1
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Wang Q, Li H, Bujupi U, Gröning J, Stolz A, Bongiorno A, Gupta R. Oxygen Activation in Aromatic Ring Cleaving Salicylate Dioxygenase: Detection of Reaction Intermediates with a Nitro-substituted Substrate Analog. Chembiochem 2024; 25:e202400023. [PMID: 38363551 DOI: 10.1002/cbic.202400023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/17/2024]
Abstract
Cupin dioxygenases such as salicylate 1,2-dioxygense (SDO) perform aromatic C-C bond scission via a 3-His motif tethered iron cofactor. Here, transient kinetics measurements are used to monitor the catalytic cycle of SDO by using a nitro-substituted substrate analog, 3-nitrogentisate. Compared to the natural substrate, the nitro group reduces the enzymatic kcat by 500-fold, thereby facilitating the detection and kinetic characterization of reaction intermediates. Sums and products of reciprocal relaxation times derived from kinetic measurements were found to be linearly dependent on O2 concentration, suggesting reversible formation of two distinct intermediates. Dioxygen binding to the metal cofactor takes place with a forward rate of 5.9×103 M-1 s-1: two orders of magnitude slower than other comparable ring-cleaving dioxygenses. Optical chromophore of the first intermediate is distinct from the in situ generated SDO Fe(III)-O2⋅- complex but closer to the enzyme-substrate precursor.
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Affiliation(s)
- Qian Wang
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
| | - Hanbin Li
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
- Ph.D. Programs in Chemistry and Physics, The Graduate Center of the City University of New York, New York, 10016, United States
| | - Uran Bujupi
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
| | - Janosch Gröning
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Andreas Stolz
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Angelo Bongiorno
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
- Ph.D. Programs in Chemistry and Physics, The Graduate Center of the City University of New York, New York, 10016, United States
| | - Rupal Gupta
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
- Ph.D. Programs in Biochemistry, The Graduate Center of the City University of New York, New York, 10016, United States
- Ph.D. Programs in Chemistry and Physics, The Graduate Center of the City University of New York, New York, 10016, United States
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2
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Huang Z, Gu Z, Abuduwupuer X, Qin D, Liu Y, Guo Z, Gao R. Engineering non-conservative substrate recognition sites of extradiol dioxygenase: Computation guided design to diversify and accelerate degradation of aromatic compounds. Int J Biol Macromol 2024; 264:130739. [PMID: 38460639 DOI: 10.1016/j.ijbiomac.2024.130739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Extradiol dioxygenases (EDOs) catalyzing meta-cleavage of catecholic compounds promise an effective way to detoxify aromatic pollutants. This work reported a novel scenario to engineer our recently identified Type I EDO from Tcu3516 for a broader substrate scope and enhanced activity, which was based on 2,3-dihydroxybiphenyl (2,3-DHB)-liganded molecular docking of Tcu3516 and multiple sequence alignment with other 22 Type I EDOs. 11 non-conservative residues of Tcu3516 within 6 Å distance to the 2,3-DHB ligand center were selected as potential hotspots and subjected to semi-rational design using 6 catecholic analogues as substrates; the mutants V186L and V212N returned with progressive evolution in substrate scope and catalytic activity. Both mutants were combined with D285A for construction of double mutants and final triple mutant V186L/V212N/D285A. Except for 2,3-DHB (the mutant V186L/D285A gave the best catalytic performance), the triple mutant prevailed all other 5 catecholic compounds for their degradation; affording the catalytic efficiency kcat/Km value increase by 10-30 folds, protein Tm (structural rigidity) increase by 15 °C and the half-life time enhancement by 10 times compared to the wild type Tcu3516. The molecular dynamic simulation suggested that a stabler core and a more flexible entrance are likely accounting for enhanced catalytic activity and stability of enzymes.
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Affiliation(s)
- Zihao Huang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zhenyu Gu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xiemuxinuer Abuduwupuer
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Deyuan Qin
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yuchen Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark.
| | - Renjun Gao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
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3
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Kass D, Larson VA, Corona T, Kuhlmann U, Hildebrandt P, Lohmiller T, Bill E, Lehnert N, Ray K. Trapping of a phenoxyl radical at a non-haem high-spin iron(II) centre. Nat Chem 2024; 16:658-665. [PMID: 38216752 DOI: 10.1038/s41557-023-01405-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 11/17/2023] [Indexed: 01/14/2024]
Abstract
The activation of dioxygen at haem and non-haem metal centres, and subsequent functionalization of unactivated C‒H bonds, has been a focal point of much research. In iron-mediated oxidation reactions, O2 binding at an iron(II) centre is often accompanied by an oxidation of the iron centre. Here we demonstrate dioxygen activation by sodium tetraphenylborate and protons in the presence of an iron(II) complex to form a reactive radical species, whereby the iron oxidation state remains unaltered in the presence of a highly oxidizing phenoxyl radical and O2. This complex, containing an unusual iron(II)-phenoxyl radical motif, represents an elusive example of a spectroscopically characterized oxygen-derived iron(II)-reactive intermediate during chemical and biological dioxygen activation at haem and non-haem iron active centres. The present report opens up strategies for the stabilization of a phenoxyl radical cofactor, with its full oxidizing capabilities, to act as an independent redox centre next to an iron(II) site during substrate oxidation reactions.
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Affiliation(s)
- Dustin Kass
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Virginia A Larson
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Teresa Corona
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Uwe Kuhlmann
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Peter Hildebrandt
- Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Thomas Lohmiller
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
- EPR4Energy Joint Lab, Department Spins in Energy Conversion and Quantum Information Science, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Mülheim an der Ruhr, Germany
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
| | - Kallol Ray
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany.
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4
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Schittich AR, Fenner K, Stedmon CA, Xu J, McKnight US, Smets BF. Coupling pathway prediction and fluorescence spectroscopy to assess the impact of auxiliary substrates on micropollutant biodegradation. Environ Microbiol 2024; 26:e16560. [PMID: 38234207 DOI: 10.1111/1462-2920.16560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024]
Abstract
Some bacteria can degrade organic micropollutants (OMPs) as primary carbon sources. Due to typically low OMP concentrations, these bacteria may benefit from supplemental assimilation of natural substrates present in the pool of dissolved organic matter (DOM). The biodegradability of such auxiliary substrates and the impacts on OMP removal are tightly linked to biotransformation pathways. Here, we aimed to elucidate the biodegradability and effect of different DOM constituents for the carbofuran degrader Novosphingobium sp. KN65.2, using a novel approach that combines pathway prediction, laboratory experiments, and fluorescence spectroscopy. Pathway prediction suggested that ring hydroxylation reactions catalysed by Rieske-type dioxygenases and flavin-dependent monooxygenases determine the transformability of the 11 aromatic compounds used as model DOM constituents. Our approach further identified two groups with distinct transformation mechanisms amongst the four growth-supporting compounds selected for mixed substrate biodegradation experiments with the pesticide carbofuran (Group 1: 4-hydroxybenzoic acid, 4-hydroxybenzaldehyde; Group 2: p-coumaric acid, ferulic acid). Carbofuran biodegradation kinetics were stable in the presence of both Group 1 and Group 2 auxiliary substrates. However, Group 2 substrates would be preferable for bioremediation processes, as they showed constant biodegradation kinetics under different experimental conditions (pre-growing KN65.2 on carbofuran vs. DOM constituent). Furthermore, Group 2 substrates were utilisable by KN65.2 in the presence of a competitor (Pseudomonas fluorescens sp. P17). Our study thus presents a simple and cost-efficient approach that reveals mechanistic insights into OMP-DOM biodegradation.
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Affiliation(s)
- Anna-Ricarda Schittich
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
- Sino-Danish Center for Education and Research, Denmark
- Department of Civil and Environmental Engineering, University of California Berkeley, Berkeley, California, USA
| | - Kathrin Fenner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- University of Zürich, Department of Chemistry, Zürich, Switzerland
| | - Colin A Stedmon
- National Institute of Aquatic Research, Technical University of Denmark, Lyngby, Denmark
| | - Jianxin Xu
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Ursula S McKnight
- Swedish Meteorological and Hydrological Institute, Norrköping, Sweden
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
- Sino-Danish Center for Education and Research, Denmark
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5
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Ehinger FJ, Niehs SP, Dose B, Dell M, Krabbe J, Pidot SJ, Stinear TP, Scherlach K, Ross C, Lackner G, Hertweck C. Analysis of Rhizonin Biosynthesis Reveals Origin of Pharmacophoric Furylalanine Moieties in Diverse Cyclopeptides. Angew Chem Int Ed Engl 2023; 62:e202308540. [PMID: 37650335 DOI: 10.1002/anie.202308540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/01/2023]
Abstract
Rhizonin A and B are hepatotoxic cyclopeptides produced by bacterial endosymbionts (Mycetohabitans endofungorum) of the fungus Rhizopus microsporus. Their toxicity critically depends on the presence of 3-furylalanine (Fua) residues, which also occur in pharmaceutically relevant cyclopeptides of the endolide and bingchamide families. The biosynthesis and incorporation of Fua by non-ribosomal peptide synthetases (NRPS), however, has remained elusive. By genome sequencing and gene inactivation we elucidated the gene cluster responsible for rhizonin biosynthesis. A suite of isotope labeling experiments identified tyrosine and l-DOPA as Fua precursors and provided the first mechanistic insight. Bioinformatics, mutational analysis and heterologous reconstitution identified dioxygenase RhzB as necessary and sufficient for Fua formation. RhzB is a novel type of heme-dependent aromatic oxygenases (HDAO) that enabled the discovery of the bingchamide biosynthesis gene cluster through genome mining.
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Affiliation(s)
- Friedrich J Ehinger
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Sarah P Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Maria Dell
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Jana Krabbe
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute, 792 Elizabeth Street, Melbourne, 3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, 792 Elizabeth Street, Melbourne, 3000, Australia
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Claudia Ross
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Gerald Lackner
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstraße 11a, 07745, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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6
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BUYUKTEMIZ M, DEDE Y. Homoprotocatechuate dioxygenase active site: Imitating the secondary sphere base via computational design. Turk J Chem 2023; 47:1116-1124. [PMID: 38173743 PMCID: PMC10760822 DOI: 10.55730/1300-0527.3598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 10/31/2023] [Accepted: 09/30/2023] [Indexed: 01/05/2024] Open
Abstract
Oxidative ring cleavage reactions have attracted great interest and various studies on the catechol ring-cleaving enzyme homoprotocatechuate dioxygenase (HPCD) have been reported in the literature. The available data on how the proton transfer takes place led us to design a potential HPCD model structure. A secondary sphere effect of utmost importance, the assistance of His200, which is critical for the catechol proton to migrate to dioxygen, was cautiously included on the first coordination shell. This was done mainly by modifying the axial ligands in the first coordination shell of HPCD such that the dual basic/acidic role in the proton transfer pathway of His200 was reproduced. Model systems with mono-, bi-, and tridentate ligands are reported. Energetically feasible reaction channels on synthetically promising ligand structures are identified. Key structural and electronic principles for obtaining viable proton transfer paths are outlined.
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Affiliation(s)
- Muhammed BUYUKTEMIZ
- Department of Chemistry, Faculty of Science, Gazi University, Ankara,
Turkiye
| | - Yavuz DEDE
- Department of Chemistry, Faculty of Science, Gazi University, Ankara,
Turkiye
- Department of Chemistry, Faculty of Science, University of Helsinki, Helsinki,
Finland
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7
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Slater JW, Lin CY, Neugebauer ME, McBride MJ, Sil D, Nair M, Katch BJ, Boal AK, Chang MC, Silakov A, Krebs C, Bollinger JM. Synergistic Binding of the Halide and Cationic Prime Substrate of l-Lysine 4-Chlorinase, BesD, in Both Ferrous and Ferryl States. Biochemistry 2023; 62:2480-2491. [PMID: 37542461 PMCID: PMC10829012 DOI: 10.1021/acs.biochem.3c00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2023]
Abstract
An aliphatic halogenase requires four substrates: 2-oxoglutarate (2OG), halide (Cl- or Br-), the halogenation target ("prime substrate"), and dioxygen. In well-studied cases, the three nongaseous substrates must bind to activate the enzyme's Fe(II) cofactor for efficient capture of O2. Halide, 2OG, and (lastly) O2 all coordinate directly to the cofactor to initiate its conversion to a cis-halo-oxo-iron(IV) (haloferryl) complex, which abstracts hydrogen (H•) from the non-coordinating prime substrate to enable radicaloid carbon-halogen coupling. We dissected the kinetic pathway and thermodynamic linkage in binding of the first three substrates of the l-lysine 4-chlorinase, BesD. After addition of 2OG, subsequent coordination of the halide to the cofactor and binding of cationic l-Lys near the cofactor are associated with strong heterotropic cooperativity. Progression to the haloferryl intermediate upon the addition of O2 does not trap the substrates in the active site and, in fact, markedly diminishes cooperativity between halide and l-Lys. The surprising lability of the BesD•[Fe(IV)=O]•Cl•succinate•l-Lys complex engenders pathways for decay of the haloferryl intermediate that do not result in l-Lys chlorination, especially at low chloride concentrations; one identified pathway involves oxidation of glycerol. The mechanistic data imply (i) that BesD may have evolved from a hydroxylase ancestor either relatively recently or under weak selective pressure for efficient chlorination and (ii) that acquisition of its activity may have involved the emergence of linkage between l-Lys binding and chloride coordination following the loss of the anionic protein-carboxylate iron ligand present in extant hydroxylases.
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Affiliation(s)
- Jeffrey W. Slater
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Monica E. Neugebauer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, United States
- Present address: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, United States
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Alliance Pharma, New York, NY 10065, United States
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Department of Chemistry, Indian Institute of Science Education & Research (IISER)-Pune, Pune-411008, India
| | - Mrutyunjay Nair
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Bryce J. Katch
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Present address: Tri-Institutional MD-PhD Program, Weill Cornell Medical College and Cornell University, New York, NY 10065, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Michelle C.Y. Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, United States
- Departments of Chemistry and of Molecular and Cell Biology, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
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8
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Sgro M, Chow N, Olyaei F, Arentshorst M, Geoffrion N, Ram AFJ, Powlowski J, Tsang A. Functional analysis of the protocatechuate branch of the β-ketoadipate pathway in Aspergillus niger. J Biol Chem 2023; 299:105003. [PMID: 37399977 PMCID: PMC10406623 DOI: 10.1016/j.jbc.2023.105003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
Bacteria and fungi catabolize plant-derived aromatic compounds by funneling into one of seven dihydroxylated aromatic intermediates, which then undergo ring fission and conversion to TCA cycle intermediates. Two of these intermediates, protocatechuic acid and catechol, converge on β-ketoadipate which is further cleaved to succinyl-CoA and acetyl-CoA. These β-ketoadipate pathways have been well characterized in bacteria. The corresponding knowledge of these pathways in fungi is incomplete. Characterization of these pathways in fungi would expand our knowledge and improve the valorization of lignin-derived compounds. Here, we used homology to characterize bacterial or fungal genes to predict the genes involved in the β-ketoadipate pathway for protocatechuate utilization in the filamentous fungus Aspergillus niger. We further used the following approaches to refine the assignment of the pathway genes: whole transcriptome sequencing to reveal genes upregulated in the presence of protocatechuic acid; deletion of candidate genes to observe their ability to grow on protocatechuic acid; determination by mass spectrometry of metabolites accumulated by deletion mutants; and enzyme assays of the recombinant proteins encoded by candidate genes. Based on the aggregate experimental evidence, we assigned the genes for the five pathway enzymes as follows: NRRL3_01405 (prcA) encodes protocatechuate 3,4-dioxygenase; NRRL3_02586 (cmcA) encodes 3-carboxy-cis,cis-muconate cyclase; NRRL3_01409 (chdA) encodes 3-carboxymuconolactone hydrolase/decarboxylase; NRRL3_01886 (kstA) encodes β-ketoadipate:succinyl-CoA transferase; and NRRL3_01526 (kctA) encodes β-ketoadipyl-CoA thiolase. Strain carrying ΔNRRL3_00837 could not grow on protocatechuic acid, suggesting that it is essential for protocatechuate catabolism. Its function is unknown as recombinant NRRL3_00837 did not affect the in vitro conversion of protocatechuic acid to β-ketoadipate.
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Affiliation(s)
- Michael Sgro
- Department of Biology, Concordia University, Montreal, Quebec, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Nicholas Chow
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Farnaz Olyaei
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Mark Arentshorst
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, The Netherlands
| | - Nicholas Geoffrion
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Arthur F J Ram
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, The Netherlands
| | - Justin Powlowski
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada; Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Adrian Tsang
- Department of Biology, Concordia University, Montreal, Quebec, Canada; Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
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9
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Runda ME, de Kok NAW, Schmidt S. Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities. Chembiochem 2023; 24:e202300078. [PMID: 36964978 DOI: 10.1002/cbic.202300078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or exploited for synthetic applications. This review aims to provide a general overview of the most important Fd-dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non-heme iron-dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure-function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.
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Affiliation(s)
- Michael E Runda
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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10
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Babicz JT, Rogers MS, DeWeese DE, Sutherlin KD, Banerjee R, Böttger LH, Yoda Y, Nagasawa N, Saito M, Kitao S, Kurokuzu M, Kobayashi Y, Tamasaku K, Seto M, Lipscomb JD, Solomon EI. Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage. J Am Chem Soc 2023; 145:15230-15250. [PMID: 37414058 PMCID: PMC10804917 DOI: 10.1021/jacs.3c02242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.
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Affiliation(s)
- Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Dory E. DeWeese
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Kyle D. Sutherlin
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Lars H. Böttger
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Nobumoto Nagasawa
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Makina Saito
- Department of Physics, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shinji Kitao
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Masayuki Kurokuzu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Yasuhiro Kobayashi
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center, RIKEN, Sayo, Hyogo 679-5148, Japan
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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11
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Łomża P, Krucoń T, Tabernacka A. Potential of Microbial Communities to Perform Dehalogenation Processes in Natural and Anthropogenically Modified Environments-A Metagenomic Study. Microorganisms 2023; 11:1702. [PMID: 37512875 PMCID: PMC10385969 DOI: 10.3390/microorganisms11071702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Halogenated organic compounds (HOCs) pose a serious problem for the environment. Many are highly toxic and accumulate both in soil and in organisms. Their biological transformation takes place by dehalogenation, in which the halogen substituents are detached from the carbon in the organic compound by enzymes produced by microorganisms. This increases the compounds' water solubility and bioavailability, reduces toxicity, and allows the resulting compound to become more susceptible to biodegradation. The microbial halogen cycle in soil is an important part of global dehalogenation processes. The aim of the study was to examine the potential of microbial communities inhabiting natural and anthropogenically modified environments to carry out the dehalogenation process. The potential of microorganisms was assessed by analyzing the metagenomes from a natural environment (forest soils) and from environments subjected to anthropopression (agricultural soil and sludge from wastewater treatment plants). Thirteen genes encoding enzymes with dehalogenase activity were identified in the metagenomes of both environments, among which, 2-haloacid dehalogenase and catechol 2,3-dioxygenase were the most abundant genes. Comparative analysis, based on comparing taxonomy, identified genes, total halogens content and content of DDT derivatives, demonstrated the ability of microorganisms to transform HOCs in both environments, indicating the presence of these compounds in the environment for a long period of time and the adaptive need to develop mechanisms for their detoxification. Metagenome analyses and comparative analyses indicate the genetic potential of microorganisms of both environments to carry out dehalogenation processes, including dehalogenation of anthropogenic HOCs.
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Affiliation(s)
- Pola Łomża
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
| | - Tomasz Krucoń
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, 1 Miecznikowa Street, 02-089 Warsaw, Poland
| | - Agnieszka Tabernacka
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
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12
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Vijayanand M, Ramakrishnan A, Subramanian R, Issac PK, Nasr M, Khoo KS, Rajagopal R, Greff B, Wan Azelee NI, Jeon BH, Chang SW, Ravindran B. Polyaromatic hydrocarbons (PAHs) in the water environment: A review on toxicity, microbial biodegradation, systematic biological advancements, and environmental fate. ENVIRONMENTAL RESEARCH 2023; 227:115716. [PMID: 36940816 DOI: 10.1016/j.envres.2023.115716] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/04/2023] [Accepted: 03/16/2023] [Indexed: 05/08/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are considered a major class of organic contaminants or pollutants, which are poisonous, mutagenic, genotoxic, and/or carcinogenic. Due to their ubiquitous occurrence and recalcitrance, PAHs-related pollution possesses significant public health and environmental concerns. Increasing the understanding of PAHs' negative impacts on ecosystems and human health has encouraged more researchers to focus on eliminating these pollutants from the environment. Nutrients available in the aqueous phase, the amount and type of microbes in the culture, and the PAHs' nature and molecular characteristics are the common factors influencing the microbial breakdown of PAHs. In recent decades, microbial community analyses, biochemical pathways, enzyme systems, gene organization, and genetic regulation related to PAH degradation have been intensively researched. Although xenobiotic-degrading microbes have a lot of potential for restoring the damaged ecosystems in a cost-effective and efficient manner, their role and strength to eliminate the refractory PAH compounds using innovative technologies are still to be explored. Recent analytical biochemistry and genetically engineered technologies have aided in improving the effectiveness of PAHs' breakdown by microorganisms, creating and developing advanced bioremediation techniques. Optimizing the key characteristics like the adsorption, bioavailability, and mass transfer of PAH boosts the microorganisms' bioremediation performance, especially in the natural aquatic water bodies. This review's primary goal is to provide an understanding of recent information about how PAHs are degraded and/or transformed in the aquatic environment by halophilic archaea, bacteria, algae, and fungi. Furthermore, the removal mechanisms of PAH in the marine/aquatic environment are discussed in terms of the recent systemic advancements in microbial degradation methodologies. The review outputs would assist in facilitating the development of new insights into PAH bioremediation.
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Affiliation(s)
- Madhumitha Vijayanand
- Department of Medical Biotechnology and Integrative Physiology, Institute of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai, 602 105, Tamil Nadu, India
| | - Abiraami Ramakrishnan
- Department of Civil Engineering, Christian College of Engineering and Technology Oddanchatram, 624619,Dindigul District, Tamilnadu, India
| | - Ramakrishnan Subramanian
- Department of Civil Engineering, Sri Krishna College of Engineering and Technology, Kuniamuthur, Coimbatore, 641008, Tamilnadu, India
| | - Praveen Kumar Issac
- Department of Medical Biotechnology and Integrative Physiology, Institute of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai, 602 105, Tamil Nadu, India.
| | - Mahmoud Nasr
- Environmental Engineering Department, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, 21934, Egypt; Sanitary Engineering Department, Faculty of Engineering, Alexandria University, 21544, Alexandria, Egypt
| | - Kuan Shiong Khoo
- Biorefinery and Bioprocess Engineering Laboratory, Department of Chemical Engineering and Material Science, Yuan Ze University, Taoyuan, Taiwan
| | - Rajinikanth Rajagopal
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
| | - Babett Greff
- Department of Food Science, Albert Casimir Faculty at Mosonmagyaróvár, Széchenyi István University, 15-17 Lucsony Street, 9200, Mosonmagyaróvár, Hungary
| | - Nur Izyan Wan Azelee
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, 81310, UTM Skudai, Johor Bahru, Johor Darul Takzim, Malaysia
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Soon Woong Chang
- Department of Environmental Energy & Engineering, Kyonggi University, Suwon-si, Gyeonggi-do, 16227, South Korea
| | - Balasubramani Ravindran
- Department of Medical Biotechnology and Integrative Physiology, Institute of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai, 602 105, Tamil Nadu, India; Department of Environmental Energy & Engineering, Kyonggi University, Suwon-si, Gyeonggi-do, 16227, South Korea.
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13
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Liu Y, Li J, Zeng J, Yu X, Sun X, Zhou Z, Xu J, Xu L, Li L. Complete oxidative degradation of diclofenac via coupling free radicals and oxygenases of a micro/nanostructured biogenic Mn oxide composite from engineered Pseudomonas sp. MB04R-2. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131657. [PMID: 37245362 DOI: 10.1016/j.jhazmat.2023.131657] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/06/2023] [Accepted: 05/16/2023] [Indexed: 05/30/2023]
Abstract
Oxidative degradation can effectively degrade aromatic emerging contaminants (ECs). However, the degradability of lone inorganic/biogenic oxides or oxidases is typically limited when treating polycyclic ECs. Herein, we report a dual-dynamic oxidative system comprising engineered Pseudomonas and biogenic Mn oxides (BMO), which completely degrades diclofenac (DCF), a representative halogen-containing polycyclic EC. Correspondingly, recombinant Pseudomonas sp. MB04R-2 was constructed via gene deletion and chromosomal insertion of a heterologous multicopper oxidase cotA, allowing for enhanced Mn(II)-oxidizing activity and rapid formation of the BMO aggregate complex. Additionally, we characterized it as a micro/nanostructured ramsdellite (MnO2) composite using multiple-phase composition and fine structure analyses. Furthermore, using real-time quantitative polymerase chain reaction, gene knockout, and expression complementation of oxygenase genes, we demonstrated the central and associative roles of intracellular oxygenases and cytogenic/BMO-derived free radicals (FRs) in degrading DCF and determined the effects of FR excitation and quenching on the DCF degradation efficiency. Finally, after identifying the degraded intermediates of 2H-labeled DCF, we constructed the DCF metabolic pathway. In addition, we evaluated the degradation and detoxification effects of the BMO composite on DCF-containing urban lake water and on biotoxicity in zebrafish embryos. Based on our findings, we proposed a mechanism for oxidative degradation of DCF by associative oxygenases and FRs.
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Affiliation(s)
- Yongxuan Liu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaoqing Li
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, School of Life Sciences, Jiaying University, Meizhou 514015, China
| | - Jie Zeng
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xun Yu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaowen Sun
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhicheng Zhou
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingjing Xu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangzheng Xu
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, School of Life Sciences, Jiaying University, Meizhou 514015, China
| | - Lin Li
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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14
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Slater JW, Neugebauer ME, McBride MJ, Sil D, Lin CY, Katch BJ, Boal AK, Chang MC, Silakov A, Krebs C, Bollinger JM. Synergistic Binding of the Halide and Cationic Prime Substrate of the l-Lysine 4-Chlorinase, BesD, in Both Ferrous and Ferryl States. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539147. [PMID: 37205437 PMCID: PMC10187165 DOI: 10.1101/2023.05.02.539147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
An aliphatic halogenase requires four substrates: 2-oxoglutarate (2OG), halide (Cl - or Br - ), the halogenation target ("prime substrate"), and dioxygen. In well-studied cases, the three non-gaseous substrates must bind to activate the enzyme's Fe(II) cofactor for efficient capture of O 2 . Halide, 2OG, and (lastly) O 2 all coordinate directly to the cofactor to initiate its conversion to a cis -halo-oxo-iron(IV) (haloferryl) complex, which abstracts hydrogen (H•) from the non-coordinating prime substrate to enable radicaloid carbon-halogen coupling. We dissected the kinetic pathway and thermodynamic linkage in binding of the first three substrates of the l -lysine 4-chlorinase, BesD. After 2OG adds, subsequent coordination of the halide to the cofactor and binding of cationic l -Lys near the cofactor are associated with strong heterotropic cooperativity. Progression to the haloferryl intermediate upon addition of O 2 does not trap the substrates in the active site and, in fact, markedly diminishes cooperativity between halide and l -Lys. The surprising lability of the BesD•[Fe(IV)=O]•Cl•succinate• l -Lys complex engenders pathways for decay of the haloferryl intermediate that do not result in l -Lys chlorination, especially at low chloride concentrations; one identified pathway involves oxidation of glycerol. The mechanistic data imply that (i) BesD may have evolved from a hydroxylase ancestor either relatively recently or under weak selective pressure for efficient chlorination and (ii) that acquisition of its activity may have involved the emergence of linkage between l -Lys binding and chloride coordination following loss of the anionic protein-carboxylate iron ligand present in extant hydroxylases.
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Affiliation(s)
- Jeffrey W. Slater
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Monica E. Neugebauer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Present address: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Debangsu Sil
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Bryce J. Katch
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Michelle C.Y. Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Departments of Chemistry and of Molecular and Cell Biology, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexey Silakov
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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15
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Jeong D, Selverstone Valentine J, Cho J. Bio-inspired mononuclear nonheme metal peroxo complexes: Synthesis, structures and mechanistic studies toward understanding enzymatic reactions. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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16
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Rafalowski A, Hassan BA, Lou K, Nguyen MC, Taylor EA. How Single Amino Acid Substitutions Can Disrupt a Protein Hetero-Dimer Interface: Computational and Experimental Studies of the LigAB Dioxygenase from Sphingobium sp. Strain SYK-6. Int J Mol Sci 2023; 24:ijms24076319. [PMID: 37047291 PMCID: PMC10094722 DOI: 10.3390/ijms24076319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Protocatechuate 4,5-dioxygenase (LigAB) is a heterodimeric enzyme that catalyzes the dioxygenation of multiple lignin derived aromatic compounds. The active site of LigAB is at the heterodimeric interface, with specificity conferred by the alpha subunit and catalytic residues contributed by the beta subunit. Previous research has indicated that the phenylalanine at the 103 position of the alpha subunit (F103α) controls selectivity for the C5 position of the aromatic substrates, and mutations of this residue can enhance the rate of catalysis for substrates with larger functional groups at this position. While several of the mutations to this position (Valine, V; Threonine, T; Leucine, L; and Histidine, H) were catalytically active, other mutations (Alanine, A; and Serine, S) were found to have reduced dimer interface affinity, leading to challenges in copurifing the catalytically active enzyme complex under high salt conditions. In this study, we aimed to experimentally and computationally interrogate residues at the dimer interface to discern the importance of position 103α for maintaining the integrity of the heterodimer. Molecular dynamic simulations and electrophoretic mobility assays revealed a preference for nonpolar/aromatic amino acids in this position, suggesting that while substitutions to polar amino acids may produce a dioxygenase with a useful substrate utilization profile, those considerations may be off-set by potential destabilization of the catalytically active oligomer. Understanding the dimerization of LigAB provides insight into the multimeric proteins within the largely uncharacterized superfamily and characteristics to consider when engineering proteins that can degrade lignin efficiently. These results shed light on the challenges associated with engineering proteins for broader substrate specificity.
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17
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Kim JH, Buyuktemiz M, Alıcı G, Baik MH, Dede Y. The Role of the Redox Non-Innocent Hydroxyl Ligand in the Activation of O 2 Performed by [Ni(H)(OH)] . Chemistry 2023; 29:e202203128. [PMID: 36447369 DOI: 10.1002/chem.202203128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022]
Abstract
The cationic complex [Ni(H)(OH)]+ was previously found to activate dioxygen and methane in gas phase under single collision conditions. These remarkable reactivities were thought to originate from a non-classical electronic structure, where the Ni-center adopts a Ni(II), instead of the classically expected Ni(III) oxidation state by formally accepting an electron from the hydroxo ligand, which formally becomes a hydroxyl radical in the process. Such radicaloid oxygen moieties are envisioned to easily react with otherwise inert substrates, mimicking familiar reactivities of free radicals. In this study, the reductive activation of dioxygen by [Ni(H)(OH)]+ to afford the hydroperoxo species was investigated using coupled cluster, multireference ab initio and density functional theory calculations. Orbital and wave function analyses indicate that O2 binding tranforms the aforementioned non-classical electronic structure to a classical Ni(III)-hydroxyl system, before O2 reduction takes place. Remarkably, we found no evidence for a direct involvement of the radicaloid hydroxyl in the reaction with O2 , as is often assumed. The function of the redox non-innocent character of the activator complex is to protect the reactive electronic structure until the complex engages O2 , upon which a dramatic electronic reorganization releases internal energy and drives the chemical reaction to completion.
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Affiliation(s)
- Jun-Hyeong Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Muhammed Buyuktemiz
- Department of Chemistry, Faculty of Science, Gazi University, Teknikokullar, Ankara, Turkey
| | - Gökçe Alıcı
- Department of Chemistry, Faculty of Science, Gazi University, Teknikokullar, Ankara, Turkey
| | - Mu-Hyun Baik
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Yavuz Dede
- Department of Chemistry, Faculty of Science, Gazi University, Teknikokullar, Ankara, Turkey
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18
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Bioconversion of 4-hydroxyestradiol by extradiol ring-cleavage dioxygenases from Novosphingobium sp. PP1Y. Sci Rep 2023; 13:1835. [PMID: 36725873 PMCID: PMC9892492 DOI: 10.1038/s41598-023-28908-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Livestock breeding activities and pharmaceutical wastes lead to considerable accumulation of steroid hormones and estrogens in wastewaters. Here estrogens act as pro-cancerogenic agents and endocrine disruptors interfering with the sexual development of aquatic animals and having toxic effects in humans. Environmental bacteria play a vital role in estrogens degradation. Their wide reservoir of enzymes, such as ring cleavage dioxygenases (RCDs), can degrade the steroid nucleus, catalyzing the meta-cleavage of A, B or D steroid rings. In this work, 4 extra-diol ring cleavage dioxygenases (ERCDs), PP28735, PP26077, PP00124 and PP00193, were isolated from the marine sphingomonad Novosphingobium sp. PP1Y and characterized. Enzymes kinetic parameters were determined on different synthetic catecholic substrates. Then, the bioconversion of catechol estrogens was evaluated. PP00124 showed to be an efficient catalyst for the degradation of 4-hydroxyestradiol (4-OHE2), a carcinogenic hydroxylated derivate of E2. 4-OHE2 complete cleavage was obtained using PP00124 both in soluble form and in whole recombinant E. coli cells. LC-MS/MS analyses confirmed the generation of a semialdehyde product, through A-ring meta cleavage. To the best of our knowledge, PP00124 is the first characterized enzyme able to directly degrade 4-OHE2 via meta cleavage. Moreover, the complete 4-OHE2 biodegradation using recombinant whole cells highlighted advantages for bioremediation purposes.
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19
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Kennes-Veiga D, Trueba-Santiso A, Gallardo-Garay V, Balboa S, Carballa M, Lema JM. Sulfamethoxazole Enhances Specific Enzymatic Activities under Aerobic Heterotrophic Conditions: A Metaproteomic Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13152-13159. [PMID: 36073795 PMCID: PMC9686132 DOI: 10.1021/acs.est.2c05001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
The growing concern about antibiotic-resistant microorganisms has focused on the sludge from wastewater treatment plants (WWTPs) as a potential hotspot for their development and spread. To this end, it seems relevant to analyze the changes on the microbiota as a consequence of the antibiotics that wastewater may contain. This study aims at determining whether the presence of sulfamethoxazole (SMX), even in relatively low concentrations, modifies the microbial activities and the enzymatic expression of an activated sludge under aerobic heterotrophic conditions. For that purpose, we applied a metaproteomic approach in combination with genomic and transformation product analyses. SMX was biotransformed, and the metabolite 2,4(1H,3H)-pteridinedione-SMX (PtO-SMX) from the pterin-conjugation pathway was detected at all concentrations tested. Metaproteomics showed that SMX at 50-2000 μg/L slightly affected the microbial community structure, which was confirmed by DNA metabarcoding. Interestingly, an enhanced activity of the genus Corynebacterium and specifically of five enzymes involved in its central carbon metabolism was found at increased SMX concentrations. Our results suggest a role of Corynebacterium genus on SMX risks mitigation in our bioreactors.
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Affiliation(s)
- David
M. Kennes-Veiga
- CRETUS,
Department of Chemical Engineering, University
of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Alba Trueba-Santiso
- CRETUS,
Department of Chemical Engineering, University
of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Valentina Gallardo-Garay
- CRETUS,
Department of Chemical Engineering, University
of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Sabela Balboa
- CRETUS,
Department of Microbiology, University of
Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Marta Carballa
- CRETUS,
Department of Chemical Engineering, University
of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Juan M. Lema
- CRETUS,
Department of Chemical Engineering, University
of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
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20
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Efficient biodegradation of di-(2-ethylhexyl) phthalate by a novel strain Nocardia asteroides LMB-7 isolated from electronic waste soil. Sci Rep 2022; 12:15262. [PMID: 36088485 PMCID: PMC9464244 DOI: 10.1038/s41598-022-19752-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 09/02/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractThe di-2-ethylhexyl phthalate (DEHP) degrading strain LMB-7 was isolated from electronic waste soil. According to its biophysical/biochemical characteristics and 16S rRNA gene analysis, the strain was identified as Nocardia asteroides. Optimal pH and temperature for DEHP degradation were 8.0 and 30 °C, respectively, and DEHP removal reached 97.11% after cultivation for 24 h at an initial concentration of 400 mg/L. As degradation intermediates, di-butyl phthalates, mono-2-ethylhexyl phthalate and 2-ethylhexanol could be identified, and it could be confirmed that DEHP was completely degraded by strain LMB-7. To our knowledge, this is a new report of DEHP degradation by a strain of Nocardia asteroides, at rates higher than those reported to date. This finding provides a new way for DEHP elimination from environment.
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21
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Li Z, Wang J, Gu C, Guo Y, Wu S. Marine bacteria-mediated abiotic-biotic coupling degradation mechanism of ibuprofen. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:128960. [PMID: 35472552 DOI: 10.1016/j.jhazmat.2022.128960] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 06/14/2023]
Abstract
Knowledge on the behavior and fate of pharmaceuticals and personal care products (PPCPs) is poorly explored in marine aphotic environment. In this study, the degradation mechanism of a typical PPCPs-ibuprofen (IBP) by a ubiquitous marine Pseudoalteromonas sp. was investigated based on transcriptome and key enzymes analysis. More importantly, a novel enzymatic-nonenzymatic coupling degradation mechanism was uncovered for the first time, namely, the degradation of IBP was firstly initiated by extracellular reactive oxygen species (ROS), then the intermediate (e.g.4-ethylresorcinol) was further degraded by intracellular enzymes. It was showed that biogenic •OH, O2•-and H2O2 were responsible for extracellular nonenzymatic degradation, in which IBP was degraded to 4-ethylresorcinol through hydrogenation, isobutyl moiety cleavage, oxidation and decarboxylation. 4-Hydroxyphenylpyruvate dioxygenase, homogentisate 1,2-dioxygenase, long-chain acyl-CoA synthetase, acetyl-CoA acyltransferase and enoyl-CoA hydratase were identified to be involved in intracellular degradation, leading 4-ethylresorcinol cracked and eventually mineralized. Ultimately, this novel degradation mechanism was demonstrated to be amino acids-driven through KEGG enrichment analysis and experimental data. Overall, our work uncovered a yet undiscovered abiotic-biotic coupling degradation mechanism in PPCPs biotransformation, thereby updating the conventional concept that contaminants transformation is solely accomplished by enzymes or non-enzymes, which can also provide new insights into PPCPs environmental behavior and fate.
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Affiliation(s)
- Zelong Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Chen Gu
- Power China Huadong Engineering Corporation Limited, Hangzhou 311122, China
| | - Yali Guo
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Shuo Wu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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22
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Medić AB, Karadžić IM. Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation. World J Microbiol Biotechnol 2022; 38:165. [PMID: 35861883 DOI: 10.1007/s11274-022-03349-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/26/2022] [Indexed: 10/17/2022]
Abstract
Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.
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Affiliation(s)
- Ana B Medić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia.
| | - Ivanka M Karadžić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia
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23
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The Novel Amidase PcnH Initiates the Degradation of Phenazine-1-Carboxamide in Sphingomonas histidinilytica DS-9. Appl Environ Microbiol 2022; 88:e0054322. [PMID: 35579476 PMCID: PMC9195955 DOI: 10.1128/aem.00543-22] [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: 12/29/2022] Open
Abstract
Phenazines are an important class of secondary metabolites and are primarily named for their heterocyclic phenazine cores, including phenazine-1-carboxylic acid (PCA) and its derivatives, such as phenazine-1-carboxamide (PCN) and pyocyanin (PYO). Although several genes involved in the degradation of PCA and PYO have been reported so far, the genetic foundations of PCN degradation remain unknown. In this study, a PCN-degrading bacterial strain, Sphingomonas histidinilytica DS-9, was isolated. The gene pcnH, encoding a novel amidase responsible for the initial step of PCN degradation, was cloned by genome comparison and subsequent experimental validation. PcnH catalyzed the hydrolysis of the amide bond of PCN to produce PCA, which shared low identity (only 26 to 33%) with reported amidases. The Km and kcat values of PcnH for PCN were 33.22 ± 5.70 μM and 18.71 ± 0.52 s-1, respectively. PcnH has an Asp-Lys-Cys motif, which is conserved among amidases of the isochorismate hydrolase-like (IHL) superfamily. The replacement of Asp37, Lys128, and Cys163 with alanine in PcnH led to the complete loss of enzymatic activity. Furthermore, the genes pcaA1A2A3A4 and pcnD were found to encode PCA 1,2-dioxygenase and 1,2-dihydroxyphenazine (2OHPC) dioxygenase, which were responsible for the subsequent degradation steps of PCN. The PCN-degradative genes were highly conserved in some bacteria of the genus Sphingomonas, with slight variations in the sequence identities. IMPORTANCE Phenazines have been widely acknowledged as a natural antibiotic for more than 150 years, but their degradation mechanisms are still not completely elucidated. Compared with the studies on the degradation mechanism of PCA and PYO, little is known regarding PCN degradation by far. Previous studies have speculated that its initial degradation step may be catalyzed by an amidase, but no further studies have been conducted. This study identified a novel amidase, PcnH, that catalyzed the hydrolysis of PCN to PCA. In addition, the PCA 1,2-dioxygenase PcaA1A2A3A4 and 2OHPC dioxygenase PcnD were also found to be involved in the subsequent degradation steps of PCN in S. histidinilytica DS-9. And the genes responsible for PCN catabolism are highly conserved in some strains of Sphingomonas. These results deepen our understanding of the PCN degradation mechanism.
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24
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Pati SG, Bopp CE, Kohler HPE, Hofstetter TB. Substrate-Specific Coupling of O 2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases. ACS Catal 2022; 12:6444-6456. [PMID: 35692249 PMCID: PMC9171724 DOI: 10.1021/acscatal.2c00383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/09/2022] [Indexed: 02/07/2023]
Abstract
![]()
Rieske dioxygenases
catalyze the initial steps in the hydroxylation
of aromatic compounds and are critical for the metabolism of xenobiotic
substances. Because substrates do not bind to the mononuclear non-heme
FeII center, elementary steps leading to O2 activation
and substrate hydroxylation are difficult to delineate, thus making
it challenging to rationalize divergent observations on enzyme mechanisms,
reactivity, and substrate specificity. Here, we show for nitrobenzene
dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes
to nitrite and substituted catechols, that unproductive O2 activation with the release of the unreacted substrate and reactive
oxygen species represents an important path in the catalytic cycle.
Through correlation of O2 uncoupling for a series of substituted
nitroaromatic compounds with 18O and 13C kinetic
isotope effects of dissolved O2 and aromatic substrates,
respectively, we show that O2 uncoupling occurs after the
rate-limiting formation of FeIII-(hydro)peroxo species
from which substrates are hydroxylated. Substituent effects on the
extent of O2 uncoupling suggest that the positioning of
the substrate in the active site rather than the susceptibility of
the substrate for attack by electrophilic oxygen species is responsible
for unproductive O2 uncoupling. The proposed catalytic
cycle provides a mechanistic basis for assessing the very different
efficiencies of substrate hydroxylation vs unproductive O2 activation and generation of reactive oxygen species in reactions
catalyzed by Rieske dioxygenases.
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Affiliation(s)
- Sarah G. Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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26
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Cheng M, Chen D, Parales RE, Jiang J. Oxygenases as Powerful Weapons in the Microbial Degradation of Pesticides. Annu Rev Microbiol 2022; 76:325-348. [PMID: 35650666 DOI: 10.1146/annurev-micro-041320-091758] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oxygenases, which catalyze the reductive activation of O2 and incorporation of oxygen atoms into substrates, are widely distributed in aerobes. They function by switching the redox states of essential cofactors that include flavin, heme iron, Rieske non-heme iron, and Fe(II)/α-ketoglutarate. This review summarizes the catalytic features of flavin-dependent monooxygenases, heme iron-dependent cytochrome P450 monooxygenases, Rieske non-heme iron-dependent oxygenases, Fe(II)/α-ketoglutarate-dependent dioxygenases, and ring-cleavage dioxygenases, which are commonly involved in pesticide degradation. Heteroatom release (hydroxylation-coupled hetero group release), aromatic/heterocyclic ring hydroxylation to form ring-cleavage substrates, and ring cleavage are the main chemical fates of pesticides catalyzed by these oxygenases. The diversity of oxygenases, specificities for electron transport components, and potential applications of oxygenases are also discussed. This article summarizes our current understanding of the catalytic mechanisms of oxygenases and a framework for distinguishing the roles of oxygenases in pesticide degradation. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Minggen Cheng
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
| | - Dian Chen
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA
| | - Jiandong Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
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27
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Abstract
Here, the choice of the first coordination shell of the metal center is analyzed from the perspective of charge maintenance in a binary enzyme-substrate complex and an O2-bound ternary complex in the nonheme iron oxygenases. Comparing homogentisate 1,2-dioxygenase and gentisate dioxygenase highlights the significance of charge maintenance after substrate binding as an important factor that drives the reaction coordinate. We then extend the charge analysis to several common types of nonheme iron oxygenases containing either a 2-His-1-carboxylate facial triad or a 3-His or 4-His ligand motif, including extradiol and intradiol ring-cleavage dioxygenases, thiol dioxygenases, α-ketoglutarate-dependent oxygenases, and carotenoid cleavage oxygenases. After forming the productive enzyme-substrate complex, the overall charge of the iron complex at the 0, +1, or +2 state is maintained in the remaining catalytic steps. Hence, maintaining a constant charge is crucial to promote the reaction of the iron center beginning from the formation of the Michaelis or ternary complex. The charge compensation to the iron ion is tuned not only by protein-derived carboxylate ligands but also by substrates. Overall, these analyses indicate that charge maintenance at the iron center is significant when all the necessary components form a productive complex. This charge maintenance concept may apply to most oxygen-activating metalloenzymes systems that do not draw electrons and protons step-by-step from a separate reactant, such as NADH, via a reductase. The charge maintenance perception may also be useful in proposing catalytic pathways or designing prototypical reactions using artificial or engineered enzymes for biotechnological applications.
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Affiliation(s)
- Ephrahime S. Traore
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
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28
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Soares DM, Gonçalves LP, Machado CO, Esteves LC, Stevani CV, Oliveira CC, Dörr FA, Pinto E, Adachi FM, Hotta CT, Bastos EL. Reannotation of Fly Amanita l-DOPA Dioxygenase Gene Enables Its Cloning and Heterologous Expression. ACS OMEGA 2022; 7:16070-16079. [PMID: 35571802 PMCID: PMC9097196 DOI: 10.1021/acsomega.2c01365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
The l-DOPA dioxygenase of Amanita muscaria (AmDODA) participates in the biosynthesis of betalain- and hygroaurin-type natural pigments. AmDODA is encoded by the dodA gene, whose DNA sequence was inferred from cDNA and gDNA libraries almost 30 years ago. However, reports on its heterologous expression rely on either the original 5'-truncated cDNA plasmid or artificial gene synthesis. We provide unequivocal evidence that the heterologous expression of AmDODA from A. muscaria specimens is not possible by using the coding sequence previously inferred for dodA. Here, we rectify and reannotate the full-length coding sequence for AmDODA and express a 205-aa His-tagged active enzyme, which was used to produce the l-DOPA hygroaurin, a rare fungal pigment. Moreover, AmDODA and other isozymes from bacteria were submitted to de novo folding using deep learning algorithms, and their putative active sites were inferred and compared. The wide catalytic pocket of AmDODA and the presence of the His-His-His and His-His-Asp motifs can provide insight into the dual cleavage of l-DOPA at positions 2,3 and 4,5 as per the mechanism proposed for nonheme dioxygenases.
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Affiliation(s)
- Douglas
M. M. Soares
- Departamento
de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05508-000 São
Paulo, São Paulo Brazil
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, São Paulo Brazil
| | - Letícia
C. P. Gonçalves
- Departamento
de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05508-000 São
Paulo, São Paulo Brazil
| | - Caroline O. Machado
- Departamento
de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05508-000 São
Paulo, São Paulo Brazil
| | - Larissa C. Esteves
- Departamento
de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05508-000 São
Paulo, São Paulo Brazil
| | - Cassius V. Stevani
- Departamento
de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05508-000 São
Paulo, São Paulo Brazil
| | - Carla C. Oliveira
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, São Paulo Brazil
| | - Felipe A. Dörr
- Departamento
de Análises Clínicas e Toxicológicas, Faculdade
de Ciências Farmacêuticas, Universidade de São Paulo, 05508-000 São Paulo, São Paulo Brazil
| | - Ernani Pinto
- Departamento
de Análises Clínicas e Toxicológicas, Faculdade
de Ciências Farmacêuticas, Universidade de São Paulo, 05508-000 São Paulo, São Paulo Brazil
- Centro
de Energia Nuclear na Agricultura, Universidade
de São Paulo, 13400-970 Piracicaba, São Paulo Brazil
| | - Flávia M.
M. Adachi
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, São Paulo Brazil
| | - Carlos T. Hotta
- Departamento
de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000 São Paulo, São Paulo Brazil
| | - Erick L. Bastos
- Departamento
de Química Fundamental, Instituto de Química, Universidade de São Paulo, 05508-000 São
Paulo, São Paulo Brazil
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29
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Liu J, Lorraine SC, Dolinar BS, Hoover JM. Aerobic Oxidation Reactivity of Well-Defined Cobalt(II) and Cobalt(III) Aminophenol Complexes. Inorg Chem 2022; 61:6008-6016. [PMID: 35414172 PMCID: PMC9328405 DOI: 10.1021/acs.inorgchem.1c03686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This paper describes the synthesis and reactivity studies of three cobalt complexes bearing aminophenol-derived ligands without nitrogen substitution: CoII(tBu2APH)2(tBu2AP)2 (1), CoIII2(tBu2APH)2(tBu2AP)2(μ-tBu2BAP)2 (2), and CoIII(tBu2AP)3 (3), where tBu2APH = 2-amino-4,6-di-tert-butylphenol, tBu2AP = 2-amino-4,6-di-tert-butylphenolate, and μ-tBu2BAP = bridging 2-amido-4,6-di-tert-butylphenolate. Stoichiometric reactivity studies of these well-defined complexes demonstrate the catalytic competency of both cobalt(II) and cobalt(III) complexes in the aerobic oxidative cyclization of tBu2APH with tert-butylisonitrile. Reactions with O2 reveal the aerobic oxidation of the cobalt(II) complex 1 to generate the cobalt(III) species 2 and 3. UV-visible time-course studies and electron paramagnetic resonance spectroscopy indicate that this oxidation proceeds through a ligand-based radical intermediate. These studies represent the first example of well-defined cobalt aminophenol complexes that participate in catalytic aerobic oxidation reactions and highlight a key role for a ligand radical in the oxidation sequence.
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30
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Navas LE, Zahn M, Bajwa H, Grigg JC, Wolf ME, Chan ACK, Murphy MEP, McGeehan JE, Eltis LD. Characterization of a phylogenetically distinct extradiol dioxygenase involved in the bacterial catabolism of lignin-derived aromatic compounds. J Biol Chem 2022; 298:101871. [PMID: 35346686 PMCID: PMC9062432 DOI: 10.1016/j.jbc.2022.101871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 10/28/2022] Open
Abstract
The actinobacterium Rhodococcus jostii RHA1 grows on a remarkable variety of aromatic compounds and has been studied for applications ranging from the degradation of polychlorinated biphenyls to the valorization of lignin, an underutilized component of biomass. In RHA1, the catabolism of two classes of lignin-derived compounds, alkylphenols and alkylguaiacols, involves a phylogenetically distinct extradiol dioxygenase, AphC, previously misannotated as BphC, an enzyme involved in biphenyl catabolism. To better understand the role of AphC in RHA1 catabolism, we first showed that purified AphC had highest apparent specificity for 4-propylcatechol (kcat/KM ∼106 M-1 s-1), and its apparent specificity for 4-alkylated substrates followed the trend for alkylguaiacols: propyl > ethyl > methyl > phenyl > unsubstituted. We also show AphC only poorly cleaved 3-phenylcatechol, the preferred substrate of BphC. Moreover, AphC and BphC cleaved 3-phenylcatechol and 4-phenylcatechol with different regiospecificities, likely due to the substrates' binding mode. A crystallographic structure of the AphC·4-ethylcatechol binary complex to 1.59 Å resolution revealed that the catechol is bound to the active site iron in a bidentate manner and that the substrate's alkyl side chain is accommodated by a hydrophobic pocket. Finally, we show RHA1 grows on a mixture of 4-ethylguaiacol and guaiacol, simultaneously catabolizing these substrates through meta-cleavage and ortho-cleavage pathways, respectively, suggesting that the specificity of AphC helps to prevent the routing of catechol through the Aph pathway. Overall, this study contributes to our understanding of the bacterial catabolism of aromatic compounds derived from lignin, and the determinants of specificity in extradiol dioxygenases.
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Affiliation(s)
- Laura E Navas
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Michael Zahn
- Centre for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Harbir Bajwa
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Jason C Grigg
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Megan E Wolf
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Anson C K Chan
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - John E McGeehan
- Centre for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada.
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31
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Csizi KS, Eckert L, Brunken C, Hofstetter TB, Reiher M. The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases. Chemistry 2022; 28:e202103937. [PMID: 35072969 PMCID: PMC9306888 DOI: 10.1002/chem.202103937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/29/2022]
Abstract
Rieske dioxygenases belong to the non‐heme iron family of oxygenases and catalyze important cis‐dihydroxylation as well as O‐/N‐dealkylation and oxidative cyclization reactions for a wide range of substrates. The lack of substrate coordination at the non‐heme ferrous iron center, however, makes it particularly challenging to delineate the role of the substrate for productive O2
activation. Here, we studied the role of the substrate in the key elementary reaction leading to O2
activation from a theoretical perspective by systematically considering (i) the 6‐coordinate to 5‐coordinate conversion of the non‐heme FeII upon abstraction of a water ligand, (ii) binding of O2
, and (iii) transfer of an electron from the Rieske cluster. We systematically evaluated the spin‐state‐dependent reaction energies and structural effects at the active site for all combinations of the three elementary processes in the presence and absence of substrate using naphthalene dioxygenase as a prototypical Rieske dioxygenase. We find that reaction energies for the generation of a coordination vacancy at the non‐heme FeII
center through thermoneutral H2O reorientation and exothermic O2
binding prior to Rieske cluster oxidation are largely insensitive to the presence of naphthalene and do not lead to formation of any of the known reactive Fe‐oxygen species. By contrast, the role of the substrate becomes evident after Rieske cluster oxidation and exclusively for the 6‐coordinate non‐heme FeII
sites in that the additional electron is found at the substrate instead of at the iron and oxygen atoms. Our results imply an allosteric control of the substrate on Rieske dioxygenase reactivity to happen prior to changes at the non‐heme FeII
in agreement with a strategy that avoids unproductive O2
activation.
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Affiliation(s)
- Katja-Sophia Csizi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Lina Eckert
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Christoph Brunken
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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33
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Ghosh I, Chakraborty B, Bera A, Paul S, Paine TK. Selective oxygenation of C-H and CC bonds with H 2O 2 by high-spin cobalt(II)-carboxylate complexes. Dalton Trans 2022; 51:2480-2492. [PMID: 35050271 DOI: 10.1039/d1dt02235k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Four cobalt(II)-carboxylate complexes [(6-Me3-TPA)CoII(benzoate)](BPh4) (1), [(6-Me3-TPA)CoII(benzilate)](ClO4) (2), [(6-Me3-TPA)CoII(mandelate)](BPh4) (3), and [(6-Me3-TPA)CoII(MPA)](BPh4) (4) (HMPA = 2-methoxy-2-phenylacetic acid) of the 6-Me3-TPA (tris((6-methylpyridin-2-yl)methyl)amine) ligand were isolated to investigate their ability in H2O2-dependent selective oxygenation of C-H and CC bonds. All six-coordinate complexes contain a high-spin cobalt(II) center. While the cobalt(II) complexes are inert toward dioxygen, each of these complexes reacts readily with hydrogen peroxide to form a diamagnetic cobalt(III) species, which decays with time leading to the oxidation of the methyl groups on the pyridine rings of the supporting ligand. Intramolecular ligand oxidation by the cobalt-based oxidant is partially inhibited in the presence of external substrates, and the substrates are converted to their corresponding oxidized products. Kinetic studies and labelling experiments indicate the involvement of a metal-based oxidant in affecting the chemo- and stereo-selective catalytic oxygenation of aliphatic C-H bonds and epoxidation of alkenes. An electrophilic cobalt-oxygen species that exhibits a kinetic isotope effect (KIE) value of 5.3 in toluene oxidation by 1 is proposed as the active oxidant. Among the complexes, the cobalt(II)-benzoate (1) and cobalt(II)-MPA (4) complexes display better catalytic activity compared to their α-hydroxy analogues (2 and 3). Catalytic studies with the cobalt(II)-acetonitrile complex [(6-Me3-TPA)CoII(CH3CN)2](ClO4)2 (5) in the presence and absence of externally added benzoate support the role of the carboxylate co-ligand in oxidation reactions. The proposed catalytic reaction involves a carboxylate-bridged dicobalt complex in the activation of H2O2 followed by the oxidation of substrates by a metal-based oxidant.
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Affiliation(s)
- Ivy Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Biswarup Chakraborty
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Abhijit Bera
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Satadal Paul
- Department of Chemistry, Bangabasi Morning College, 19, Rajkumar Chakraborty Sarani, Kolkata - 700 009, India
| | - Tapan Kanti Paine
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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Characterization of Gentisate 1,2-Dioxygenase from Pseudarthrobacter phenanthrenivorans Sphe3 and Its Stabilization by Immobilization on Nickel-Functionalized Magnetic Nanoparticles. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The aim of this study was the biochemical and kinetic characterization of the gentisate 1,2-dioxygenase (GDO) from Pseudarthrobacter phenanthrenivorans Sphe3 and the development of a nanobiocatalyst by its immobilization on Ni2+-functionalized Fe3O4-polydopamine magnetic nanoparticles (Ni2+-PDA-MNPs). This is the first GDO to be immobilized. The gene encoding the GDO was cloned with an N-terminal His-tag and overexpressed in E. coli. The nanoparticles showed a high purification efficiency of GDO from crude cell lysates with a maximum activity recovery of 97%. The immobilized enzyme was characterized by Fourier transform infrared spectroscopy (FTIR). The reaction product was identified by 1H NMR. Both free and immobilized GDO exhibited Michaelis–Menten kinetics with Km values of 25.9 ± 4.4 and 82.5 ± 14.2 μM and Vmax values of 1.2 ± 0.1 and 0.03 ± 0.002 mM*s−1, respectively. The thermal stability of the immobilized GDO was enhanced at 30 °C, 40 °C, and 50 °C, compared to the free GDO. Stored at −20 °C, immobilized GDO retained more than 60% of its initial activity after 30 d, while the free enzyme completely lost its activity after 10 d. Furthermore, the immobilized nanoparticle–enzyme conjugate retained more than 50% enzyme activity up to the fifth cycle.
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Wei J, Wang Y, Li X, Zhang X, Liu Y. Mechanistic Insights into Pyridine Ring Degradation Catalyzed by 2,5-Dihydroxypyridine Dioxygenase NicX. Inorg Chem 2022; 61:2517-2529. [DOI: 10.1021/acs.inorgchem.1c03370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xue Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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Rodrigues RC, Berenguer-Murcia Á, Carballares D, Morellon-Sterling R, Fernandez-Lafuente R. Stabilization of enzymes via immobilization: Multipoint covalent attachment and other stabilization strategies. Biotechnol Adv 2021; 52:107821. [PMID: 34455028 DOI: 10.1016/j.biotechadv.2021.107821] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 08/21/2021] [Indexed: 12/22/2022]
Abstract
The use of enzymes in industrial processes requires the improvement of their features in many instances. Enzyme immobilization, a requirement to facilitate the recovery and reuse of these water-soluble catalysts, is one of the tools that researchers may utilize to improve many of their properties. This review is focused on how enzyme immobilization may improve enzyme stability. Starting from the stabilization effects that an enzyme may experience by the mere fact of being inside a solid particle, we detail other possibilities to stabilize enzymes: generation of favorable enzyme environments, prevention of enzyme subunit dissociation in multimeric enzymes, generation of more stable enzyme conformations, or enzyme rigidification via multipoint covalent attachment. In this last point, we will discuss the features of an "ideal" immobilization protocol to maximize the intensity of the enzyme-support interactions. The most interesting active groups in the support (glutaraldehyde, epoxide, glyoxyl and vinyl sulfone) will be also presented, discussing their main properties and uses. Some instances in which the number of enzyme-support bonds is not directly related to a higher stabilization will be also presented. Finally, the possibility of coupling site-directed mutagenesis or chemical modification to get a more intense multipoint covalent immobilization will be discussed.
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Affiliation(s)
- Rafael C Rodrigues
- Biocatalysis and Enzyme Technology Lab, Institute of Food Science and Technology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, P.O. Box 15090, Porto Alegre, RS, Brazil
| | | | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC Cantoblanco, Madrid, Spain
| | | | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC Cantoblanco, Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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Cheng M, Qian Y, Xing Z, Zylstra GJ, Huang X. The low-nanomolar 4-nitrobenzoate-responsive repressor PnbX negatively regulates the actinomycete-derived 4-nitrobenzoate-degrading pnb locus. Environ Microbiol 2021; 23:7028-7041. [PMID: 34554625 DOI: 10.1111/1462-2920.15787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022]
Abstract
Nitroaromatic compounds pose severe threats to public health and environmental safety. Nitro group removal via ammonia release is an important strategy for bacterial detoxification of nitroaromatic compounds, such as the conversion of 4-nitrobenzoate (4-NBA) to protocatechuate by the bacterial pnb operon. In contrast to the LysR-family transcriptional regulator PnbR in proteobacteria, the actinomycete-derived pnb locus (4-NBA degradation structural genes) formed an operon with the TetR-family transcriptional regulator gene pnbX, implying that it has a distinct regulatory mechanism. Here, pnbBA from the actinomycete Nocardioides sp. strain LMS-CY was biochemically confirmed to express 4-NBA degradation enzymes, and pnbX was essential for inducible degradation of 4-NBA. Purified PnbX-6His could bind the promoter probe of the pnb locus in vitro, and 4-NBA prevented this binding. 4-NBA could bind PnbX at a 1:1 molar ratio with KD = 26.7 ± 4.2 nM. Low-nanomolar levels of 4-NBA induced the transcription of the pnb operon in strain LMS-CY. PnbX bound a palindromic sequence motif (5'-TTACGTTACA-N8 -TGTAACGTAA-3') that encompasses the pnb promoter. This study identified a TetR-family repressor for the actinomycete-derived pnb operon that recognizes 10-8 M 4-NBA as its ligand, implying that nitro group removal of nitroaromatic compounds may be especially important for actinomycetes.
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Affiliation(s)
- Minggen Cheng
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yingying Qian
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ziyu Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Gerben J Zylstra
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Xing Huang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Tsagogiannis E, Vandera E, Primikyri A, Asimakoula S, Tzakos AG, Gerothanassis IP, Koukkou AI. Characterization of Protocatechuate 4,5-Dioxygenase from Pseudarthrobacter phenanthrenivorans Sphe3 and In Situ Reaction Monitoring in the NMR Tube. Int J Mol Sci 2021; 22:9647. [PMID: 34502555 PMCID: PMC8431788 DOI: 10.3390/ijms22179647] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
The current study aims at the functional and kinetic characterization of protocatechuate (PCA) 4,5-dioxygenase (PcaA) from Pseudarthrobacter phenanthrenivorans Sphe3. This is the first single subunit Type II dioxygenase characterized in Actinobacteria. RT-PCR analysis demonstrated that pcaA and the adjacent putative genes implicated in the PCA meta-cleavage pathway comprise a single transcriptional unit. The recombinant PcaA is highly specific for PCA and exhibits Michaelis-Menten kinetics with Km and Vmax values of 21 ± 1.6 μM and 44.8 ± 4.0 U × mg-1, respectively, in pH 9.5 and at 20 °C. PcaA also converted gallate from a broad range of substrates tested. The enzymatic reaction products were identified and characterized, for the first time, through in situ biotransformation monitoring inside an NMR tube. The PCA reaction product demonstrated a keto-enol tautomerization, whereas the gallate reaction product was present only in the keto form. Moreover, the transcriptional levels of pcaA and pcaR (gene encoding a LysR-type regulator of the pathway) were also determined, showing an induction when cells were grown on PCA and phenanthrene. Studying key enzymes in biodegradation pathways is significant for bioremediation and for efficient biocatalysts development.
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Affiliation(s)
- Epameinondas Tsagogiannis
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
| | - Elpiniki Vandera
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
| | - Alexandra Primikyri
- Laboratory of Organic Chemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (A.G.T.); (I.P.G.)
| | - Stamatia Asimakoula
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
| | - Andreas G. Tzakos
- Laboratory of Organic Chemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (A.G.T.); (I.P.G.)
| | - Ioannis P. Gerothanassis
- Laboratory of Organic Chemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (A.P.); (A.G.T.); (I.P.G.)
| | - Anna-Irini Koukkou
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (E.V.); (S.A.)
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Sonwani RK, Kim KH, Zhang M, Tsang YF, Lee SS, Giri BS, Singh RS, Rai BN. Construction of biotreatment platforms for aromatic hydrocarbons and their future perspectives. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125968. [PMID: 34492879 DOI: 10.1016/j.jhazmat.2021.125968] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 04/05/2021] [Accepted: 04/22/2021] [Indexed: 06/13/2023]
Abstract
Aromatic hydrocarbons (AHCs) are one of the major environmental pollutants introduced from both natural and anthropogenic sources. Many AHCs are well known for their toxic, carcinogenic, and mutagenic impact on human health and ecological systems. Biodegradation is an eco-friendly and cost-effective option as microorganisms (e.g., bacteria, fungi, and algae) can efficiently breakdown or transform such pollutants into less harmful and simple metabolites (e.g., carbon dioxide (aerobic), methane (anaerobic), water, and inorganic salts). This paper is organized to offer a state-of-the-art review on the biodegradation of AHCs (monocyclic aromatic hydrocarbons (MAHs) and polycyclic aromatic hydrocarbons (PAHs)) and associated mechanisms. The recent progress in biological treatment using suspended and attached growth bioreactors for the biodegradation of AHCs is also discussed. In addition, various substrate growth and inhibition models are introduced along with the key factors governing their biodegradation kinetics. The growth and inhibition models have helped gain a better understanding of substrate inhibition in biodegradation. Techno-economic analysis (TEA) and life cycle assessment (LCA) aspects are also described to assess the technical, economical, and environmental impacts of the biological treatment system.
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Affiliation(s)
- Ravi Kumar Sonwani
- Department of Chemical Engineering & Technology Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
| | - Ming Zhang
- Department of Environmental Engineering, China Jiliang University, Hangzhou 310018, China
| | - Yiu Fai Tsang
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, New Territories 999077, Hong Kong
| | - Sang Soo Lee
- Department of Environmental Engineering, Yonsei University, Wonju 26493, Republic of Korea
| | - Balendu Shekher Giri
- Department of Chemical Engineering & Technology Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Ram Sharan Singh
- Department of Chemical Engineering & Technology Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Birendra Nath Rai
- Department of Chemical Engineering & Technology Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
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Physiological Role of the Previously Unexplained Benzenetriol Dioxygenase Homolog in the Burkholderia sp. Strain SJ98 4-Nitrophenol Catabolism Pathway. Appl Environ Microbiol 2021; 87:e0000721. [PMID: 33990303 DOI: 10.1128/aem.00007-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
4-Nitrophenol, a priority pollutant, is degraded by Gram-positive and Gram-negative bacteria via 1,2,4-benzenetriol (BT) and hydroquinone (HQ), respectively. All enzymes involved in the two pathways have been functionally identified. So far, all Gram-negative 4-nitrophenol utilizers are from the genera Pseudomonas and Burkholderia. But it remains a mystery why pnpG, an apparently superfluous BT 1,2-dioxygenase-encoding gene, always coexists in the catabolic cluster (pnpABCDEF) encoding 4-nitrophenol degradation via HQ. Here, the physiological role of pnpG in Burkholderia sp. strain SJ98 was investigated. Deletion and complementation experiments established that pnpG is essential for strain SJ98 growing on 4-nitrocatechol rather than 4-nitrophenol. During 4-nitrophenol degradation by strain SJ98 and its two variants (pnpG deletion and complementation strains), 1,4-benzoquinone and HQ were detected, but neither 4-nitrocatechol nor BT was observed. When the above-mentioned three strains (the wild type and complementation strains with 2,2'-dipyridyl) were incubated with 4-nitrocatechol, BT was the only intermediate detected. The results established the physiological role of pnpG that encodes BT degradation in vivo. Biotransformation analyses showed that the pnpA-deleted strain was unable to degrade both 4-nitrophenol and 4-nitrocatechol. Thus, the previously characterized 4-nitrophenol monooxygenase PnpASJ98 is also essential for the conversion of 4-nitrocatechol to BT. Among 775 available complete genomes for Pseudomonas and Burkholderia, as many as 89 genomes were found to contain the putative pnpBCDEFG genes. The paucity of pnpA (3 in 775 genomes) implies that the extension of BT and HQ pathways enabling the degradation of 4-nitrophenol and 4-nitrocatechol is rarer, more recent, and likely due to the release of xenobiotic nitroaromatic compounds. IMPORTANCE An apparently superfluous gene (pnpG) encoding BT 1,2-dioxygenase is always found in the catabolic clusters involved in 4-nitrophenol degradation via HQ by Gram-negative bacteria. Our experiments reveal that pnpG is not essential for 4-nitrophenol degradation in Burkholderia sp. strain SJ98 but instead enables its degradation of 4-nitrocatechol via BT. The presence of pnpG genes broadens the range of growth substrates to include 4-nitrocatechol or BT, intermediates from the microbial degradation of many aromatic compounds in natural ecosystems. In addition, the existence of pnpCDEFG in 11.6% of the above-mentioned two genera suggests that the ability to degrade BT and HQ simultaneously is ancient. The extension of BT and HQ pathways including 4-nitrophenol degradation seems to be an adaptive evolution for responding to synthetic nitroaromatic compounds entering the environment since the industrial revolution.
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Bacosa HP, Mabuhay-Omar JA, Balisco RAT, Omar DM, Inoue C. Biodegradation of binary mixtures of octane with benzene, toluene, ethylbenzene or xylene (BTEX): insights on the potential of Burkholderia, Pseudomonas and Cupriavidus isolates. World J Microbiol Biotechnol 2021; 37:122. [PMID: 34151386 DOI: 10.1007/s11274-021-03093-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/14/2021] [Indexed: 01/20/2023]
Abstract
The contamination of the environment by crude oil and its by-products, mainly composed of aliphatic and aromatic hydrocarbons, is a widespread problem. Biodegradation by bacteria is one of the processes responsible for the removal of these pollutants. This study was conducted to determine the abilities of Burkholderia sp. B5, Cupriavidus sp. B1, Pseudomonas sp. T1, and another Cupriavidus sp. X5 to degrade binary mixtures of octane (representing aliphatic hydrocarbons) with benzene, toluene, ethylbenzene, or xylene (BTEX as aromatic hydrocarbons) at a final concentration of 100 ppm under aerobic conditions. These strains were isolated from an enriched bacterial consortium (Yabase or Y consortium) that prefer to degrade aromatic hydrocarbon over aliphatic hydrocarbons. We found that B5 degraded all BTEX compounds more rapidly than octane. In contrast, B1, T1 and X5 utilized more of octane over BTX compounds. B5 also preferred to use benzene over octane with varying concentrations of up to 200 mg/l. B5 possesses alkane hydroxylase (alkB) and catechol 2,3-dioxygenase (C23D) genes, which are responsible for the degradation of alkanes and aromatic hydrocarbons, respectively. This study strongly supports our notion that Burkholderia played a key role in the preferential degradation of aromatic hydrocarbons over aliphatic hydrocarbons in the previously characterized Y consortium. The preferential degradation of more toxic aromatic hydrocarbons over aliphatics is crucial in risk-based bioremediation.
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Affiliation(s)
- Hernando P Bacosa
- Environmental Science Program, Department of Biological Sciences, College of Science and Mathematics, Mindanao State University-Iligan Institute of Technology, Tibanga, 9200, Iligan, Lanao del Norte, Philippines.,Graduate School of Environmental Studies, Tohoku University, 6-6-20 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Jhonamie A Mabuhay-Omar
- College of Fisheries and Aquatic Sciences, Western Philippines University-Puerto Princesa, Sta. Monica, 5300, Puerto Princesa, Palawan, Philippines.
| | - Rodulf Anthony T Balisco
- College of Fisheries and Aquatic Sciences, Western Philippines University-Puerto Princesa, Sta. Monica, 5300, Puerto Princesa, Palawan, Philippines
| | - Dawin M Omar
- College of Engineering, Architecture and Technology, Palawan State University, Tiniguiban, 5300, Puerto Princesa, Palawan, Philippines
| | - Chihiro Inoue
- Graduate School of Environmental Studies, Tohoku University, 6-6-20 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
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Mainka T, Weirathmüller D, Herwig C, Pflügl S. Potential applications of halophilic microorganisms for biological treatment of industrial process brines contaminated with aromatics. J Ind Microbiol Biotechnol 2021; 48:kuab015. [PMID: 33928348 PMCID: PMC9113102 DOI: 10.1093/jimb/kuab015] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/20/2021] [Indexed: 11/13/2022]
Abstract
Saline wastewater contaminated with aromatic compounds can be frequently found in various industrial sectors. Those compounds need to be degraded before reuse of wastewater in other process steps or release to the environment. Halophiles have been reported to efficiently degrade aromatics, but their application to treat industrial wastewater is rare. Halophilic processes for industrial wastewater treatment need to satisfy certain requirements: a continuous process mode, low operational expenditures, suitable reactor systems and a monitoring and control strategy. The aim of this review is to provide an overview of halophilic microorganisms, principles of aromatic biodegradation, and sources of saline wastewater containing aromatics and other contaminants. Finally, process examples for halophilic wastewater treatment and potential process monitoring strategies are discussed. To further illustrate the significant potential of halophiles for saline wastewater treatment and to facilitate development of ready-to-implement processes, future research should focus on scale-up and innovative process monitoring and control strategies.
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Affiliation(s)
- Thomas Mainka
- Institute for Chemical, Environmental and Bioscience
Engineering, TU Wien, Gumpendorfer Straße 1a, 1060
Vienna, Austria
- Competence Center CHASE GmbH,
Altenbergerstraße 69, 4040 Linz, Austria
| | - David Weirathmüller
- Institute for Chemical, Environmental and Bioscience
Engineering, TU Wien, Gumpendorfer Straße 1a, 1060
Vienna, Austria
| | - Christoph Herwig
- Institute for Chemical, Environmental and Bioscience
Engineering, TU Wien, Gumpendorfer Straße 1a, 1060
Vienna, Austria
- Competence Center CHASE GmbH,
Altenbergerstraße 69, 4040 Linz, Austria
| | - Stefan Pflügl
- Institute for Chemical, Environmental and Bioscience
Engineering, TU Wien, Gumpendorfer Straße 1a, 1060
Vienna, Austria
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Yi X, Mei J, Lin L, Wang W. Overexpression of Dioxygenase Encoding Gene Accelerates the Phenolic Aldehyde Conversion and Ethanol Fermentability of Zymomonas mobilis. Appl Biochem Biotechnol 2021; 193:3017-3027. [PMID: 33826067 DOI: 10.1007/s12010-021-03551-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/22/2021] [Indexed: 11/27/2022]
Abstract
NADH-dependent reductase enzyme catalyzes the phenolic aldehyde conversion and correspondingly improves the ethanol fermentability of the ethanologenic Zymomonas mobilis. This study constructed the transcriptional landscape of mono/dioxygenase genes in Z. mobilis ZM4 under the stress of the toxic phenolic aldehyde inhibitors of 4-hydroxybenzaldehyde, syringaldehyde, and vanillin. One specific dioxygenase encoding gene ZMO1721 was differentially expressed by 3.07-folds under the stress of 4-hydroxybenzaldehyde among the eleven mono/dioxygenase genes. The purified ZMO1721 shared 99.9% confidence and 48.0% identity with the oxidoreductase in Rhodoferax ferrireducens T118 was assayed and the NADH-dependent reduction activity was confirmed for phenolic aldehyde vanillin conversion. The ZMO1721 gene was then overexpressed in Z. mobilis ZM4 and the 4-hydroxybenzaldehyde conversion rate was accelerated. The cell growth, glucose consumption, and ethanol productivity of Z. mobilis ZM4 were also improved by ZMO1721 overexpression. The genes identified on improving phenolic aldehyde tolerance and ethanol fermentability in this study could be used as the synthetic biology tools for modification of ethanologenic strains.
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Affiliation(s)
- Xia Yi
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000, China.
| | - Jun Mei
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000, China
| | - Ling Lin
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000, China
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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Redundancy in aromatic O-demethylation and ring opening reactions in Novosphingobium aromaticivorans and their impact in the metabolism of plant derived phenolics. Appl Environ Microbiol 2021; 87:AEM.02794-20. [PMID: 33579679 PMCID: PMC8091115 DOI: 10.1128/aem.02794-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lignin is a plant heteropolymer composed of phenolic subunits. Because of its heterogeneity and recalcitrance, the development of efficient methods for its valorization still remains an open challenge. One approach to utilize lignin is its chemical deconstruction into mixtures of monomeric phenolic compounds followed by biological funneling into a single product. Novosphingobium aromaticivorans DSM12444 has been previously engineered to produce 2-pyrone-4,6-dicarboxylic acid (PDC) from depolymerized lignin by simultaneously metabolizing multiple aromatics through convergent routes involving the intermediates 3-methoxygallic acid (3-MGA) and protocatechuic acid (PCA). We investigated enzymes predicted to be responsible for O-demethylation and oxidative aromatic ring opening, two critical reactions involved in the metabolism of phenolics compounds by N. aromaticivorans The results showed the involvement of DesA in O-demethylation of syringic and vanillic acids, LigM in O-demethylation of vanillic acid and 3-MGA, and a new O-demethylase, DmtS, in the conversion of 3-MGA into gallic acid (GA). In addition, we found that LigAB was the main aromatic ring opening dioxygenase involved in 3-MGA, PCA, and GA metabolism, and that a previously uncharacterized dioxygenase, LigAB2, had high activity with GA. Our results indicate a metabolic route not previously identified in N. aromaticivorans that involves O-demethylation of 3-MGA to GA. We predict this pathway channels ∼15% of the carbon flow from syringic acid, with the rest following ring opening of 3-MGA. The new knowledge obtained in this study allowed for the creation of an improved engineered strain for the funneling of aromatic compounds that exhibits stoichiometric conversion of syringic acid into PDC.IMPORTANCE For lignocellulosic biorefineries to effectively contribute to reduction of fossil fuel use, they need to become efficient at producing chemicals from all major components of plant biomass. Making products from lignin will require engineering microorganisms to funnel multiple phenolic compounds to the chemicals of interest, and N. aromaticivorans is a promising chassis for this technology. The ability of N. aromaticivorans to efficiently and simultaneously degrade many phenolic compounds may be linked to having functionally redundant aromatic degradation pathways and enzymes with broad substrate specificity. A detailed knowledge of aromatic degradation pathways is thus essential to identify genetic engineering targets to maximize product yields. Furthermore, knowledge of enzyme substrate specificity is critical to redirect flow of carbon to desired pathways. This study described an uncharacterized pathway in N. aromaticivorans and the enzymes that participate in this pathway, allowing the engineering of an improved strain for production of PDC from lignin.
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Identifying metabolic pathway intermediates that modulate the gallate dioxygenase (DesB) from Sphingobium sp. strain SYK-6. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Chatterjee S, Banerjee S, Jana RD, Bhattacharya S, Chakraborty B, Jannuzzi SAV. Tuning the stereoelectronic factors of iron(II)-2-aminophenolate complexes for the reaction with dioxygen: oxygenolytic C-C bond cleavage vs. oxidation of complex. Dalton Trans 2021; 50:1901-1912. [PMID: 33475662 DOI: 10.1039/d0dt03316b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxidative C-C bond cleavage of 2-aminophenols mediated by transition metals and dioxygen is a topic of great interest. While the oxygenolytic C-C bond cleavage reaction relies on the inherent redox non-innocent property of 2-aminophenols, the metal complexes of 2-aminophenolates often undergo 1e-/2e- oxidation events (metal or ligand oxidation), instead of the direct addition of O2 for subsequent C-C bond cleavage. In this work, we report the isolation, characterization and dioxygen reactivity of a series of ternary iron(ii)-2-aminophenolate complexes [(TpPh,Me)FeII(X)], where X = 2-amino-4-tert-butylphenolate (4-tBu-HAP) (1); X = 2-amino-4,6-di-tert-butylphenolate (4,6-di-tBu-HAP) (2); X = 2-amino-4-nitrophenolate (4-NO2-HAP)(3); and X = 2-anilino-4,6-di-tert-butylphenolate (NH-Ph-4,6-di-tBu-HAP) (4) supported by a facial tridentate nitrogen donor ligand (TpPh,Me = hydrotris(3-phenyl-5-methylpyrazol-1-yl)borate). Another facial N3 ligand (TpPh2 = hydrotris(3,5-diphenyl-pyrazol-1-yl)borate) has been used to isolate an iron(ii)-2-anilino-4,6-di-tert-butylphenolate complex (5) for comparison. Both [(TpPh,Me)FeII(4-tBu-HAP)] (1) and [(TpPh,Me)FeII(4,6-di-tBu-HAP)] (2) undergo regioselective oxidative aromatic ring fission reaction of the coordinated 2-aminophenols to the corresponding 2-picolinic acids in the reaction with dioxygen. In contrast, complex [(TpPh,Me)FeII(4-NO2-HAP)] (3) displays metal based oxidation to form an iron(iii)-2-amidophenolate complex. Complexes [(TpPh,Me)FeII(NH-Ph-4,6-di-tBu-HAP)] (4) and [(TpPh2)FeII(NH-Ph-4,6-di-tBu-HAP)] (5) react with dioxygen to undergo 2e- oxidation with the formation of the corresponding iron(iii)-2-iminobenzosemiquinonato radical species implicating the importance of the -NH2 group in directing the C-C bond cleavage reactivity of 2-aminophenols. The systematic study presented in this work unravels the effect of the electronic and structural properties of the redox non-innocent 2-aminophenolate ring and the supporting ligand on the C-C bond cleavage reactivity vs. the metal/ligand oxidation of the complexes. The study further reveals that proper modulation of the stereoelectronic factors enables us to design a well synchronised proton transfer (PT) and dioxygen binding events for complexes 1 and 2 that mimic the structure and function of the nonheme enzyme 2-aminophenol-1,6-dioxygenase (APD).
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Affiliation(s)
- Sayanti Chatterjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
| | - Sridhar Banerjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
| | - Rahul Dev Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
| | - Shrabanti Bhattacharya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
| | - Biswarup Chakraborty
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
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Leal C, Fontaine F, Aziz A, Egas C, Clément C, Trotel-Aziz P. Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol. ENVIRONMENTAL MICROBIOME 2021; 16:3. [PMID: 33902737 PMCID: PMC8067347 DOI: 10.1186/s40793-021-00372-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 01/07/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Bacillus subtilis strains have been widely studied for their numerous benefits in agriculture, including viticulture. Providing several assets, B. subtilis spp. are described as promising plant-protectors against many pathogens and as influencers to adaptations in a changing environment. This study reports the draft genome sequence of the beneficial Bacillus subtilis PTA-271, isolated from the rhizospheric soil of healthy Vitis vinifera cv. Chardonnay at Champagne Region in France, attempting to draw outlines of its full biocontrol capacity. RESULTS The PTA-271 genome has a size of 4,001,755 bp, with 43.78% of G + C content and 3945 protein coding genes. The draft genome of PTA-271 putatively highlights a functional swarming motility system hypothesizing a colonizing capacity and a strong interacting capacity, strong survival capacities and a set of genes encoding for bioactive substances. Predicted bioactive compounds are known to: stimulate plant growth or defenses such as hormones and elicitors, influence beneficial microbiota, and counteract pathogen aggressiveness such as effectors and many kinds of detoxifying enzymes. CONCLUSIONS Plurality of the putatively encoded biomolecules by Bacillus subtilis PTA-271 genome suggests environmentally robust biocontrol potential of PTA-271, protecting plants against a broad spectrum of pathogens.
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Affiliation(s)
- Catarina Leal
- SFR Condorcet - FR CNRS 3417, University of Reims Champagne-Ardenne, Induced Resistance and Plant Bioprotection (RIBP) - EA 4707, BP1039, Cedex 2, F-51687, Reims, France
| | - Florence Fontaine
- SFR Condorcet - FR CNRS 3417, University of Reims Champagne-Ardenne, Induced Resistance and Plant Bioprotection (RIBP) - EA 4707, BP1039, Cedex 2, F-51687, Reims, France
| | - Aziz Aziz
- SFR Condorcet - FR CNRS 3417, University of Reims Champagne-Ardenne, Induced Resistance and Plant Bioprotection (RIBP) - EA 4707, BP1039, Cedex 2, F-51687, Reims, France
| | - Conceiçao Egas
- UC-Biotech_CNC, Biocant Park, Biotechnology Innovation Center, P-3060-197, Cantanhede, Portugal
| | - Christophe Clément
- SFR Condorcet - FR CNRS 3417, University of Reims Champagne-Ardenne, Induced Resistance and Plant Bioprotection (RIBP) - EA 4707, BP1039, Cedex 2, F-51687, Reims, France
| | - Patricia Trotel-Aziz
- SFR Condorcet - FR CNRS 3417, University of Reims Champagne-Ardenne, Induced Resistance and Plant Bioprotection (RIBP) - EA 4707, BP1039, Cedex 2, F-51687, Reims, France.
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Mahto KU, Das S. Whole genome characterization and phenanthrene catabolic pathway of a biofilm forming marine bacterium Pseudomonas aeruginosa PFL-P1. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 206:111087. [PMID: 32871516 DOI: 10.1016/j.ecoenv.2020.111087] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 05/02/2023]
Abstract
Pseudomonas aeruginosa is a small rod shaped Gram-negative bacterium of Gammaproteobacteria class known for its metabolic versatility. P. aeruginosa PFL-P1 was isolated from Polycyclic Aromatic Hydrocarbons (PAHs) contaminated site of Paradip Port, Odisha Coast, India. The strain showed excellent biofilm formation and could retain its ability to form biofilm grown with different PAHs in monoculture as well as co-cultures. To explore mechanistic insights of PAHs metabolism, the whole genome of the strain was sequenced. Next generation sequencing unfolded a genome size of 6,333,060 bp encoding 5857 CDSs. Gene ontology distribution assigned to a total of 2862 genes, wherein 2235 genes were allocated to biological process, 1549 genes to cellular component and 2339 genes to molecular function. A total of 318 horizontally transferred genes were identified when the genome was compared with the reference genomes of P. aeruginosa PAO1 and P. aeruginosa DSM 50071. Further comparison of P. aeruginosa PFL-P1 genome with P. putida containing TOL plasmids revealed similarities in the meta cleavage pathway employed for degradation of aromatic compounds like xylene and toluene. Gene annotation and pathway analysis unveiled 145 genes involved in xenobiotic biodegradation and metabolism. The biofilm cultures of P. aeruginosa PFL-P1 could degrade ~74% phenanthrene within 120 h while degradation increased up to ~76% in co-culture condition. GC-MS analysis indicated presence of diverse metabolites indicating the involvement of multiple pathways for one of the PAHs (phenanthrene) degradation. The strain also possesses the genetic machinery to utilize diverse toxic aromatic compounds such as naphthalene, benzoate, aminobenzoate, fluorobenzoate, toluene, xylene, styrene, atrazine, caprolactam etc. Common catabolic gene clusters such as benABCD, xylXYZ and catAB were observed within the genome of P. aeruginosa PFL-P1 which play key roles in the degradation of various toxic aromatic compounds.
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Affiliation(s)
- Kumari Uma Mahto
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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Nunes OC, Manaia CM, Kolvenbach BA, Corvini PFX. Living with sulfonamides: a diverse range of mechanisms observed in bacteria. Appl Microbiol Biotechnol 2020; 104:10389-10408. [PMID: 33175245 DOI: 10.1007/s00253-020-10982-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/18/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022]
Abstract
Sulfonamides are the oldest class of synthetic antibiotics still in use in clinical and veterinary settings. The intensive utilization of sulfonamides has been leading to the widespread contamination of the environment with these xenobiotic compounds. Consequently, in addition to pathogens and commensals, also bacteria inhabiting a wide diversity of environmental compartments have been in contact with sulfonamides for almost 90 years. This review aims at giving an overview of the effect of sulfonamides on bacterial cells, including the strategies used by bacteria to cope with these bacteriostatic agents. These include mechanisms of antibiotic resistance, co-metabolic transformation, and partial or total mineralization of sulfonamides. Possible implications of these mechanisms on the ecosystems and dissemination of antibiotic resistance are also discussed. KEY POINTS: • Sulfonamides are widespread xenobiotic pollutants; • Target alteration is the main sulfonamide resistance mechanism observed in bacteria; • Sulfonamides can be modified, degraded, or used as nutrients by some bacteria.
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Affiliation(s)
- Olga C Nunes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.
| | - Célia M Manaia
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Boris A Kolvenbach
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Philippe F-X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
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Li X, Zhu W, Liu Y. Mechanistic Insights into the Oxidative Rearrangement Catalyzed by the Unprecedented Dioxygenase ChaP Involved in Chartreusin Biosynthesis. Inorg Chem 2020; 59:13988-13999. [PMID: 32951427 DOI: 10.1021/acs.inorgchem.0c01706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ChaP is a non-heme iron-dependent dioxygenase belonging to the vicinal oxygen chelate (VOC) enzyme superfamily that catalyzes the final α-pyrone ring formation in the biosynthesis of chartreusin. In contrast to other common dioxygenases, for example, 2,3-catechol dioxygenase which uses the dioxygen molecule as the oxidant, ChaP requires the flavin-activated oxygen (O22-) as the equivalent. Previous experiments showed that the ChaP-catalyzed ring rearrangement contains two successive C-C bond cleavages and one lactonization; however, the detailed reaction mechanism is unknown. In this work, on the basis of the recently obtained crystal structure of ChaP, the computational model was constructed and the catalytic mechanism of ChaP was explored by performing quantum mechanical/molecular mechanical (QM/MM) calculations. Our calculation results reveal that ChaP uses the proximal oxygen in iron-coordinated HOO- to attack the carbonyl carbon of the substrate, whereas the previous proposal that Asp49 acts as a base to deprotonate the iron-coordinated HOO- to generate O22- is unlikely. In the first stage reaction, owing to the coordination of the substrate with iron, the substrate is activated by accepting an electron from iron and the resulting oxy-radical intermediate formed by O-O cleavage can easily trigger the ring rearrangement. In the final decarboxylation, the phenolic anion of the substrate cooperatively accepts the proton of iron-coordinated HOO- to facilitate the attack of the distal oxygen, and the proton-coupled electron transfer (PCET) from the substrate to the FeIV═O plays a key role for the decarboxylation. These findings may provide useful information for understanding the ChaP-catalyzed oxidative rearrangement and other flavin-dependent non-heme dioxygenases.
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Affiliation(s)
- Xinyi Li
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Wenyou Zhu
- College of Chemistry and Chemical Engineering, Xuzhou Institute of Technology, Xuzhou, Jiangsu 221111, China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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