1
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Gemmecker Y, Winiarska A, Hege D, Kahnt J, Seubert A, Szaleniec M, Heider J. A pH-dependent shift of redox cofactor specificity in a benzyl alcohol dehydrogenase of aromatoleum aromaticum EbN1. Appl Microbiol Biotechnol 2024; 108:410. [PMID: 38976076 PMCID: PMC11231019 DOI: 10.1007/s00253-024-13225-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/09/2024]
Abstract
We characterise a reversible bacterial zinc-containing benzyl alcohol dehydrogenase (BaDH) accepting either NAD+ or NADP+ as a redox cofactor. Remarkably, its redox cofactor specificity is pH-dependent with the phosphorylated cofactors favored at lower and the dephospho-forms at higher pH. BaDH also shows different steady-state kinetic behavior with the two cofactor forms. From a structural model, the pH-dependent shift may affect the charge of a histidine in the 2'-phosphate-binding pocket of the redox cofactor binding site. The enzyme is phylogenetically affiliated to a new subbranch of the Zn-containing alcohol dehydrogenases, which share this conserved residue. BaDH appears to have some specificity for its substrate, but also turns over many substituted benzyl alcohol and benzaldehyde variants, as well as compounds containing a conjugated C=C double bond with the aldehyde carbonyl group. However, compounds with an sp3-hybridised C next to the alcohol/aldehyde group are not or only weakly turned over. The enzyme appears to contain a Zn in its catalytic site and a mixture of Zn and Fe in its structural metal-binding site. Moreover, we demonstrate the use of BaDH in an enzyme cascade reaction with an acid-reducing tungsten enzyme to reduce benzoate to benzyl alcohol. KEY POINTS: •Zn-containing BaDH has activity with either NAD + or NADP+ at different pH optima. •BaDH converts a broad range of substrates. •BaDH is used in a cascade reaction for the reduction of benzoate to benzyl alcohol.
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Affiliation(s)
- Yvonne Gemmecker
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Agnieszka Winiarska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland
| | - Dominik Hege
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany
| | - Jörg Kahnt
- Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Andreas Seubert
- Faculty of Chemistry, Analytical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.
| | - Johann Heider
- Laboratory for Microbial Biochemistry, Philipps University of Marburg, 35043, Marburg, Germany.
- Center for Synthetic Microbiology, Marburg, Germany.
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2
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Tataruch M, Illeová V, Kluza A, Cabadaj P, Polakovič M. Catalytic Stability of S-1-(4-Hydroxyphenyl)-Ethanol Dehydrogenase from Aromatoleum aromaticum. Int J Mol Sci 2024; 25:7385. [PMID: 39000491 PMCID: PMC11242144 DOI: 10.3390/ijms25137385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Derived from the denitrifying bacterium Aromatoleum aromaticum EbN1 (Azoarcus sp.), the enzyme S-1-(4-hydroxyphenyl)-ethanol dehydrogenase (S-HPED) belongs to the short-chain dehydrogenase/reductase family. Using research techniques like UV-Vis spectroscopy, dynamic light scattering, thermal-shift assay and HPLC, we investigated the catalytic and structural stability of S-HPED over a wide temperature range and within the pH range of 5.5 to 9.0 under storage and reaction conditions. The relationship between aggregation and inactivation of the enzyme in various pH environments was also examined and interpreted. At pH 9.0, where the enzyme exhibited no aggregation, we characterized thermally induced enzyme inactivation. Through isothermal and multitemperature analysis of inactivation data, we identified and confirmed the first-order inactivation mechanism under these pH conditions and determined the kinetic parameters of the inactivation process. Additionally, we report the positive impact of glucose as an enzyme stabilizer, which slows down the dynamics of S-HPED inactivation over a wide range of pH and temperature and limits enzyme aggregation. Besides characterizing the stability of S-HPED, the enzyme's catalytic activity and high stereospecificity for 10 prochiral carbonyl compounds were positively verified, thus expanding the spectrum of substrates reduced by S-HPED. Our research contributes to advancing knowledge about the biocatalytic potential of this catalyst.
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Affiliation(s)
- Mateusz Tataruch
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland; (M.T.); (A.K.)
| | - Viera Illeová
- Institute of Chemical and Environmental Engineering, Slovak Technical University, Radlinského 9, 812 37 Bratislava, Slovakia; (V.I.); (P.C.)
| | - Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland; (M.T.); (A.K.)
| | - Patrik Cabadaj
- Institute of Chemical and Environmental Engineering, Slovak Technical University, Radlinského 9, 812 37 Bratislava, Slovakia; (V.I.); (P.C.)
| | - Milan Polakovič
- Institute of Chemical and Environmental Engineering, Slovak Technical University, Radlinského 9, 812 37 Bratislava, Slovakia; (V.I.); (P.C.)
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3
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Nissen LS, Moon J, Hitschler L, Basen M. A Versatile Aldehyde: Ferredoxin Oxidoreductase from the Organic Acid Reducing Thermoanaerobacter sp. Strain X514. Int J Mol Sci 2024; 25:1077. [PMID: 38256150 PMCID: PMC10816221 DOI: 10.3390/ijms25021077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Aldehyde:ferredoxin oxidoreductases (AORs) have been isolated and biochemically-characterized from a handful of anaerobic or facultative aerobic archaea and bacteria. They catalyze the ferredoxin (Fd)-dependent oxidation of aldehydes to acids. Recently, the involvement of AOR in the reduction of organic acids to alcohols with electrons derived from sugar or synthesis gas was demonstrated, with alcohol dehydrogenases (ADHs) carrying out the reduction of the aldehyde to the alcohol (AOR-ADH pathway). Here, we describe the biochemical characterization of an AOR of the thermophilic fermentative bacterium Thermoanaerobacter sp. strain X514 (AORX514). The putative aor gene (Teth514_1380) including a 6x-His-tag was introduced into the genome of the genetically-accessible, related species Thermoanaerobacter kivui. The protein was purified to apparent homogeneity, and indeed revealed AOR activity, as measured by acetaldehyde-dependent ferredoxin reduction. AORX514 was active over a wide temperature (10 to 95 °C) and pH (5.5 to 11.5) range, utilized a wide variety of aldehydes (short and branched-chained, aliphatic, aromatic) and resembles archaeal sensu stricto AORs, as the protein is active in a homodimeric form. The successful, recombinant production of AORX514 in a related, well-characterized and likewise strict anaerobe paves the road towards structure-function analyses of this enzyme and possibly similar oxygen-sensitive or W/Mo-dependent proteins in the future.
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Affiliation(s)
- Laura Sofie Nissen
- Microbiology, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany;
| | - Jimyung Moon
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt/Main, Germany; (J.M.)
| | - Lisa Hitschler
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt/Main, Germany; (J.M.)
| | - Mirko Basen
- Microbiology, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany;
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt/Main, Germany; (J.M.)
- Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, 18059 Rostock, Germany
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4
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Winiarska A, Ramírez-Amador F, Hege D, Gemmecker Y, Prinz S, Hochberg G, Heider J, Szaleniec M, Schuller JM. A bacterial tungsten-containing aldehyde oxidoreductase forms an enzymatic decorated protein nanowire. SCIENCE ADVANCES 2023; 9:eadg6689. [PMID: 37267359 PMCID: PMC10413684 DOI: 10.1126/sciadv.adg6689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/28/2023] [Indexed: 06/04/2023]
Abstract
Aldehyde oxidoreductases (AORs) are tungsten enzymes catalyzing the oxidation of many different aldehydes to the corresponding carboxylic acids. In contrast to other known AORs, the enzyme from the denitrifying betaproteobacterium Aromatoleum aromaticum (AORAa) consists of three different subunits (AorABC) and uses nicotinamide adenine dinucleotide (NAD) as an electron acceptor. Here, we reveal that the enzyme forms filaments of repeating AorAB protomers that are capped by a single NAD-binding AorC subunit, based on solving its structure via cryo-electron microscopy. The polyferredoxin-like subunit AorA oligomerizes to an electron-conducting nanowire that is decorated with enzymatically active and W-cofactor (W-co) containing AorB subunits. Our structure further reveals the binding mode of the native substrate benzoate in the AorB active site. This, together with quantum mechanics:molecular mechanics (QM:MM)-based modeling for the coordination of the W-co, enables formulation of a hypothetical catalytic mechanism that paves the way to further engineering for applications in synthetic biology and biotechnology.
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Affiliation(s)
- Agnieszka Winiarska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków, Poland
| | - Fidel Ramírez-Amador
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
| | - Dominik Hege
- Faculty of Biology, Philipps-University of Marburg, Marburg, Germany
| | - Yvonne Gemmecker
- Faculty of Biology, Philipps-University of Marburg, Marburg, Germany
| | - Simone Prinz
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Georg Hochberg
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Johann Heider
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
- Faculty of Biology, Philipps-University of Marburg, Marburg, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków, Poland
| | - Jan Michael Schuller
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University of Marburg, Marburg, Germany
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5
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Tataruch M, Illeová V, Miłaczewska A, Borowski T, Mihal' M, Polakovič M. Inactivation and aggregation of R-specific 1-(4-hydroxyphenyl)-ethanol dehydrogenase from Aromatoleum aromaticum. Int J Biol Macromol 2023; 234:123772. [PMID: 36812967 DOI: 10.1016/j.ijbiomac.2023.123772] [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: 07/23/2022] [Revised: 12/11/2022] [Accepted: 02/15/2023] [Indexed: 02/22/2023]
Abstract
R-specific 1-(4-hydroxyphenyl)-ethanol dehydrogenase (R-HPED) is a promising biotool for stereoselective synthesis of chiral aromatic alcohols. This work focused on the evaluation of its stability under storage and in-process conditions in the pH range from 5.5 to 8.5. The relationship between the dynamics of aggregation and activity loss under various pH conditions and in the presence of glucose, serving as a stabilizer, was analysed using spectrophotometric techniques and dynamic light scattering. pH 8.5 was indicated as a representative environment in which the enzyme, despite relatively low activity, shows high stability and the highest total product yield. Based on a series of inactivation experiments, the mechanism of thermal inactivation at pH 8.5 was modelled. The irreversible first-order mechanism of R-HPED inactivation in the temperature range of 47.5-60 °C was verified by isothermal and multi-temperature evaluation of data, confirming that in the alkaline pH 8.5, R-HPED aggregation is the secondary process occurring at already inactivated protein molecules. The rate constants were from 0.029 min-1 to 0.380 min-1 for a buffer solution but they decreased to 0.011 min-1 and 0.161 min-1, respectively, when 1.5 M glucose was added as a stabilizer. The activation energy was however about 200 kJ mol-1 in both cases.
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Affiliation(s)
- Mateusz Tataruch
- Institute of Chemical and Environmental Engineering, Slovak Technical University, Radlinského 9, 812 37 Bratislava, Slovakia; Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, PL-30-239 Krakow, Poland
| | - Viera Illeová
- Institute of Chemical and Environmental Engineering, Slovak Technical University, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Anna Miłaczewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, PL-30-239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, PL-30-239 Krakow, Poland
| | - Mario Mihal'
- Institute of Chemical and Environmental Engineering, Slovak Technical University, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Milan Polakovič
- Institute of Chemical and Environmental Engineering, Slovak Technical University, Radlinského 9, 812 37 Bratislava, Slovakia.
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6
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Shalygin MG, Kozlova AA, Heider J, Sapegin DA, Netrusov AA, Teplyakov VV. Polymeric Membranes for Vapor-Phase Concentrating Volatile Organic Products from Biomass Processing. MEMBRANES AND MEMBRANE TECHNOLOGIES 2023. [DOI: 10.1134/s2517751623010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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7
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Systems Biology of Aromatic Compound Catabolism in Facultative Anaerobic Aromatoleum aromaticum EbN1 T. mSystems 2022; 7:e0068522. [PMID: 36445109 PMCID: PMC9765128 DOI: 10.1128/msystems.00685-22] [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] [Indexed: 12/03/2022] Open
Abstract
Members of the genus Aromatoleum thrive in diverse habitats and use a broad range of recalcitrant organic molecules coupled to denitrification or O2 respiration. To gain a holistic understanding of the model organism A. aromaticum EbN1T, we studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate, and acetate utilized under nitrate-reducing versus oxic conditions. Integrated multi-omics (transcriptome, proteome, and metabolome) covered most of the catabolic network (199 genes) and allowed for the refining of knowledge of the degradation modules studied. Their substrate-dependent regulation showed differing degrees of specificity, ranging from high with 3-(4-hydroxyphenyl)propanoate to mostly relaxed with benzoate. For benzoate, the transcript and protein formation were essentially constitutive, contrasted by that of anoxia-specific versus oxia-specific metabolite profiles. The matrix factorization of transcriptomic data revealed that the anaerobic modules accounted for most of the variance across the degradation network. The respiration network appeared to be constitutive, both on the transcript and protein levels, except for nitrate reductase (with narGHI expression occurring only under nitrate-reducing conditions). The anoxia/nitrate-dependent transcription of denitrification genes is apparently controlled by three FNR-type regulators as well as by NarXL (all constitutively formed). The resequencing and functional reannotation of the genome fostered a genome-scale metabolic model, which is comprised of 655 enzyme-catalyzed reactions and 731 distinct metabolites. The model predictions for growth rates and biomass yields agreed well with experimental stoichiometric data, except for 3-(4-hydroxyphenyl)propanoate, with which 4-hydroxybenzoate was exported. Taken together, the combination of multi-omics, growth physiology, and a metabolic model advanced our knowledge of an environmentally relevant microorganism that differs significantly from other bacterial model strains. IMPORTANCE Aromatic compounds are abundant constituents not only of natural organic matter but also of bulk industrial chemicals and fuel components of environmental concern. Considering the widespread occurrence of redox gradients in the biosphere, facultative anaerobic degradation specialists can be assumed to play a prominent role in the natural mineralization of organic matter and in bioremediation at contaminated sites. Surprisingly, differential multi-omics profiling of the A. aromaticum EbN1T studied here revealed relaxed regulatory stringency across its four main physiological modi operandi (i.e., O2-independent and O2-dependent degradation reactions versus denitrification and O2 respiration). Combining multi-omics analyses with a genome-scale metabolic model aligned with measured growth performances establishes A. aromaticum EbN1T as a systems-biology model organism and provides unprecedented insights into how this bacterium functions on a holistic level. Moreover, this experimental platform invites future studies on eco-systems and synthetic biology of the environmentally relevant betaproteobacterial Aromatoleum/Azoarcus/Thauera cluster.
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8
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Thorgersen MP, Schut GJ, Poole FL, Haja DK, Putumbaka S, Mycroft HI, de Vries WJ, Adams MWW. Obligately aerobic human gut microbe expresses an oxygen resistant tungsten-containing oxidoreductase for detoxifying gut aldehydes. Front Microbiol 2022; 13:965625. [PMID: 36051760 PMCID: PMC9424855 DOI: 10.3389/fmicb.2022.965625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Brevibacillus massiliensis strain phR is an obligately aerobic microbe that was isolated from human feces. Here, we show that it readily takes up tungsten (W), a metal previously associated only with anaerobes. The W is incorporated into an oxidoreductase enzyme (BmWOR) that was purified from native biomass. BmWOR consists of a single 65 kDa subunit and contains a single W-pyranopterin cofactor and a single [4Fe-4S] cluster. It exhibited high aldehyde-oxidizing activity with very high affinities (apparent Km < 6 μM) for aldehydes common in the human gut and in cooked foods, including furfural, propionaldehyde, benzaldehyde and tolualdehyde, suggesting that BmWOR plays a key role in their detoxification. B. massiliensis converted added furfural to furoic acid when grown in the presence of W, but not in the presence of the analogous element molybdenum. B. massiliensis ferredoxin (BmFd) served as the electron acceptor (apparent Km < 5 μM) for BmWOR suggesting it is the physiological electron carrier. Genome analysis revealed a Fd-dependent rather than NADH-dependent Complex I, suggesting that WOR not only serves a detoxification role but its aldehyde substrates could also serve as a source of energy. BmWOR is the first tungstoenzyme and the first member of the WOR family to be obtained from a strictly aerobic microorganism. Remarkably, BmWOR oxidized furfural in the presence of air (21% O2, v/v) but only if BmFd was also present. BmWOR is the first characterized member of the Clade 83 WORs, which are predominantly found in extremely halophilic and aerobic archaea (Clade 83A), with many isolated from food sources, while the remaining bacterial members (Clade 83B) include both aerobes and anaerobes. The potential advantages for microbes found in foods and involved in human gut health that harbor O2-resistant WORs, including in Bacillus and Brevibacillus based-probiotics, are discussed.
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9
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Winiarska A, Hege D, Gemmecker Y, Kryściak-Czerwenka J, Seubert A, Heider J, Szaleniec M. Tungsten Enzyme Using Hydrogen as an Electron Donor to Reduce Carboxylic Acids and NAD . ACS Catal 2022; 12:8707-8717. [PMID: 35874620 PMCID: PMC9295118 DOI: 10.1021/acscatal.2c02147] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Tungsten-dependent
aldehyde oxidoreductases (AORs) catalyze the
oxidation of aldehydes to acids and are the only known enzymes reducing
non-activated acids using electron donors with low redox potentials.
We report here that AOR from Aromatoleum aromaticum (AORAa) catalyzes the reduction of organic
acids not only with low-potential Eu(II) or Ti(III) complexes but
also with H2 as an electron donor. Additionally, AORAa catalyzes the H2-dependent reduction
of NAD+ or benzyl viologen. The rate of H2-dependent
NAD+ reduction equals to 10% of that of aldehyde oxidation,
representing the highest H2 turnover rate observed among
the Mo/W enzymes. As AORAa simultaneously
catalyzes the reduction of acids and NAD+, we designed
a cascade reaction utilizing a NAD(P)H-dependent alcohol dehydrogenase
to reduce organic acids to the corresponding alcohols with H2 as the only reductant. The newly discovered W-hydrogenase side activity
of AORAa may find applications in either
NADH recycling or conversion of carboxylic acids to more useful biochemicals.
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Affiliation(s)
- Agnieszka Winiarska
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
| | - Dominik Hege
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Yvonne Gemmecker
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Joanna Kryściak-Czerwenka
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
| | - Andreas Seubert
- Faculty of Chemistry, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Johann Heider
- Faculty of Biology, Philipps-Universität Marburg, Marburg D-35043, Germany.,Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg D-35043, Germany
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Kraków 30-239, Poland
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10
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Reji L, Cardarelli EL, Boye K, Bargar JR, Francis CA. Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics. THE ISME JOURNAL 2022; 16:1140-1152. [PMID: 34873295 PMCID: PMC8940955 DOI: 10.1038/s41396-021-01167-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 11/17/2021] [Accepted: 11/26/2021] [Indexed: 02/03/2023]
Abstract
The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.
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Affiliation(s)
- Linta Reji
- grid.168010.e0000000419368956Department of Earth System Science, Stanford University, Stanford, CA USA ,grid.16750.350000 0001 2097 5006Present Address: Department of Geosciences, Princeton University, Princeton, NJ USA
| | - Emily L. Cardarelli
- grid.168010.e0000000419368956Department of Earth System Science, Stanford University, Stanford, CA USA ,grid.20861.3d0000000107068890Present Address: Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Kristin Boye
- grid.445003.60000 0001 0725 7771Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - John R. Bargar
- grid.445003.60000 0001 0725 7771Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Christopher A. Francis
- grid.168010.e0000000419368956Department of Earth System Science, Stanford University, Stanford, CA USA
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11
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González PJ, Rivas MG, Ferroni FM, Rizzi AC, Brondino CD. Electron transfer pathways and spin–spin interactions in Mo- and Cu-containing oxidoreductases. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Tungsten enzymes play a role in detoxifying food and antimicrobial aldehydes in the human gut microbiome. Proc Natl Acad Sci U S A 2021; 118:2109008118. [PMID: 34686601 DOI: 10.1073/pnas.2109008118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/20/2022] Open
Abstract
Tungsten (W) is a metal that is generally thought to be seldom used in biology. We show here that a W-containing oxidoreductase (WOR) family is diverse and widespread in the microbial world. Surprisingly, WORs, along with the tungstate-specific transporter Tup, are abundant in the human gut microbiome, which contains 24 phylogenetically distinct WOR types. Two model gut microbes containing six types of WOR and Tup were shown to assimilate W. Two of the WORs were natively purified and found to contain W. The enzymes catalyzed the conversion of toxic aldehydes to the corresponding acid, with one WOR carrying out an electron bifurcation reaction coupling aldehyde oxidation to the simultaneous reduction of NAD+ and of the redox protein ferredoxin. Such aldehydes are present in cooked foods and are produced as antimicrobials by gut microbiome metabolism. This aldehyde detoxification strategy is dependent on the availability of W to the microbe. The functions of other WORs in the gut microbiome that do not oxidize aldehydes remain unknown. W is generally beyond detection (<6 parts per billion) in common foods and at picomolar concentrations in drinking water, suggesting that W availability could limit some gut microbial functions and might be an overlooked micronutrient.
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13
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Sproules S. Oxo versus Sulfido Coordination at Tungsten: A Spectroscopic and Correlated Ab Initio Electronic Structure Study. Inorg Chem 2021; 60:9057-9063. [PMID: 34096284 DOI: 10.1021/acs.inorgchem.1c01055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tungsten ion that resides at the active site of a unique class of enzymes only found in esoteric hyperthermophilic archaea bacteria is known to possess at least one terminal chalcogenide ligand. The identity of this as either an oxo or sulfido (or both) is difficult to ascertain from structural studies; therefore, small-molecule analogues are developed to calibrate and substantiate spectroscopic signatures obtained from native proteins. The electronic structures of Tp*WECl2 (E = O, S; Tp* = hydrotris(3,5-dimethylpyrazol-1-yl)borate) have been scrutinized using electronic, electron paramagnetic resonance (EPR), and X-ray absorption spectroscopy to assess the impact of terminal chalcogen on the adjacent cis chloride ligands. Examination at the Cl K-edge provides a direct probe of the bonding and therein lability of these chloride ligands, and in conjunction with density functional theoretical and multireference calculations reveals greater bond covalency in Tp*WOCl2 compared to Tp*WSCl2. The computational model and electronic structure assignment are corroborated by the reproduction of spin-Hamiltonian parameters, whose magnitude is dominated by the sizeable spin-orbit coupling of tungsten.
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Affiliation(s)
- Stephen Sproules
- WestCHEM, School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
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Abstract
Tungsten is the heaviest element used in biological systems. It occurs in the active sites of several bacterial or archaeal enzymes and is ligated to an organic cofactor (metallopterin or metal binding pterin; MPT) which is referred to as tungsten cofactor (Wco). Wco-containing enzymes are found in the dimethyl sulfoxide reductase (DMSOR) and the aldehyde:ferredoxin oxidoreductase (AOR) families of MPT-containing enzymes. Some depend on Wco, such as aldehyde oxidoreductases (AORs), class II benzoyl-CoA reductases (BCRs) and acetylene hydratases (AHs), whereas others may incorporate either Wco or molybdenum cofactor (Moco), such as formate dehydrogenases, formylmethanofuran dehydrogenases or nitrate reductases. The obligately tungsten-dependent enzymes catalyze rather unusual reactions such as ones with extremely low-potential electron transfers (AOR, BCR) or an unusual hydration reaction (AH). In recent years, insights into the structure and function of many tungstoenzymes have been obtained. Though specific and unspecific ABC transporter uptake systems have been described for tungstate and molybdate, only little is known about further discriminative steps in Moco and Wco biosynthesis. In bacteria producing Moco- and Wco-containing enzymes simultaneously, paralogous isoforms of the metal insertase MoeA may be specifically involved in the molybdenum- and tungsten-insertion into MPT, and in targeting Moco or Wco to their respective apo-enzymes. Wco-containing enzymes are of emerging biotechnological interest for a number of applications such as the biocatalytic reduction of CO2, carboxylic acids and aromatic compounds, or the conversion of acetylene to acetaldehyde.
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Nissen LS, Basen M. The emerging role of aldehyde:ferredoxin oxidoreductases in microbially-catalyzed alcohol production. J Biotechnol 2019; 306:105-117. [DOI: 10.1016/j.jbiotec.2019.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022]
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Two Different Quinohemoprotein Amine Dehydrogenases Initiate Anaerobic Degradation of Aromatic Amines in Aromatoleum aromaticum EbN1. J Bacteriol 2019; 201:JB.00281-19. [PMID: 31138631 DOI: 10.1128/jb.00281-19] [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: 04/18/2019] [Accepted: 05/23/2019] [Indexed: 11/20/2022] Open
Abstract
Aromatic amines like 2-phenylethylamine (2-PEA) and benzylamine (BAm) have been identified as novel growth substrates of the betaproteobacterium Aromatoleum aromaticum EbN1, which degrades a wide variety of aromatic compounds in the absence of oxygen under denitrifying growth conditions. The catabolic pathway of these amines was identified, starting with their oxidative deamination to the corresponding aldehydes, which are then further degraded via the enzymes of the phenylalanine or benzyl alcohol metabolic pathways. Two different periplasmic quinohemoprotein amine dehydrogenases involved in 2-PEA or BAm metabolism were identified and characterized. Both enzymes consist of three subunits, contain two heme c cofactors in their α-subunits, and exhibit extensive processing of their γ-subunits, generating four intramolecular thioether bonds and a cysteine tryptophylquinone (CTQ) cofactor. One of the enzymes was present in cells grown with 2-PEA or other substrates, showed an α2β2γ2 composition, and had a rather broad substrate spectrum, which included 2-PEA, BAm, tyramine, and 1-butylamine. In contrast, the other enzyme was specifically induced in BAm-grown cells, showing an αβγ composition and activity only with BAm and 2-PEA. Since the former enzyme showed the highest catalytic efficiency with 2-PEA and the latter with BAm, they were designated 2-PEADH and benzylamine dehydrogenase (BAmDH). The catalytic properties and inhibition patterns of 2-PEADH and BAmDH showed considerable differences and were compared to previously characterized quinohemoproteins of the same enzyme family.IMPORTANCE The known substrate spectrum of A. aromaticum EbN1 is expanded toward aromatic amines, which are metabolized as sole substrates coupled to denitrification. The characterization of the two quinohemoprotein isoenzymes involved in degrading either 2-PEA or BAm expands the knowledge of this enzyme family and establishes for the first time that the necessary maturation of their quinoid CTQ cofactors does not require the presence of molecular oxygen. Moreover, the study revealed a highly interesting regulatory phenomenon, suggesting that growth with BAm leads to a complete replacement of 2-PEADH by BAmDH, which has considerably different catalytic and inhibition properties.
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Scott IM, Rubinstein GM, Poole FL, Lipscomb GL, Schut GJ, Williams-Rhaesa AM, Stevenson DM, Amador-Noguez D, Kelly RM, Adams MWW. The thermophilic biomass-degrading bacterium Caldicellulosiruptor bescii utilizes two enzymes to oxidize glyceraldehyde 3-phosphate during glycolysis. J Biol Chem 2019; 294:9995-10005. [PMID: 31097544 DOI: 10.1074/jbc.ra118.007120] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/13/2019] [Indexed: 01/22/2023] Open
Abstract
Caldicellulosiruptor bescii is an extremely thermophilic, cellulolytic bacterium with a growth optimum at 78 °C and is the most thermophilic cellulose degrader known. It is an attractive target for biotechnological applications, but metabolic engineering will require an in-depth understanding of its primary pathways. A previous analysis of its genome uncovered evidence that C. bescii may have a completely uncharacterized aspect to its redox metabolism, involving a tungsten-containing oxidoreductase of unknown function. Herein, we purified and characterized this new member of the aldehyde ferredoxin oxidoreductase family of tungstoenzymes. We show that it is a heterodimeric glyceraldehyde-3-phosphate (GAP) ferredoxin oxidoreductase (GOR) present not only in all known Caldicellulosiruptor species, but also in 44 mostly anaerobic bacterial genera. GOR is phylogenetically distinct from the monomeric GAP-oxidizing enzyme found previously in several Archaea. We found that its large subunit (GOR-L) contains a single tungstopterin site and one iron-sulfur [4Fe-4S] cluster, that the small subunit (GOR-S) contains four [4Fe-4S] clusters, and that GOR uses ferredoxin as an electron acceptor. Deletion of either subunit resulted in a distinct growth phenotype on both C5 and C6 sugars, with an increased lag phase, but higher cell densities. Using metabolomics and kinetic analyses, we show that GOR functions in parallel with the conventional GAP dehydrogenase, providing an alternative ferredoxin-dependent glycolytic pathway. These two pathways likely facilitate the recycling of reduced redox carriers (NADH and ferredoxin) in response to environmental H2 concentrations. This metabolic flexibility has important implications for the future engineering of this and related species.
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Affiliation(s)
- Israel M Scott
- From the Department of Biochemistry and Molecular Biology and
| | | | - Farris L Poole
- From the Department of Biochemistry and Molecular Biology and
| | - Gina L Lipscomb
- From the Department of Biochemistry and Molecular Biology and
| | - Gerrit J Schut
- From the Department of Biochemistry and Molecular Biology and
| | | | - David M Stevenson
- the Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, and
| | - Daniel Amador-Noguez
- the Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, and
| | - Robert M Kelly
- the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
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