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Lequan Q, Yanan F, Xianda Z, Mengyuan B, Chenyu L, Shijin W. Mechanisms and high-value applications of phthalate isomers degradation pathways in bacteria. World J Microbiol Biotechnol 2024; 40:247. [PMID: 38904858 DOI: 10.1007/s11274-024-04060-5] [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: 04/30/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024]
Abstract
Phthalate isomers are key intermediates in the biodegradation of pollutants including waste polyethylene terephthalate (PET) plastics and plasticizers. So far, an increasing number of phthalate isomer-degrading strains have been isolated, and their degradation pathways show significant diversity. In this paper, we comprehensively review the current status of research on the degrading bacteria, degradation characteristics, aerobic and anaerobic degradation pathways, and degradation genes (clusters) of phthalate isomers, and discuss the current shortcomings and challenges. Moreover, the degradation process of phthalate isomers produces many important aromatic precursor molecules, which can be used to produce higher-value derivative chemicals, and the modification of their degradation pathways holds good prospects. Therefore, this review also highlights the current progress made in modifying the phthalate isomer degradation pathway and explores its potential for high-value applications.
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Affiliation(s)
- Qiu Lequan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.
| | - Fu Yanan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhou Xianda
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Bao Mengyuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Li Chenyu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Wu Shijin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.
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2
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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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3
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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4
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Zhang L, Toplak M, Saleem-Batcha R, Höing L, Jakob R, Jehmlich N, von Bergen M, Maier T, Teufel R. Bacterial Dehydrogenases Facilitate Oxidative Inactivation and Bioremediation of Chloramphenicol. Chembiochem 2023; 24:e202200632. [PMID: 36353978 DOI: 10.1002/cbic.202200632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/09/2022] [Indexed: 11/11/2022]
Abstract
Antimicrobial resistance represents a major threat to human health and knowledge of the underlying mechanisms is therefore vital. Here, we report the discovery and characterization of oxidoreductases that inactivate the broad-spectrum antibiotic chloramphenicol via dual oxidation of the C3-hydroxyl group. Accordingly, chloramphenicol oxidation either depends on standalone glucose-methanol-choline (GMC)-type flavoenzymes, or on additional aldehyde dehydrogenases that boost overall turnover. These enzymes also enable the inactivation of the chloramphenicol analogues thiamphenicol and azidamfenicol, but not of the C3-fluorinated florfenicol. Notably, distinct isofunctional enzymes can be found in Gram-positive (e. g., Streptomyces sp.) and Gram-negative (e. g., Sphingobium sp.) bacteria, which presumably evolved their selectivity for chloramphenicol independently based on phylogenetic analyses. Mechanistic and structural studies provide further insights into the catalytic mechanisms of these biotechnologically interesting enzymes, which, in sum, are both a curse and a blessing by contributing to the spread of antibiotic resistance as well as to the bioremediation of chloramphenicol.
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Affiliation(s)
- Lei Zhang
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Raspudin Saleem-Batcha
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Lars Höing
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Roman Jakob
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research UFZ GmbH, Leipzig, Germany.,German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.,University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research UFZ GmbH, Leipzig, Germany.,German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.,University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
| | - Timm Maier
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Robin Teufel
- Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
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5
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Li Z, Gao J, Zhao Y, Wang Z, Cui Y, Li D, Guo Y, Wu Z, Zeng L. Different acesulfame potassium fate and antibiotic resistance propagation pattern in nitrifying and denitrifying sludge systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159238. [PMID: 36208732 DOI: 10.1016/j.scitotenv.2022.159238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/16/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Acesulfame potassium (ACE-K) is a widely utilized sugar substitute with increasing demand, which is frequently detected in various environmental matrix due to recalcitrance. However, a general consensus on the contribution of nitrifying and denitrifying process to ACE-K removal is lacking. Therefore, ACE-K removal, its effects on antibiotic resistant genes (ARGs) propagation and microbial community in nitrifying sequencing batch reactor (N-SBR) and denitrifying sequencing batch reactor (D-SBR) inoculated with the identical activated sludge were investigated. In this study, ACE-K can be eliminated in N-SBR with satisfying removal efficiency (96.76 ± 8.33 %) after 13 d acclimation, while it remained persistent (average ACE-K removal efficiency of 2.24 ± 1.86 %) in D-SBR during 84 d exposure. Moreover, ACE-K hardly affected the performances of these two types of reactors and had little impact on nitrifying and denitrifying functional genes. However, initial contact with ACE-K would increase ARGs abundance, network analysis showed functional bacteria in each reactor were possible ARGs hosts. Potential ACE-K degrading genera Chelatococcus, Bosea and Aquamicrobium were found in both reactors. LefSe analysis showed that Phyllobacteriaceae containing Aquamicrobium genus was a differentially enriched family in N-SBR. This research might provide a perspective for better understanding factor affecting ACE-K fate in wastewater treatment process and its ecological risks.
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Affiliation(s)
- Ziqiao Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
| | - Yifan Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Zhiqi Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yingchao Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Dingchang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Yi Guo
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Zejie Wu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Liqin Zeng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
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6
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Junghare M, Frey J, Naji KM, Spiteller D, Vaaje-Kolstad G, Schink B. Isophthalate:coenzyme A ligase initiates anaerobic degradation of xenobiotic isophthalate. BMC Microbiol 2022; 22:227. [PMID: 36171563 PMCID: PMC9516798 DOI: 10.1186/s12866-022-02630-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/02/2022] [Indexed: 11/25/2022] Open
Abstract
Background Environmental contamination from synthetic plastics and their additives is a widespread problem. Phthalate esters are a class of refractory synthetic organic compounds which are widely used in plastics, coatings, and for several industrial applications such as packaging, pharmaceuticals, and/or paints. They are released into the environment during production, use and disposal, and some of them are potential mutagens and carcinogens. Isophthalate (1,3-benzenedicarboxylic acid) is a synthetic chemical that is globally produced at a million-ton scale for industrial applications and is considered a priority pollutant. Here we describe the biochemical characterization of an enzyme involved in anaerobic degradation of isophthalate by the syntrophically fermenting bacterium Syntrophorhabdus aromaticivorans strain UI that activate isophthalate to isophthalyl-CoA followed by its decarboxylation to benzoyl-CoA. Results Isophthalate:Coenzyme A ligase (IPCL, AMP-forming) that activates isophthalate to isophthalyl-CoA was heterologously expressed in E. coli (49.6 kDa) for biochemical characterization. IPCL is homologous to phenylacetate-CoA ligase that belongs to the family of ligases that form carbon-sulfur bonds. In the presence of coenzyme A, Mg2+ and ATP, IPCL converts isophthalate to isophthalyl-CoA, AMP and pyrophosphate (PPi). The enzyme was specifically induced after anaerobic growth of S. aromaticivorans in a medium containing isophthalate as the sole carbon source. Therefore, IPCL exhibited high substrate specificity and affinity towards isophthalate. Only substrates that are structurally related to isophthalate, such as glutarate and 3-hydroxybenzoate, could be partially converted to the respective coenzyme A esters. Notably, no activity could be measured with substrates such as phthalate, terephthalate and benzoate. Acetyl-CoA or succinyl-CoA did not serve as CoA donors. The enzyme has a theoretical pI of 6.8 and exhibited optimal activity between pH 7.0 to 7.5. The optimal temperature was between 25 °C and 37 °C. Denaturation temperature (Tm) of IPCL was found to be at about 63 °C. The apparent KM values for isophthalate, CoA, and ATP were 409 μM, 642 μM, and 3580 μM, respectively. Although S. aromaticivorans is a strictly anaerobic bacterium, the enzyme was found to be oxygen-insensitive and catalysed isophthalyl-CoA formation under both anoxic and oxic conditions. Conclusion We have successfully cloned the ipcl gene, expressed and characterized the corresponding IPCL enzyme, which plays a key role in isophthalate activation that initiates its activation and further degradation by S. aromaticivorans. Its biochemical characterization represents an important step in the elucidation of the complete degradation pathway of isophthalate. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02630-x.
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Affiliation(s)
- Madan Junghare
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany. .,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1430, Ås, Norway.
| | - Jasmin Frey
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Khalid M Naji
- Chemical Ecology and Biological Chemistry, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Dieter Spiteller
- Chemical Ecology and Biological Chemistry, Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1430, Ås, Norway
| | - Bernhard Schink
- General Microbiology and Microbial Ecology, Department of Biology, University of Konstanz, D-78457, Constance, Germany
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7
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Roberts GW, Leys D. Structural insights into UbiD reversible decarboxylation. Curr Opin Struct Biol 2022; 75:102432. [PMID: 35843126 DOI: 10.1016/j.sbi.2022.102432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 11/03/2022]
Abstract
The ubiquitous UbiX-UbiD system is associated with a wide range of microbial (de)carboxylation reactions. Recent X-ray crystallographic studies have contributed to elucidating the enigmatic mechanism underpinning the conversion of α,β-unsaturated acids by this system. The UbiD component utilises a unique cofactor, prenylated flavin (prFMN), generated by the bespoke action of the associated UbiX flavin prenyltransferase. Structure determination of a range of UbiX/UbiD representatives has revealed a generic mode of action for both the flavin-to-prFMN metamorphosis and the (de)carboxylation. In contrast to the conserved UbiX, the UbiD superfamily is associated with a versatile substrate range. The latter is reflected in the considerable variety of UbiD quaternary structure, dynamic behaviour and active site architecture. Directed evolution of UbiD enzymes has taken advantage of this apparent malleability to generate new variants supporting in vivo hydrocarbon production. Other applications include coupling UbiD to carboxylic acid reductase to convert alkenes into α,β-unsaturated aldehydes via enzymatic CO2 fixation.
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Affiliation(s)
- George W Roberts
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - David Leys
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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8
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Toolbox for the structure-guided evolution of ferulic acid decarboxylase (FDC). Sci Rep 2022; 12:3347. [PMID: 35232989 PMCID: PMC8888657 DOI: 10.1038/s41598-022-07110-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/19/2022] [Indexed: 11/08/2022] Open
Abstract
The interest towards ferulic acid decarboxylase (FDC), piqued by the enzyme's unique 1,3-dipolar cycloaddition mechanism and its atypic prFMN cofactor, provided several applications of the FDC mediated decarboxylations, such as the synthesis of styrenes, or its diverse derivatives, including 1,3-butadiene and the enzymatic activation of C-H bonds through the reverse carboligation reactions. While rational design-based protein engineering was successfully employed for tailoring FDC towards diverse substrates of interest, the lack of high-throughput FDC-activity assay hinders its directed evolution-based protein engineering. Herein we report a toolbox, useful for the directed evolution based and/or structure-guided protein engineering of FDC, which was validated representatively on the well described FDC, originary from Saccharomyces cerevisiae (ScFDC). Accordingly, the developed fluorescent plate-assay allows in premiere the FDC-activity screens of a mutant library in a high-throughput manner. Moreover, using the plate-assay for the activity screens of a rationally designed 23-membered ScFDC variant library against a substrate panel comprising of 16, diversely substituted cinnamic acids, revealed several variants of improved activity. The superior catalytic properties of the hits revealed by the plate-assay, were also supported by the conversion values from their analytical scale biotransformations. The computational results further endorsed the experimental findings, showing inactive binding poses of several non-transformed substrate analogues within the active site of the wild-type ScFDC, but favorable ones within the catalytic site of the variants of improved activity. The results highlight several 'hot-spot' residues involved in substrate specificity modulation of FDC, such as I189, I330, F397, I398 or Q192, of which mutations to sterically less demanding residues increased the volume of the active site, thus facilitated proper binding and increased conversions of diverse non-natural substrates. Upon revealing which mutations improve the FDC activity towards specific substrate analogues, we also provide key for the rational substrate-tailoring of FDC.
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9
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Bloor S, Michurin I, Titchiner GR, Leys D. Prenylated flavins: structures and mechanisms. FEBS J 2022; 290:2232-2245. [PMID: 35073609 DOI: 10.1111/febs.16371] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/05/2022] [Accepted: 01/21/2022] [Indexed: 11/28/2022]
Abstract
The UbiX/UbiD system is widespread in microbes and responsible for the reversible decarboxylation of unsaturated carboxylic acids. The UbiD enzyme catalyzes this unusual reaction using a prenylated flavin (prFMN) as cofactor, the latter formed by the flavin prenyltransferase UbiX. A detailed picture of the biochemistry of flavin prenylation, oxidative maturation, and covalent catalysis underpinning reversible decarboxylation is emerging. This reveals the prFMN cofactor can undergo a wide range of transformations, complemented by considerable UbiD-variability. These provide a blueprint for biotechnological applications aimed at producing hydrocarbons or aromatic C-H activation through carboxylation.
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Affiliation(s)
- Samuel Bloor
- Department of Chemistry, Manchester Institute of Biotechnology, UK
| | | | | | - David Leys
- Department of Chemistry, Manchester Institute of Biotechnology, UK
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10
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Marshall SA, Payne KAP, Fisher K, Titchiner GR, Levy C, Hay S, Leys D. UbiD domain dynamics underpins aromatic decarboxylation. Nat Commun 2021; 12:5065. [PMID: 34417452 PMCID: PMC8379154 DOI: 10.1038/s41467-021-25278-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
The widespread UbiD enzyme family utilises the prFMN cofactor to achieve reversible decarboxylation of acrylic and (hetero)aromatic compounds. The reaction with acrylic compounds based on reversible 1,3-dipolar cycloaddition between substrate and prFMN occurs within the confines of the active site. In contrast, during aromatic acid decarboxylation, substantial rearrangement of the substrate aromatic moiety associated with covalent catalysis presents a molecular dynamic challenge. Here we determine the crystal structures of the multi-subunit vanillic acid decarboxylase VdcCD. We demonstrate that the small VdcD subunit acts as an allosteric activator of the UbiD-like VdcC. Comparison of distinct VdcCD structures reveals domain motion of the prFMN-binding domain directly affects active site architecture. Docking of substrate and prFMN-adduct species reveals active site reorganisation coupled to domain motion supports rearrangement of the substrate aromatic moiety. Together with kinetic solvent viscosity effects, this establishes prFMN covalent catalysis of aromatic (de)carboxylation is afforded by UbiD dynamics.
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Affiliation(s)
- Stephen A. Marshall
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK ,grid.4991.50000 0004 1936 8948Present Address: Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Karl A. P. Payne
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Karl Fisher
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Gabriel R. Titchiner
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Colin Levy
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Sam Hay
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - David Leys
- grid.5379.80000000121662407Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
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11
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The In Vitro Production of prFMN for Reconstitution of UbiD Enzymes. Methods Mol Biol 2021; 2280:219-227. [PMID: 33751438 DOI: 10.1007/978-1-0716-1286-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Prenylated flavin (prFMN) is a modified FMN cofactor, the isoalloxazine is extended by an additional six membered nonaromatic ring. The modification confers azomethine ylide characteristics on the oxidised prFMN, allowing it to support the reversible nonoxidative decarboxylation of unsaturated acids by the UbiD family of decarboxylases. In absence of a chemical synthesis route for prFMN, enzymatic production by the flavin prenyltransferase, UbiX, is required for in vitro reconstitution of prFMN-dependent enzymes. Here we provide an overview of the methods for producing prFMN in vitro using the flavin prenyltransferase UbiX, and the subsequent reconstitution and activation of UbiD enzymes.
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12
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Balaikaite A, Chisanga M, Fisher K, Heyes DJ, Spiess R, Leys D. Ferulic Acid Decarboxylase Controls Oxidative Maturation of the Prenylated Flavin Mononucleotide Cofactor. ACS Chem Biol 2020; 15:2466-2475. [PMID: 32840348 DOI: 10.1021/acschembio.0c00456] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prenylated flavin mononucleotide (prFMN) is a recently discovered modified flavin cofactor containing an additional nonaromatic ring, connected to the N5 and C6 atoms. This cofactor underpins reversible decarboxylation catalyzed by members of the widespread UbiD enzyme family and is produced by the flavin prenyltransferase UbiX. Oxidative maturation of the UbiX product prFMNH2 to the corresponding oxidized prFMNiminium is required for ferulic acid decarboxylase (Fdc1; a UbiD-type enzyme) activity. However, it is unclear what role the Fdc1 enzyme plays in this process. Here, we demonstrate that, in the absence of Fdc1, prFMNH2 oxidation by O2 proceeds via a transient semiquinone prFMNradical species and culminates in a remarkably stable prFMN-hydroperoxide species. Neither forms of prFMN are able to support Fdc1 activity. Instead, enzyme activation using O2-mediated oxidation requires prFMNH2 binding prior to oxygen exposure, confirming that UbiD enzymes play a role in O2-mediated oxidative maturation. In marked contrast, alternative oxidants such as potassium ferricyanide support prFMNiminium formation both in solution and in Fdc1.
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Affiliation(s)
- Arune Balaikaite
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Malama Chisanga
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- Department of Chemistry, School of Mathematics and Natural Sciences, Copperbelt University, Kitwe, Zambia
| | - Karl Fisher
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Derren J. Heyes
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Reynard Spiess
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - David Leys
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
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13
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Sanz D, García JL, Díaz E. Expanding the current knowledge and biotechnological applications of the oxygen-independent ortho-phthalate degradation pathway. Environ Microbiol 2020; 22:3478-3493. [PMID: 32510798 DOI: 10.1111/1462-2920.15119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/31/2020] [Accepted: 06/03/2020] [Indexed: 11/29/2022]
Abstract
ortho-Phthalate derives from industrially produced phthalate esters, which are massively used as plasticizers and constitute major emerging environmental pollutants. The pht pathway for the anaerobic bacterial biodegradation of o-phthalate involves its activation to phthaloyl-CoA followed by decarboxylation to benzoyl-CoA. Here, we have explored further the pht peripheral pathway in denitrifying bacteria and shown that it requires also an active transport system for o-phthalate uptake that belongs to the poorly characterized class of TAXI-TRAP transporters. The construction of a fully functional pht cassette combining both catabolic and transport genes allowed to expand the o-phthalate degradation ecological trait to heterologous hosts. Unexpectedly, the pht cassette also allowed the aerobic conversion of o-phthalate to benzoyl-CoA when coupled to a functional box central pathway. Hence, the pht pathway may constitute an evolutionary acquisition for o-phthalate degradation by bacteria that thrive either in anoxic environments or in environments that face oxygen limitations and that rely on benzoyl-CoA, rather than on catecholic central intermediates, for the aerobic catabolism of aromatic compounds. Finally, the recombinant pht cassette was used both to screen for functional aerobic box pathways in bacteria and to engineer recombinant biocatalysts for o-phthalate bioconversion into sustainable bioplastics, e.g., polyhydroxybutyrate, in plastic recycling industrial processes.
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Affiliation(s)
- David Sanz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
| | - José L García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
| | - Eduardo Díaz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
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14
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An Aerobic Hybrid Phthalate Degradation Pathway via Phthaloyl-Coenzyme A in Denitrifying Bacteria. Appl Environ Microbiol 2020; 86:AEM.00498-20. [PMID: 32220846 DOI: 10.1128/aem.00498-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/16/2020] [Indexed: 11/20/2022] Open
Abstract
The degradation of the xenobiotic phthalic acid esters by microorganisms is initiated by the hydrolysis to the respective alcohols and ortho-phthalate (hereafter, phthalate). In aerobic bacteria and fungi, oxygenases are involved in the conversion of phthalate to protocatechuate, the substrate for ring-cleaving dioxygenases. In contrast, anaerobic bacteria activate phthalate to the extremely unstable phthaloyl-coenzyme A (CoA), which is decarboxylated by oxygen-sensitive UbiD-like phthaloyl-CoA decarboxylase (PCD) to the central benzoyl-CoA intermediate. Here, we demonstrate that the facultatively anaerobic, denitrifying Thauera chlorobenzoica 3CB-1 and Aromatoleum evansii KB740 strains use phthalate as a growth substrate under aerobic and denitrifying conditions. In vitro assays with extracts from cells grown aerobically with phthalate demonstrated the succinyl-CoA-dependent activation of phthalate followed by decarboxylation to benzoyl-CoA. In T. chlorobenzoica 3CB-1, we identified PCD as a highly abundant enzyme in both aerobically and anaerobically grown cells, whereas genes for phthalate dioxygenases are missing in the genome. PCD was highly enriched from aerobically grown T. chlorobenzoica cells and was identified as an identical enzyme produced under denitrifying conditions. These results indicate that the initial steps of aerobic phthalate degradation in denitrifying bacteria are accomplished by the anaerobic enzyme inventory, whereas the benzoyl-CoA oxygenase-dependent pathway is used for further conversion to central intermediates. Such a hybrid pathway requires intracellular oxygen homeostasis at concentrations low enough to prevent PCD inactivation but sufficiently high to supply benzoyl-CoA oxygenase with its cosubstrate.IMPORTANCE Phthalic acid esters (PAEs) are industrially produced on a million-ton scale per year and are predominantly used as plasticizers. They are classified as environmentally relevant xenobiotics with a number of adverse health effects, including endocrine-disrupting activity. Biodegradation by microorganisms is considered the most effective process to eliminate PAEs from the environment. It is usually initiated by the hydrolysis of PAEs to alcohols and o-phthalic acid. Degradation of o-phthalic acid fundamentally differs in aerobic and anaerobic microorganisms; aerobic phthalate degradation heavily depends on dioxygenase-dependent reactions, whereas anaerobic degradation employs the oxygen-sensitive key enzyme phthaloyl-CoA decarboxylase. We demonstrate that aerobic phthalate degradation in facultatively anaerobic bacteria proceeds via a previously unknown hybrid degradation pathway involving oxygen-sensitive and oxygen-dependent key enzymes. Such a strategy is essential for facultatively anaerobic bacteria that frequently switch between oxic and anoxic environments.
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15
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Boll M, Geiger R, Junghare M, Schink B. Microbial degradation of phthalates: biochemistry and environmental implications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:3-15. [PMID: 31364812 DOI: 10.1111/1758-2229.12787] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 05/10/2023]
Abstract
The environmentally relevant xenobiotic esters of phthalic acid (PA), isophthalic acid (IPA) and terephthalic acid (TPA) are produced on a million ton scale annually and are predominantly used as plastic polymers or plasticizers. Degradation by microorganisms is considered as the most effective means of their elimination from the environment and proceeds via hydrolysis to the corresponding PA isomers and alcohols under oxic and anoxic conditions. Further degradation of PA, IPA and TPA differs fundamentally between anaerobic and aerobic microorganisms. The latter introduce hydroxyl functionalities by dioxygenases to facilitate subsequent decarboxylation by either aromatizing dehydrogenases or cofactor-free decarboxylases. In contrast, anaerobic bacteria activate the PA isomers to the respective thioesters using CoA ligases or CoA transferases followed by decarboxylation to the central intermediate benzoyl-CoA. Decarboxylases acting on the three PA CoA thioesters belong to the UbiD enzyme family that harbour a prenylated flavin mononucleotide (FMN) cofactor to achieve the mechanistically challenging decarboxylation. Capture of the extremely instable PA-CoA intermediate is accomplished by a massive overproduction of phthaloyl-CoA decarboxylase and a balanced production of PA-CoA forming/decarboxylating enzymes. The strategy of anaerobic phthalate degradation probably represents a snapshot of an ongoing evolution of a xenobiotic degradation pathway via a short-lived reaction intermediate.
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Affiliation(s)
- Matthias Boll
- Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Robin Geiger
- Faculty of Biology, Microbiology, University of Freiburg, Freiburg, Germany
| | - Madan Junghare
- Department of Biology and Microbial Ecology, University of Konstanz, Constance, Germany
| | - Bernhard Schink
- Department of Biology and Microbial Ecology, University of Konstanz, Constance, Germany
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16
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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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17
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Geiger RA, Junghare M, Mergelsberg M, Ebenau‐Jehle C, Jesenofsky VJ, Jehmlich N, von Bergen M, Schink B, Boll M. Enzymes involved in phthalate degradation in sulphate‐reducing bacteria. Environ Microbiol 2019; 21:3601-3612. [DOI: 10.1111/1462-2920.14681] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/03/2019] [Accepted: 05/11/2019] [Indexed: 12/31/2022]
Affiliation(s)
| | - Madan Junghare
- Department of Biology, Microbial EcologyUniversity of Konstanz, 78457 Constance Germany
| | - Mario Mergelsberg
- Faculty of Biology–MicrobiologyUniversity of Freiburg, 79104 Freiburg Germany
| | | | | | - Nico Jehmlich
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research UFZ 04318 Leipzig Germany
| | - Martin von Bergen
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research UFZ 04318 Leipzig Germany
- Institute of Biochemistry, Faculty of Life SciencesUniversity of Leipzig Brüderstr. 34, 04103 Leipzig Germany
| | - Bernhard Schink
- Department of Biology, Microbial EcologyUniversity of Konstanz, 78457 Constance Germany
| | - Matthias Boll
- Faculty of Biology–MicrobiologyUniversity of Freiburg, 79104 Freiburg Germany
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18
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Marshall SA, Payne KAP, Fisher K, Gahloth D, Bailey SS, Balaikaite A, Saaret A, Gostimskaya I, Aleku G, Huang H, Rigby SEJ, Procter D, Leys D. Heterologous production, reconstitution and EPR spectroscopic analysis of prFMN dependent enzymes. Methods Enzymol 2019; 620:489-508. [PMID: 31072499 DOI: 10.1016/bs.mie.2019.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recent discovery of the prenylated FMN (prFMN) cofactor has led to a renewed interest in the prFMN-dependent UbiD family of enzymes. The latter catalyses the reversible decarboxylation of alpha-beta unsaturated carboxylic acids and features widely in microbial metabolism. The flavin prenyltransferase UbiX synthesizes prFMN from reduced FMN and phosphorylated dimethylallyl precursors. Oxidative maturation of the resulting prFMNreduced species to the active prFMNiminium form is required for UbiD activity. Heterologous production of active holo-UbiD requires co-expression of UbiX, but the levels of prFMN incorporation and oxidative maturation appear variable. Detailed protocols and strategies for in vitro reconstitution and oxidative maturation of UbiD are presented that can yield an alternative source of active holo-UbiD for biochemical studies.
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Affiliation(s)
- Stephen A Marshall
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Karl A P Payne
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Karl Fisher
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Deepankar Gahloth
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Samuel S Bailey
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Arune Balaikaite
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Annica Saaret
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Irina Gostimskaya
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Godwin Aleku
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Huanming Huang
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Stephen E J Rigby
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - David Procter
- School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - David Leys
- School of Chemistry, University of Manchester, Manchester, United Kingdom.
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19
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Junghare M, Spiteller D, Schink B. Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans. ISME JOURNAL 2019; 13:1252-1268. [PMID: 30647456 DOI: 10.1038/s41396-019-0348-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 12/13/2022]
Abstract
Syntrophorhabdus aromaticivorans is a syntrophically fermenting bacterium that can degrade isophthalate (3-carboxybenzoate). It is a xenobiotic compound which has accumulated in the environment for more than 50 years due to its global industrial usage and can cause negative effects on the environment. Isophthalate degradation by the strictly anaerobic S. aromaticivorans was investigated to advance our understanding of the degradation of xenobiotics introduced into nature, and to identify enzymes that might have ecological significance for bioremediation. Differential proteome analysis of isophthalate- vs benzoate-grown cells revealed over 400 differentially expressed proteins of which only four were unique to isophthalate-grown cells. The isophthalate-induced proteins include a phenylacetate:CoA ligase, a UbiD-like decarboxylase, a UbiX-like flavin prenyltransferase, and a hypothetical protein. These proteins are encoded by genes forming a single gene cluster that putatively codes for anaerobic conversion of isophthalate to benzoyl-CoA. Subsequently, benzoyl-CoA is metabolized by the enzymes of the anaerobic benzoate degradation pathway that were identified in the proteomic analysis. In vitro enzyme assays with cell-free extracts of isophthalate-grown cells indicated that isophthalate is activated to isophthalyl-CoA by an ATP-dependent isophthalate:CoA ligase (IPCL), and subsequently decarboxylated to benzoyl-CoA by a UbiD family isophthalyl-CoA decarboxylase (IPCD) that requires a prenylated flavin mononucleotide (prFMN) cofactor supplied by UbiX to effect decarboxylation. Phylogenetic analysis revealed that IPCD is a novel member of the functionally diverse UbiD family (de)carboxylases. Homologs of the IPCD encoding genes are found in several other bacteria, such as aromatic compound-degrading denitrifiers, marine sulfate-reducers, and methanogenic communities in a terephthalate-degrading reactor. These results suggest that metabolic strategies adapted for degradation of isophthalate and other phthalate are conserved between microorganisms that are involved in the anaerobic degradation of environmentally relevant aromatic compounds.
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Affiliation(s)
- Madan Junghare
- Microbial Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
| | - Dieter Spiteller
- Chemical Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Bernhard Schink
- Microbial Ecology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
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20
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Leys D. Flavin metamorphosis: cofactor transformation through prenylation. Curr Opin Chem Biol 2018; 47:117-125. [PMID: 30326424 DOI: 10.1016/j.cbpa.2018.09.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 11/28/2022]
Abstract
Prenylated flavin (prFMN) is a recently discovered cofactor that underpins catalysis in the ubiquitous microbial UbiDX system. UbiX acts as a flavin prenyltransferase while UbiD is a prFMN-dependent reversible (de)carboxylase. The extensive modification of flavin by prenylation, and the consecutive oxidation to the prFMNiminium azomethine ylide, leads to cofactor metamorphosis. While prFMN is no longer able to perform N5-based classical flavin chemistry, it is capable of forming cycloadducts with dipolarophiles, long-lived C4a-based radical species as well as undergoing extensive light driven isomerization. An ever-expanding range of distinct prFMN forms hints at the possibility of novel prFMN driven biochemistry yet to be discovered.
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Affiliation(s)
- David Leys
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street Manchester, M1 7DN, UK.
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21
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Four Molybdenum-Dependent Steroid C-25 Hydroxylases: Heterologous Overproduction, Role in Steroid Degradation, and Application for 25-Hydroxyvitamin D 3 Synthesis. mBio 2018; 9:mBio.00694-18. [PMID: 29921665 PMCID: PMC6016249 DOI: 10.1128/mbio.00694-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Side chain-containing steroids are ubiquitous constituents of biological membranes that are persistent to biodegradation. Aerobic, steroid-degrading bacteria employ oxygenases for isoprenoid side chain and tetracyclic steran ring cleavage. In contrast, a Mo-containing steroid C-25 dehydrogenase (S25DH) of the dimethyl sulfoxide (DMSO) reductase family catalyzes the oxygen-independent hydroxylation of tertiary C-25 in the anaerobic, cholesterol-degrading bacterium Sterolibacterium denitrificans Its genome contains eight paralogous genes encoding active site α-subunits of putative S25DH-like proteins. The difficult enrichment of labile, oxygen-sensitive S25DH from the wild-type bacteria and the inability of its active heterologous production have largely hampered the study of S25DH-like gene products. Here we established a heterologous expression platform for the three structural genes of S25DH subunits together with an essential chaperone in the denitrifying betaproteobacterium Thauera aromatica K172. Using this system, S25DH1 and three isoenzymes (S25DH2, S25DH3, and S25DH4) were overproduced in a soluble, active form allowing a straightforward purification of nontagged αβγ complexes. All S25DHs contained molybdenum, four [4Fe-4S] clusters, one [3Fe-4S] cluster, and heme B and catalyzed the specific, water-dependent C-25 hydroxylations of various 4-en-3-one forms of phytosterols and zoosterols. Crude extracts from T. aromatica expressing genes encoding S25DH1 catalyzed the hydroxylation of vitamin D3 (VD3) to the clinically relevant 25-OH-VD3 with >95% yield at a rate 6.5-fold higher than that of wild-type bacterial extracts; the specific activity of recombinant S25DH1 was twofold higher than that of wild-type enzyme. These results demonstrate the potential application of the established expression platform for 25-OH-VD3 synthesis and pave the way for the characterization of previously genetically inaccessible S25DH-like Mo enzymes of the DMSO reductase family.IMPORTANCE Steroids are ubiquitous bioactive compounds, some of which are considered an emerging class of micropollutants. Their degradation by microorganisms is the major process of steroid elimination from the environment. While oxygenase-dependent steroid degradation in aerobes has been studied for more than 40 years, initial insights into the anoxic steroid degradation have only recently been obtained. Molybdenum-dependent steroid C25 dehydrogenases (S25DHs) have been proposed to catalyze oxygen-independent side chain hydroxylations of globally abundant zoo-, phyto-, and mycosterols; however, so far, their lability has allowed only the initial characterization of a single S25DH. Here we report on a heterologous gene expression platform that allowed for easy isolation and characterization of four highly active S25DH isoenzymes. The results obtained demonstrate the key role of S25DHs during anoxic degradation of various steroids. Moreover, the platform is valuable for the efficient enzymatic hydroxylation of vitamin D3 to its clinically relevant C-25-OH form.
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22
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Sawers RG. o-Phthalate derived from plastics’ plasticizers and a bacterium's solution to its anaerobic degradation. Mol Microbiol 2018; 108:595-600. [DOI: 10.1111/mmi.13975] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2018] [Indexed: 12/18/2022]
Affiliation(s)
- R. G. Sawers
- Institute of Biology/Microbiology; Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3; Halle (Saale) 06120, Germany
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23
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Mergelsberg M, Egle V, Boll M. Evolution of a xenobiotic degradation pathway: formation and capture of the labile phthaloyl-CoA intermediate during anaerobic phthalate degradation. Mol Microbiol 2018; 108:614-626. [PMID: 29645305 DOI: 10.1111/mmi.13962] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2018] [Indexed: 12/21/2022]
Abstract
Xenobiotic phthalates are industrially produced on the annual million ton scale. The oxygen-independent enzymatic reactions involved in anaerobic phthalate degradation have only recently been elucidated. In vitro assays suggested that phthalate is first activated to phthaloyl-CoA followed by decarboxylation to benzoyl-CoA. Here, we report the heterologous production and characterization of the enzyme initiating anaerobic phthalate degradation from 'Aromatoleum aromaticum': a highly specific succinyl-CoA:phthalate CoA transferase (SPT, class III CoA transferase). Phthaloyl-CoA formed by SPT accumulated only to sub-micromolar concentrations due to the extreme lability of the product towards intramolecular substitution with a half-life of around 7 min. Upon addition of excess phthaloyl-CoA decarboxylase (PCD), the combined activity of both enzymes was drastically shifted towards physiologically relevant benzoyl-CoA formation. In conclusion, a massive overproduction of PCD in phthalate-grown cells to concentrations >140 μM was observed that allowed for efficient phthaloyl-CoA conversion at concentrations 250-fold below the apparent Km -value of PCD. The results obtained provide insights into an only recently evolved xenobiotic degradation pathway where a massive cellular overproduction of PCD compensates for the formation of the probably most unstable CoA ester intermediate in biology.
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Affiliation(s)
- Mario Mergelsberg
- Faculty of Biology - Microbiology, University of Freiburg, Freiburg, Germany
| | - Valentin Egle
- Faculty of Biology - Microbiology, University of Freiburg, Freiburg, Germany
| | - Matthias Boll
- Faculty of Biology - Microbiology, University of Freiburg, Freiburg, Germany
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24
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The UbiX-UbiD system: The biosynthesis and use of prenylated flavin (prFMN). Arch Biochem Biophys 2017; 632:209-221. [DOI: 10.1016/j.abb.2017.07.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/17/2022]
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