extended proteomic database represents a new landmark in understanding the metabolic versatility of Desulfitobacterium spp. and provides a solid basis for addressing future research questions.
Collapse
Affiliation(s)
- Mathilde Stéphanie Willemin
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Romain Hamelin
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Armand
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland,*Correspondence: Julien Maillard, ✉
| |
Collapse
|
9
|
Brazelton WJ, McGonigle JM, Motamedi S, Pendleton HL, Twing KI, Miller BC, Lowe WJ, Hoffman AM, Prator CA, Chadwick GL, Anderson RE, Thomas E, Butterfield DA, Aquino KA, Früh-Green GL, Schrenk MO, Lang SQ. Metabolic Strategies Shared by Basement Residents of the Lost City Hydrothermal Field. Appl Environ Microbiol 2022; 88:e0092922. [PMID: 35950875 PMCID: PMC9469722 DOI: 10.1128/aem.00929-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/28/2022] [Indexed: 12/14/2022] Open
Abstract
Alkaline fluids venting from chimneys of the Lost City hydrothermal field flow from a potentially vast microbial habitat within the seafloor where energy and organic molecules are released by chemical reactions within rocks uplifted from Earth's mantle. In this study, we investigated hydrothermal fluids venting from Lost City chimneys as windows into subseafloor environments where the products of geochemical reactions, such as molecular hydrogen (H2), formate, and methane, may be the only available sources of energy for biological activity. Our deep sequencing of metagenomes and metatranscriptomes from these hydrothermal fluids revealed a few key species of archaea and bacteria that are likely to play critical roles in the subseafloor microbial ecosystem. We identified a population of Thermodesulfovibrionales (belonging to phylum Nitrospirota) as a prevalent sulfate-reducing bacterium that may be responsible for much of the consumption of H2 and sulfate in Lost City fluids. Metagenome-assembled genomes (MAGs) classified as Methanosarcinaceae and Candidatus Bipolaricaulota were also recovered from venting fluids and represent potential methanogenic and acetogenic members of the subseafloor ecosystem. These genomes share novel hydrogenases and formate dehydrogenase-like sequences that may be unique to hydrothermal environments where H2 and formate are much more abundant than carbon dioxide. The results of this study include multiple examples of metabolic strategies that appear to be advantageous in hydrothermal and subsurface alkaline environments where energy and carbon are provided by geochemical reactions. IMPORTANCE The Lost City hydrothermal field is an iconic example of a microbial ecosystem fueled by energy and carbon from Earth's mantle. Uplift of mantle rocks into the seafloor can trigger a process known as serpentinization that releases molecular hydrogen (H2) and creates unusual environmental conditions where simple organic carbon molecules are more stable than dissolved inorganic carbon. This study provides an initial glimpse into the kinds of microbes that live deep within the seafloor where serpentinization takes place, by sampling hydrothermal fluids exiting from the Lost City chimneys. The metabolic strategies that these microbes appear to be using are also shared by microbes that inhabit other sites of serpentinization, including continental subsurface environments and natural springs. Therefore, the results of this study contribute to a broader, interdisciplinary effort to understand the general principles and mechanisms by which serpentinization-associated processes can support life on Earth and perhaps other worlds.
Collapse
Affiliation(s)
| | - Julia M. McGonigle
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Shahrzad Motamedi
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Katrina I. Twing
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Briggs C. Miller
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - William J. Lowe
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Cecilia A. Prator
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Grayson L. Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Rika E. Anderson
- Department of Biology, Carleton College, Northfield, Minnesota, USA
| | - Elaina Thomas
- Department of Biology, Carleton College, Northfield, Minnesota, USA
| | - David A. Butterfield
- Joint Institute for the Study of Atmosphere and Ocean, University of Washington, Seattle, Washington, USA
| | | | | | - Matthew O. Schrenk
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Susan Q. Lang
- School of the Earth, Ocean, and Environment, University of South Carolina, Columbia, South Carolina, USA
| |
Collapse
|
10
|
Trutschel LR, Chadwick GL, Kruger B, Blank JG, Brazelton WJ, Dart ER, Rowe AR. Investigation of microbial metabolisms in an extremely high pH marine-like terrestrial serpentinizing system: Ney Springs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155492. [PMID: 35476949 DOI: 10.1016/j.scitotenv.2022.155492] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Ney Springs, a continental serpentinizing spring in northern California, has an exceptionally high reported pH (12.4) for a naturally occurring water source. With high conductivity fluids, it is geochemically more akin to marine serpentinizing systems than other terrestrial locations. Our geochemical analyses also revealed high sulfide concentrations (544 mg/L) and methane emissions (83% volume gas content) relative to other serpentinizing systems. Thermodynamic calculations were used to investigate the potential for substrates resulting from serpentinization to fuel microbial life, and were found to support the energetic feasibility of sulfate reduction, anaerobic methane oxidation, denitrification, and anaerobic sulfide oxidation within this system. Assessment of the microbial community via 16S rRNA taxonomic gene surveys and metagenome sequencing revealed a community composition dominated by poorly characterized members of the Izemoplasmatales and Clostridiales. The genomes of these dominant taxa point to a fermentative lifestyle, though other highly complete (>90%) metagenome assembled genomes support the potential for organisms to perform sulfate reduction, sulfur disproportionation and/or sulfur oxidation (aerobic and anaerobic). Two chemolithoheterotrophs identified in the metagenome, a Halomonas sp. and a Rhodobacteraceae sp., were isolated and shown to oxidize thiosulfate and were capable of growth in conditions up to pH 12.4. Despite being characteristic products of serpentinization reactions, little evidence was seen for hydrogen and methane utilization in the Ney Springs microbial community. Hydrogen is not highly abundant and could be consumed prior to reaching the spring community. Other metabolic strategies may be outcompeted by more energetically favorable heterotrophic or fermentation reactions, or even inhibited by other compounds in the spring such as ammonia. The unique geochemistry of Ney Springs provides an opportunity to study how local geology interacts with serpentinized fluids, while its microbial community can better inform us of the metabolic strategies employed in hyperalkaline environments.
Collapse
Affiliation(s)
- Leah R Trutschel
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Grayson L Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Jennifer G Blank
- Blue Marble Space Institute of Science, Livermore, CA, USA; NASA Ames Research Center in Silicon Valley, Moffett Field, CA, USA
| | | | - Emily R Dart
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Annette R Rowe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
| |
Collapse
|
11
|
Graham JE, Niks D, Zane GM, Gui Q, Hom K, Hille R, Wall JD, Raman CS. How a Formate Dehydrogenase Responds to Oxygen: Unexpected O 2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel E. Graham
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Qin Gui
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - C. S. Raman
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| |
Collapse
|
12
|
Morra S. Fantastic [FeFe]-Hydrogenases and Where to Find Them. Front Microbiol 2022; 13:853626. [PMID: 35308355 PMCID: PMC8924675 DOI: 10.3389/fmicb.2022.853626] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/10/2022] [Indexed: 01/01/2023] Open
Abstract
[FeFe]-hydrogenases are complex metalloenzymes, key to microbial energy metabolism in numerous organisms. During anaerobic metabolism, they dissipate excess reducing equivalents by using protons from water as terminal electron acceptors, leading to hydrogen production. This reaction is coupled to reoxidation of specific redox partners [ferredoxins, NAD(P)H or cytochrome c3], that can be used either individually or simultaneously (via flavin-based electron bifurcation). [FeFe]-hydrogenases also serve additional physiological functions such as H2 uptake (oxidation), H2 sensing, and CO2 fixation. This broad functional spectrum is enabled by a modular architecture and vast genetic diversity, which is not fully explored and understood. This Mini Review summarises recent advancements in identifying and characterising novel [FeFe]-hydrogenases, which has led to expanding our understanding of their multiple roles in metabolism and functional mechanisms. For example, while numerous well-known [FeFe]-hydrogenases are irreversibly damaged by oxygen, some newly discovered enzymes display intrinsic tolerance. These findings demonstrate that oxygen sensitivity varies between different [FeFe]-hydrogenases: in some cases, protection requires the presence of exogenous compounds such as carbon monoxide or sulphide, while in other cases it is a spontaneous built-in mechanism that relies on a reversible conformational change. Overall, it emerges that additional research is needed to characterise new [FeFe]-hydrogenases as this will reveal further details on the physiology and mechanisms of these enzymes that will enable potential impactful applications.
Collapse
Affiliation(s)
- Simone Morra
- Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| |
Collapse
|
13
|
Feng X, Schut GJ, Haja DK, Adams MWW, Li H. Structure and electron transfer pathways of an electron-bifurcating NiFe-hydrogenase. SCIENCE ADVANCES 2022; 8:eabm7546. [PMID: 35213221 PMCID: PMC8880783 DOI: 10.1126/sciadv.abm7546] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Electron bifurcation enables thermodynamically unfavorable biochemical reactions. Four groups of bifurcating flavoenzyme are known and three use FAD to bifurcate. FeFe-HydABC hydrogenase represents the fourth group, but its bifurcation site is unknown. We report cryo-EM structures of the related NiFe-HydABCSL hydrogenase that reversibly oxidizes H2 and couples endergonic reduction of ferredoxin with exergonic reduction of NAD. FMN surrounded by a unique arrangement of iron sulfur clusters forms the bifurcating center. NAD binds to FMN in HydB, and electrons from H2 via HydA to a HydB [4Fe-4S] cluster enable the FMN to reduce NAD. Low-potential electron transfer from FMN to the HydC [2Fe-2S] cluster and subsequent reduction of a uniquely penta-coordinated HydB [2Fe-2S] cluster require conformational changes, leading to ferredoxin binding and reduction by a [4Fe-4S] cluster in HydB. This work clarifies the electron transfer pathways for a large group of hydrogenases underlying many essential functions in anaerobic microorganisms.
Collapse
Affiliation(s)
- Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Gerrit J. Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Dominik K. Haja
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| |
Collapse
|
14
|
Payne N, Kpebe A, Guendon C, Baffert C, Ros J, Lebrun R, Denis Y, Shintu L, Brugna M. The electron-bifurcating FeFe-hydrogenase Hnd is involved in ethanol metabolism in Desulfovibrio fructosovorans grown on pyruvate. Mol Microbiol 2022; 117:907-920. [PMID: 35066935 DOI: 10.1111/mmi.14881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 11/28/2022]
Abstract
Desulfovibrio fructosovorans, a sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases catalyzing the reversible oxidation of H2 into protons and electrons. Among them, Hnd is an electron-bifurcating hydrogenase, coupling the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin with electrons derived from H2 . It was previously hypothesized that its biological function involves the production of NADPH necessary for biosynthetic purposes. However, it was subsequently demonstrated that Hnd is instead a NAD+ -reducing enzyme, thus its specific function has yet to be established. To understand the physiological role of Hnd in D. fructosovorans, we compared the hnd deletion mutant with the wild-type strain grown on pyruvate. Growth, metabolites production and comsumption, and gene expression were compared under three different growth conditions. Our results indicate that hnd is strongly regulated at the transcriptional level and that its deletion has a drastic effect on the expression of genes for two enzymes, an aldehyde ferredoxin oxidoreductase and an alcohol dehydrogenase. We demonstrated here that Hnd is involved in ethanol metabolism when bacteria grow fermentatively and proposed that Hnd might oxidize part of the H2 produced during fermentation generating both NADH and reduced ferredoxin for ethanol production via its electron bifurcation mechanism.
Collapse
Affiliation(s)
| | | | | | | | - Julien Ros
- CNRS, Aix Marseille Univ, BIP, Marseille, France
| | - Régine Lebrun
- CNRS, Aix Marseille Univ, Plate-forme Protéomique de l'IMM, FR 3479, Marseille Protéomique (MaP), Marseille, France
| | - Yann Denis
- CNRS, Aix Marseille Univ, Plate-forme Transcriptomique, Marseille, France
| | - Laetitia Shintu
- CNRS, Aix Marseille Univ, Centrale Marseille, ISM2, Marseille, France
| | | |
Collapse
|
15
|
Williams TJ, Allen MA, Berengut JF, Cavicchioli R. Shedding Light on Microbial "Dark Matter": Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake. Front Microbiol 2021; 12:741077. [PMID: 34707591 PMCID: PMC8542988 DOI: 10.3389/fmicb.2021.741077] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
The potential metabolism and ecological roles of many microbial taxa remain unknown because insufficient genomic data are available to assess their functional potential. Two such microbial "dark matter" taxa are the Candidatus bacterial phyla Cloacimonadota and Omnitrophota, both of which have been identified in global anoxic environments, including (but not limited to) organic-carbon-rich lakes. Using 24 metagenome-assembled genomes (MAGs) obtained from an Antarctic lake (Ace Lake, Vestfold Hills), novel lineages and novel metabolic traits were identified for both phyla. The Cloacimonadota MAGs exhibited a capacity for carbon fixation using the reverse tricarboxylic acid cycle driven by oxidation of hydrogen and sulfur. Certain Cloacimonadota MAGs encoded proteins that possess dockerin and cohesin domains, which is consistent with the assembly of extracellular cellulosome-like structures that are used for degradation of polypeptides and polysaccharides. The Omnitrophota MAGs represented phylogenetically diverse taxa that were predicted to possess a strong biosynthetic capacity for amino acids, nucleosides, fatty acids, and essential cofactors. All of the Omnitrophota were inferred to be obligate fermentative heterotrophs that utilize a relatively narrow range of organic compounds, have an incomplete tricarboxylic acid cycle, and possess a single hydrogenase gene important for achieving redox balance in the cell. We reason that both Cloacimonadota and Omnitrophota form metabolic interactions with hydrogen-consuming partners (methanogens and Desulfobacterota, respectively) and, therefore, occupy specific niches in Ace Lake.
Collapse
Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| |
Collapse
|
16
|
Yuan H, Wang X, Lin TY, Kim J, Liu WT. Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning. Sci Rep 2021; 11:15140. [PMID: 34302023 PMCID: PMC8302695 DOI: 10.1038/s41598-021-94628-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/12/2021] [Indexed: 01/04/2023] Open
Abstract
Interspecies hydrogen transfer (IHT) and direct interspecies electron transfer (DIET) are two syntrophy models for methanogenesis. Their relative importance in methanogenic environments is still unclear. Our recent discovery of a novel species Candidatus Geobacter eutrophica with the genetic potential of IHT and DIET may serve as a model species to address this knowledge gap. To experimentally demonstrate its DIET ability, we performed electrochemical enrichment of Ca. G. eutrophica-dominating communities under 0 and 0.4 V vs. Ag/AgCl based on the presumption that DIET and extracellular electron transfer (EET) share similar metabolic pathways. After three batches of enrichment, Geobacter OTU650, which was phylogenetically close to Ca. G. eutrophica, was outcompeted in the control but remained abundant and active under electrochemical stimulation, indicating Ca. G. eutrophica's EET ability. The high-quality draft genome further showed high phylogenomic similarity with Ca. G. eutrophica, and the genes encoding outer membrane cytochromes and enzymes for hydrogen metabolism were actively expressed. A Bayesian network was trained with the genes encoding enzymes for alcohol metabolism, hydrogen metabolism, EET, and methanogenesis from dominant fermentative bacteria, Geobacter, and Methanobacterium. Methane production could not be accurately predicted when the genes for IHT were in silico knocked out, inferring its more important role in methanogenesis. The genomics-enabled machine learning modeling approach can provide predictive insights into the importance of IHT and DIET.
Collapse
Affiliation(s)
- Heyang Yuan
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA.
| | - Xuehao Wang
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jinha Kim
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA.
| |
Collapse
|
17
|
Yuly JL, Zhang P, Ru X, Terai K, Singh N, Beratan DN. Efficient and reversible electron bifurcation with either normal or inverted potentials at the bifurcating cofactor. Chem 2021. [DOI: 10.1016/j.chempr.2021.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
18
|
Dietrich HM, Kremp F, Öppinger C, Ribaric L, Müller V. Biochemistry of methanol-dependent acetogenesis in Eubacterium callanderi KIST612. Environ Microbiol 2021; 23:4505-4517. [PMID: 34125457 DOI: 10.1111/1462-2920.15643] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/13/2021] [Indexed: 11/26/2022]
Abstract
Methanol is the simplest of all alcohols, is universally distributed in anoxic sediments as a result of plant material decomposition and is constantly attracting attention as an interesting substrate for anaerobes like acetogens that can convert bio-renewable methanol into value-added chemicals. A major drawback in the development of environmentally friendly but economically attractive biotechnological processes is the present lack of information on biochemistry and bioenergetics during methanol conversion in these bacteria. The mesophilic acetogen Eubacterium callanderi KIST612 is naturally able to consume methanol and produce acetate as well as butyrate. To grasp the full potential of methanol-based production of chemicals, we analysed the genes and enzymes involved in methanol conversion to acetate and identified the redox carriers involved. We will display a complete model for methanol-derived acetogenesis and butyrogenesis in Eubacterium callanderi KIST612, tracing the electron transfer routes and shed light on the bioenergetics during the process.
Collapse
Affiliation(s)
- Helge M Dietrich
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Florian Kremp
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Christian Öppinger
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Luna Ribaric
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| |
Collapse
|
19
|
Zuchan K, Baymann F, Baffert C, Brugna M, Nitschke W. The dyad of the Y-junction- and a flavin module unites diverse redox enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148401. [PMID: 33684340 DOI: 10.1016/j.bbabio.2021.148401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 11/26/2022]
Abstract
The concomitant presence of two distinctive polypeptide modules, which we have chosen to denominate as the "Y-junction" and the "flavin" module, is observed in 3D structures of enzymes as functionally diverse as complex I, NAD(P)-dependent [NiFe]-hydrogenases and NAD(P)-dependent formate dehydrogenases. Amino acid sequence conservation furthermore suggests that both modules are also part of NAD(P)-dependent [FeFe]-hydrogenases for which no 3D structure model is available yet. The flavin module harbours the site of interaction with the substrate NAD(P) which exchanges two electrons with a strictly conserved flavin moiety. The Y-junction module typically contains four iron-sulphur centres arranged to form a Y-shaped electron transfer conduit and mediates electron transfer between the flavin module and the catalytic units of the respective enzymes. The Y-junction module represents an electron transfer hub with three potential electron entry/exit sites. The pattern of specific redox centres present both in the Y-junction and the flavin module is correlated to present knowledge of these enzymes' functional properties. We have searched publicly accessible genomes for gene clusters containing both the Y-junction and the flavin module to assemble a comprehensive picture of the diversity of enzymes harbouring this dyad of modules and to reconstruct their phylogenetic relationships. These analyses indicate the presence of the dyad already in the last universal common ancestor and the emergence of complex I's EFG-module out of a subgroup of NAD(P)- dependent formate dehydrogenases.
Collapse
Affiliation(s)
- Kilian Zuchan
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
| | - Frauke Baymann
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
| | - Carole Baffert
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
| | - Myriam Brugna
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France.
| | - Wolfgang Nitschke
- Aix Marseille Univ, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 09, France
| |
Collapse
|
20
|
Jacq-Bailly A, Benvenuti M, Payne N, Kpebe A, Felbek C, Fourmond V, Léger C, Brugna M, Baffert C. Electrochemical Characterization of a Complex FeFe Hydrogenase, the Electron-Bifurcating Hnd From Desulfovibrio fructosovorans. Front Chem 2021; 8:573305. [PMID: 33490032 PMCID: PMC7820892 DOI: 10.3389/fchem.2020.573305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/10/2020] [Indexed: 12/02/2022] Open
Abstract
Hnd, an FeFe hydrogenase from Desulfovibrio fructosovorans, is a tetrameric enzyme that can perform flavin-based electron bifurcation. It couples the oxidation of H2 to both the exergonic reduction of NAD+ and the endergonic reduction of a ferredoxin. We previously showed that Hnd retains activity even when purified aerobically unlike other electron-bifurcating hydrogenases. In this study, we describe the purification of the enzyme under O2-free atmosphere and its biochemical and electrochemical characterization. Despite its complexity due to its multimeric composition, Hnd can catalytically and directly exchange electrons with an electrode. We characterized the catalytic and inhibition properties of this electron-bifurcating hydrogenase using protein film electrochemistry of Hnd by purifying Hnd aerobically or anaerobically, then comparing the electrochemical properties of the enzyme purified under the two conditions via protein film electrochemistry. Hydrogenases are usually inactivated under oxidizing conditions in the absence of dioxygen and can then be reactivated, to some extent, under reducing conditions. We demonstrate that the kinetics of this high potential inactivation/reactivation for Hnd show original properties: it depends on the enzyme purification conditions and varies with time, suggesting the coexistence and the interconversion of two forms of the enzyme. We also show that Hnd catalytic properties (Km for H2, diffusion and reaction at the active site of CO and O2) are comparable to those of standard hydrogenases (those which cannot catalyze electron bifurcation). These results suggest that the presence of the additional subunits, needed for electron bifurcation, changes neither the catalytic behavior at the active site, nor the gas diffusion kinetics but induces unusual rates of high potential inactivation/reactivation.
Collapse
Affiliation(s)
| | | | - Natalie Payne
- CNRS, Aix Marseille University, BIP, Marseille, France
| | - Arlette Kpebe
- CNRS, Aix Marseille University, BIP, Marseille, France
| | | | | | | | - Myriam Brugna
- CNRS, Aix Marseille University, BIP, Marseille, France
| | | |
Collapse
|
21
|
Wise CE, Ledinina AE, Yuly JL, Artz JH, Lubner CE. The role of thermodynamic features on the functional activity of electron bifurcating enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148377. [PMID: 33453185 DOI: 10.1016/j.bbabio.2021.148377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 11/25/2022]
Abstract
Electron bifurcation is a biological mechanism to drive a thermodynamically unfavorable redox reaction through direct coupling with an exergonic reaction. This process allows microorganisms to generate high energy reducing equivalents in order to sustain life and is often found in anaerobic metabolism, where the energy economy of the cell is poor. Recent work has revealed details of the redox energy landscapes for a variety of electron bifurcating enzymes, greatly expanding the understanding of how energy is transformed by this unique mechanism. Here we highlight the plasticity of these emerging landscapes, what is known regarding their mechanistic underpinnings, and provide a context for interpreting their biochemical activity within the physiological framework. We conclude with an outlook for propelling the field toward an integrative understanding of the impact of electron bifurcation.
Collapse
Affiliation(s)
| | | | | | - Jacob H Artz
- National Renewable Energy Laboratory, Golden, CO, USA
| | | |
Collapse
|
22
|
Maus I, Tubbesing T, Wibberg D, Heyer R, Hassa J, Tomazetto G, Huang L, Bunk B, Spröer C, Benndorf D, Zverlov V, Pühler A, Klocke M, Sczyrba A, Schlüter A. The Role of Petrimonas mucosa ING2-E5A T in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses. Microorganisms 2020; 8:E2024. [PMID: 33348776 PMCID: PMC7768429 DOI: 10.3390/microorganisms8122024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/17/2022] Open
Abstract
Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.
Collapse
Affiliation(s)
- Irena Maus
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Tom Tubbesing
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Robert Heyer
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany; (R.H.); (D.B.)
- Database and Software Engineering Group, Department of Computer Science, Institute for Technical and Business Information Systems, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Geizecler Tomazetto
- Biological and Chemical Engineering Section (BCE), Department of Engineering, Aarhus University, 8000 Aarhus, Denmark;
| | - Liren Huang
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Boyke Bunk
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (B.B.); (C.S.)
| | - Cathrin Spröer
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (B.B.); (C.S.)
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Universitätspl. 2, 39106 Magdeburg, Germany; (R.H.); (D.B.)
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106 Magdeburg, Germany
- Microbiology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06354 Köthen, Germany
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany;
- Institute of Molecular Genetics, National Research Centre «Kurchatov Institute», Kurchatov Sq. 2, 123128 Moscow, Russia
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| | - Michael Klocke
- Institute of Agricultural and Urban Ecological Projects Affiliated to Berlin Humboldt University (IASP), Philippstraße 13, 10115 Berlin, Germany;
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany; (T.T.); (L.H.); (A.S.)
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany; (I.M.); (D.W.); (J.H.); (A.P.)
| |
Collapse
|
23
|
Kremp F, Roth J, Müller V. The Sporomusa type Nfn is a novel type of electron-bifurcating transhydrogenase that links the redox pools in acetogenic bacteria. Sci Rep 2020; 10:14872. [PMID: 32913242 PMCID: PMC7483475 DOI: 10.1038/s41598-020-71038-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/07/2020] [Indexed: 11/15/2022] Open
Abstract
Flavin-based electron bifurcation is a long hidden mechanism of energetic coupling present mainly in anaerobic bacteria and archaea that suffer from energy limitations in their environment. Electron bifurcation saves precious cellular ATP and enables lithotrophic life of acetate-forming (acetogenic) bacteria that grow on H2 + CO2 by the only pathway that combines CO2 fixation with ATP synthesis, the Wood–Ljungdahl pathway. The energy barrier for the endergonic reduction of NADP+, an electron carrier in the Wood–Ljungdahl pathway, with NADH as reductant is overcome by an electron-bifurcating, ferredoxin-dependent transhydrogenase (Nfn) but many acetogens lack nfn genes. We have purified a ferredoxin-dependent NADH:NADP+ oxidoreductase from Sporomusa ovata, characterized the enzyme biochemically and identified the encoding genes. These studies led to the identification of a novel, Sporomusa type Nfn (Stn), built from existing modules of enzymes such as the soluble [Fe–Fe] hydrogenase, that is widespread in acetogens and other anaerobic bacteria.
Collapse
Affiliation(s)
- Florian Kremp
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Jennifer Roth
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, 60438, Frankfurt, Germany.
| |
Collapse
|
24
|
Losey NA, Poudel S, Boyd ES, McInerney MJ. The Beta Subunit of Non-bifurcating NADH-Dependent [FeFe]-Hydrogenases Differs From Those of Multimeric Electron-Bifurcating [FeFe]-Hydrogenases. Front Microbiol 2020; 11:1109. [PMID: 32625172 PMCID: PMC7311640 DOI: 10.3389/fmicb.2020.01109] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/04/2020] [Indexed: 12/29/2022] Open
Abstract
A non-bifurcating NADH-dependent, dimeric [FeFe]-hydrogenase (HydAB) from Syntrophus aciditrophicus was heterologously produced in Escherichia coli, purified and characterized. Purified recombinant HydAB catalyzed NAD+ reduction coupled to hydrogen oxidation and produced hydrogen from NADH without the involvement of ferredoxin. Hydrogen partial pressures (2.2-40.2 Pa) produced by the purified recombinant HydAB at NADH to NAD+ ratios of 1-5 were similar to the hydrogen partial pressures generated by pure and cocultures of S. aciditrophicus (5.9-36.6 Pa). Thus, the hydrogen partial pressures observed in metabolizing cultures and cocultures of S. aciditrophicus can be generated by HydAB if S. aciditrophicus maintains NADH to NAD+ ratios greater than one. The flavin-containing beta subunits from S. aciditrophicus HydAB and the non-bifurcating NADH-dependent S. wolfei Hyd1ABC share a number of conserved residues with the flavin-containing beta subunits from non-bifurcating NADH-dependent enzymes such as NADH:quinone oxidoreductases and formate dehydrogenases. A number of differences were observed between sequences of these non-bifurcating NADH-dependent enzymes and [FeFe]-hydrogenases and formate dehydrogenases known to catalyze electron bifurcation including differences in the number of [Fe-S] centers and in conserved residues near predicted cofactor binding sites. These differences can be used to distinguish members of these two groups of enzymes and may be relevant to the differences in ferredoxin-dependence and ability to mediate electron-bifurcation. These results show that two phylogenetically distinct syntrophic fatty acid-oxidizing bacteria, Syntrophomonas wolfei a member of the phylum Firmicutes, and S. aciditrophicus, a member of the class Deltaproteobacteria, possess functionally similar [FeFe]-hydrogenases that produce hydrogen from NADH during syntrophic fatty acid oxidation without the involvement of reduced ferredoxin. The reliance on a non-bifurcating NADH-dependent [FeFe]-hydrogenases may explain the obligate requirement that many syntrophic metabolizers have for a hydrogen-using partner microorganism when grown on fatty, aromatic and alicyclic acids.
Collapse
Affiliation(s)
- Nathaniel A Losey
- Department of Plant Biology and Microbiology, The University of Oklahoma, Norman, OK, United States
| | - Saroj Poudel
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Michael J McInerney
- Department of Plant Biology and Microbiology, The University of Oklahoma, Norman, OK, United States
| |
Collapse
|
25
|
Land H, Senger M, Berggren G, Stripp ST. Current State of [FeFe]-Hydrogenase Research: Biodiversity and Spectroscopic Investigations. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01614] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Henrik Land
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
| | - Moritz Senger
- Physical Chemistry, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
- Bioinorganic Spectroscopy, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Gustav Berggren
- Molecular Biomimetics, Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala 75120, Sweden
| | - Sven T. Stripp
- Bioinorganic Spectroscopy, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| |
Collapse
|
26
|
Chongdar N, Pawlak K, Rüdiger O, Reijerse EJ, Rodríguez-Maciá P, Lubitz W, Birrell JA, Ogata H. Spectroscopic and biochemical insight into an electron-bifurcating [FeFe] hydrogenase. J Biol Inorg Chem 2019; 25:135-149. [PMID: 31823008 PMCID: PMC7064455 DOI: 10.1007/s00775-019-01747-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 11/21/2019] [Indexed: 01/28/2023]
Abstract
Abstract The heterotrimeric electron-bifurcating [FeFe] hydrogenase (HydABC) from Thermotoga maritima (Tm) couples the endergonic reduction of protons (H+) by dihydronicotinamide adenine dinucleotide (NADH) (∆G0 ≈ 18 kJ mol−1) to the exergonic reduction of H+ by reduced ferredoxin (Fdred) (∆G0 ≈ − 16 kJ mol−1). The specific mechanism by which HydABC functions is not understood. In the current study, we describe the biochemical and spectroscopic characterization of TmHydABC recombinantly produced in Escherichia coli and artificially maturated with a synthetic diiron cofactor. We found that TmHydABC catalyzed the hydrogen (H2)-dependent reduction of nicotinamide adenine dinucleotide (NAD+) in the presence of oxidized ferredoxin (Fdox) at a rate of ≈17 μmol NADH min−1 mg−1. Our data suggest that only one flavin is present in the enzyme and is not likely to be the site of electron bifurcation. FTIR and EPR spectroscopy, as well as FTIR spectroelectrochemistry, demonstrated that the active site for H2 conversion, the H-cluster, in TmHydABC behaves essentially the same as in prototypical [FeFe] hydrogenases, and is most likely also not the site of electron bifurcation. The implications of these results are discussed with respect to the current hypotheses on the electron bifurcation mechanism of [FeFe] hydrogenases. Overall, the results provide insight into the electron-bifurcating mechanism and present a well-defined system for further investigations of this fascinating class of [FeFe] hydrogenases. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-019-01747-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nipa Chongdar
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
| | - Krzysztof Pawlak
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Edward J Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Patricia Rodríguez-Maciá
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - James A Birrell
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany.
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany. .,Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan.
| |
Collapse
|
27
|
Slobodkin A, Slobodkina G, Allioux M, Alain K, Jebbar M, Shadrin V, Kublanov I, Toshchakov S, Bonch-Osmolovskaya E. Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres. Genes (Basel) 2019; 10:genes10110849. [PMID: 31717820 PMCID: PMC6896113 DOI: 10.3390/genes10110849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 01/12/2023] Open
Abstract
Information on the biochemical pathways of carbon and energy metabolism in representatives of the deep lineage bacterial phylum Deferribacteres are scarce. Here, we report the results of the sequencing and analysis of the high-quality draft genome of the thermophilic chemolithoautotrophic anaerobe Deferribacter autotrophicus. Genomic data suggest that CO2 assimilation is carried out by recently proposed reversible tricarboxylic acid cycle (“roTCA cycle”). The predicted genomic ability of D. autotrophicus to grow due to the oxidation of carbon monoxide was experimentally proven. CO oxidation was coupled with the reduction of nitrate to ammonium. Utilization of CO most likely involves anaerobic [Ni, Fe]-containing CO dehydrogenase. This is the first evidence of CO oxidation in the phylum Deferribacteres. The genome of D. autotrophicus encodes a Nap-type complex of nitrate reduction. However, the conversion of produced nitrite to ammonium proceeds via a non-canonical pathway with the participation of hydroxylamine oxidoreductase (Hao) and hydroxylamine reductase. The genome contains 17 genes of putative multiheme c-type cytochromes and “e-pilin” genes, some of which are probably involved in Fe(III) reduction. Genomic analysis indicates that the roTCA cycle of CO2 fixation and putative Hao-enabled ammonification may occur in several members of the phylum Deferribacteres.
Collapse
Affiliation(s)
- Alexander Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
- Correspondence:
| | - Galina Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Maxime Allioux
- Univ Brest, CNRS, Ifremer, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, F-29280 Plouzané, France; (M.A.); (K.A.); (M.J.)
| | - Karine Alain
- Univ Brest, CNRS, Ifremer, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, F-29280 Plouzané, France; (M.A.); (K.A.); (M.J.)
| | - Mohamed Jebbar
- Univ Brest, CNRS, Ifremer, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, F-29280 Plouzané, France; (M.A.); (K.A.); (M.J.)
| | - Valerian Shadrin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Stepan Toshchakov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Elizaveta Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| |
Collapse
|
28
|
Baffert C, Kpebe A, Avilan L, Brugna M. Hydrogenases and H 2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus. Adv Microb Physiol 2019; 74:143-189. [PMID: 31126530 DOI: 10.1016/bs.ampbs.2019.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H2 metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H2 metabolism.
Collapse
Affiliation(s)
- Carole Baffert
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Arlette Kpebe
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Luisana Avilan
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Myriam Brugna
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| |
Collapse
|
29
|
Clostridial whole cell and enzyme systems for hydrogen production: current state and perspectives. Appl Microbiol Biotechnol 2018; 103:567-575. [PMID: 30446778 DOI: 10.1007/s00253-018-9514-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
Abstract
Strictly anaerobic bacteria of the Clostridium genus have attracted great interest as potential cell factories for molecular hydrogen production purposes. In addition to being a useful approach to this process, dark fermentation has the advantage of using the degradation of cheap agricultural residues and industrial wastes for molecular hydrogen production. However, many improvements are still required before large-scale hydrogen production from clostridial metabolism is possible. Here we review the literature on the basic biological processes involved in clostridial hydrogen production, and present the main advances obtained so far in order to enhance the hydrogen productivity, as well as suggesting some possible future prospects.
Collapse
|