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Kountz DJ, Balskus EP. A diversified, widespread microbial gene cluster encodes homologs of methyltransferases involved in methanogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551370. [PMID: 37577662 PMCID: PMC10418091 DOI: 10.1101/2023.07.31.551370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Analyses of microbial genomes have revealed unexpectedly wide distributions of enzymes from specialized metabolism, including methanogenesis, providing exciting opportunities for discovery. Here, we identify a family of gene clusters (the type 1 mlp gene clusters (MGCs)) that encodes homologs of the soluble coenzyme M methyltransferases (SCMTs) involved in methylotrophic methanogenesis and is widespread in bacteria and archaea. Type 1 MGCs are expressed and regulated in medically, environmentally, and industrially important organisms, making them likely to be physiologically relevant. Enzyme annotation, analysis of genomic context, and biochemical experiments suggests these gene clusters play a role in methyl-sulfur and/or methyl-selenide metabolism in numerous anoxic environments, including the human gut microbiome, potentially impacting sulfur and selenium cycling in diverse, anoxic environments.
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Affiliation(s)
- Duncan J. Kountz
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, United States
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2
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Lazar CS, Schwab VF, Ueberschaar N, Pohnert G, Trumbore S, Küsel K. Microbial degradation and assimilation of veratric acid in oxic and anoxic groundwaters. Front Microbiol 2023; 14:1252498. [PMID: 37901809 PMCID: PMC10602745 DOI: 10.3389/fmicb.2023.1252498] [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: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 10/31/2023] Open
Abstract
Microbial communities are key players in groundwater ecosystems. In this dark environment, heterotrophic microbes rely on biomass produced by the activity of lithoautotrophs or on the degradation of organic matter seeping from the surface. Most studies on bacterial diversity in groundwater habitats are based on 16S gene sequencing and full genome reconstructions showing potential metabolic pathways used in these habitats. However, molecular-based studies do not allow for the assessment of population dynamics over time or the assimilation of specific compounds and their biochemical transformation by microbial communities. Therefore, in this study, we combined DNA-, phospholipid fatty acid-, and metabolomic-stable isotope probing to target and identify heterotrophic bacteria in the groundwater setting of the Hainich Critical Zone Exploratory (CZE), focusing on 2 aquifers with different physico-chemical conditions (oxic and anoxic). We incubated groundwater from 4 different wells using either 13C-labeled veratric acid (a lignin-derived compound) (single labeling) or a combination of 13CO2 and D-labeled veratric acid (dual labeling). Our results show that heterotrophic activities dominate all groundwater sites. We identified bacteria with the potential to break down veratric acid (Sphingobium or Microbacterium). We observed differences in heterotrophic activities between the oxic and anoxic aquifers, indicating local adaptations of bacterial populations. The dual labeling experiments suggested that the serine pathway is an important carbon assimilation pathway and that organic matter was an important source of hydrogen in the newly produced lipids. These experiments also yielded different labeled taxa compared to the single labeling experiments, showing that there exists a complex interaction network in the groundwater habitats.
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Affiliation(s)
- Cassandre Sara Lazar
- Department of Biological Sciences, University of Quebec at Montreal (UQAM), Montreal, QC, Canada
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Valérie F. Schwab
- Department Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Nico Ueberschaar
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Susan Trumbore
- Department Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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3
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Moon J, Schubert A, Waschinger LM, Müller V. Reprogramming the metabolism of an acetogenic bacterium to homoformatogenesis. THE ISME JOURNAL 2023:10.1038/s41396-023-01411-2. [PMID: 37061584 DOI: 10.1038/s41396-023-01411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/17/2023]
Abstract
Methyl groups are abundant in anoxic environments and their utilization as carbon and energy sources by microorganisms involves oxidation of the methyl groups to CO2, followed by transfer of the electrons to an acceptor. In acetogenic bacteria, the electron acceptor is CO2 that is reduced to enzyme bound carbon monoxide, the precursor of the carboxyl group in acetate. Here, we describe the generation of a mutant of the acetogen Acetobacterium woodii in which the last step in methyl group oxidation, formate oxidation to CO2 catalyzed by the HDCR enzyme, has been genetically deleted. The mutant grew on glycine betaine as methyl group donor, and in contrast to the wild type, formed formate alongside acetate, in a 1:2 ratio, demonstrating that methyl group oxidation stopped at the level of formate and reduced electron carriers were reoxidized by CO2 reduction to acetate. In the presence of the alternative electron acceptor caffeate, CO2 was no longer reduced to acetate, formate was the only product and all the carbon went to formate. Apparently, acetogenesis was not required to sustain formatogenic growth. This is the first demonstration of a genetic reprogramming of an acetogen into a formatogen that grows by homoformatogenesis from methyl groups. Formate production from methyl groups is not only of biotechnological interest but also for the mechanism of electron transfer in syntrophic interactions in anoxic environments.
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Affiliation(s)
- Jimyung Moon
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Anja Schubert
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Lara M Waschinger
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany.
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Identification of a Phylogenetically Divergent Vanillate O-Demethylase from Rhodococcus ruber R1 Supporting Growth on Meta-Methoxylated Aromatic Acids. Microorganisms 2022; 11:microorganisms11010078. [PMID: 36677370 PMCID: PMC9867520 DOI: 10.3390/microorganisms11010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Rieske-type two-component vanillate O-demethylases (VanODs) catalyze conversion of the lignin-derived monomer vanillate into protocatechuate in several bacterial species. Currently, VanODs have received attention because of the demand of effective lignin valorization technologies, since these enzymes own the potential to catalyze methoxy group demethylation of distinct lignin monomers. In this work, we identified a phylogenetically divergent VanOD from Rhodococcus ruber R1, only distantly related to previously described homologues and whose presence, along with a 3-hydroxybenzoate/gentisate pathway, correlated with the ability to grow on other meta-methoxylated aromatics, such as 3-methoxybenzoate and 5-methoxysalicylate. The complementation of catabolic abilities by heterologous expression in a host strain unable to grow on vanillate, and subsequent resting cell assays, suggest that the vanAB genes of R1 strain encode a proficient VanOD acting on different vanillate-like substrates; and also revealed that a methoxy group in the meta position and a carboxylic acid moiety in the aromatic ring are key for substrate recognition. Phylogenetic analysis of the oxygenase subunit of bacterial VanODs revealed three divergent groups constituted by homologues found in Proteobacteria (Type I), Actinobacteria (Type II), or Proteobacteria/Actinobacteria (Type III) in which the R1 VanOD is placed. These results suggest that VanOD from R1 strain, and its type III homologues, expand the range of methoxylated aromatics used as substrates by bacteria.
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5
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Litty D, Kremp F, Müller V. One substrate, many fates: different ways of methanol utilization in the acetogen Acetobacterium woodii. Environ Microbiol 2022; 24:3124-3133. [PMID: 35416389 DOI: 10.1111/1462-2920.16011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 11/28/2022]
Abstract
Acetogenic bacteria such as Acetobacterium woodii use the Wood-Ljungdahl pathway (WLP) for fixation of CO2 and energy conservation. This pathway enables conversion of diverse substrates to the main product of acetogenesis, acetate. Methyl group containing substrates such as methanol or methylated compounds, derived from pectin, are abundant in the environment and a source for CO2 . Methyl groups enter the WLP at the level of methyltetrahydrofolic acid (methyl-THF). For methyl transfer from methanol to THF a substrate specific methyltransferase system is required. In this study, we used genetic methods to identify mtaBC2A (Awo_c22760- Awo_c22740) as the methanol specific methyltransferase system of A. woodii. After methyl transfer, methyl-THF serves as carbon and/or electron- source and the respiratory Rnf complex is required for redox homeostasis if methanol+CO2 is the substrate. Resting cells fed with methanol+CO2 , indeed converted methanol to acetate in a 4:3 stoichiometry. When methanol was fed in combination with other electron sources such as H2 + CO2 or CO, methanol was converted Rnf-independently and the methyl group was condensed with CO to build acetate. When fed in combination with alternative electron sinks such as caffeate methanol was oxidized only and resulting electrons were used for non-acetogenic growth. These different pathways for the conversion of methyl-group containing substrates enable acetogens to adapt to various ecological niches and to syntrophic communities. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Dennis Litty
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Florian Kremp
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
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6
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Shigeno M, Hayashi K, Korenaga T, Nozawa-Kumada K, Kondo Y. Organic superbase t-Bu-P4-catalyzed demethylations of methoxyarenes. Org Chem Front 2022. [DOI: 10.1039/d2qo00483f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The organic superbase t-Bu-P4 catalyzes the demethylation reactions of methoxyarenes in the presence of alkanethiol and hexamethyldisilazane.
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Affiliation(s)
- Masanori Shigeno
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Science, Tohoku University, Aoba, Sendai, 980-8578, Japan
| | - Kazutoshi Hayashi
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Science, Tohoku University, Aoba, Sendai, 980-8578, Japan
| | - Toshinobu Korenaga
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Ueda, Morioka, 020-8551, Japan
- Soft-Path Science and Engineering Research Center (SPERC), Iwate University, Ueda, Morioka, 020-8551, Japan
| | - Kanako Nozawa-Kumada
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Science, Tohoku University, Aoba, Sendai, 980-8578, Japan
| | - Yoshinori Kondo
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Science, Tohoku University, Aoba, Sendai, 980-8578, Japan
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7
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Pompei S, Grimm C, Schiller C, Schober L, Kroutil W. Thiols Act as Methyl Traps in the Biocatalytic Demethylation of Guaiacol Derivatives. Angew Chem Int Ed Engl 2021; 60:16906-16910. [PMID: 34057803 PMCID: PMC8361964 DOI: 10.1002/anie.202104278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Indexed: 12/13/2022]
Abstract
Demethylating methyl phenyl ethers is challenging, especially when the products are catechol derivatives prone to follow-up reactions. For biocatalytic demethylation, monooxygenases have previously been described requiring molecular oxygen which may cause oxidative side reactions. Here we show that such compounds can be demethylated anaerobically by using cobalamin-dependent methyltransferases exploiting thiols like ethyl 3-mercaptopropionate as a methyl trap. Using just two equivalents of this reagent, a broad spectrum of substituted guaiacol derivatives were demethylated, with conversions mostly above 90 %. This strategy was used to prepare the highly valuable antioxidant hydroxytyrosol on a one-gram scale in 97 % isolated yield.
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Affiliation(s)
- Simona Pompei
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI GrazHeinrichstrasse 288010GrazAustria
| | - Christopher Grimm
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI GrazHeinrichstrasse 288010GrazAustria
| | - Christine Schiller
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI GrazHeinrichstrasse 288010GrazAustria
| | - Lukas Schober
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI GrazHeinrichstrasse 288010GrazAustria
| | - Wolfgang Kroutil
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI GrazHeinrichstrasse 288010GrazAustria
- BioTechMed Graz8010GrazAustria
- Field of Excellence BioHealth-University of Graz8010GrazAustria
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8
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Pompei S, Grimm C, Schiller C, Schober L, Kroutil W. Thiols Act as Methyl Traps in the Biocatalytic Demethylation of Guaiacol Derivatives. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:17043-17047. [PMID: 38505659 PMCID: PMC10946705 DOI: 10.1002/ange.202104278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Indexed: 11/10/2022]
Abstract
Demethylating methyl phenyl ethers is challenging, especially when the products are catechol derivatives prone to follow-up reactions. For biocatalytic demethylation, monooxygenases have previously been described requiring molecular oxygen which may cause oxidative side reactions. Here we show that such compounds can be demethylated anaerobically by using cobalamin-dependent methyltransferases exploiting thiols like ethyl 3-mercaptopropionate as a methyl trap. Using just two equivalents of this reagent, a broad spectrum of substituted guaiacol derivatives were demethylated, with conversions mostly above 90 %. This strategy was used to prepare the highly valuable antioxidant hydroxytyrosol on a one-gram scale in 97 % isolated yield.
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Affiliation(s)
- Simona Pompei
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI GrazHeinrichstrasse 288010GrazAustria
| | - Christopher Grimm
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI GrazHeinrichstrasse 288010GrazAustria
| | - Christine Schiller
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI GrazHeinrichstrasse 288010GrazAustria
| | - Lukas Schober
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI GrazHeinrichstrasse 288010GrazAustria
| | - Wolfgang Kroutil
- Institute of Chemistry, Biocatalytic SynthesisUniversity of Graz, NAWI GrazHeinrichstrasse 288010GrazAustria
- BioTechMed Graz8010GrazAustria
- Field of Excellence BioHealth-University of Graz8010GrazAustria
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9
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Venkatesagowda B, Dekker RFH. Microbial demethylation of lignin: Evidence of enzymes participating in the removal of methyl/methoxyl groups. Enzyme Microb Technol 2021; 147:109780. [PMID: 33992403 DOI: 10.1016/j.enzmictec.2021.109780] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 02/27/2021] [Accepted: 03/11/2021] [Indexed: 11/30/2022]
Abstract
Lignin is an abundant natural plant aromatic biopolymer containing various functional groups that can be exploited for activating lignin for potential commercial applications. Applications are hindered due to the presence of a high content of methyl/methoxyl groups that affects reactiveness. Various chemical and enzymatic approaches have been investigated to increase the functionality in transforming lignin. Among these is demethylation/demethoxylation, which increases the potential numbers of vicinal hydroxyl groups for applications as phenol-formaldehyde resins. Although the chemical route to lignin demethylation is well-studied, the biological route is still poorly explored. Bacteria and fungi have the ability to demethylate lignin and lignin-related compounds. Considering that appropriate microorganisms possess the biochemical machinery to demethylate lignin by cleaving O-methyl groups liberating methanol, and modify lignin by increasing the vicinal diol content that allows lignin to substitute for phenol in organic polymer syntheses. Certain bacteria through the actions of specific O-demethylases can modify various lignin-related compounds generating vicinal diols and liberating methanol or formaldehyde as end-products. The enzymes include: cytochrome P450-aryl-O-demethylase, monooxygenase, veratrate 3-O-demethylase, DDVA O-demethylase (LigX; lignin-related biphenyl 5,5'-dehydrodivanillate (DDVA)), vanillate O-demethylase, syringate O-demethylase, and tetrahydrofolate-dependent-O-demethylase. Although, the fungal counterparts have not been investigated in depth as in bacteria, O-demethylases, nevertheless, have been reported in demethylating various lignin substrates providing evidence of a fungal enzyme system. Few fungi appear to have the ability to secrete O-demethylases. The fungi can mediate lignin demethylation enzymatically (laccase, lignin peroxidase, manganese peroxidase, O-demethylase), or non-enzymatically in brown-rot fungi through the Fenton reaction. This review discusses details on the aspects of microbial (bacterial and fungal) demethylation of lignins and lignin-model compounds and provides evidence of enzymes identified as specific O-demethylases involved in demethylation.
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Affiliation(s)
- Balaji Venkatesagowda
- Biorefining Research Institute, Lakehead University, Thunder Bay, Ontario, P7B 5E1, Canada.
| | - Robert F H Dekker
- Biorefining Research Institute, Lakehead University, Thunder Bay, Ontario, P7B 5E1, Canada; Universidade Tecnológica Federal do Paraná, Programa de Pós-Graduação em Engenharia Ambiental, Câmpus Londrina, CEP: 86036-370, Londrina, PR, Brazil.
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10
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Ma Y, Donohue TJ, Noguera DR. Kinetic modeling of anaerobic degradation of plant-derived aromatic mixtures by Rhodopseudomonas palustris. Biodegradation 2021; 32:179-192. [PMID: 33675449 PMCID: PMC7997838 DOI: 10.1007/s10532-021-09932-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/23/2021] [Indexed: 11/23/2022]
Abstract
Rhodopseudomonas palustris is a model microorganism for studying the anaerobic metabolism of aromatic compounds. While it is well documented which aromatics can serve as sole organic carbon sources, co-metabolism of other aromatics is poorly understood. This study used kinetic modeling to analyze the simultaneous degradation of aromatic compounds present in corn stover hydrolysates and model the co-metabolism of aromatics not known to support growth of R. palustris as sole organic substrates. The simulation predicted that p-coumaroyl amide and feruloyl amide were hydrolyzed to p-coumaric acid and ferulic acid, respectively, and further transformed via p-coumaroyl-CoA and feruloyl-CoA. The modeling also suggested that metabolism of p-hydroxyphenyl aromatics was slowed by substrate inhibition, whereas the transformation of guaiacyl aromatics was inhibited by their p-hydroxyphenyl counterparts. It also predicted that substrate channeling may occur during degradation of p-coumaroyl-CoA and feruloyl-CoA, resulting in no detectable accumulation of p-hydroxybenzaldehyde and vanillin, during the transformation of these CoA ligated compounds to p-hydroxybenzoic acid and vanillic acid, respectively. While the simulation correctly represented the known transformation of p-hydroxybenzoic acid via the benzoyl-CoA pathway, it also suggested co-metabolism of vanillic acid and syringic acid, which are known not to serve as photoheterotrophic growth substrate for R. palustris.
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Affiliation(s)
- Yanjun Ma
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Timothy J Donohue
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Daniel R Noguera
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA. .,Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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11
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Kißling L, Greiser Y, Dürichen H, Studenik S. Flavodoxin hydroquinone provides electrons for the ATP-dependent reactivation of protein-bound corrinoid cofactors. FEBS J 2020; 287:4971-4981. [PMID: 32160390 DOI: 10.1111/febs.15290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/31/2020] [Accepted: 03/10/2020] [Indexed: 12/01/2022]
Abstract
Corrinoid-dependent enzyme systems rely on the super-reduced state of the protein-bound corrinoid cofactor to be functional, for example, in methyl transfer reactions. Due to the low redox potential of the [CoII ]/[CoI ] couple, autoxidation of the corrinoid cofactor occurs and leads to the formation of the inactive [CoII ]-state. For the reactivation, which is an energy-demanding process, electrons have to be transferred from a physiological donor to the corrinoid cofactor by the help of a reductive activator protein. In this study, we identified reduced flavodoxin as electron donor for the ATP-dependent reduction of protein-bound corrinoid cofactors of bacterial O-demethylase enzyme systems. Reduced flavodoxin was generated enzymatically using pyruvate:ferredoxin/flavodoxin oxidoreductase rather than hydrogenase. Two of the four flavodoxins identified in Acetobacterium dehalogenans and Desulfitobacterium hafniense DCB-2 were functional in supplying electrons for corrinoid reduction. They exhibited a midpoint potential of about -400 mV (ESHE , pH 7.5) for the semiquinone/hydroquinone transition. Reduced flavodoxin could be replaced by reduced clostridial ferredoxin. It was shown that the low-potential electrons of reduced flavodoxin are first transferred to the iron-sulfur cluster of the reductive activator and finally to the protein-bound corrinoid cofactor. This study further highlights the importance of reduced flavodoxin, which allows maintaining a variety of enzymatic reaction cycles by delivering low-potential electrons.
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Affiliation(s)
- Lena Kißling
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Yvonne Greiser
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hendrike Dürichen
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Sandra Studenik
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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12
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Retroconversion of estrogens into androgens by bacteria via a cobalamin-mediated methylation. Proc Natl Acad Sci U S A 2019; 117:1395-1403. [PMID: 31848239 DOI: 10.1073/pnas.1914380117] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Steroid estrogens modulate physiology and development of vertebrates. Conversion of C19 androgens into C18 estrogens is thought to be an irreversible reaction. Here, we report a denitrifying Denitratisoma sp. strain DHT3 capable of catabolizing estrogens or androgens anaerobically. Strain DHT3 genome contains a polycistronic gene cluster, emtABCD, differentially transcribed under estrogen-fed conditions and predicted to encode a cobalamin-dependent methyltransferase system conserved among estrogen-utilizing anaerobes; an emtA-disrupted DHT3 derivative could catabolize androgens but not estrogens. These data, along with the observed androgen production in estrogen-fed strain DHT3 cultures, suggested the occurrence of a cobalamin-dependent estrogen methylation to form androgens. Consistently, the estrogen conversion into androgens in strain DHT3 cell extracts requires methylcobalamin and is inhibited by propyl iodide, a specific inhibitor of cobalamin-dependent enzymes. The identification of the cobalamin-dependent estrogen methylation thus represents an unprecedented metabolic link between cobalamin and steroid metabolism and suggests that retroconversion of estrogens into androgens occurs in the biosphere.
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13
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Li B, Liu XN, Tang C, Zhou J, Wu XY, Xie XX, Wei P, Jia HH, Yong XY. Degradation of phenolic compounds with simultaneous bioelectricity generation in microbial fuel cells: Influence of the dynamic shift in anode microbial community. BIORESOURCE TECHNOLOGY 2019; 291:121862. [PMID: 31357047 DOI: 10.1016/j.biortech.2019.121862] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/16/2019] [Accepted: 07/20/2019] [Indexed: 06/10/2023]
Abstract
This study evaluated the feasibility of microbial fuel cells (MFCs) for simultaneous electricity generation and degradation of phenolic compounds. The voltage generation was inhibited by 36.18-63.90%, but the degradation rate increased by 146.15-392.31% when the initial concentration of syringic acid (SA), vanillic acid (VA), and 4-hydroxybenzoic acid (HBA) increased from 0.3 to 3.0 g/L. The collaboration among the functional microbes significantly enhanced the degradation rate of parent compounds and their intermediates in MFCs systems, while the accumulated intermediates severely inhibited their complete mineralization in fermentative systems. High-throughput sequencing showed that the growth of fermentative bacteria prevailed, but electrogenic bacteria were inhibited in the anode microbial community (AMC) under high concentrations of phenolic compounds (3.0 g/L). These findings provide a better understanding of the dynamic shift and synergy effects of the AMC to evaluate its potential for the treatment of phenolic-containing wastewater.
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Affiliation(s)
- Biao Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing 211816, China
| | - Xiao-Na Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing 211816, China
| | - Chen Tang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing 211816, China
| | - Jun Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing 211816, China
| | - Xia-Yuan Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing 211816, China
| | - Xin-Xin Xie
- College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing 211816, China
| | - Ping Wei
- College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing 211816, China
| | - Hong-Hua Jia
- College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing 211816, China
| | - Xiao-Yu Yong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing TECH University, Nanjing 211816, China.
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14
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Li X, Zheng Y. Biotransformation of lignin: Mechanisms, applications and future work. Biotechnol Prog 2019; 36:e2922. [PMID: 31587530 DOI: 10.1002/btpr.2922] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 01/04/2023]
Abstract
As one of the most abundant polymers in biosphere, lignin has attracted extensive attention as a kind of promising feedstock for biofuel and bio-based products. However, the utilization of lignin presents various challenges in that its complex composition and structure and high resistance to degradation. Lignin conversion through biological platform harnesses the catalytic power of microorganisms to decompose complex lignin molecules and obtain value-added products through biosynthesis. Given the heterogeneity of lignin, various microbial metabolic pathways are involved in lignin bioconversion processes, which has been characterized in extensive research work. With different types of lignin substrates (e.g., model compounds, technical lignin, and lignocellulosic biomass), several bacterial and fungal species have been proved to own lignin-degrading abilities and accumulate microbial products (e.g., lipid and polyhydroxyalkanoates), while the lignin conversion efficiencies are still relatively low. Genetic and metabolic strategies have been developed to enhance lignin biodegradation by reprogramming microbial metabolism, and diverse products, such as vanillin and dicarboxylic acids were also produced from lignin. This article aims at presenting a comprehensive review on lignin bioconversion including lignin degradation mechanisms, metabolic pathways, and applications for the production of value-added bioproducts. Advanced techniques on genetic and metabolic engineering are also covered in the recent development of biological platforms for lignin utilization. To conclude this article, the existing challenges for efficient lignin bioprocessing are analyzed and possible directions for future work are proposed.
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Affiliation(s)
- Xiang Li
- Department of Grain Science and Industry, Kansas State University, Manhattan, Kansas
| | - Yi Zheng
- Department of Grain Science and Industry, Kansas State University, Manhattan, Kansas
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15
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Venkatesagowda B. Enzymatic demethylation of lignin for potential biobased polymer applications. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2019.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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16
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Farnberger JE, Richter N, Hiebler K, Bierbaumer S, Pickl M, Skibar W, Zepeck F, Kroutil W. Biocatalytic methylation and demethylation via a shuttle catalysis concept involving corrinoid proteins. Commun Chem 2018. [DOI: 10.1038/s42004-018-0083-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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17
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Kremp F, Poehlein A, Daniel R, Müller V. Methanol metabolism in the acetogenic bacterium Acetobacterium woodii. Environ Microbiol 2018; 20:4369-4384. [PMID: 30003650 DOI: 10.1111/1462-2920.14356] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/07/2018] [Indexed: 11/29/2022]
Abstract
Methanol derived from plant tissue is ubiquitous in anaerobic sediments and a good substrate for anaerobes growing on C1 compounds such as methanogens and acetogens. In contrast to methanogens little is known about the physiology, biochemistry and bioenergetics of methanol utilization in acetogenic bacteria. To fill this gap, we have used the model acetogen Acetobacterium woodii to study methanol metabolism using physiological and biochemical experiments paired with molecular studies and transcriptome analysis. These studies identified the genes and enzymes involved in acetogenesis from methanol and the redox carriers involved. We will present the first comprehensive model for carbon and electron flow from methanol in an acetogen and the bioenergetics of acetogenesis from methanol.
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Affiliation(s)
- Florian Kremp
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
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18
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Marjamaa K, Kruus K. Enzyme biotechnology in degradation and modification of plant cell wall polymers. PHYSIOLOGIA PLANTARUM 2018; 164:106-118. [PMID: 29987848 DOI: 10.1111/ppl.12800] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 05/28/2023]
Abstract
Lignocelluloses are abundant raw materials for production of fuels, chemicals and materials. The purpose of this paper is to review the enzyme-types and enzyme-technologies studied and applied in the processing of the lignocelluloses into different products. The enzymes here are mostly glycoside hydrolases, esterases and different redox enzymes. Enzymatic hydrolysis of lignocellulosic polysaccharides to platform sugars has been widely studied leading to development of advanced commercial products for this purpose. Restricted hydrolysis or oxidation of cellulosic fibers have been applied in processing of pulps to paper products, nanocelluloses and textile fibers. Oxidation, transglycosylation and derivatization have been utilized in functionalization of fibers, cellulosic surfaces and polysaccharides. Enzymatic polymerization, depolymerization and grafting methods are being developed for lignin valorization.
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Affiliation(s)
- Kaisa Marjamaa
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, Espoo, 02044, Finland
| | - Kristiina Kruus
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, Espoo, 02044, Finland
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19
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Wright J, Kirchner V, Bernard W, Ulrich N, McLimans C, Campa MF, Hazen T, Macbeth T, Marabello D, McDermott J, Mackelprang R, Roth K, Lamendella R. Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation. Front Microbiol 2017; 8:2300. [PMID: 29213257 PMCID: PMC5702783 DOI: 10.3389/fmicb.2017.02300] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023] Open
Abstract
The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.
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Affiliation(s)
- Justin Wright
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States.,Wright Labs, LLC, Huntingdon, PA, United States
| | - Veronica Kirchner
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - William Bernard
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Nikea Ulrich
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Christopher McLimans
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Maria F Campa
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
| | - Terry Hazen
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory (DOE), Oak Ridge, TN, United States.,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States.,Department of Microbiology, University of Tennessee, Knoxville, TN, United States.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
| | | | | | | | - Rachel Mackelprang
- Department of Biology, California State University Northridge, Northridge, PA, United States
| | - Kimberly Roth
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States
| | - Regina Lamendella
- Lamendella Laboratory, Juniata College, Department of Biology, Huntingdon, PA, United States.,Wright Labs, LLC, Huntingdon, PA, United States
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20
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Chen G, Kleindienst S, Griffiths DR, Mack EE, Seger ES, Löffler FE. Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture. Environ Microbiol 2017; 19:4784-4796. [DOI: 10.1111/1462-2920.13945] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Gao Chen
- Center for Environmental Biotechnology; University of Tennessee; Knoxville TN 37996 USA
- Department of Civil and Environmental Engineering; University of Tennessee; Knoxville TN 37996 USA
| | - Sara Kleindienst
- Center for Environmental Biotechnology; University of Tennessee; Knoxville TN 37996 USA
- Oak Ridge National Laboratory; University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division; Oak Ridge TN 37831 USA
- Center for Applied Geosciences; Department of Geosciences, Eberhard Karls University Tübingen; Tübingen 72074 Germany
| | | | - E. Erin Mack
- Corporate Remediation Group; E. I. DuPont de Nemours and Company; Wilmington DE 19805 USA
| | | | - Frank E. Löffler
- Center for Environmental Biotechnology; University of Tennessee; Knoxville TN 37996 USA
- Department of Civil and Environmental Engineering; University of Tennessee; Knoxville TN 37996 USA
- Oak Ridge National Laboratory; University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division; Oak Ridge TN 37831 USA
- Department of Microbiology; University of Tennessee; Knoxville TN 37996 USA
- Department of Biosystems Engineering and Soil Science; University of Tennessee; Knoxville TN 37996 USA
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21
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Ghattas AK, Fischer F, Wick A, Ternes TA. Anaerobic biodegradation of (emerging) organic contaminants in the aquatic environment. WATER RESEARCH 2017; 116:268-295. [PMID: 28347952 DOI: 10.1016/j.watres.2017.02.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 05/22/2023]
Abstract
Although strictly anaerobic conditions prevail in several environmental compartments, up to now, biodegradation studies with emerging organic contaminants (EOCs), such as pharmaceuticals and personal care products, have mainly focused on aerobic conditions. One of the reasons probably is the assumption that the aerobic degradation is more energetically favorable than degradation under strictly anaerobic conditions. Certain aerobically recalcitrant contaminants, however, are biodegraded under strictly anaerobic conditions and little is known about the organisms and enzymatic processes involved in their degradation. This review provides a comprehensive survey of characteristic anaerobic biotransformation reactions for a variety of well-studied, structurally rather simple contaminants (SMOCs) bearing one or a few different functional groups/structural moieties. Furthermore it summarizes anaerobic degradation studies of more complex contaminants with several functional groups (CMCs), in soil, sediment and wastewater treatment. While strictly anaerobic conditions are able to promote the transformation of several aerobically persistent contaminants, the variety of observed reactions is limited, with reductive dehalogenations and the cleavage of ether bonds being the most prevalent. Thus, it becomes clear that the transferability of degradation mechanisms deduced from culture studies of SMOCs to predict the degradation of CMCs, such as EOCs, in environmental matrices is hampered due the more complex chemical structure bearing different functional groups, different environmental conditions (e.g. matrix, redox, pH), the microbial community (e.g. adaptation, competition) and the low concentrations typical for EOCs.
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Affiliation(s)
- Ann-Kathrin Ghattas
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Ferdinand Fischer
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Arne Wick
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Thomas A Ternes
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany.
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22
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Zeng X, Collins MA, Borole AP, Pavlostathis SG. The extent of fermentative transformation of phenolic compounds in the bioanode controls exoelectrogenic activity in a microbial electrolysis cell. WATER RESEARCH 2017; 109:299-309. [PMID: 27914260 DOI: 10.1016/j.watres.2016.11.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
Phenolic compounds in hydrolysate/pyrolysate and wastewater streams produced during the pretreatment of lignocellulosic biomass for biofuel production present a significant challenge in downstream processes. Bioelectrochemical systems are increasingly recognized as an alternative technology to handle biomass-derived streams and to promote water reuse in biofuel production. Thus, a thorough understanding of the fate of phenolic compounds in bioanodes is urgently needed. The present study investigated the biotransformation of three structurally similar phenolic compounds (syringic acid, SA; vanillic acid, VA; 4-hydroxybenzoic acid, HBA), and their individual contribution to exoelectrogenesis in a microbial electrolysis cell (MEC) bioanode. Fermentation of SA resulted in the highest exoelectrogenic activity among the three compounds tested, with 50% of the electron equivalents converted to current, compared to 12 and 9% for VA and HBA, respectively. The biotransformation of SA, VA and HBA was initiated by demethylation and decarboxylation reactions common to all three compounds, resulting in their corresponding hydroxylated analogs. SA was transformed to pyrogallol (1,2,3-trihydroxybenzene), whose aromatic ring was then cleaved via a phloroglucinol pathway, resulting in acetate production, which was then used in exoelectrogenesis. In contrast, more than 80% of VA and HBA was converted to catechol (1,2-dihydroxybenzene) and phenol (hydroxybenzene) as their respective dead-end products. The persistence of catechol and phenol is explained by the fact that the phloroglucinol pathway does not apply to di- or mono-hydroxylated benzenes. Previously reported, alternative ring-cleaving pathways were either absent in the bioanode microbial community or unfavorable due to high energy-demand reactions. With the exception of acetate oxidation, all biotransformation steps in the bioanode occurred via fermentation, independently of exoelectrogenesis. Therefore, the observed exoelectrogenic activity in batch runs conducted with SA, VA and HBA was controlled by the extent of fermentative transformation of the three phenolic compounds in the bioanode, which is related to the number and position of the methoxy and hydroxyl substituents.
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Affiliation(s)
- Xiaofei Zeng
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0512, United States
| | - Maya A Collins
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0512, United States
| | - Abhijeet P Borole
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Bredesen Center for Interdisciplinary Research and Education, The University of Tennessee, Knoxville, TN 37996, United States
| | - Spyros G Pavlostathis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0512, United States.
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23
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Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization. Proc Natl Acad Sci U S A 2016; 113:E5802-E5811. [PMID: 27634497 DOI: 10.1073/pnas.1606043113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Sphingobium sp. SYK-6 is a soil bacterium boasting a well-studied ligninolytic pathway and the potential for development into a microbial chassis for lignin valorization. An improved understanding of its metabolism will help researchers in the engineering of SYK-6 for the production of value-added chemicals through lignin valorization. We used 13C-fingerprinting, 13C metabolic flux analysis (13C-MFA), and RNA-sequencing differential expression analysis to uncover the following metabolic traits: (i) SYK-6 prefers alkaline conditions, making it an efficient host for the consolidated bioprocessing of lignin, and it also lacks the ability to metabolize sugars or organic acids; (ii) the CO2 release (i.e., carbon loss) from the ligninolysis-based metabolism of SYK-6 is significantly greater than the CO2 release from the sugar-based metabolism of Escherichia coli; (iii) the vanillin catabolic pathway (which is the converging point of majority of the lignin catabolic pathways) is coupled with the tetrahydrofolate-dependent C1 pathway that is essential for the biosynthesis of serine, histidine, and methionine; (iv) catabolic end products of lignin (pyruvate and oxaloacetate) must enter the tricarboxylic acid (TCA) cycle first and then use phosphoenolpyruvate carboxykinase to initiate gluconeogenesis; and (v) 13C-MFA together with RNA-sequencing differential expression analysis establishes the vanillin catabolic pathway as the major contributor of NAD(P)H synthesis. Therefore, the vanillin catabolic pathway is essential for SYK-6 to obtain sufficient reducing equivalents for its healthy growth; cosubstrate experiments support this finding. This unique energy feature of SYK-6 is particularly interesting because most heterotrophs rely on the transhydrogenase, the TCA cycle, and the oxidative pentose phosphate pathway to obtain NADPH.
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24
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Richter N, Zepeck F, Kroutil W. Cobalamin-dependent enzymatic O-, N-, and S-demethylation. Trends Biotechnol 2015; 33:371-3. [DOI: 10.1016/j.tibtech.2015.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 11/25/2022]
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25
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Sjuts H, Dunstan MS, Fisher K, Leys D. Structure of the cobalamin-binding protein of a putative O-demethylase from Desulfitobacterium hafniense DCB-2. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1609-16. [PMID: 23897483 PMCID: PMC3727330 DOI: 10.1107/s0907444913011323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 04/25/2013] [Indexed: 11/10/2022]
Abstract
This study describes the identification and the structural and spectroscopic analysis of a cobalamin-binding protein (termed CobDH) implicated in O-demethylation by the organohalide-respiring bacterium Desulfitobacterium hafniense DCB-2. The 1.5 Å resolution crystal structure of CobDH is presented in the cobalamin-bound state and reveals that the protein is composed of an N-terminal helix-bundle domain and a C-terminal Rossmann-fold domain, with the cobalamin coordinated in the base-off/His-on conformation similar to other cobalamin-binding domains that catalyse methyl-transfer reactions. EPR spectroscopy of CobDH confirms cobalamin binding and reveals the presence of a cob(III)alamin superoxide, indicating binding of oxygen to the fully oxidized cofactor. These data provide the first structural insights into the methyltransferase reactions that occur during O-demethylation by D. hafniense.
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Affiliation(s)
- Hanno Sjuts
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, England
| | - Mark S. Dunstan
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, England
| | - Karl Fisher
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, England
| | - David Leys
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, England
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26
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Nguyen HD, Studenik S, Diekert G. Corrinoid activation by a RACE protein: studies on the interaction of the proteins involved. FEMS Microbiol Lett 2013; 345:31-8. [DOI: 10.1111/1574-6968.12178] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/17/2013] [Accepted: 05/13/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Hai Dang Nguyen
- Institut für Mikrobiologie; Friedrich-Schiller-Universität Jena; Lehrstuhl für Angewandte und Ökologische Mikrobiologie; Jena; Germany
| | - Sandra Studenik
- Institut für Mikrobiologie; Friedrich-Schiller-Universität Jena; Lehrstuhl für Angewandte und Ökologische Mikrobiologie; Jena; Germany
| | - Gabriele Diekert
- Institut für Mikrobiologie; Friedrich-Schiller-Universität Jena; Lehrstuhl für Angewandte und Ökologische Mikrobiologie; Jena; Germany
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27
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Anderson I, Held B, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)). Stand Genomic Sci 2012; 6:174-84. [PMID: 22768361 PMCID: PMC3387795 DOI: 10.4056/sigs.2746047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Holophaga foetida Liesack et al. 1995 is a member of the phylum Acidobacteria and is of interest for its ability to anaerobically degrade aromatic compounds and for its production of volatile sulfur compounds through a unique pathway. The genome of H. foetida strain TMBS4(T) is the first to be sequenced for a representative of the class Holophagae. Here we describe the features of this organism, together with the complete genome sequence (improved high quality draft), and annotation. The 4,127,237 bp long chromosome with its 3,615 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Iain Anderson
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Brittany Held
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne A. Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Evelyne-Marie Brambilla
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Bristow
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A. Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA
- University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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28
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Abstract
Besides acetogenic bacteria, only Desulfitobacterium has been described to utilize and cleave phenyl methyl ethers under anoxic conditions; however, no ether-cleaving O-demethylases from the latter organisms have been identified and investigated so far. In this study, genes of an operon encoding O-demethylase components of Desulfitobacterium hafniense strain DCB-2 were cloned and heterologously expressed in Escherichia coli. Methyltransferases I and II were characterized. Methyltransferase I mediated the ether cleavage and the transfer of the methyl group to the superreduced corrinoid of a corrinoid protein. Desulfitobacterium methyltransferase I had 66% identity (80% similarity) to that of the vanillate-demethylating methyltransferase I (OdmB) of Acetobacterium dehalogenans. The substrate spectrum was also similar to that of the latter enzyme; however, Desulfitobacterium methyltransferase I showed a higher level of activity for guaiacol and used methyl chloride as a substrate. Methyltransferase II catalyzed the transfer of the methyl group from the methylated corrinoid protein to tetrahydrofolate. It also showed a high identity (∼70%) to methyltransferases II of A. dehalogenans. The corrinoid protein was produced in E. coli as cofactor-free apoprotein that could be reconstituted with hydroxocobalamin or methylcobalamin to function in the methyltransferase I and II assays. Six COG3894 proteins, which were assumed to function as activating enzymes mediating the reduction of the corrinoid protein after an inadvertent oxidation of the corrinoid cofactor, were studied with respect to their abilities to reduce the recombinant reconstituted corrinoid protein. Of these six proteins, only one was found to catalyze the reduction of the corrinoid protein.
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Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction. BMC Microbiol 2012; 12:21. [PMID: 22316246 PMCID: PMC3306737 DOI: 10.1186/1471-2180-12-21] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 02/08/2012] [Indexed: 12/13/2022] Open
Abstract
Background The genome of the Gram-positive, metal-reducing, dehalorespiring Desulfitobacterium hafniense DCB-2 was sequenced in order to gain insights into its metabolic capacities, adaptive physiology, and regulatory machineries, and to compare with that of Desulfitobacterium hafniense Y51, the phylogenetically closest strain among the species with a sequenced genome. Results The genome of Desulfitobacterium hafniense DCB-2 is composed of a 5,279,134-bp circular chromosome with 5,042 predicted genes. Genome content and parallel physiological studies support the cell's ability to fix N2 and CO2, form spores and biofilms, reduce metals, and use a variety of electron acceptors in respiration, including halogenated organic compounds. The genome contained seven reductive dehalogenase genes and four nitrogenase gene homologs but lacked the Nar respiratory nitrate reductase system. The D. hafniense DCB-2 genome contained genes for 43 RNA polymerase sigma factors including 27 sigma-24 subunits, 59 two-component signal transduction systems, and about 730 transporter proteins. In addition, it contained genes for 53 molybdopterin-binding oxidoreductases, 19 flavoprotein paralogs of the fumarate reductase, and many other FAD/FMN-binding oxidoreductases, proving the cell's versatility in both adaptive and reductive capacities. Together with the ability to form spores, the presence of the CO2-fixing Wood-Ljungdahl pathway and the genes associated with oxygen tolerance add flexibility to the cell's options for survival under stress. Conclusions D. hafniense DCB-2's genome contains genes consistent with its abilities for dehalogenation, metal reduction, N2 and CO2 fixation, anaerobic respiration, oxygen tolerance, spore formation, and biofilm formation which make this organism a potential candidate for bioremediation at contaminated sites.
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The limited deglucosylation process of β-glucosidase in Bacillus cereus H62L for biotransforming secoisolariciresinol diglucoside into mammalian lignans. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Studenik S, Kreher S, Diekert G. The ether-cleaving methyltransferase of the strict anaerobe Acetobacterium dehalogenans: analysis of the zinc-binding site. FEMS Microbiol Lett 2011; 318:131-6. [DOI: 10.1111/j.1574-6968.2011.02251.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Kreher S, Studenik S, Diekert G. Ether cleaving methyltransferases of the strict anaerobe Acetobacterium dehalogenans: controlling the substrate spectrum by genetic engineering of the N-terminus. Mol Microbiol 2010; 78:230-7. [PMID: 20923421 DOI: 10.1111/j.1365-2958.2010.07333.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The anaerobic cleavage of ether bonds of methoxylated substrates such as vanillate or veratrol in acetogenic bacteria is mediated by multi-component enzyme systems, the O-demethylases. Acetobacterium dehalogenans harbours different inducible O-demethylases with various substrate spectra. Two of these enzyme systems, the vanillate- and the veratrol-O-demethylases, have been characterized so far. One component of this enzyme system, the methyltransferase I (MT I), catalyses the cleavage of the substrate ether bond and the subsequent transfer of the methyl group to a corrinoid protein. For the C-termini of the methyltransferases I of the vanillate- and the veratrol-O-demethylases, a TIM barrel structure of the enzymes was predicted, whereas the N-termini are not part of this conserved structure. The deletion of the N-terminal regions led to a significant increase of activity (up to 20-fold) and an extended substrate spectrum of the mutants, which also comprised non-aromatic compounds such as the thioether methionine and diethylether. The exchange of the N-termini of the two methyltransferases I resulted in chimeric enzymes whose substrate specificities were those of the enzymes from which the N-termini were derived. This demonstrated the crucial role of the N-termini for the substrate specificity of the methyltransferases.
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Affiliation(s)
- Sandra Kreher
- Institut für Mikrobiologie, Lehrstuhl für Angewandte und Ökologische Mikrobiologie, Friedrich-Schiller-Universität Jena, Philosophenweg 12, 07743 Jena, Germany
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Sonoki T, Masai E, Sato K, Kajita S, Katayama Y. Methoxyl groups of lignin are essential carbon donors in C1 metabolism of Sphingobium sp. SYK-6. J Basic Microbiol 2009; 49 Suppl 1:S98-102. [PMID: 19718680 DOI: 10.1002/jobm.200800367] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Sphingobium sp. SYK-6 can utilize lignin biphenyl compounds, such as 2,2'-dihydroxy-3,3'-dimethoxy-5,5'-dicarboxybiphenyl (DDVA). In the metabolism of DDVA, this microorganism exploits two O -demethylation systems with different substrate specificities, namely, a DDVA-specific oxygenative O -demethylation system and a vanillate-specific (VA-specific) tetrahydrofolate-dependent (THF-dependent) methyltransferase system. We examined the way in which these two systems interact in the metabolism of lignin in Sphingobium sp. SYK-6. Our results indicate that THF accepts methyl groups derived not only from the THF-dependent O -demethylation of VA but also from the oxygenative O -demethylation of DDVA. Thus, the methoxyl groups of lignin model compounds are an essential source of carbon in Sphingobium sp. SYK-6. ((c) 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim).
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Affiliation(s)
- Tomonori Sonoki
- Faculty of Agriculture and Life Sciences, Hirosaki University, Bunkyo-cho, Hirosaki, Aomori, Japan
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Matthews RG, Koutmos M, Datta S. Cobalamin-dependent and cobamide-dependent methyltransferases. Curr Opin Struct Biol 2009; 18:658-66. [PMID: 19059104 DOI: 10.1016/j.sbi.2008.11.005] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 11/02/2008] [Indexed: 11/18/2022]
Abstract
Methyltransferases that employ cobalamin cofactors, or their analogs the cobamides, as intermediates in catalysis of methyl transfer play vital roles in energy generation in anaerobic unicellular organisms. In a broader range of organisms they are involved in the conversion of homocysteine to methionine. Although the individual methyl transfer reactions catalyzed are simple S(N)2 displacements, the required change in coordination at the cobalt of the cobalamin or cobamide cofactors and the lability of the reduced Co(+1) intermediates introduces the necessity for complex conformational changes during the catalytic cycle. Recent spectroscopic and structural studies on several of these methyltransferases have helped to reveal the strategies by which these conformational changes are facilitated and controlled.
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Affiliation(s)
- Rowena G Matthews
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA.
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Abstract
This chapter reviews the literature on cobalamin- and corrinoid-containing enzymes. These enzymes fall into two broad classes, those using methylcobalamin or related methylcorrinoids as prosthetic groups and catalyzing methyl transfer reactions, and those using adenosylcobalamin as the prosthetic group and catalyzing the generation of substrate radicals that in turn undergo rearrangements and/or eliminations.
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Affiliation(s)
- Rowena G Matthews
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor MI 48109-2216, USA
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Ragsdale SW, Pierce E. Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1784:1873-98. [PMID: 18801467 PMCID: PMC2646786 DOI: 10.1016/j.bbapap.2008.08.012] [Citation(s) in RCA: 680] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 08/12/2008] [Accepted: 08/13/2008] [Indexed: 01/04/2023]
Abstract
Conceptually, the simplest way to synthesize an organic molecule is to construct it one carbon at a time. The Wood-Ljungdahl pathway of CO(2) fixation involves this type of stepwise process. The biochemical events that underlie the condensation of two one-carbon units to form the two-carbon compound, acetate, have intrigued chemists, biochemists, and microbiologists for many decades. We begin this review with a description of the biology of acetogenesis. Then, we provide a short history of the important discoveries that have led to the identification of the key components and steps of this usual mechanism of CO and CO(2) fixation. In this historical perspective, we have included reflections that hopefully will sketch the landscape of the controversies, hypotheses, and opinions that led to the key experiments and discoveries. We then describe the properties of the genes and enzymes involved in the pathway and conclude with a section describing some major questions that remain unanswered.
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Affiliation(s)
- Stephen W Ragsdale
- Department of Biological Chemistry, MSRB III, 5301, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109-0606, USA.
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The ether-cleaving methyltransferase system of the strict anaerobe Acetobacterium dehalogenans: analysis and expression of the encoding genes. J Bacteriol 2008; 191:588-99. [PMID: 19011025 DOI: 10.1128/jb.01104-08] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic O-demethylases are inducible multicomponent enzymes which mediate the cleavage of the ether bond of phenyl methyl ethers and the transfer of the methyl group to tetrahydrofolate. The genes of all components (methyltransferases I and II, CP, and activating enzyme [AE]) of the vanillate- and veratrol-O-demethylases of Acetobacterium dehalogenans were sequenced and analyzed. In A. dehalogenans, the genes for methyltransferase I, CP, and methyltransferase II of both O-demethylases are clustered. The single-copy gene for AE is not included in the O-demethylase gene clusters. It was found that AE grouped with COG3894 proteins, the function of which was unknown so far. Genes encoding COG3894 proteins with 20 to 41% amino acid sequence identity with AE are present in numerous genomes of anaerobic microorganisms. Inspection of the domain structure and genetic context of these orthologs predicts that these are also reductive activases for corrinoid enzymes (RACEs), such as carbon monoxide dehydrogenase/acetyl coenzyme A synthases or anaerobic methyltransferases. The genes encoding the O-demethylase components were heterologously expressed with a C-terminal Strep-tag in Escherichia coli, and the recombinant proteins methyltransferase I, CP, and AE were characterized. Gel shift experiments showed that the AE comigrated with the CP. The formation of other protein complexes with the O-demethylase components was not observed under the conditions used. The results point to a strong interaction of the AE with the CP. This is the first report on the functional heterologous expression of acetogenic phenyl methyl ether-cleaving O-demethylases.
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Ragsdale SW. Catalysis of methyl group transfers involving tetrahydrofolate and B(12). VITAMINS AND HORMONES 2008; 79:293-324. [PMID: 18804699 PMCID: PMC3037834 DOI: 10.1016/s0083-6729(08)00410-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review focuses on the reaction mechanism of enzymes that use B(12) and tetrahydrofolate (THF) to catalyze methyl group transfers. It also covers the related reactions that use B(12) and tetrahydromethanopterin (THMPT), which is a THF analog used by archaea. In the past decade, our understanding of the mechanisms of these enzymes has increased greatly because the crystal structures for three classes of B(12)-dependent methyltransferases have become available and because biophysical and kinetic studies have elucidated the intermediates involved in catalysis. These steps include binding of the cofactors and substrates, activation of the methyl donors and acceptors, the methyl transfer reaction itself, and product dissociation. Activation of the methyl donor in one class of methyltransferases is achieved by an unexpected proton transfer mechanism. The cobalt (Co) ion within the B(12) macrocycle must be in the Co(I) oxidation state to serve as a nucleophile in the methyl transfer reaction. Recent studies have uncovered important principles that control how this highly reducing active state of B(12) is generated and maintained.
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Affiliation(s)
- Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0606, USA
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Das A, Fu ZQ, Tempel W, Liu ZJ, Chang J, Chen L, Lee D, Zhou W, Xu H, Shaw N, Rose JP, Ljungdahl LG, Wang BC. Characterization of a corrinoid protein involved in the C1 metabolism of strict anaerobic bacterium Moorella thermoacetica. Proteins 2007; 67:167-76. [PMID: 17211893 DOI: 10.1002/prot.21094] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The strict anaerobic, thermophilic bacterium Moorella thermoacetica metabolizes C1 compounds for example CO(2)/H(2), CO, formate, and methanol into acetate via the Wood/Ljungdahl pathway. Some of the key steps in this pathway include the metabolism of the C1 compounds into the methyl group of methylenetetrahydrofolate (MTHF) and the transfer of the methyl group from MTHF to the methyl group of acetyl-CoA catalyzed by methyltransferase, corrinoid protein and CO dehydrogenase/acetyl CoA synthase. Recently, we reported the crystallization of a 25 kDa methanol-induced corrinoid protein from M. thermoacetica (Zhou et al., Acta Crystallogr F 2005; 61:537-540). In this study we analyzed the crystal structure of the 25 kDa protein and provide genetic and biochemical evidences supporting its role in the methanol metabolism of M. thermoacetia. The 25 kDa protein was encoded by orf1948 of contig 303 in the M. thermoacetica genome. It resembles similarity to MtaC the corrinoid protein of the methanol:CoM methyltransferase system of methane producing archaea. The latter enzyme system also contains two additional enzymes MtaA and MtaB. Homologs of MtaA and MtaB were found to be encoded by orf2632 of contig 303 and orf1949 of contig 309, respectively, in the M. thermoacetica genome. The orf1948 and orf1949 were co-transcribed from a single polycistronic operon. Metal analysis and spectroscopic data confirmed the presence of cobalt and the corrinoid in the purified 25 kDa protein. High resolution X-ray crystal structure of the purified 25 kDa protein revealed corrinoid as methylcobalamin with the imidazole of histidine as the alpha-axial ligand replacing benziimidazole, suggesting base-off configuration for the corrinoid. Methanol significantly activated the expression of the 25 kDa protein. Cyanide and nitrate inhibited methanol metabolism and suppressed the level of the 25 kDa protein. The results suggest a role of the 25 kDa protein in the methanol metabolism of M. thermoacetica.
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Affiliation(s)
- Amaresh Das
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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Dilling S, Imkamp F, Schmidt S, Müller V. Regulation of caffeate respiration in the acetogenic bacterium Acetobacterium woodii. Appl Environ Microbiol 2007; 73:3630-6. [PMID: 17416687 PMCID: PMC1932707 DOI: 10.1128/aem.02060-06] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The anaerobic acetogenic bacterium Acetobacterium woodii can conserve energy by oxidation of various substrates coupled to either carbonate or caffeate respiration. We used a cell suspension system to study the regulation and kinetics of induction of caffeate respiration. After addition of caffeate to suspensions of fructose-grown cells, there was a lag phase of about 90 min before caffeate reduction commenced. However, in the presence of tetracycline caffeate was not reduced, indicating that de novo protein synthesis is required for the ability to respire caffeate. Induction also took place in the presence of CO(2), and once a culture was induced, caffeate and CO(2) were used simultaneously as electron acceptors. Induction of caffeate reduction was also observed with H(2) plus CO(2) as the substrate, but the lag phase was much longer. Again, caffeate and CO(2) were used simultaneously as electron acceptors. In contrast, during oxidation of methyl groups derived from methanol or betaine, acetogenesis was the preferred energy-conserving pathway, and caffeate reduction started only after acetogenesis was completed. The differential flow of reductants was also observed with suspensions of resting cells in which caffeate reduction was induced prior to harvest of the cells. These cell suspensions utilized caffeate and CO(2) simultaneously with fructose or hydrogen as electron donors, but CO(2) was preferred over caffeate during methyl group oxidation. Caffeate-induced resting cells could reduce caffeate and also p-coumarate or ferulate with hydrogen as the electron donor. p-Coumarate or ferulate also served as an inducer for caffeate reduction. Interestingly, caffeate-induced cells reduced ferulate in the absence of an external reductant, indicating that caffeate also induces the enzymes required for oxidation of the methyl group of ferulate.
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Affiliation(s)
- Sabrina Dilling
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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Nonaka H, Keresztes G, Shinoda Y, Ikenaga Y, Abe M, Naito K, Inatomi K, Furukawa K, Inui M, Yukawa H. Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195. J Bacteriol 2006; 188:2262-74. [PMID: 16513756 PMCID: PMC1428132 DOI: 10.1128/jb.188.6.2262-2274.2006] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Desulfitobacterium strains have the ability to dechlorinate halogenated compounds under anaerobic conditions by dehalorespiration. The complete genome of the tetrachloroethene (PCE)-dechlorinating strain Desulfitobacterium hafniense Y51 is a 5,727,534-bp circular chromosome harboring 5,060 predicted protein coding sequences. This genome contains only two reductive dehalogenase genes, a lower number than reported in most other dehalorespiring strains. More than 50 members of the dimethyl sulfoxide reductase superfamily and 30 paralogs of the flavoprotein subunit of the fumarate reductase are encoded as well. A remarkable feature of the genome is the large number of O-demethylase paralogs, which allow utilization of lignin-derived phenyl methyl ethers as electron donors. The large genome reveals a more versatile microorganism that can utilize a larger set of specialized electron donors and acceptors than previously thought. This is in sharp contrast to the PCE-dechlorinating strain Dehalococcoides ethenogenes 195, which has a relatively small genome with a narrow metabolic repertoire. A genomic comparison of these two very different strains allowed us to narrow down the potential candidates implicated in the dechlorination process. Our results provide further impetus to the use of desulfitobacteria as tools for bioremediation.
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Affiliation(s)
- Hiroshi Nonaka
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizu-Cho, Soraku-Gun, Kyoto 619-0292, Japan
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Clavel T, Borrmann D, Braune A, Doré J, Blaut M. Occurrence and activity of human intestinal bacteria involved in the conversion of dietary lignans. Anaerobe 2005; 12:140-7. [PMID: 16765860 DOI: 10.1016/j.anaerobe.2005.11.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Revised: 11/07/2005] [Accepted: 11/09/2005] [Indexed: 12/12/2022]
Abstract
The human intestinal microbiota is necessary for the production of enterolignans from the dietary lignan secoisolariciresinol diglucoside (SDG). However, little is known about the bacteria that contribute to SDG conversion. Therefore, we aimed at describing the occurrence and activity of SDG metabolising bacteria. The data showed differences in conversion efficiency between SDG deglycosylating species, but SDG was completely deglycosylated within 20 h by five of six strains. The strain Clostridium sp. SDG-Mt85-3Db showed the highest initial rate of SDG deglycosylation. Furthermore, we found that Bacteroides distasonis and B. fragilis made up 0.5% and 3.3% of total faecal bacteria, respectively. However, Clostridium sp. SDG-Mt85-3Db was detected within the dominant microbiota of only two out of 20 faecal samples. Bacteria involved in the demethylation step of SDG conversion also demethylated a variety of compounds other than SDG. In particular, Peptostreptococcus productus demethylated the lignans pinoresinol, lariciresinol and matairesinol. Finally, Eggerthella lenta catalysed the reduction of pinoresinol and lariciresinol to secoisolariciresinol.
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Affiliation(s)
- Thomas Clavel
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 155, 14558 Nuthetal, Germany
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Siebert A, Schubert T, Engelmann T, Studenik S, Diekert G. Veratrol-O-demethylase of Acetobacterium dehalogenans: ATP-dependent reduction of the corrinoid protein. Arch Microbiol 2005; 183:378-84. [PMID: 15968525 DOI: 10.1007/s00203-005-0001-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2004] [Revised: 03/31/2005] [Accepted: 05/04/2005] [Indexed: 10/25/2022]
Abstract
The anaerobic veratrol O-demethylase mediates the transfer of the methyl group of the phenyl methyl ether veratrol to tetrahydrofolate. The primary methyl group acceptor is the cobalt of a corrinoid protein, which has to be in the +1 oxidation state to bind the methyl group. Due to the negative redox potential of the cob(II)/cob(I)alamin couple, autoxidation of the cobalt may accidentally occur. In this study, the reduction of the corrinoid to the superreduced [Co(I)] state was investigated. The ATP-dependent reduction of the corrinoid protein of the veratrol O-demethylase was shown to be dependent on titanium(III) citrate as electron donor and on an activating enzyme. In the presence of ATP, activating enzyme, and Ti(III), the redox potential versus the standard hydrogen electrode (E (SHE)) of the cob(II)alamin/cob(I)alamin couple in the corrinoid protein was determined to be -290 mV (pH 7.5), whereas E (SHE) at pH 7.5 was lower than -450 mV in the absence of either activating enzyme or ATP. ADP, AMP, or GTP could not replace ATP in the activation reaction. The ATP analogue adenosine-5'-(beta,gamma-imido)triphosphate (AMP-PNP, 2-4 mM) completely inhibited the corrinoid reduction in the presence of ATP (2 mM).
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Affiliation(s)
- Anke Siebert
- Institut für Mikrobiologie, FSU Jena, Lehrstuhl für Angewandte und Okologische Mikrobiologie, Philosophenweg 12, 07743 Jena, Germany
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Abe T, Masai E, Miyauchi K, Katayama Y, Fukuda M. A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6. J Bacteriol 2005; 187:2030-7. [PMID: 15743951 PMCID: PMC1064056 DOI: 10.1128/jb.187.6.2030-2037.2005] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vanillate and syringate are converted into protocatechuate (PCA) and 3-O-methylgallate (3MGA), respectively, by O-demethylases in Sphingomonas paucimobilis SYK-6. PCA is further degraded via the PCA 4,5-cleavage pathway, while 3MGA is degraded through multiple pathways in which PCA 4,5-dioxygenase (LigAB), 3MGA 3,4-dioxygenase (DesZ), and an unidentified 3MGA O-demethylase and gallate dioxygenase are participants. For this study, we isolated a 4.7-kb SmaI fragment that conferred on Escherichia coli the activity required for the conversion of vanillate to PCA. The nucleotide sequence of this fragment revealed an open reading frame of 1,413 bp (ligM), the deduced amino acid sequence of which showed 49% identity with that of the tetrahydrofolate (H4folate)-dependent syringate O-demethylase gene (desA). The metF and ligH genes, which are thought to be involved in H4folate-mediated C1 metabolism, were located just downstream of ligM. The crude LigM enzyme expressed in E. coli converted vanillate and 3MGA to PCA and gallate, respectively, with similar specific activities, and only in the presence of H4folate; however, syringate was not a substrate for LigM. The disruption of ligM led to significant growth retardation on both vanillate and syringate, indicating that ligM is involved in the catabolism of these substrates. The ability of the ligM mutant to transform vanillate was markedly decreased, and this mutant completely lost the 3MGA O-demethylase activity. A ligM desA double mutant completely lost the ability to transform vanillate, thus indicating that desA also contributes to vanillate degradation. All of these results indicate that ligM encodes vanillate/3MGA O-demethylase and plays an important role in the O demethylation of vanillate and 3MGA, respectively.
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Affiliation(s)
- Tomokuni Abe
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
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Braune A, Engst W, Blaut M. Degradation of neohesperidin dihydrochalcone by human intestinal bacteria. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2005; 53:1782-1790. [PMID: 15740074 DOI: 10.1021/jf0484982] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The degradation of neohesperidin dihydrochalcone by human intestinal microbiota was studied in vitro. Human fecal slurries converted neohesperidin dihydrochalcone anoxically to 3-(3-hydroxy-4-methoxyphenyl)propionic acid or 3-(3,4-dihydroxyphenyl)propionic acid. Two transient intermediates were identified as hesperetin dihydrochalcone 4'-beta-d-glucoside and hesperetin dihydrochalcone. These metabolites suggest that neohesperidin dihydrochalcone is first deglycosylated to hesperetin dihydrochalcone 4'-beta-d-glucoside and subsequently to the aglycon hesperetin dihydrochalcone. The latter is hydrolyzed to the corresponding 3-(3-hydroxy-4-methoxyphenyl)propionic acid and probably phloroglucinol. Eubacterium ramulus and Clostridium orbiscindens were not capable of converting neohesperidin dihydrochalcone. However, hesperetin dihydrochalcone 4'-beta-d-glucoside was converted by E. ramulus to hesperetin dihydrochalcone and further to 3-(3-hydroxy-4-methoxyphenyl)propionic acid, but not by C. orbiscindens. In contrast, hesperetin dihydrochalcone was cleaved to 3-(3-hydroxy-4-methoxyphenyl)propionic acid by both species. The latter reaction was shown to be catalyzed by the phloretin hydrolase from E. ramulus.
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Affiliation(s)
- Annett Braune
- Department of Gastrointestinal Microbiology and of Nutritional Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, D-14558 Nuthetal, Germany.
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Kim YH, Engesser KH. Degradation of alkyl ethers, aralkyl ethers, and dibenzyl ether by Rhodococcus sp. strain DEE5151, isolated from diethyl ether-containing enrichment cultures. Appl Environ Microbiol 2004; 70:4398-401. [PMID: 15240329 PMCID: PMC444782 DOI: 10.1128/aem.70.7.4398-4401.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty strains isolated from sewage sludge were found to degrade various ethers, including alkyl ethers, aralkyl ethers, and dibenzyl ether. In Rhodococcus strain DEE5151, induction of ether degradation needed substrates exhibiting at least one unsubstituted Calpha-methylene moiety as the main structural prerequisite. The cleavage reaction observed with anisole, phenetole, and dibenzyl ether indicates that the initial oxidation occurs at such respective Calpha positions. Diethyl ether-induced strain DEE5151 degraded dibenzyl ether via intermediately accumulated benzoic acid. Phenetole seems to be subject also to another ether-cleaving enzyme. Other strains of this group showed different enzymatic activities towards the substrate classes investigated.
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Affiliation(s)
- Yong-Hak Kim
- Institut für Siedlungswasserbau, Wassergüte- und Abfallwirtschaft, Universität Stuttgart, Abteilung Biologische Abluftreinigung, Bandtäle 2, D-70569 Stuttgart (Büsnau), Germany
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47
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Masai E, Sasaki M, Minakawa Y, Abe T, Sonoki T, Miyauchi K, Katayama Y, Fukuda M. A novel tetrahydrofolate-dependent O-demethylase gene is essential for growth of Sphingomonas paucimobilis SYK-6 with syringate. J Bacteriol 2004; 186:2757-65. [PMID: 15090517 PMCID: PMC387776 DOI: 10.1128/jb.186.9.2757-2765.2004] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sphingomonas paucimobilis SYK-6 degrades syringate to 3-O-methylgallate (3MGA), which is finally converted to pyruvate and oxaloacetate via multiple pathways in which protocatechuate 4,5-dioxygenase, 3MGA dioxygenase, and gallate dioxygenase are involved. Here we isolated the syringate O-demethylase gene (desA), which complemented the growth deficiency on syringate of a Tn5 mutant of the SYK-6 derivative strain. The desA gene is located 929 bp downstream of ferA, encoding feruloyl-coenzyme A synthetase, and consists of a 1,386-bp open reading frame encoding a polypeptide with a molecular mass of 50,721 Da. The deduced amino acid sequence of desA showed 26% identity in a 325-amino-acid overlap with that of gcvT of Escherichia coli, which encodes the tetrahydrofolate (H(4)folate)-dependent aminomethyltransferase involved in glycine cleavage. The cell extract of E. coli carrying desA converted syringate to 3MGA only when H(4)folate was added to the reaction mixture. DesA catalyzes the transfer of the methyl moiety of syringate to H(4)folate, forming 5-methyl-H(4)folate. Vanillate and 3MGA were also used as substrates for DesA; however, the relative activities toward them were 3 and 0.4% of that toward syringate, respectively. Disruption of desA in SYK-6 resulted in a growth defect on syringate but did not affect growth on vanillate, indicating that desA is essential to syringate degradation. In a previous study the ligH gene, which complements the growth deficiency on vanillate and syringate of a chemical-induced mutant of SYK-6, DC-49, was isolated (S. Nishikawa, T. Sonoki, T. Kasahara, T. Obi, S. Kubota, S. Kawai, N. Morohoshi, and Y. Katayama, Appl. Environ. Microbiol. 64:836-842, 1998). Disruption of ligH resulted in the same phenotype as DC-49; its cell extract, however, was found to be able to convert vanillate and syringate in the presence of H(4)folate. The possible role of ligH is discussed.
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Affiliation(s)
- Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.
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Abstract
Vitamin B12 is a complex organometallic cofactor associated with three subfamilies of enzymes: the adenosylcobalamin-dependent isomerases, the methylcobalamin-dependent methyltransferases, and the dehalogenases. Different chemical aspects of the cofactor are exploited during catalysis by the isomerases and the methyltransferases. Thus, the cobalt-carbon bond ruptures homolytically in the isomerases, whereas it is cleaved heterolytically in the methyltransferases. The reaction mechanism of the dehalogenases, the most recently discovered class of B12 enzymes, is poorly understood. Over the past decade our understanding of the reaction mechanisms of B12 enzymes has been greatly enhanced by the availability of large amounts of enzyme that have afforded detailed structure-function studies, and these recent advances are the subject of this review.
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Affiliation(s)
- Ruma Banerjee
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA. ;
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Naidu D, Ragsdale SW. Characterization of a three-component vanillate O-demethylase from Moorella thermoacetica. J Bacteriol 2001; 183:3276-81. [PMID: 11344134 PMCID: PMC99624 DOI: 10.1128/jb.183.11.3276-3281.2001] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Moorella thermoacetica aromatic O-demethylase was characterized as an inducible three-component system with similarity to the methanogenic methanol, methylamine, and methanethiol methyltransferases and to the O-demethylase system from Acetobacterium dehalogenans. MtvB catalyzes methyl transfer from a phenylmethylether to the cobalt center of MtvC, a corrinoid protein. MtvA catalyzes transmethylation from MtvC to tetrahydrofolate, forming methyltetrahydrofolate. Cobalamin can substitute for MtvC.
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Affiliation(s)
- D Naidu
- Department of Biochemistry, Beadle Center, University of Nebraska-Lincoln, Lincoln, NE 68588-0664, USA
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Jansen M, Hansen TA. Non-growth-associated demethylation of dimethylsulfoniopropionate by (homo)acetogenic bacteria. Appl Environ Microbiol 2001; 67:300-6. [PMID: 11133459 PMCID: PMC92569 DOI: 10.1128/aem.67.1.300-306.2001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The demethylation of the algal osmolyte dimethylsulfoniopropionate (DMSP) to methylthiopropionate (MTPA) by (homo)acetogenic bacteria was studied. Five Eubacterium limosum strains (including the type strain), Sporomusa ovata DSM 2662(T), Sporomusa sphaeroides DSM 2875(T), and Acetobacterium woodii DSM 1030(T) were shown to demethylate DMSP stoichiometrically to MTPA. The (homo)acetogenic fermentation based on this demethylation did not result in any significant increase in biomass. The analogous demethylation of glycine betaine to dimethylglycine does support growth of acetogens. In batch cultures of E. limosum PM31 DMSP and glycine betaine were demethylated simultaneously. In mixed substrates experiments with fructose-DMSP or methanol-DMSP, DMSP was used rapidly but only after exhaustion of the fructose or the methanol. In steady-state fructose-limited chemostat cultures (at a dilution rate of 0.03 h(-1)) with DMSP as a second reservoir substrate, DMSP was biotransformed to MTPA but this did not result in higher biomass values than in cultures without DMSP; cells from such cultures demethylated DMSP at rates of approximately 50 nmol min(-1) mg of protein(-1), both after growth in the presence of DMSP and after growth in its absence. In cell extracts of glycine betaine-grown strain PM31, DMSP demethylation activities of 21 to 24 nmol min(-1) mg of protein(-1) were detected with tetrahydrofolate as a methyl acceptor; the activities seen with glycine betaine were approximately 10-fold lower. A speculative explanation for the demethylation of DMSP without an obvious benefit for the organism is that the DMSP-demethylating activity is catalyzed by the glycine betaine-demethylating enzyme and that a transport-related factor, in particular a higher energy demand for DMSP transport across the cytoplasmic membrane than for glycine betaine transport, may reduce the overall ATP yield of the fermentation to virtually zero.
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Affiliation(s)
- M Jansen
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, NL-9750 AA Haren, The Netherlands
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