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Heker I, Haberhauer G, Meckenstock RU. Naphthalene Carboxylation in the Sulfate-Reducing Enrichment Culture N47 Is Proposed to Proceed via 1,3-Dipolar Cycloaddition to the Cofactor Prenylated Flavin Mononucleotide. Appl Environ Microbiol 2023; 89:e0192722. [PMID: 36815794 PMCID: PMC10057960 DOI: 10.1128/aem.01927-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/12/2023] [Indexed: 02/24/2023] Open
Abstract
Polycyclic aromatic hydrocarbons are persistent pollutants of anthropogenic or natural origin in the environment and accumulate in anoxic habitats. In this study, we investigated the mechanism of the enzyme naphthalene carboxylase as a model reaction for polycyclic aromatic hydrocarbon activation by carboxylation. An enzyme assay was established with cell extracts of the highly enriched culture N47. In assays without addition of ATP, naphthalene carboxylase catalyzed a stable isotope exchange of the carboxyl group of naphthoate with 13C-labeled bicarbonate buffer, which can only occur via a partial backwards reaction of the naphthalene carboxylase reaction to an intermediate that does not include the carboxyl group. Hence, a new carboxyl group from the labeled bicarbonate is added upon forward reaction to the naphthoate. This indicates that the reaction mechanism consists of two or more steps and that at least the latter steps are reversible and ATP independent. Naphthalene carboxylation assays were carried out in deuterated buffer and revealed the incorporation of 0, 1, 2, or 3 deuterium atoms in the final product naphthoyl-coenzyme A, indicating that the reaction is fully reversible. Putative reaction mechanisms were tested by quantum mechanical calculations. The proposed mechanism of the reaction consists of three steps: the activation of the naphthalene by 1,3-dipolar cycloaddition of the cofactor prFMN to naphthalene, release of a proton and rearomatization producing a stable intermediate, and a carboxylation with a reverse 1,3-dipolar cycloaddition and cleavage of the bond to the cofactor producing 2-naphthoate. IMPORTANCE Pollution with polycyclic aromatic hydrocarbons poses a great hazard to humans and animals, with considerable long-term effects. The anaerobic degradation of polycyclic aromatic hydrocarbons in anoxic zones and anaerobic growth of such organisms is very slow, leading to only poor investigation of the degradation pathways, so far. In this work, we elucidated the mechanism of naphthalene carboxylase, a key enzyme in anaerobic naphthalene degradation. This is the first mechanism proposed for a carboxylase targeting nonsubstituted (polycyclic) aromatic compounds and can serve as a model for the initial activation reaction in the anaerobic degradation of benzene or nonsubstituted polycyclic aromatic hydrocarbons, as well as similar enzymatic reactions from the expanding class of UbiD-like (de)carboxylases.
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Affiliation(s)
- Isabelle Heker
- Institute for Environmental Microbiology and Biotechnology, Aquatic Microbiology, University Duisburg-Essen, Essen, Germany
| | - Gebhard Haberhauer
- Institute for Organic Chemistry, University Duisburg-Essen, Essen, Germany
| | - Rainer U. Meckenstock
- Institute for Environmental Microbiology and Biotechnology, Aquatic Microbiology, University Duisburg-Essen, Essen, Germany
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2
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The Catabolic System of Acetovanillone and Acetosyringone in Sphingobium sp. Strain SYK-6 Useful for Upgrading Aromatic Compounds Obtained through Chemical Lignin Depolymerization. Appl Environ Microbiol 2022; 88:e0072422. [PMID: 35938864 PMCID: PMC9397112 DOI: 10.1128/aem.00724-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Acetovanillone is a major aromatic monomer produced in oxidative/base-catalyzed lignin depolymerization. However, the production of chemical products from acetovanillone has not been explored due to the lack of information on the microbial acetovanillone catabolic system. Here, the acvABCDEF genes were identified as specifically induced genes during the growth of Sphingobium sp. strain SYK-6 cells with acetovanillone and these genes were essential for SYK-6 growth on acetovanillone and acetosyringone (a syringyl-type acetophenone derivative). AcvAB and AcvF produced in Escherichia coli phosphorylated acetovanillone/acetosyringone and dephosphorylated the phosphorylated acetovanillone/acetosyringone, respectively. AcvCDE produced in Sphingobium japonicum UT26S carboxylated the reaction products generated from acetovanillone/acetosyringone by AcvAB and AcvF into vanilloyl acetic acid/3-(4-hydroxy-3,5-dimethoxyphenyl)-3-oxopropanoic acid. To demonstrate the feasibility of producing cis,cis-muconic acid from acetovanillone, a metabolic modification on a mutant of Pseudomonas sp. strain NGC7 that accumulates cis,cis-muconic acid from catechol was performed. The resulting strain expressing vceA and vceB required for converting vanilloyl acetic acid to vanillic acid and aroY encoding protocatechuic acid decarboxylase in addition to acvABCDEF successfully converted 1.2 mM acetovanillone to approximately equimolar cis,cis-muconic acid. Our results are expected to help improve the yield and purity of value-added chemical production from lignin through biological funneling. IMPORTANCE In the alkaline oxidation of lignin, aromatic aldehydes (vanillin, syringaldehyde, and p-hydroxybenzaldehyde), aromatic acids (vanillic acid, syringic acid, and p-hydroxybenzoic acid), and acetophenone-related compounds (acetovanillone, acetosyringone, and 4'-hydroxyacetophenone) are produced as major aromatic monomers. Also, base-catalyzed depolymerization of guaiacyl lignin resulted in vanillin, vanillic acid, guaiacol, and acetovanillone as primary aromatic monomers. To date, microbial catabolic systems of vanillin, vanillic acid, and guaiacol have been well characterized, and the production of value-added chemicals from them has also been explored. However, due to the lack of information on the microbial acetovanillone and acetosyringone catabolic system, chemical production from acetovanillone and acetosyringone has not been achieved. This study elucidated the acetovanillone/acetosyringone catabolic system and demonstrates the potential of using these genes for the production of value-added chemicals from these compounds.
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Rawat A, Dhakla S, Lama P, Pal TK. Fixation of carbon dioxide to aryl/aromatic carboxylic acids. J CO2 UTIL 2022. [DOI: 10.1016/j.jcou.2022.101939] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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4
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Schweitzer HD, Smith HJ, Barnhart EP, McKay LJ, Gerlach R, Cunningham AB, Malmstrom RR, Goudeau D, Fields MW. Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics. NPJ Biofilms Microbiomes 2022; 8:7. [PMID: 35177633 PMCID: PMC8854433 DOI: 10.1038/s41522-022-00267-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 01/05/2022] [Indexed: 11/18/2022] Open
Abstract
Environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities under in situ conditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled coal seams. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways was observed but with a predominance of aerobic dioxygenases. The putative low-molecular-weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The methods used in this study—subsurface environmental samplers in combination with metagenomic sequencing of both total and translationally active metagenomes—offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox conditions broadening the understanding of degradation strategies for subsurface carbon.
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Affiliation(s)
- Hannah D Schweitzer
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA. .,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA. .,UiT-The Arctic University of Norway, 9019, Tromsø, Norway.
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA. .,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
| | - Elliott P Barnhart
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.,US Geological Survey, Wyoming-Montana Water Science Center, Helena, MT, 59601, USA
| | - Luke J McKay
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.,Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Robin Gerlach
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.,Energy Research Institute, Montana State University, Bozeman, MT, 59717, USA.,Department of Biological and Chemical Engineering, Montana State University, Bozeman, MT, 59717, USA
| | - Alfred B Cunningham
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.,Energy Research Institute, Montana State University, Bozeman, MT, 59717, USA.,Department of Civil Engineering, Montana State University, Bozeman, MT, 59717, USA
| | | | | | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA. .,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA. .,Energy Research Institute, Montana State University, Bozeman, MT, 59717, USA.
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Nanomolar Responsiveness of an Anaerobic Degradation Specialist to Alkylphenol Pollutants. J Bacteriol 2020; 202:JB.00595-19. [PMID: 31843798 DOI: 10.1128/jb.00595-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022] Open
Abstract
Anaerobic degradation of p-cresol (4-methylphenol) by the denitrifying betaproteobacterium Aromatoleum aromaticum EbN1 is regulated with high substrate specificity, presumed to be mediated by the predicted σ54-dependent two-component system PcrSR. An unmarked, in-frame ΔpcrSR deletion mutant showed reduced expression of the genes cmh (21-fold) and hbd (8-fold) that encode the two enzymes for initial oxidation of p-cresol to p-hydroxybenzoate compared to their expression in the wild type. The expression of cmh and hbd was restored by in trans complementation with pcrSR in the ΔpcrSR background to even higher levels than in the wild type. This is likely due to ∼200-/∼30-fold more transcripts of pcrSR in the complemented mutant. The in vivo responsiveness of A. aromaticum EbN1 to p-cresol was studied in benzoate-limited anaerobic cultures by the addition of p-cresol at various concentrations (from 100 μM down to 0.1 nM). Time-resolved transcript profiling by quantitative reverse transcription-PCR (qRT-PCR) revealed that the lowest p-cresol concentrations just affording cmh and hbd expression (response threshold) ranged between 1 and 10 nM, which is even more sensitive than the respective odor receptors of insects. A similar response threshold was determined for another alkylphenol, p-ethylphenol, which strain EbN1 anaerobically degrades via a different route and senses by the σ54-dependent one-component system EtpR. Based on these data and theoretical considerations, p-cresol or p-ethylphenol added as a single pulse (10 nM) requires less than a fraction of a second to reach equilibrium between intra- and extracellular space (∼20 molecules per cell), with an estimated Kd (dissociation constant) of <100 nM alkylphenol (p-cresol or p-ethylphenol) for its respective sensory protein (PcrS or EtpR).IMPORTANCE Alkylphenols (like p-cresol and p-ethylphenol) represent bulk chemicals for industrial syntheses. Besides massive local damage events, large-scale micropollution is likewise of environmental and health concern. Next to understanding how such pollutants can be degraded by microorganisms, it is also relevant to determine the microorganisms' lower threshold of responsiveness. Aromatoleum aromaticum EbN1 is a specialist in anaerobic degradation of aromatic compounds, employing a complex and substrate-specifically regulated catabolic network. The present study aims at verifying the predicted role of the PcrSR system in sensing p-cresol and at determining the threshold of responsiveness for alkylphenols. The findings have implications for the enigmatic persistence of dissolved organic matter (escape from biodegradation) and for the lower limits of aromatic compounds required for bacterial growth.
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Payer SE, Faber K, Glueck SM. Non-Oxidative Enzymatic (De)Carboxylation of (Hetero)Aromatics and Acrylic Acid Derivatives. Adv Synth Catal 2019; 361:2402-2420. [PMID: 31379472 PMCID: PMC6644310 DOI: 10.1002/adsc.201900275] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/16/2019] [Indexed: 12/20/2022]
Abstract
The utilization of carbon dioxide as a C1-building block for the production of valuable chemicals has recently attracted much interest. Whereas chemical CO2 fixation is dominated by C-O and C-N bond forming reactions, the development of novel concepts for the carboxylation of C-nucleophiles, which leads to the formation of carboxylic acids, is highly desired. Beside transition metal catalysis, biocatalysis has emerged as an attractive method for the highly regioselective (de)carboxylation of electron-rich (hetero)aromatics, which has been recently further expanded to include conjugated α,β-unsaturated (acrylic) acid derivatives. Depending on the type of substrate, different classes of enzymes have been explored for (i) the ortho-carboxylation of phenols catalyzed by metal-dependent ortho-benzoic acid decarboxylases and (ii) the side-chain carboxylation of para-hydroxystyrenes mediated by metal-independent phenolic acid decarboxylases. Just recently, the portfolio of bio-carboxylation reactions was complemented by (iii) the para-carboxylation of phenols and the decarboxylation of electron-rich heterocyclic and acrylic acid derivatives mediated by prenylated FMN-dependent decarboxylases, which is the main focus of this review. Bio(de)carboxylation processes proceed under physiological reaction conditions employing bicarbonate or (pressurized) CO2 when running in the energetically uphill carboxylation direction. Aiming to facilitate the application of these enzymes in preparative-scale biotransformations, their catalytic mechanism and substrate scope are analyzed in this review.
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Affiliation(s)
- Stefan E. Payer
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Kurt Faber
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
| | - Silvia M. Glueck
- Institute of ChemistryUniversity of GrazHeinrichstrasse 288010GrazAustria
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7
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Carboxylation of Hydroxyaromatic Compounds with HCO3− by Enzyme Catalysis: Recent Advances Open the Perspective for Valorization of Lignin-Derived Aromatics. Catalysts 2019. [DOI: 10.3390/catal9010037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
This review focuses on recent advances in the field of enzymatic carboxylation reactions of hydroxyaromatic compounds using HCO3− (as a CO2 source) to produce hydroxybenzoic and other phenolic acids in mild conditions with high selectivity and moderate to excellent yield. Nature offers an extensive portfolio of enzymes catalysing reversible decarboxylation of hydroxyaromatic acids, whose equilibrium can be pushed towards the side of the carboxylated products. Extensive structural and mutagenesis studies have allowed recent advances in the understanding of the reaction mechanism of decarboxylase enzymes, ultimately enabling an improved yield and expansion of the scope of the reaction. The topic is of particular relevance today as the scope of the carboxylation reactions can be extended to include lignin-related compounds in view of developing lignin biorefinery technology.
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8
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Pesci L, Gurikov P, Liese A, Kara S. Amine-Mediated Enzymatic Carboxylation of Phenols Using CO 2 as Substrate Increases Equilibrium Conversions and Reaction Rates. Biotechnol J 2017; 12. [PMID: 28862371 DOI: 10.1002/biot.201700332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/18/2017] [Indexed: 01/08/2023]
Abstract
A variety of strategies is applied to alleviate thermodynamic and kinetic limitations in biocatalytic carboxylation of metabolites in vivo. A key feature to consider in enzymatic carboxylations is the nature of the cosubstrate: CO2 or its hydrated form, bicarbonate. The substrate binding and activation mechanism determine what the actual carboxylation agent is. Dihydroxybenzoic acid (de)carboxylases catalyze the reversible regio-selective ortho-(de)carboxylation of phenolics. These enzymes have attracted considerable attention in the last 10 years due to their potential in substituting harsh conditions typical of chemical carboxylations (100-200 °C, 5-100 bar) with, ideally, greener ones (20-40 °C, 1 bar). They are reported to use bicarbonate as substrate, needed in large excess to overcome thermodynamic and kinetic limitations. Therefore, CO2 can be used as substrate by these enzymes only if it is converted into bicarbonate in situ. In this contribution, we report the simultaneous amine-mediated conversion of CO2 into bicarbonate and the ortho-carboxylation of different phenolic molecules catalyzed by 2,3-dihydroxybenzoic acid (de)carboxylase from Aspergillus oryzae. Our results show that under the newly developed conditions a significant thermodynamic (up to twofold increase in conversion) and kinetic improvement (up to approx. fivefold increase in rate) of the biocatalytic carboxylation of catechol is achieved.
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Affiliation(s)
- Lorenzo Pesci
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
| | - Pavel Gurikov
- Institute of Thermal Separation Processes, Hamburg University of Technology, Hamburg, Germany
| | - Andreas Liese
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
| | - Selin Kara
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
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Wang W, Wu B, Pan S, Yang K, Hu Z, Yuan S. Performance robustness of the UASB reactors treating saline phenolic wastewater and analysis of microbial community structure. JOURNAL OF HAZARDOUS MATERIALS 2017; 331:21-27. [PMID: 28242525 DOI: 10.1016/j.jhazmat.2017.02.025] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/06/2017] [Accepted: 02/14/2017] [Indexed: 06/06/2023]
Abstract
Anaerobic digestion was an important way to remove phenols from saline wastewater; however the anaerobic microorganisms were adversely affected by high concentration of salts. In order to clarify the performance robustness and microbial community structure for anaerobic digestion of saline phenolic wastewater, the UASB reactors were compared to treat phenolic wastewater under saline and non-saline conditions. The saline reactors were operated stably with phenols concentration increasing from 100 to 500mgL-1 at 10g Na+ L-1. The robustness of the saline reactors was weakened at 1000mg phenols L-1 and 10g Na+ L-1. However, the substrate utilization rates (SURs) for phenol, catechol, resorcinol, hydroquinone, and the specific methanogenic activity (SMA) of sludge were decreased by 95%, 85%, 97%, 78%, and 68%, respectively with phenols concentration enhancing from 1000 to 2000mgL-1. Moreover, the SURs for phenol, catechol, resorcinol, hydroquinone, and the SMA of sludge were reduced by 32%, 65%, 74%, 45%, and 59%, respectively with Na+ concentration increasing from 10 to 20gL-1, in comparison with the values obtained at 10g Na+ L-1 and 1000mg phenols L-1. Finally, the analysis of microbial community structure demonstrated that phenols degraders were less tolerant to high concentrations of Na+ and phenols than methanogens.
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Affiliation(s)
- Wei Wang
- Department of Municipal Engineering, School of Civil and Hydraulic Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Benteng Wu
- Department of Municipal Engineering, School of Civil and Hydraulic Engineering, Hefei University of Technology, Hefei 230009, China
| | - Shanglei Pan
- Department of Municipal Engineering, School of Civil and Hydraulic Engineering, Hefei University of Technology, Hefei 230009, China
| | - Kai Yang
- Department of Municipal Engineering, School of Civil and Hydraulic Engineering, Hefei University of Technology, Hefei 230009, China
| | - Zhenhu Hu
- Department of Municipal Engineering, School of Civil and Hydraulic Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Shoujun Yuan
- Department of Municipal Engineering, School of Civil and Hydraulic Engineering, Hefei University of Technology, Hefei 230009, China
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Meckenstock RU, Boll M, Mouttaki H, Koelschbach JS, Cunha Tarouco P, Weyrauch P, Dong X, Himmelberg AM. Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons. J Mol Microbiol Biotechnol 2016; 26:92-118. [DOI: 10.1159/000441358] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers.
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Wei X, Gilevska T, Wetzig F, Dorer C, Richnow HH, Vogt C. Characterization of phenol and cresol biodegradation by compound-specific stable isotope analysis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 210:166-73. [PMID: 26716730 DOI: 10.1016/j.envpol.2015.11.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/21/2015] [Accepted: 11/02/2015] [Indexed: 05/06/2023]
Abstract
Microbial degradation of phenol and cresols can occur under oxic and anoxic conditions by different degradation pathways. One recent technique to take insight into reaction mechanisms is compound-specific isotope analysis (CSIA). While enzymes and reaction mechanisms of several degradation pathways have been characterized in (bio)chemical studies, associated isotope fractionation patterns have been rarely reported, possibly due to constraints in current analytical methods. In this study, carbon enrichment factors and apparent kinetic isotope effects (AKIEc) of the initial steps of different aerobic and anaerobic phenol and cresols degradation pathways were analyzed by isotope ratio mass spectrometry connected with liquid chromatography (LC-IRMS). Significant isotope fractionation was detected for aerobic ring hydroxylation, anoxic side chain hydroxylation, and anoxic fumarate addition, while anoxic carboxylation reactions produced small and inconsistent fractionation. The results suggest that several microbial degradation pathways of phenol and cresols are detectable in the environment by CSIA.
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Affiliation(s)
- Xi Wei
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany; Friedrich Schiller University Jena, Institute for Microbiology, Department of Applied and Ecological Microbiology, Jena, Germany
| | - Tetyana Gilevska
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany
| | - Felix Wetzig
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany; Friedrich Schiller University Jena, Faculty of Chemistry and Earth Science, Jena, Germany
| | - Conrad Dorer
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany; University of Freiburg, Faculty of Biology, Schänzlestrasse 1, Freiburg, Germany
| | - Hans-Hermann Richnow
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany
| | - Carsten Vogt
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, Leipzig, Germany.
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12
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Muhr E, Schühle K, Clermont L, Sünwoldt K, Kleinsorge D, Seyhan D, Kahnt J, Schall I, Cordero PR, Schmitt G, Heider J. Enzymes of anaerobic ethylbenzene and p-ethylphenol catabolism in 'Aromatoleum aromaticum': differentiation and differential induction. Arch Microbiol 2015; 197:1051-62. [PMID: 26275558 DOI: 10.1007/s00203-015-1142-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/24/2015] [Accepted: 08/06/2015] [Indexed: 01/18/2023]
Abstract
The denitrifying bacterium 'Aromatoleum aromaticum' strain EbN1 is one of the best characterized bacteria regarding anaerobic ethylbenzene degradation. EbN1 also degrades various other aromatic and phenolic compounds in the absence of oxygen, one of them being p-ethylphenol. Despite having similar chemical structures, ethylbenzene and p-ethylphenol have been proposed to be metabolized by completely separate pathways. In this study, we established and applied biochemical and molecular biological methods to show the (almost) exclusive presence and specificity of enzymes involved in the respective degradation pathways by recording enzyme activities, complemented by heme staining, immuno- and biotin-blotting analyses. These combined results substantiated the predicted p-ethylphenol degradation pathway. The identified enzymes include a heme c-containing p-ethylphenol-hydroxylase, both an (R)- and an (S)-specific alcohol dehydrogenase as well as a novel biotin-dependent carboxylase. We also establish an activity assay for benzoylacetate-CoA ligases likely being involved in both metabolic pathways.
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Affiliation(s)
- Enrico Muhr
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Karola Schühle
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Lina Clermont
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Katharina Sünwoldt
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Daniel Kleinsorge
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Deniz Seyhan
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Iris Schall
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Paul R Cordero
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Georg Schmitt
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Johann Heider
- Laboratory of Microbial Biochemistry, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany. .,LOEWE-Center for Synthetic Microbiology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany.
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Rabus R, Trautwein K, Wöhlbrand L. Towards habitat-oriented systems biology of "Aromatoleum aromaticum" EbN1: chemical sensing, catabolic network modulation and growth control in anaerobic aromatic compound degradation. Appl Microbiol Biotechnol 2014; 98:3371-88. [PMID: 24493567 DOI: 10.1007/s00253-013-5466-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 12/11/2013] [Accepted: 12/11/2013] [Indexed: 12/29/2022]
Abstract
The denitrifying betaproteobacterium "Aromatoleum aromaticum" EbN1 is a well-studied model organism for anaerobic degradation of aromatic compounds. Following publication of its genome in 2005, comprehensive physiological-proteomic studies were conducted to deduce functional understanding from the genomic blueprint. A catabolic network (85 predicted, 65 identified proteins) for anaerobic degradation of 24 aromatic growth substrates (including 11 newly recognized) was established. Newly elucidated pathways include those for 4-ethylphenol and plant-derived 3-phenylpropanoids, involving functional assignment of several paralogous genes. The substrate-specific regulation of individual peripheral degradation pathways is probably initiated by highly specific chemical sensing via dedicated sensory/regulatory proteins, e.g. three different σ⁵⁴-dependent one-component sensory/regulatory proteins are predicted to discriminate between three phenolic substrates (phenol, p-cresol and 4-ethylphenol) and two different two-component systems are assumed to differentiate between two alkylbenzenes (toluene, ethylbenzene). Investigations under in situ relevant growth conditions revealed (a) preferred utilization of benzoate from a mixture with succinate results from repressed synthesis of a C₄-dicarboxylate TRAP transporter; (b) response to alkylbenzene-induced solvent stress comprises metabolic re-routing of acetyl-CoA and reducing equivalents to poly(3-hydroxybutyrate) synthesis, alteration of cellular membrane composition and formation of putative solvent efflux systems; and (c) multifaceted adaptation to slow growth includes adjustment of energy demand for maintenance and preparedness for future nutritional opportunities, i.e. provision of uptake systems and catabolic enzymes for multiple aromatic substrates despite their absence. This broad knowledge base taken together with the recent development of a genetic system will facilitate future functional, biotechnological (stereospecific dehydrogenases) and habitat re-enacting ("eco-"systems biology) studies with "A. aromaticum" EbN1.
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Affiliation(s)
- Ralf Rabus
- Institut für Chemie und Biologie des Meeres (ICBM), AG Allgemeine und Molekulare Mikrobiologie, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky Str. 9-11, 26111, Oldenburg, Germany,
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Boll M, Löffler C, Morris BEL, Kung JW. Anaerobic degradation of homocyclic aromatic compounds via arylcarboxyl-coenzyme A esters: organisms, strategies and key enzymes. Environ Microbiol 2013; 16:612-27. [PMID: 24238333 DOI: 10.1111/1462-2920.12328] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/03/2013] [Indexed: 11/28/2022]
Abstract
Next to carbohydrates, aromatic compounds are the second most abundant class of natural organic molecules in living organic matter but also make up a significant proportion of fossil carbon sources. Only microorganisms are capable of fully mineralizing aromatic compounds. While aerobic microbes use well-studied oxygenases for the activation and cleavage of aromatic rings, anaerobic bacteria follow completely different strategies to initiate catabolism. The key enzymes related to aromatic compound degradation in anaerobic bacteria are comprised of metal- and/or flavin-containing cofactors, of which many use unprecedented radical mechanisms for C-H bond cleavage or dearomatization. Over the past decade, the increasing number of completed genomes has helped to reveal a large variety of anaerobic degradation pathways in Proteobacteria, Gram-positive microbes and in one archaeon. This review aims to update our understanding of the occurrence of aromatic degradation capabilities in anaerobic microorganisms and serves to highlight characteristic enzymatic reactions involved in (i) the anoxic oxidation of alkyl side chains attached to aromatic rings, (ii) the carboxylation of aromatic rings and (iii) the reductive dearomatization of central arylcarboxyl-coenzyme A intermediates. Depending on the redox potential of the electron acceptors used and the metabolic efficiency of the cell, different strategies may be employed for identical overall reactions.
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Affiliation(s)
- Matthias Boll
- Institute for Biology II, University of Freiburg, Freiburg, Germany
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Philipp B, Schink B. Different strategies in anaerobic biodegradation of aromatic compounds: nitrate reducers versus strict anaerobes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:469-478. [PMID: 23760891 DOI: 10.1111/j.1758-2229.2011.00304.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Mononuclear aromatic compounds are degraded anaerobically through pathways that are basically different from those used in the presence of oxygen. Whereas aerobic degradation destabilizes the aromatic π-electron system by oxidative steps through oxygenase reactions, anaerobic degradation is most often initiated by a reductive attack. The benzoyl-CoA pathway is the most important metabolic route in this context, and a broad variety of mononuclear aromatics, including phenol, cresols, toluene, xylenes and ethylbenzene, are channelled into this pathway through various modification reactions. Multifunctional phenolic compounds are metabolized via the reductive resorcinol pathway, the oxidative resorcinol pathway with hydroxyhydroquinone as key intermediate, and the phloroglucinol pathway. Comparison of the various pathways used for modification and degradation of aromatics in the absence of oxygen indicates that the strategies of breakdown of these compounds are largely determined by the redox potentials of the electron acceptors used, and by the overall reaction energetics. Consequently, nitrate reducers quite often use strategies for primary attack on aromatic compounds that differ from those used by sulfate-reducing, iron-reducing or fermenting bacteria.
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Affiliation(s)
- Bodo Philipp
- Department of Biology, University of Konstanz, Universitätsstr. 10, D-78457 Konstanz, Germany
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Schaarschmidt J, Wischgoll S, Hofmann HJ, Boll M. Conversion of a decarboxylating to a non-decarboxylating glutaryl-coenzyme A dehydrogenase by site-directed mutagenesis. FEBS Lett 2011; 585:1317-21. [PMID: 21477586 DOI: 10.1016/j.febslet.2011.03.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 03/30/2011] [Accepted: 03/31/2011] [Indexed: 11/26/2022]
Abstract
Glutaryl-coenzyme A (CoA) dehydrogenases (GDHs) are acyl-CoA dehydrogenases, which usually dehydrogenate and decarboxylate the substrate to crotonyl-CoA. In some anaerobic bacteria, non-decarboxylating GDHs exist that release glutaconyl-CoA (2,3-dehydroglutaryl-CoA) without decarboxylation. The differing mechanisms of decarboxylating and non-decarboxylating GDHs were investigated by site-directed mutagenesis of the gene coding for the crotonyl-CoA-forming GDH from Geobacter metallireducens. Exchange of single amino acids involved in substrate carboxylate binding impaired the decarboxylation step, resulting in relative glutaconyl-CoA:crotonyl-CoA formation rates of 1:1 (S97A) or 13:1 (Y370A). The total amount of glutaconyl-CoA formed was maximal in the Y370V+S97A double mutant. The results obtained indicate that an invariant deprotonated Tyr plays a crucial role for optimizing the leaving group potential of CO(2) in decarboxylating GDHs.
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