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Suman J, Sredlova K, Fraraccio S, Jerabkova M, Strejcek M, Kabickova H, Cajthaml T, Uhlik O. Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase. CHEMOSPHERE 2024; 349:140909. [PMID: 38070605 DOI: 10.1016/j.chemosphere.2023.140909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/18/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Monohydroxylated PCBs (OH-PCBs) are an (eco)toxicologically significant group of compounds, as they arise from the oxidation of polychlorinated biphenyls (PCBs) and, at the same time, may exert even more severe toxic effects than their parent PCB molecules. Despite having been widely detected in environmental samples, plants, and animals, information on the fate of OH-PCBs in the environment is scarce, including on the enzymatic machinery behind their degradation. To date, only a few bacterial taxa capable of OH-PCB transformation have been reported. In this study, we aimed to obtain a deeper insight into the transformation of OH-PCBs in soil bacteria and isolated a Pseudomonas sp. strain P1B16 based on its ability to use o-phenylphenol (2-PP) which, when exposed to the Delor 103-derived OH-PCB mixture, depleted a wide spectrum of mono-, di, and trichlorinated OH-PCBs. In the P1B16 genome, a region designated as hbp was identified, which bears a set of putative genes involved in the transformation of OH-PCBs, namely hbpA encoding for a putative flavin-dependent 2-hydroxybiphenyl monooxygenase, hbpC (2,3-dihydroxybiphenyl-1,2-dioxygenase), hbpD (2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase), and the transcriptional activator-encoding gene hbpR. The hbpA coding sequence was heterologously expressed, purified, and its substrate specificity was investigated towards the Delor 103-derived OH-PCB mixture, individual OH-PCBs, and multiple (chlorinated) phenolics. Apart from 2-PP and 2-chlorophenol, HbpA was also demonstrated to transform a range of OH-PCBs, including a 3-hydroxy-2,2',4',5,5'-pentachlorobiphenyl. Importantly, this is the first direct evidence of HbpA homologs being involved in the degradation of OH-PCBs. Moreover, using a P1B16-based biosensor strain, the specific induction of hbp genes by 2-PP, 3-phenylphenol, 4-phenylphenol, and the OH-PCB mixture was demonstrated. This study provides direct evidence on the specific enzymatic machinery responsible for the transformation of OH-PCBs in bacteria, with many implications in ecotoxicology, environmental restoration, and microbial ecology in habitats burdened with PCB contamination.
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Affiliation(s)
- Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
| | - Kamila Sredlova
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Serena Fraraccio
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Martina Jerabkova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Hana Kabickova
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske Nemocnice 1200, 169 02, Prague, Czech Republic
| | - Tomas Cajthaml
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
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Paul CE, Eggerichs D, Westphal AH, Tischler D, van Berkel WJH. Flavoprotein monooxygenases: Versatile biocatalysts. Biotechnol Adv 2021; 51:107712. [PMID: 33588053 DOI: 10.1016/j.biotechadv.2021.107712] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.
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Affiliation(s)
- Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Eggerichs
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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Jia Y, Zhang H, Khanal SK, Yin L, Lu H. Insights into pharmaceuticals removal in an anaerobic sulfate-reducing bacteria sludge system. WATER RESEARCH 2019; 161:191-201. [PMID: 31195335 DOI: 10.1016/j.watres.2019.06.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 06/09/2023]
Abstract
In this study, we examined eight typical and widely detected pharmaceuticals (PhAs) removal in an anaerobic sulfate-reducing bacteria (SRB) sludge system (five antibiotics: sulfadiazine (SD), sulfamethoxazole (SMX), trimethoprim (TMP), ciprofloxacin (CIP) and enoxacin (ENO), and three nonsteroidal anti-inflammatory drugs (NSAIDs): ibuprofen (IBU), ketoprofen (KET) and diclofenac (DIC)). The results showed that the SRB sludge had the higher removal efficacy (20 to 90%) for antibiotics (SD, SMX, TMP, CIP and ENO) than NSAIDs (<20%) via adsorption and biodegradation under different operating conditions. Based on a series of batch studies, fluoroquinolone antibiotics (CIP and ENO) were instantly (<15 min) removed (∼98%) via adsorption on SRB sludge with adsorption coefficient (Kd) as high as 25.3 ± 1.8 L/g-suspended solids (SS). And thermodynamics results indicated that the adsorption of CIP and ENO on SRB sludge was spontaneous (Gibbs free energy change (ΔG°) <0 kJ/mol), exothermic (enthalpy change (ΔH°) <0 kJ/mol), and the adsorption process involved both physisorption and chemisorption (absolute value of ΔH° = 20 to 80 kJ/mol). Three widely prescribed antibiotics (SMX, TMP and CIP) were further investigated for their possible biodegradation pathways along with functional enzymes involved through a series of batch experiments. The biotransformation intermediates indicated that biotransformations of SMX and CIP in SRB sludge system could be initiated from the cleavage of isoxazole and piperazinyl rings catalyzed by sulfite reductase (SR) and cytochrome P450 (CYP450) enzymes, respectively. TMP was likely biotransformed via O-demethylation and N-acetylation coupled with hydroxylation reactions with CYP450 enzymes as the main functional enzymes. This study provided new insight into PhAs removal in SRB sludge system, and has significant potential of implementing sulfur-mediated biological process for the treatment of PhAs containing wastewater.
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Affiliation(s)
- Yanyan Jia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China; Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong
| | - Huiqun Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, PR China
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, USA
| | - Linwan Yin
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, PR China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, PR China.
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Catalytic mechanism for the conversion of salicylate into catechol by the flavin-dependent monooxygenase salicylate hydroxylase. Int J Biol Macromol 2019; 129:588-600. [DOI: 10.1016/j.ijbiomac.2019.01.135] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 11/17/2022]
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Biodegradation of 7-Hydroxycoumarin in Pseudomonas mandelii 7HK4 via ipso-Hydroxylation of 3-(2,4-Dihydroxyphenyl)-propionic Acid. Molecules 2018; 23:molecules23102613. [PMID: 30321993 PMCID: PMC6222606 DOI: 10.3390/molecules23102613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 11/17/2022] Open
Abstract
A gene cluster, denoted as hcdABC, required for the degradation of 3-(2,4-dihydroxyphenyl)-propionic acid has been cloned from 7-hydroxycoumarin-degrading Pseudomonas mandelii 7HK4 (DSM 107615), and sequenced. Bioinformatic analysis shows that the operon hcdABC encodes a flavin-binding hydroxylase (HcdA), an extradiol dioxygenase (HcdB), and a putative hydroxymuconic semialdehyde hydrolase (HcdC). The analysis of the recombinant HcdA activity in vitro confirms that this enzyme belongs to the group of ipso-hydroxylases. The activity of the proteins HcdB and HcdC has been analyzed by using recombinant Escherichia coli cells. Identification of intermediate metabolites allowed us to confirm the predicted enzyme functions and to reconstruct the catabolic pathway of 3-(2,4-dihydroxyphenyl)-propionic acid. HcdA catalyzes the conversion of 3-(2,4-dihydroxyphenyl)-propionic acid to 3-(2,3,5-trihydroxyphenyl)-propionic acid through an ipso-hydroxylation followed by an internal (1,2-C,C)-shift of the alkyl moiety. Then, in the presence of HcdB, a subsequent oxidative meta-cleavage of the aromatic ring occurs, resulting in the corresponding linear product (2E,4E)-2,4-dihydroxy-6-oxonona-2,4-dienedioic acid. Here, we describe a Pseudomonas mandelii strain 7HK4 capable of degrading 7-hydroxycoumarin via 3-(2,4-dihydroxyphenyl)-propionic acid pathway.
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Reis AC, Čvančarová M, Liu Y, Lenz M, Hettich T, Kolvenbach BA, Corvini PFX, Nunes OC. Biodegradation of sulfamethoxazole by a bacterial consortium of Achromobacter denitrificans PR1 and Leucobacter sp. GP. Appl Microbiol Biotechnol 2018; 102:10299-10314. [PMID: 30294753 DOI: 10.1007/s00253-018-9411-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 11/26/2022]
Abstract
In the last decade, biological degradation and mineralization of antibiotics have been increasingly reported feats of environmental bacteria. The most extensively described example is that of sulfonamides that can be degraded by several members of Actinobacteria and Proteobacteria. Previously, we reported sulfamethoxazole (SMX) degradation and partial mineralization by Achromobacter denitrificans strain PR1, isolated from activated sludge. However, further studies revealed an apparent instability of this metabolic trait in this strain. Here, we investigated this instability and describe the finding of a low-abundance and slow-growing actinobacterium, thriving only in co-culture with strain PR1. This organism, named GP, shared highest 16S rRNA gene sequence similarity (94.6-96.9%) with the type strains of validly described species of the genus Leucobacter. This microbial consortium was found to harbor a homolog to the sulfonamide monooxygenase gene (sadA) also found in other sulfonamide-degrading bacteria. This gene is overexpressed in the presence of the antibiotic, and evidence suggests that it codes for a group D flavin monooxygenase responsible for the ipso-hydroxylation of SMX. Additional side reactions were also detected comprising an NIH shift and a Baeyer-Villiger rearrangement, which indicate an inefficient biological transformation of these antibiotics in the environment. This work contributes to further our knowledge in the degradation of this ubiquitous micropollutant by environmental bacteria.
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Affiliation(s)
- Ana C Reis
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Monika Čvančarová
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Ying Liu
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Markus Lenz
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Timm Hettich
- Institute for Chemistry and Bioanalytics, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Boris A Kolvenbach
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Philippe F-X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Olga C Nunes
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.
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Ji L, Ji S, Wang C, Kepp KP. Molecular Mechanism of Alternative P450-Catalyzed Metabolism of Environmental Phenolic Endocrine-Disrupting Chemicals. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:4422-4431. [PMID: 29490136 DOI: 10.1021/acs.est.8b00601] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the bioactivation mechanisms to predict toxic metabolites is critical for risk assessment of phenolic endocrine-disrupting chemicals (EDCs). One mechanism involves ipso-substitution, which may contribute to the total turnover of phenolic EDCs, yet the detailed mechanism and its relationship with other mechanisms are unknown. We used density functional theory to investigate the P450-catalyzed ipso-substitution mechanism of the prominent xenoestrogen bisphenol A. The ipso-substitution proceeds via H-abstraction from bisphenol A by Compound I, followed by essentially barrierless OH-rebound onto the ipso-position forming a quinol, which can spontaneously decompose into the carbocation and hydroquinone. This carbocation can further evolve into the highly estrogenic hydroxylated and dimer-type metabolites. The H-abstraction/OH-rebound reaction mechanism has been verified as a general reaction mode for many other phenolic EDCs, such as bisphenol analogues, alkylphenols and chlorophenols. The identified mechanism enables us to effectively distinguish between type I (eliminating-substituent as anion) and type II (eliminating-substituent as cation) ipso-substitution in various phenolic EDCs. We envision that the identified pathways will be applicable for prediction of metabolites from phenolic EDCs whose fate are affected by this alternative type of P450 reactivity, and accordingly enable the screening of these metabolites for endocrine-disrupting activity.
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Affiliation(s)
- Li Ji
- College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , P. R. China
- UFZ Department of Ecological Chemistry , Helmholtz Centre for Environmental Research , Permoserstrasse 15 , 04318 Leipzig , Germany
| | - Shujing Ji
- College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , P. R. China
| | - Chenchen Wang
- College of Environmental and Resource Sciences , Zhejiang University , Hangzhou 310058 , P. R. China
| | - Kasper P Kepp
- DTU Chemistry , Technical University of Denmark , Building 206 , Kongens Lyngby , DK-2800 , Denmark
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Deng Y, Mao Y, Li B, Yang C, Zhang T. Aerobic Degradation of Sulfadiazine by Arthrobacter spp.: Kinetics, Pathways, and Genomic Characterization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:9566-9575. [PMID: 27477918 DOI: 10.1021/acs.est.6b02231] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Two aerobic sulfadiazine (SDZ) degrading bacterial strains, D2 and D4, affiliated with the genus Arthrobacter, were isolated from SDZ-enriched activated sludge. The degradation of SDZ by the two isolates followed first-order decay kinetics. The half-life time of complete SDZ degradation was 11.3 h for strain D2 and 46.4 h for strain D4. Degradation kinetic changed from nongrowth to growth-linked when glucose was introduced as the cosubstrate, and accelerated biodegradation rate was observed after the adaption period. Both isolates could degrade SDZ into 12 biodegradation products via 3 parallel pathways, of which 2-amino-4-hydroxypyrimidine was detected as the principal intermediate product toward the pyrimidine ring cleavage. Compared with five Arthrobacter strains reported previously, D2 and D4 were the only Arthrobacter strains which could degrade SDZ as the sole carbon source. The draft genomes of D2 and D4, with the same completeness of 99.7%, were compared to other genomes of related species. Overall, these two isolates shared high genomic similarities with the s-triazine-degrading Arthrobacter sp. AK-YN10 and the sulfonamide-degrading bacteria Microbacterium sp. C448. In addition, the two genomes contained a few significant regions of difference which may carry the functional genes involved in sulfonamide degradation.
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Affiliation(s)
- Yu Deng
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong , Pokfulam Road, Hong Kong, China
| | - Yanping Mao
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong , Pokfulam Road, Hong Kong, China
| | - Bing Li
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong , Pokfulam Road, Hong Kong, China
| | - Chao Yang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong , Pokfulam Road, Hong Kong, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong , Pokfulam Road, Hong Kong, China
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