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Hu M, Scott C. Toward the development of a molecular toolkit for the microbial remediation of per-and polyfluoroalkyl substances. Appl Environ Microbiol 2024; 90:e0015724. [PMID: 38477530 PMCID: PMC11022551 DOI: 10.1128/aem.00157-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024] Open
Abstract
Per- and polyfluoroalkyl substances (PFAS) are highly fluorinated synthetic organic compounds that have been used extensively in various industries owing to their unique properties. The PFAS family encompasses diverse classes, with only a fraction being commercially relevant. These substances are found in the environment, including in water sources, soil, and wildlife, leading to human exposure and fueling concerns about potential human health impacts. Although PFAS degradation is challenging, biodegradation offers a promising, eco-friendly solution. Biodegradation has been effective for a variety of organic contaminants but is yet to be successful for PFAS due to a paucity of identified microbial species capable of transforming these compounds. Recent studies have investigated PFAS biotransformation and fluoride release; however, the number of specific microorganisms and enzymes with demonstrable activity with PFAS remains limited. This review discusses enzymes that could be used in PFAS metabolism, including haloacid dehalogenases, reductive dehalogenases, cytochromes P450, alkane and butane monooxygenases, peroxidases, laccases, desulfonases, and the mechanisms of microbial resistance to intracellular fluoride. Finally, we emphasize the potential of enzyme and microbial engineering to advance PFAS degradation strategies and provide insights for future research in this field.
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Affiliation(s)
- Miao Hu
- CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Colin Scott
- CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
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2
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Yue Y, Chen J, Bao L, Wang J, Li Y, Zhang Q. Fluoroacetate dehalogenase catalyzed dehalogenation of halogenated carboxylic acids: A QM/MM approach. CHEMOSPHERE 2020; 254:126803. [PMID: 32361540 DOI: 10.1016/j.chemosphere.2020.126803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 04/11/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
Abstract
Dehalogenation is one of the most important reactions in environmental pollution control, for instance, the degradation of persistent organic pollutants (POPs). Recently, fluoroacetate dehalogenase (FAcD) has been reported to catalyze the dehalogenation reactions, which shows great potential in treating halogenated pollutants. Here the dehalogenation mechanism catalyzed by FAcD was fully deciphered with the aid of quantum mechanics/molecular mechanics method. The results show that FAcD catalyzed dehalogenation efficiency follows the order of defluorination > dechlorination > debromination. The corresponding Boltzmann-weighted average barriers are 10.1, 19.7, and 20.9 kcal mol-1. Positive/negative correlations between activation barriers and structural parameters (e.g. distance and angle) for FAcD catalyzed dechlorination and debromination were established. Based on the structure-energy relationship, we propose that mutation of the binding pocket amino acids (e.g. His155, Trp156, Tyr219) to smaller proton donor amino acids (e.g. Serine, Threonine, Cysteine, Asparagine) may increase the efficiency for dechlorination and debromination. The results may of practical value for the efficient degradation of chlorined and bromined pollutants by harnessing FAcD.
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Affiliation(s)
- Yue Yue
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
| | - Jinfeng Chen
- School of Life Sciences, Westlake University, Hangzhou, 310000, PR China
| | - Lei Bao
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
| | - Junjie Wang
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Jinan, 250100, PR China.
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
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Li Y, Yue Y, Zhang H, Yang Z, Wang H, Tian S, Wang JB, Zhang Q, Wang W. Harnessing fluoroacetate dehalogenase for defluorination of fluorocarboxylic acids: in silico and in vitro approach. ENVIRONMENT INTERNATIONAL 2019; 131:104999. [PMID: 31319293 DOI: 10.1016/j.envint.2019.104999] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/02/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
Widely distributed fluorocarboxylic acids have aroused worldwide environmental concerns due to its toxicity, persistence, and bioaccumulation. Enzyme-based eco-friendly biodegradation techniques have become increasingly important in treating fluorocarboxylic acids. Here we utilized in silico and in vitro approaches to investigate the defluorination mechanism of fluoroacetate dehalogenase (FAcD) toward monofluoropropionic acids at atomic-level. The experimentally determined kcat and kM for defluorination of 2-fluoropropionic acid are 330 ± 60 min-1 and 6.12 ± 0.13 mM. The in silico results demonstrated positive/negative correlations between activation barriers and structural parameters (e.g. distance and angle) under different enzymatic conformations. We also screened computationally and tested in vitro (enzyme assay and kinetic study) the catalytic proficiency of FAcD toward polyfluoropropionic acids and perfluoropropionic acids which are known to be challenging for enzymatic degradation. The results revealed potential degradation activity of FAcD enzyme toward 2,3,3,3-tetrafluoropropionic acids. Our work will initiate the development of a new "integrated approach" for enzyme engineering to degrade environmentally persistent fluorocarboxylic acids.
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Affiliation(s)
- Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Yue Yue
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Hongxia Zhang
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China; Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China
| | - Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Hui Wang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Shaixiao Tian
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China; Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China
| | - Jian-Bo Wang
- Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China; Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, PR China.
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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Leong LEX, Khan S, Davis CK, Denman SE, McSweeney CS. Fluoroacetate in plants - a review of its distribution, toxicity to livestock and microbial detoxification. J Anim Sci Biotechnol 2017; 8:55. [PMID: 28674607 PMCID: PMC5485738 DOI: 10.1186/s40104-017-0180-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/11/2017] [Indexed: 02/08/2023] Open
Abstract
Fluoroacetate producing plants grow worldwide and it is believed they produce this toxic compound as a defence mechanism against grazing by herbivores. Ingestion by livestock often results in fatal poisonings, which causes significant economic problems to commercial farmers in many countries such as Australia, Brazil and South Africa. Several approaches have been adopted to protect livestock from the toxicity with limited success including fencing, toxic plant eradication and agents that bind the toxin. Genetically modified bacteria capable of degrading fluoroacetate have been able to protect ruminants from fluoroacetate toxicity under experimental conditions but concerns over the release of these microbes into the environment have prevented the application of this technology. Recently, a native bacterium from an Australian bovine rumen was isolated which can degrade fluoroacetate. This bacterium, strain MFA1, which belongs to the Synergistetes phylum degrades fluoroacetate to fluoride ions and acetate. The discovery and isolation of this bacterium provides a new opportunity to detoxify fluoroacetate in the rumen. This review focuses on fluoroacetate toxicity in ruminant livestock, the mechanism of fluoroacetate toxicity, tolerance of some animals to fluoroaceate, previous attempts to mitigate toxicity, aerobic and anaerobic microbial degradation of fluoroacetate, and future directions to overcome fluoroacetate toxicity.
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Affiliation(s)
- Lex Ee Xiang Leong
- School of Chemistry and Molecular Bioscience, University of Queensland, St Lucia, 4072 QLD Australia
| | - Shahjalal Khan
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, 4072 QLD Australia
| | - Carl K Davis
- School of Chemistry and Molecular Bioscience, University of Queensland, St Lucia, 4072 QLD Australia
| | - Stuart E Denman
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, 4072 QLD Australia
| | - Chris S McSweeney
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, 4072 QLD Australia
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Li Y, Zhang R, Du L, Zhang Q, Wang W. Catalytic mechanism of C–F bond cleavage: insights from QM/MM analysis of fluoroacetate dehalogenase. Catal Sci Technol 2016. [DOI: 10.1039/c5cy00777a] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The catalytic mechanisms of fluoroacetate dehalogenase (FAcD) toward substrates fluoroacetate and chloroacetate were studied by a combined quantum mechanics/molecular mechanics (QM/MM) method.
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Affiliation(s)
- Yanwei Li
- Environment Research Institute
- Shandong University
- Jinan 250100
- PR China
| | - Ruiming Zhang
- Environment Research Institute
- Shandong University
- Jinan 250100
- PR China
| | - Likai Du
- Key Laboratory of Bio-based Materials
- Qingdao Institute of Bio-energy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- PR China
| | - Qingzhu Zhang
- Environment Research Institute
- Shandong University
- Jinan 250100
- PR China
| | - Wenxing Wang
- Environment Research Institute
- Shandong University
- Jinan 250100
- PR China
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Satpathy R, Konkimalla VB, Ratha J. Application of bioinformatics tools and databases in microbial dehalogenation research: A review. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683815010147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hamid AAA, Wong EL, Joyce-Tan KH, Shamsir MS, Hamid THTA, Huyop F. Molecular Modelling and Functional Studies of the Non-Stereospecific α-Haloalkanoic Acid Dehalogenase (DehE) fromRhizobiumSP. RC1 and its Association with 3-Chloropropionic Acid (β-Chlorinated Aliphatic Acid). BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2012.0142] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Davis CK, Webb RI, Sly LI, Denman SE, McSweeney CS. Isolation and survey of novel fluoroacetate-degrading bacteria belonging to the phylum Synergistetes. FEMS Microbiol Ecol 2012; 80:671-84. [PMID: 22372434 DOI: 10.1111/j.1574-6941.2012.01338.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 01/16/2012] [Accepted: 02/12/2012] [Indexed: 11/29/2022] Open
Abstract
Microbial dehalogenation of chlorinated compounds in anaerobic environments is well known, but the degradation of fluorinated compounds under similar conditions has rarely been described. Here, we report on the isolation of a bovine rumen bacterium that metabolizes fluoroacetate under anaerobic conditions, the mode of degradation and its presence in gut ecosystems. The bacterium was identified using 16S rRNA gene sequence analysis as belonging to the phylum Synergistetes and was designated strain MFA1. Growth was stimulated by amino acids with greater quantities of amino acids metabolized in the presence of fluoroacetate, but sugars were not fermented. Acetate, formate, propionate, isobutryate, isovalerate, ornithine and H(2) were end products of amino acid metabolism. Acetate was the primary end product of fluoroacetate dehalogenation, and the amount produced correlated with the stoichiometric release of fluoride which was confirmed using fluorine nuclear magnetic resonance ((19) F NMR) spectroscopy. Hydrogen and formate produced in situ were consumed during dehalogenation. The growth characteristics of strain MFA1 indicated that the bacterium may gain energy via reductive dehalogenation. This is the first study to identify a bacterium that can anaerobically dehalogenate fluoroacetate. Nested 16S rRNA gene-specific PCR assays detected the bacterium at low numbers in the gut of several herbivore species.
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Affiliation(s)
- Carl K Davis
- CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Qld, Australia
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Davis CK, Denman SE, Sly LI, McSweeney CS. Development of a colorimetric colony-screening assay for detection of defluorination by micro-organisms. Lett Appl Microbiol 2011; 53:417-23. [PMID: 21767280 DOI: 10.1111/j.1472-765x.2011.03123.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To develop a colorimetric colony-screening assay to facilitate the isolation of micro-organisms capable of defluorination. METHODS AND RESULTS A metal-dye chelate, zirconium-xylenol orange was used to detect fluoride ions released from a fluorinated substrate through microbial metabolism. Depolymerised zirconium reagent gave the greatest visual contrast for the presence of fluoride compared to more polymerised forms of zirconium reagent. The sensitivity of the assay was greatest when the molar ratio of depolymerised zirconium to xylenol orange was 1:2. Using depolymerised zirconium and xylenol orange (150 and 300 nmol l(-1) respectively), the assay could detect a fluoride application spot (5 mmol l(-1)) containing 50 nmoles of fluoride ions. Most media constituents were well tolerated by the assay, although phosphate ions needed to be restricted to 0.1 g l(-1) and some proteins digest to between 1 and 5 g l(-1). A microbial enrichment culture growing on solidified medium containing 20 mmol l(-1) fluoroacetate was screened using the assay, and defluorinating bacteria belonging to the genus Burkholderia isolated. CONCLUSIONS A method was developed that is sensitive, rapid and reliable for detecting defluorination by micro-organisms growing on solidified medium. SIGNIFICANCE AND IMPACT OF THE STUDY This method can be used to facilitate the isolation of micro-organisms capable of defluorination.
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Affiliation(s)
- C K Davis
- CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Qld, Australia
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Kamachi T, Nakayama T, Shitamichi O, Jitsumori K, Kurihara T, Esaki N, Yoshizawa K. The catalytic mechanism of fluoroacetate dehalogenase: a computational exploration of biological dehalogenation. Chemistry 2009; 15:7394-403. [PMID: 19551770 DOI: 10.1002/chem.200801813] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The biological dehalogenation of fluoroacetate carried out by fluoroacetate dehalogenase is discussed by using quantum mechanical/molecular mechanical (QM/MM) calculations for a whole-enzyme model of 10 800 atoms. Substrate fluoroacetate is anchored by a hydrogen-bonding network with water molecules and the surrounding amino acid residues of Arg105, Arg108, His149, Trp150, and Tyr212 in the active site in a similar way to haloalkane dehalogenase. Asp104 is likely to act as a nucleophile to attack the alpha-carbon of fluoroacetate, resulting in the formation of an ester intermediate, which is subsequently hydrolyzed by the nucleophilic attack of a water molecule to the carbonyl carbon atom. The cleavage of the strong C-F bond is greatly facilitated by the hydrogen-bonding interactions between the leaving fluorine atom and the three amino acid residues of His149, Trp150, and Tyr212. The hydrolysis of the ester intermediate is initiated by a proton transfer from the water molecule to His271 and by the simultaneous nucleophilic attack of the water molecule. The transition state and produced tetrahedral intermediate are stabilized by Asp128 and the oxyanion hole composed of Phe34 and Arg105.
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Affiliation(s)
- Takashi Kamachi
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
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X-Ray crystallographic and mutational studies of fluoroacetate dehalogenase from Burkholderia sp. strain FA1. J Bacteriol 2009; 191:2630-7. [PMID: 19218394 DOI: 10.1128/jb.01654-08] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluoroacetate dehalogenase catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. The enzyme is unique in that it catalyzes the cleavage of a carbon-fluorine bond of an aliphatic compound: the bond energy of the carbon-fluorine bond is among the highest found in natural products. The enzyme also acts on chloroacetate, although much less efficiently. We here determined the X-ray crystal structure of the enzyme from Burkholderia sp. strain FA1 as the first experimentally determined three-dimensional structure of fluoroacetate dehalogenase. The enzyme belongs to the alpha/beta hydrolase superfamily and exists as a homodimer. Each subunit consists of core and cap domains. The catalytic triad, Asp104-His271-Asp128, of which Asp104 serves as the catalytic nucleophile, was found in the core domain at the domain interface. The active site was composed of Phe34, Asp104, Arg105, Arg108, Asp128, His271, and Phe272 of the core domain and Tyr147, His149, Trp150, and Tyr212 of the cap domain. An electron density peak corresponding to a chloride ion was found in the vicinity of the N(epsilon1) atom of Trp150 and the N(epsilon2) atom of His149, suggesting that these are the halide ion acceptors. Site-directed replacement of each of the active-site residues, except for Trp150, by Ala caused the total loss of the activity toward fluoroacetate and chloroacetate, whereas the replacement of Trp150 caused the loss of the activity only toward fluoroacetate. An interaction between Trp150 and the fluorine atom is probably an absolute requirement for the reduction of the activation energy for the cleavage of the carbon-fluorine bond.
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