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Jeschke P. Recent developments in fluorine-containing pesticides. PEST MANAGEMENT SCIENCE 2024; 80:3065-3087. [PMID: 38073050 DOI: 10.1002/ps.7921] [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: 10/21/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
To ensure ongoing sustainability, the modern agrochemical industry is faced with enormous challenges. These arise from provision of high-quality food to increasing water use and environmental impact as well as a growing world population. The loss of previous agrochemicals due to consumer perception, changing grower needs and ever-changing regulatory requirements is higher than the number of active ingredients that are being introduced into the crop protection market. Therefore, the development of novel agrochemicals is essential to provide improved efficacy and environmental profiles. In this context, the introduction of fluorine atoms and fluorine-containing motifs into a molecule is an important method to influence its physicochemical properties. These include, for example, small difluoro- and trifluoromethyl, or trifluoromethoxy groups at aryl or heterocyclic aryl moieties but also fragments like 2,2,2-trifluoroethoxycarbonyl, trifluoromethylsulfonyl, trifluoroacetyl, as well as the so far unusal rest like heptafluoro-iso-propyl. This review gives an overview of recent developments of fluorine-containing pesticides launched over the past 7 years and describes a selection of current fluorine-containing development candidates. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Peter Jeschke
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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2
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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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3
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Khusnutdinova AN, Batyrova KA, Brown G, Fedorchuk T, Chai YS, Skarina T, Flick R, Petit AP, Savchenko A, Stogios P, Yakunin AF. Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases. FEBS J 2023; 290:4966-4983. [PMID: 37437000 DOI: 10.1111/febs.16903] [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: 05/18/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/14/2023]
Abstract
Fluorine forms the strongest single bond to carbon with the highest bond dissociation energy among natural products. However, fluoroacetate dehalogenases (FADs) have been shown to hydrolyze this bond in fluoroacetate under mild reaction conditions. Furthermore, two recent studies demonstrated that the FAD RPA1163 from Rhodopseudomonas palustris can also accept bulkier substrates. In this study, we explored the substrate promiscuity of microbial FADs and their ability to defluorinate polyfluorinated organic acids. Enzymatic screening of eight purified dehalogenases with reported fluoroacetate defluorination activity revealed significant hydrolytic activity against difluoroacetate in three proteins. Product analysis using liquid chromatography-mass spectrometry identified glyoxylic acid as the final product of enzymatic DFA defluorination. The crystal structures of DAR3835 from Dechloromonas aromatica and NOS0089 from Nostoc sp. were determined in the apo-state along with the DAR3835 H274N glycolyl intermediate. Structure-based site-directed mutagenesis of DAR3835 demonstrated a key role for the catalytic triad and other active site residues in the defluorination of both fluoroacetate and difluoroacetate. Computational analysis of the dimer structures of DAR3835, NOS0089, and RPA1163 indicated the presence of one substrate access tunnel in each protomer. Moreover, protein-ligand docking simulations suggested similar catalytic mechanisms for the defluorination of both fluoroacetate and difluoroacetate, with difluoroacetate being defluorinated via two consecutive defluorination reactions producing glyoxylate as the final product. Thus, our findings provide molecular insights into substrate promiscuity and catalytic mechanism of FADs, which are promising biocatalysts for applications in synthetic chemistry and bioremediation of fluorochemicals.
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Affiliation(s)
- Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
- Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, UK
| | - Khorcheska A Batyrova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Tatiana Fedorchuk
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Russia
| | - Yao Sheng Chai
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Alain-Pierre Petit
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Biological Chemistry and Drug Discovery Division, School of Life Sciences, University of Dundee, UK
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Health Research Innovation Centre, University of Calgary, AB, Canada
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, UK
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4
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Xiang Y, Li S, Rene ER, Lun X, Zhang P, Ma W. Detoxification of fluoroglucocorticoid by Acinetobacter pittii C3 via a novel defluorination pathway with hydrolysis, oxidation and reduction: Performance, genomic characteristics, and mechanism. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131302. [PMID: 37031670 DOI: 10.1016/j.jhazmat.2023.131302] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/10/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Biological dehalogenation degradation was an important detoxification method for the ecotoxicity and teratogenic toxicity of fluorocorticosteroids (FGCs). The functional strain Acinetobacter pittii C3 can effectively biodegrade and defluorinate to 1 mg/L Triamcinolone acetonide (TA), a representative FGCs, with 86 % and 79 % removal proportion in 168 h with the biodegradation and detoxification kinetic constant of 0.031/h and 0.016/h. The dehalogenation and degradation ability of strain C3 was related to its dehalogenation genomic characteristics, which manifested in the functional gene expression of dehalogenation, degradation, and toxicity tolerance. Three detoxification mechanisms were positively correlated with defluorination pathways through hydrolysis, oxidation, and reduction, which were regulated by the expression of the haloacid dehalogenase (HAD) gene (mupP, yrfG, and gph), oxygenase gene (dmpA and catA), and reductase gene (nrdAB and TgnAB). Hydrolysis defluorination was the most critical way for TA detoxification metabolism, which could rapidly generate low-toxicity metabolites and reduce toxic bioaccumulation due to hydrolytic dehalogenase-induced defluorination. The mechanism of hydrolytic defluorination was that the active pocket of hydrolytic dehalogenase was matched well with the spatial structure of TA under the adjustment of the hydrogen bond, and thus induced molecular recognition to promote the catalytic hydrolytic degradation of various amino acid residues. This work provided an effective bioremediation method and mechanism for improving defluorination and detoxification performance.
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Affiliation(s)
- Yayun Xiang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Sinuo Li
- Beijing No. 80 High School, Beijing 100102, China
| | - Eldon R Rene
- IHE-Delft, Institute for Water Education, Department of Environmental Engineering and Water Technology, Westvest 7, 2611AX Delft, the Netherlands
| | - Xiaoxiu Lun
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Panyue Zhang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Weifang Ma
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
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5
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Sarma H, Narayan M, Peralta-Videa JR, Lam SS. Exploring the significance of nanomaterials and organic amendments - Prospect for phytoremediation of contaminated agroecosystem. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119601. [PMID: 35709913 DOI: 10.1016/j.envpol.2022.119601] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/10/2022] [Accepted: 06/07/2022] [Indexed: 05/22/2023]
Abstract
Emerging micro-pollutants have rapidly contaminated the agro-ecosystem, posing serious challenges to a sustainable future. The vast majority of them have infiltrated the soil and damaged agricultural fields and crops after being released from industry. These pollutants and their transformed products are also transported in vast quantities which further exacerbate the damage. Sustainable remediation techniques are warranted for such large amounts of contaminants. As aforementioned, many of them have been detected at very high concentrations in soil and water which adversely affect crop physiology by disrupting different metabolic processes. To combat this situation, nanomaterials and other organic amendments assisted phytoremediation ware considered as a viable alternative. It is a potent synergistic activity between the biological system and the supplied organic or nanomaterial material to eliminate emerging contaminants and micropollutants from crop fields. This can be effectively be applied to degraded crop fields and could potentially embody a green technology for sustainable agriculture.
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Affiliation(s)
- Hemen Sarma
- Bioremediation Technology Research Group, Department of Botany, Bodoland University, Rangalikhata, Deborgaon, Kokrajhar(BTR), Assam, 783370, India; Institutional Biotech Hub, Department of Botany, Nanda Nath Saikia College, Titabar, Assam, 785630, India.
| | - Mahesh Narayan
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 W. University Ave., El Paso, TX, 79968, USA
| | - Jose R Peralta-Videa
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 W. University Ave., El Paso, TX, 79968, USA
| | - Su Shiung Lam
- Pyrolysis Technology Research Group, Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia; Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India
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6
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Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes. THE ISME JOURNAL 2022; 16:1397-1408. [PMID: 35039616 PMCID: PMC9038774 DOI: 10.1038/s41396-022-01188-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 12/13/2022]
Abstract
Viruses significantly influence local and global biogeochemical cycles and help bacteria to survive in different environments by encoding various auxiliary metabolic genes (AMGs) associated with energy acquisition, stress tolerance and degradation of xenobiotics. Here we studied whether bacterial (dsDNA) virus encoded AMGs are enriched in organochlorine pesticide (OCP) contaminated soil in China and if viral AMGs include genes linked to OCP biodegradation. Using metagenomics, we found that OCP-contaminated soils displayed a lower bacterial, but higher diversity of viruses that harbored a higher relative abundance of AMGs linked to pesticide degradation and metabolism. Furthermore, the diversity and relative abundance of AMGs significantly increased along with the severity of pesticide contamination, and several biodegradation genes were identified bioinformatically in viral metagenomes. Functional assays were conducted to experimentally demonstrate that virus-encoded L-2-haloacid dehalogenase gene (L-DEX) is responsible for the degradation of L-2-haloacid pesticide precursors, improving bacterial growth at sub-inhibitory pesticide concentrations. Taken together, these results demonstrate that virus-encoded AMGs are linked to bacterial metabolism and biodegradation, being more abundant and diverse in soils contaminated with pesticides. Moreover, our findings highlight the importance of virus-encoded accessory genes for bacterial ecology in stressful environments, providing a novel avenue for using viruses in the bioremediation of contaminated soils.
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7
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Sarma H, Joshi SJ. Metagenomics Combined with Stable Isotope Probe (SIP) for the Discovery of Novel Dehalogenases Producing Bacteria. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 108:478-484. [PMID: 32978646 DOI: 10.1007/s00128-020-03004-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Halogenated compounds are one of the largest groups of environmental-hazardous chemicals. The removal of the halogen atom from the substrate is possible by the catalytic activity of a type of enzyme called dehalogenase. Hydrolytic dehalogenases are suggested to be a good biodegradation catalyst for halogenated compounds with potential bioremediation applications. Therefore, the identification of possible bacterial strains that produce dehalogenase is of great importance. Soil microorganisms that are regularly exposed to halogenated pesticides are a major source of hydrolytic dehalogenase. Their proper identification may be useful in the production of high-quality dehalogenase. DNA stable isotope probing (DNA-SIP) is quite a useful technique for the identification of active microorganisms that assimilate specific carbon substrates and nutrients. Metagenomics combined with a stable isotope probe (SIP) technique could therefore be used to detect bacterial dehalogenases in pesticides exposed agricultural soil.
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Affiliation(s)
- Hemen Sarma
- Department of Botany, N. N. Saikia College, Titabar, Assam, 785630, India.
| | - Sanket J Joshi
- Oil & Gas Research Center, Central Analytical and Applied Research Unit, Sultan Qaboos University, Muscat, Oman.
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8
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Chan PWY, Chakrabarti N, Ing C, Halgas O, To TKW, Wälti M, Petit AP, Tran C, Savchenko A, Yakunin AF, Edwards EA, Pomès R, Pai EF. Defluorination Capability of l-2-Haloacid Dehalogenases in the HAD-Like Hydrolase Superfamily Correlates with Active Site Compactness. Chembiochem 2022; 23:e202100414. [PMID: 34643018 PMCID: PMC10281000 DOI: 10.1002/cbic.202100414] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/07/2021] [Indexed: 11/11/2022]
Abstract
l-2-Haloacid dehalogenases, industrially and environmentally important enzymes that catalyse cleavage of the carbon-halogen bond in S-2-halocarboxylic acids, were known to hydrolyse chlorinated, brominated and iodinated substrates but no activity towards fluorinated compounds had been reported. A screen for novel dehalogenase activities revealed four l-2-haloacid dehalogenases capable of defluorination. We now report crystal structures for two of these enzymes, Bpro0530 and Rha0230, as well as for the related proteins PA0810 and RSc1362, which hydrolyse chloroacetate but not fluoroacetate, all at ∼2.2 Å resolution. Overall structure and active sites of these enzymes are highly similar. In molecular dynamics (MD) calculations, only the defluorinating enzymes sample more compact conformations, which in turn allow more effective interactions with the small fluorine atom. Structural constraints, based on X-ray structures and MD calculations, correctly predict the defluorination activity of the homologous enzyme ST2570.
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Affiliation(s)
- Peter W Y Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Present address: Zymeworks, Inc., 1385 West 8th Avenue Suite 540, Vancouver, British Columbia, V6H 3 V9, Canada
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | | | - Chris Ing
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
- Present address: ProteinQure, Inc., 119 Spadina Avenue suite 304, Toronto, Ontario, M5V 2L1, Canada
| | - Ondrej Halgas
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Terence K W To
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- Present address: International Point of Care, Inc., 135 The West Mall, Unit 9, Toronto, Ontario, M9C 1C2, Canada
| | - Marielle Wälti
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- Present address: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0510, USA
| | - Alain-Pierre Petit
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
- Present address: Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Christopher Tran
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
- Present address: Ramboll Environment & Health, 2400 Meadowpine Boulevard, Suite 100, Mississauga, Ontario, L5N 6S2, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
- Present address: Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Health Research Innovation Centre, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, M5S 3G5, Canada
| | - Régis Pomès
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Molecular Medicine, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Princess Margaret Cancer Centre, The Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
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9
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6577122. [DOI: 10.1093/femsec/fiac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
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10
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Wang Y, Xiang Q, Zhou Q, Xu J, Pei D. Mini Review: Advances in 2-Haloacid Dehalogenases. Front Microbiol 2021; 12:758886. [PMID: 34721367 PMCID: PMC8554231 DOI: 10.3389/fmicb.2021.758886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
The 2-haloacid dehalogenases (EC 3.8.1.X) are industrially important enzymes that catalyze the cleavage of carbon-halogen bonds in 2-haloalkanoic acids, releasing halogen ions and producing corresponding 2-hydroxyl acids. These enzymes are of particular interest in environmental remediation and environmentally friendly synthesis of optically pure chiral compounds due to their ability to degrade a wide range of halogenated compounds with astonishing efficiency for enantiomer resolution. The 2-haloacid dehalogenases have been extensively studied with regard to their biochemical characterization, protein crystal structures, and catalytic mechanisms. This paper comprehensively reviews the source of isolation, classification, protein structures, reaction mechanisms, biochemical properties, and application of 2-haloacid dehalogenases; current trends and avenues for further development have also been included.
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Affiliation(s)
- Yayue Wang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Qiao Xiang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Qingfeng Zhou
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, China
- Zhengzhou Tuoyang Industrial Co., Ltd., Zhengzhou, China
| | - Dongli Pei
- College of Biology and Food, Shangqiu Normal University, Shangqiu, China
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11
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Grigorian E, Groisillier A, Thomas F, Leblanc C, Delage L. Functional Characterization of a L-2-Haloacid Dehalogenase From Zobellia galactanivorans Dsij T Suggests a Role in Haloacetic Acid Catabolism and a Wide Distribution in Marine Environments. Front Microbiol 2021; 12:725997. [PMID: 34621253 PMCID: PMC8490876 DOI: 10.3389/fmicb.2021.725997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/31/2021] [Indexed: 12/21/2022] Open
Abstract
L-2-halocid dehalogenases (L-2-HADs) have been mainly characterized from terrestrial polluted environments. By contrast, knowledge is still scarce about their role in detoxification of predominant halocarbons in marine environments. Here, phylogenetic analyses showed a wide diversity of homologous L-2-HADs, especially among those belonging to marine bacteria. Previously characterized terrestrial L-2-HADs were part of a monophyletic group (named group A) including proteins of terrestrial and marine origin. Another branch (named group B) contained mostly marine L-2-HADs, with two distinct clades of Bacteroidetes homologs, closely linked to Proteobacteria ones. This study further focused on the characterization of the only L-2-HAD from the flavobacterium Zobellia galactanivorans DsijT (ZgHAD), belonging to one of these Group B clades. The recombinant ZgHAD was shown to dehalogenate bromo- and iodoacetic acids, and gene knockout in Z. galactanivorans revealed a direct role of ZgHAD in tolerance against both haloacetic acids. Analyses of metagenomic and metatranscriptomic datasets confirmed that L-2-HADs from group A were well-represented in terrestrial and marine bacteria, whereas ZgHAD homologs (group B L-2-HADs) were mainly present in marine bacteria, and particularly in host-associated species. Our results suggest that ZgHAD homologs could be key enzymes for marine Bacteroidetes, by conferring selective advantage for the recycling of toxic halogen compounds produced in particular marine habitats, and especially during interactions with macroalgae.
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Affiliation(s)
- Eugénie Grigorian
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Agnès Groisillier
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - François Thomas
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Catherine Leblanc
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Ludovic Delage
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
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12
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Yue Y, Fan J, Xin G, Huang Q, Wang JB, Li Y, Zhang Q, Wang W. Comprehensive Understanding of Fluoroacetate Dehalogenase-Catalyzed Degradation of Fluorocarboxylic Acids: A QM/MM Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9817-9825. [PMID: 34080849 DOI: 10.1021/acs.est.0c08811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fluorochemicals are persistent, bioaccumulative, and toxic compounds that are widely tributed in the environment. Developing efficient biodegradation strategies to decompose the fluorochemicals via breaking the inert C-F bonds presents a holistic challenge. As a promising biodegradation enzyme candidate, fluoroacetate dehalogenase (FAcD) has been reported as the only non-metallic enzyme to catalyze the cleavage of the strong C-F bond. Here, we systematically investigated the catalytic actions of FAcD toward its natural substrate fluoroacetate using molecular dynamics simulations and quantum mechanism/molecular mechanism calculations. We propose that the enzymatic transformation involves four elementary steps, (I) C-F bond activation, (II) nucleophilic attack, (III) C-O bond cleavage, and (IV) proton transfer. Our results show that nucleophilic attack is the rate-determining step. However, for difluoroacetate and trifluoroacetate, C-F bond activation, instead of nucleophilic attack, becomes the rate-determining step. We show that FAcD, originally recognized as α-fluorocarboxylic acid degradation enzyme, can catalyze the defluorination of difluoroacetate to glyoxylate, which is captured by our high-resolution mass spectrometry experiments. In addition, we employed amino acid electrostatic analysis method to screen potential mutation hotspots for tuning FAcD's electrostatic environment to favor substrate conversion. The comprehensive understanding of catalytic mechanism will inform a rational enzyme engineering strategy to degrade fluorochemicals for benefits of environmental sustainability.
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Affiliation(s)
- Yue Yue
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Jiaqian Fan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P. R. China
| | - Guoqing Xin
- Wuhan National High Magnetic Field Center (WHMFC), Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Qun Huang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P. R. China
| | - Jian-Bo Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P. R. China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
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13
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Chen G, Jiang N, Villalobos Solis MI, Kara Murdoch F, Murdoch RW, Xie Y, Swift CM, Hettich RL, Löffler FE. Anaerobic Microbial Metabolism of Dichloroacetate. mBio 2021; 12:e00537-21. [PMID: 33906923 PMCID: PMC8092247 DOI: 10.1128/mbio.00537-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 12/23/2022] Open
Abstract
Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising "Candidatus Dichloromethanomonas elyunquensis" strain RM utilizes DCA as an energy source, and the transient formation of formate, H2, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated "Candidatus Dichloromethanomonas elyunquensis" strain RM in DCA degradation. An (S)-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg-1 protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota.IMPORTANCE Dichloroacetate (DCA) is ubiquitous in the environment due to natural formation via biological and abiotic chlorination processes and the turnover of chlorinated organic materials (e.g., humic substances). Additional sources include DCA usage as a chemical feedstock and cancer drug and its unintentional formation during drinking water disinfection by chlorination. Despite the ubiquitous presence of DCA, its fate under anoxic conditions has remained obscure. We discovered an anaerobic bacterium capable of metabolizing DCA, identified the enzyme responsible for DCA dehalogenation, and elucidated a novel DCA fermentation pathway. The findings have implications for the turnover of DCA and the carbon and electron flow in electron acceptor-depleted environments and the human gastrointestinal tract.
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Affiliation(s)
- Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Nannan Jiang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Fadime Kara Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert Waller Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Yongchao Xie
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Cynthia M Swift
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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14
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Grabowski Ł, Łepek K, Stasiłojć M, Kosznik-Kwaśnicka K, Zdrojewska K, Maciąg-Dorszyńska M, Węgrzyn G, Węgrzyn A. Bacteriophage-encoded enzymes destroying bacterial cell membranes and walls, and their potential use as antimicrobial agents. Microbiol Res 2021; 248:126746. [PMID: 33773329 DOI: 10.1016/j.micres.2021.126746] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 01/22/2023]
Abstract
Appearance of pathogenic bacteria resistant to most, if not all, known antibiotics is currently one of the most significant medical problems. Therefore, development of novel antibacterial therapies is crucial for efficient treatment of bacterial infections in the near future. One possible option is to employ enzymes, encoded by bacteriophages, which cause destruction of bacterial cell membranes and walls. Bacteriophages use such enzymes to destroy bacterial host cells at the final stage of their lytic development, in order to ensure effective liberation of progeny virions. Nevertheless, to use such bacteriophage-encoded proteins in medicine and/or biotechnology, it is crucial to understand details of their biological functions and biochemical properties. Therefore, in this review article, we will present and discuss our current knowledge on the processes of bacteriophage-mediated bacterial cell lysis, with special emphasis on enzymes involved in them. Regulation of timing of the lysis is also discussed. Finally, possibilities of the practical use of these enzymes as antibacterial agents will be underlined and perspectives of this aspect will be presented.
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Affiliation(s)
- Łukasz Grabowski
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Krzysztof Łepek
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Małgorzata Stasiłojć
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Katarzyna Kosznik-Kwaśnicka
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Karolina Zdrojewska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Monika Maciąg-Dorszyńska
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
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15
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Wahhab BHA, Samsulrizal NH, Edbeib MF, Wahab RA, Al-Nimer MSM, Hamid AAA, Oyewusi HA, Kaya Y, Notarte KIR, Shariff AHM, Huyop F. Genomic analysis of a functional haloacid-degrading gene of Bacillus megaterium strain BHS1 isolated from Blue Lake (Mavi Gölü, Turkey). ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01625-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Bacillus megaterium strain BHS1, isolated from an alkaline water sample taken from Mavi Gölü (Blue Lake, Turkey), can grow on minimal medium containing 2,2-dichloropropionic acid. We characterized this bacterium at the genomic level.
Methods
The HiSeq platform was used to carry out genome sequencing, de novo assembly, and scaffolding with strain BHS1. Next, genome data were analyzed to demarcate DNA regions containing protein-coding genes and determine the function of certain BHS1 genes. Finally, results from a colorimetric chloride ion–release assay demonstrated that strain BHS1 produces dehalogenase.
Results
De novo assembly of the BHS1 genomic sequence revealed a genome size of ~ 5.37 Mb with an average G+C content of 38%. The predicted nuclear genome harbors 5509 protein-coding genes, 1353 tRNA genes, 67 rRNA genes, and 6 non-coding (mRNA) genes. Genomic mapping of strain BHS1 revealed its amenability to synthesize two families of dehalogenases (Cof-type haloacid dehalogenase IIB family hydrolase and haloacid dehalogenase type II), suggesting that these enzymes can participate in the catabolism of halogenated organic acids. The mapping identified seven Na+/H+ antiporter subunits that are vital for adaptation of the bacterium to an alkaline environment. Apart from a pairwise analysis to the well-established L-2-haloacid dehalogenases, whole-cell analysis strongly suggested that the haloacid dehalogenase type II might act stereospecifically on L-2-chloropropionic acid, D,L-2-chloropropionic acid, and 2,2-dichloropropionic acid. Whole-cell studies confirmed the utilization of these three substrates and the gene’s role in dehalogenation.
Conclusions
To our knowledge, this is the first report of the full genome sequence for strain BHS1, which enabled the characterization of selected genes having specific metabolic activities and their roles in the biodegradation of halogenated compounds.
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Gul I, Le W, Jie Z, Ruiqin F, Bilal M, Tang L. Recent advances on engineered enzyme-conjugated biosensing modalities and devices for halogenated compounds. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116145] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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17
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Sobrado P. Role of reduced flavin in dehalogenation reactions. Arch Biochem Biophys 2020; 697:108696. [PMID: 33245912 DOI: 10.1016/j.abb.2020.108696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022]
Abstract
Halogenated organic compounds are extensively used in the cosmetic, pharmaceutical, and chemical industries. Several naturally occurring halogen-containing natural products are also produced, mainly by marine organisms. These compounds accumulate in the environment due to their chemical stability and lack of biological pathways for their degradation. However, a few enzymes have been identified that perform dehalogenation reactions in specific biological pathways and others have been identified to have secondary activities toward halogenated compounds. Various mechanisms for dehalogenation of I, Cl, Br, and F containing compounds have been elucidated. These have been grouped into reductive, oxidative, and hydrolytic mechanisms. Flavin-dependent enzymes have been shown to catalyze oxidative dehalogenation reactions utilizing the C4a-hydroperoxyflavin intermediate. In addition, flavoenzymes perform reductive dehalogenation, forming transient flavin semiquinones. Recently, flavin-dependent enzymes have also been shown to perform dehalogenation reactions where the reduced form of the flavin produces a covalent intermediate. Here, recent studies on the reactions of flavoenzymes in dehalogenation reactions, with a focus on covalent catalytic dehalogenation mechanisms, are described.
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Affiliation(s)
- Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA.
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18
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Biotechnological Approach for the Production of Enantiomeric Hydroxylactones Derived from Benzaldehyde and Evaluation of Their Cytotoxic Activity. Catalysts 2020. [DOI: 10.3390/catal10111313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The β-aryl-δ-halo-γ-lactones are known for their antiproliferative activity towards numerous cancer cell lines. The aim of this study was to obtain in the biotransformation process new β-aryl-δ-hydroxy-γ-lactones and compare their activity with the antiproliferative activity of parent compounds. The racemic cis-5-(1-iodoethyl)-4-phenyldihydrofuran-2-one as well as separate enantiomers were transformed in fungal cultures. Among ten tested biocatalysts, three (Absidia cylindrospora AM336, Absidia glauca AM254, and Fusarium culmorum AM10) were able to catalyze the hydrolytic dehalogenation process. The biotransformations processes were highly stereoselective and enantiomerically pure hydroxylactones were obtained (ee ≥ 99%). The iodo- and hydroxylactone enantiomers were subjected to cytotoxic activity evaluation on canine leukemia and lymphoma cell lines. The iodolactones exhibited higher biological potential towards tested cell lines than hydroxylactones. Higher cytotoxic potential was also characteristic for (+)-(4S,5S,6R)-enantiomer of iodolactone compared to its antipode.
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19
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Gul I, Wang Q, Jiang Q, Fang R, Tang L. Enzyme immobilization on glass fiber membrane for detection of halogenated compounds. Anal Biochem 2020; 609:113971. [PMID: 32979368 DOI: 10.1016/j.ab.2020.113971] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 01/19/2023]
Abstract
Enzyme immobilization using inorganic membranes has enticed increased attention as they not only improve enzyme stability, but also furnish user-friendly biodevices that can be tailored to different applications. Herein, we explored the suitability of the glass fiber membrane for enzyme immobilization and its application for halocarbon detection. For this, halohydrin dehalogenase (HheC) and bovine serum albumin were crosslinked and immobilized on a glass fiber membrane without membrane functionalization. Immobilized HheC exhibited higher storage stability than its free counterpart over 60 days at 4 °C (67% immobilized vs. 8.1% free) and 30 °C (77% immobilized vs. 57% free). Similarly, the thermal endurance of the immobilized HheC was significantly improved. The practical utility of the membrane-immobilized enzyme was demonstrated by colorimetric detection of 1,3-dichloro-2-propanol (1,3-DCP) and 2,3-dibromo-1-propanol (2,3-DBP) as model analytes. Under optimized conditions, the detection limits of 0.06 mM and 0.09 mM were achieved for 1,3-DCP and 2,3-DBP, respectively. The satisfactory recoveries were observed with spiked river and lake water samples, which demonstrate the application potential of immobilized HheC for screening contaminants in water samples. Our results revealed that the proposed frugal and facile approach could be useful for enzyme stabilization, and mitigation of halocarbon pollution.
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Affiliation(s)
- Ijaz Gul
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Qian Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Qifa Jiang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Ruiqin Fang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Lixia Tang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
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20
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Crystal structure of ClA1, a type of chlorinase from soil bacteria. Biochem Biophys Res Commun 2020; 530:42-46. [PMID: 32828313 DOI: 10.1016/j.bbrc.2020.06.129] [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] [Received: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 11/23/2022]
Abstract
Halogenated compounds are widely discovered in nature, and many of them exhibit biological activities, such as an important chlorinated natural product salinosporamide A serving as a potential anticancer agent. Compared with bromination, iodination and fluorination, chlorination is the mainly important modification. To shed light on the mechanism of SAM-dependent chlorinases, a recombinant chlorinase ClA1 was expressed in Escherichia coli and further purified for crystallization and X-ray diffraction experiments. The flake crystals of ClA1 were able to diffract to a resolution of 1.85 Å. The crystals belonged to space group R3, with unit-cell parameters α = β = 90.0°, γ = 120.0°. By determining the structure of ClA1, it is revealed that the side chain of Arg242 in ClA1 may have contacts with the L-Met. However, in SalL the equivalent Arg243's side chain is far from L-Met. Considering the ClA1 and SalL are from different environments and their enzyme kinetics are quite different, it is suggested that the side chain conformation differences of the conserved arginine are possibly related with the enzyme activity differences of the two chlorinases.
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21
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Structure-guided protein design of fluoroacetate dehalogenase for kinetic resolution of rac-2-bromobutyric acid. GREEN SYNTHESIS AND CATALYSIS 2020. [DOI: 10.1016/j.gresc.2020.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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Bollinger A, Thies S, Katzke N, Jaeger K. The biotechnological potential of marine bacteria in the novel lineage of Pseudomonas pertucinogena. Microb Biotechnol 2020; 13:19-31. [PMID: 29943398 PMCID: PMC6922532 DOI: 10.1111/1751-7915.13288] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 01/20/2023] Open
Abstract
Marine habitats represent a prolific source for molecules of biotechnological interest. In particular, marine bacteria have attracted attention and were successfully exploited for industrial applications. Recently, a group of Pseudomonas species isolated from extreme habitats or living in association with algae or sponges were clustered in the newly established Pseudomonas pertucinogena lineage. Remarkably for the predominantly terrestrial genus Pseudomonas, more than half (9) of currently 16 species within this lineage were isolated from marine or saline habitats. Unlike other Pseudomonas species, they seem to have in common a highly specialized metabolism. Furthermore, the marine members apparently possess the capacity to produce biomolecules of biotechnological interest (e.g. dehalogenases, polyester hydrolases, transaminases). Here, we summarize the knowledge regarding the enzymatic endowment of the marine Pseudomonas pertucinogena bacteria and report on a genomic analysis focusing on the presence of genes encoding esterases, dehalogenases, transaminases and secondary metabolites including carbon storage compounds.
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Affiliation(s)
- Alexander Bollinger
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Stephan Thies
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Nadine Katzke
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich‐Heine‐University DüsseldorfForschungszentrum JülichD‐52425JülichGermany
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyForschungszentrum Jülich GmbHD‐52425JülichGermany
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23
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Wu JH, Chen WY, Kuo HC, Li YM. Redox fluctuations shape the soil microbiome in the hypoxic bioremediation of octachlorinated dibenzodioxin- and dibenzofuran-contaminated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 248:506-515. [PMID: 30831347 DOI: 10.1016/j.envpol.2019.02.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/16/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
The biodegradation of polychlorinated-p-dioxins and dibenzofurans (PCDD/Fs) has been recently demonstrated in a single reactor under hypoxic conditions. Maintaining hypoxic conditions through periodic aerations results in a marked fluctuation of reduction-oxidation (redox) potential. To further assess the effects of redox fluctuations, we operated two fed-batch continuously stirred tank reactors (CSTRs) with sophisticated redox controls at different anoxic/oxic fluctuations to reduce PCDD/Fs in contaminated soil. The results of long-term reactor operation showed that the CSTR with redox fluctuations at a narrow range (-63 ± 68 mV) (CSTR_A) revealed a higher substrate hydrolysis level and PCDD/F degradation rate than did the CSTR with a redox potential that fluctuated at a broad range (-13 ± 118 mV) (CSTR_B). In accordance with analyses of bacterial 16S rRNA genes, the designated hypoxic conditions with added compost supported survival of bacterial populations at a density of approximately 109 copies/g slurry. The evolved core microbiome was dominated by anoxic/oxic fluctuation-adapted Bacteroidetes, Alphaproteobacteria, and Actinobacteria, with higher species diversity and functionality, including hydrolysis and degradation of dioxin-like compounds in CSTR_A than in CSTR_B. Taken together, the overall results of this study expand the understanding of redox fluctuations in association with the degradation of recalcitrant substrates in soil and the corresponding microbiome.
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Affiliation(s)
- Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan.
| | - Wei-Yu Chen
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Hung-Chih Kuo
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Yun-Ming Li
- Mass Laboratory, National Chiao-Tung University, Hsinchu, Taiwan
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24
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Comparative Genomic Analysis of Lactobacillus plantarum: An Overview. Int J Genomics 2019; 2019:4973214. [PMID: 31093491 PMCID: PMC6481158 DOI: 10.1155/2019/4973214] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/19/2019] [Accepted: 03/12/2019] [Indexed: 01/21/2023] Open
Abstract
Background Lactobacillus plantarum is widely used in the manufacture of dairy products, fermented foods, and bacteriocins. The genomes of the strains contain multiple genes which may have been acquired by horizontal gene transfer. Many of these genes are important for the regulation, metabolism, and transport of various sugars; however, other genes may carry and spread virulence and antibiotic resistance determinants. In this way, monitoring these genomes is essential to the manufacture of food. In this study, we aim to provide an overview of the genomic properties of L. plantarum based on approaches of comparative genomics. Results The finding of the current study indicates that the core genome of L. plantarum presents 1425 protein-coding genes and is mostly related to the metabolic process. The accessory genome has on average 1320 genes that encodes protein involved in processes as the formation of bacteriocins, degradation of halogen, arsenic detoxification, and nisin resistance. Most of the strains show an ancestral synteny, similar to the one described in the genomes of L. pentosus KCA1 and L. plantarum WCFS1. The lifestyle island analyses did not show a pattern of arrangement or gene content according to habitat. Conclusions Our results suggest that there is a high rate of transfer of genetic material between the strains. We did not identify any virulence factors and antibiotic resistance genes on the genomes. Thus, the strains may be useful for the biotechnology, bioremediation, and production of bacteriocins. The potential applications are, however, restricted to particular strains.
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25
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Atashgahi S, Liebensteiner MG, Janssen DB, Smidt H, Stams AJM, Sipkema D. Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds. Front Microbiol 2018; 9:3079. [PMID: 30619161 PMCID: PMC6299022 DOI: 10.3389/fmicb.2018.03079] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/29/2018] [Indexed: 12/26/2022] Open
Abstract
Organic and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | | | - Dick B. Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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26
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Biodegradation of mono-, di- and trifluoroacetate by microbial cultures with different origins. N Biotechnol 2018; 43:23-29. [DOI: 10.1016/j.nbt.2017.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 05/10/2017] [Accepted: 08/14/2017] [Indexed: 02/07/2023]
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27
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Ang TF, Maiangwa J, Salleh AB, Normi YM, Leow TC. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications. Molecules 2018; 23:E1100. [PMID: 29735886 PMCID: PMC6100074 DOI: 10.3390/molecules23051100] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/07/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.
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Affiliation(s)
- Thiau-Fu Ang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Jonathan Maiangwa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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Tailoring cyanobacterial cell factory for improved industrial properties. Biotechnol Adv 2018; 36:430-442. [DOI: 10.1016/j.biotechadv.2018.01.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/07/2018] [Accepted: 01/08/2018] [Indexed: 11/20/2022]
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29
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Cuozzo SA, Sineli PE, Davila Costa J, Tortella G. Streptomyces sp. is a powerful biotechnological tool for the biodegradation of HCH isomers: biochemical and molecular basis. Crit Rev Biotechnol 2017; 38:719-728. [PMID: 29124958 DOI: 10.1080/07388551.2017.1398133] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Actinobacteria are well-known degraders of toxic materials that have the ability to tolerate and remove organochloride pesticides; thus, they are used for bioremediation. The biodegradation of organochlorines by actinobacteria has been demonstrated in pure and mixed cultures with the concomitant production of metabolic intermediates including γ-pentachlorocyclohexene (γ-PCCH); 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN); 1,2-dichlorobenzene (1,2-DCB), 1,3-dichlorobenzene (1,3-DCB), or 1,4-dichlorobenzene (1,4-DCB); 1,2,3-trichlorobenzene (1,2,3-TCB), 1,2,4-trichlorobenzene (1,2,4-TCB), or 1,3,5-trichlorobenzene (1,3,5-TCB); 1,3-DCB; and 1,2-DCB. Chromatography coupled to mass spectrometric detection, especially GC-MS, is typically used to determine HCH-isomer metabolites. The important enzymes involved in HCH isomer degradation metabolic pathways include hexachlorocyclohexane dehydrochlorinase (LinA), haloalkane dehalogenase (LinB), and alcohol dehydrogenase (LinC). The metabolic versatility of these enzymes is known. Advances have been made in the identification of actinobacterial haloalkane dehydrogenase, which is encoded by linB. This knowledge will permit future improvements in biodegradation processes using Actinobacteria. The enzymatic and genetic characterizations of the molecular mechanisms involved in these processes have not been fully elucidated, necessitating further studies. New advances in this area suggest promising results. The scope of this paper encompasses the following: (i) the aerobic degradation pathways of hexachlorocyclohexane (HCH) isomers; (ii) the important genes and enzymes involved in the metabolic pathways of HCH isomer degradation; and (iii) the identification and quantification of intermediate metabolites through gas chromatography coupled to mass spectrometry (GC-MS).
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Affiliation(s)
- S A Cuozzo
- a Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET) , Tucumán , Argentina.,b Facultad de Ciencias Naturales e Instituto Miguel Lillo , Universidad Nacional de Tucumán , Tucumán , Argentina
| | - P E Sineli
- a Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET) , Tucumán , Argentina
| | - J Davila Costa
- a Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET) , Tucumán , Argentina
| | - G Tortella
- c Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA) , Universidad de La Frontera , Temuco , Chile.,d Departamento de Ingeniería Química , Universidad de La Frontera , Temuco , Chile
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30
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Homogeneous and heterogeneous electrocatalytic reduction of halo-organic compounds by (NiIILi)2+ (Li= tetraaza-macrocyclic ligand) in aqueous solutions. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2017.06.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Wang JB, Ilie A, Yuan S, Reetz MT. Investigating Substrate Scope and Enantioselectivity of a Defluorinase by a Stereochemical Probe. J Am Chem Soc 2017; 139:11241-11247. [DOI: 10.1021/jacs.7b06019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jian-bo Wang
- Department
of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Adriana Ilie
- Department
of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Shuguang Yuan
- Laboratory
of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station
6, CH-1015 Lausanne, Switzerland
| | - Manfred T. Reetz
- Department
of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
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In silico characterization of a novel dehalogenase (DehHX) from the halophile Pseudomonas halophila HX isolated from Tuz Gölü Lake, Turkey: insights into a hypersaline-adapted dehalogenase. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1266-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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34
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Emma MG, Lombardo M, Trombini C, Quintavalla A. The Organocatalytic α-Fluorination of Chiral γ-Nitroaldehydes: the Challenge of Facing the Construction of a Quaternary Fluorinated Stereocenter. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600378] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marco Giuseppe Emma
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Marco Lombardo
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Claudio Trombini
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Arianna Quintavalla
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum; University of Bologna; Via Selmi 2 40126 Bologna Italy
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35
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Adamu A, Wahab RA, Huyop F. l-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1. SPRINGERPLUS 2016; 5:695. [PMID: 27347470 PMCID: PMC4899344 DOI: 10.1186/s40064-016-2328-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 05/11/2016] [Indexed: 11/10/2022]
Abstract
l-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1 is a stereospecific enzyme that acts exclusively on l-isomers of 2-chloropropionate and dichloroacetate. The amino acid sequence of this enzyme is substantially different from those of other l-specific dehalogenases produced by other organisms. DehL has not been crystallised, and hence its three-dimensional structure is unavailable. Herein, we review what is known concerning DehL and tentatively identify the amino acid residues important for catalysis based on a comparative structural and sequence analysis with well-characterised l-specific dehalogenases.
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Affiliation(s)
- Aliyu Adamu
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Baharu, Johor Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Baharu, Johor Malaysia
| | - Fahrul Huyop
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Baharu, Johor Malaysia
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36
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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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37
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Wang Y, Cao X, Feng Y, Xue S. Environment-induced conformational and functional changes of L-2-haloacid dehalogenase. J Biosci Bioeng 2015; 121:491-6. [PMID: 26508534 DOI: 10.1016/j.jbiosc.2015.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/11/2015] [Accepted: 09/11/2015] [Indexed: 11/29/2022]
Abstract
2-Haloacid dehalogenases have been highly studied due to their potential applications in chemical industries and bioremediation. Although biochemical and structural characterizations of the enzyme have been detailed, no information was available regarding environmental effects on the structure-function relationship. Here, circular dichroism spectroscopy (CD) was used to investigate the correlation between changes on the conformation and the function of l-2-haloacid dehalogenase (HadL AJ1) from the Pseudomonas putida induced by the environmental factors. Decreased α-helix and increased β-sheet contents were observed in the structure of HadL AJ1 along with activity losses caused by pH, temperature and inhibitors. Regardless of which factor above-mentioned existed, more than 65.0% of HadL AJ1 activity could be remained if its α-helix content was over 12.0%. The maintenance of α-helical structure in HadL AJ1 was indispensable to its catalysis, while β-sheet increase restricts its activity. This study revealed the variation of enzymatic activity due to environmental conditions resulting in structural changes monitored by CD, which contributed to rational modification and was instructive for predicting changes of the enzymatic activity during application.
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Affiliation(s)
- Yayue Wang
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xupeng Cao
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yanbin Feng
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Song Xue
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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38
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Properties and biotechnological applications of natural and engineered haloalkane dehalogenases. Appl Microbiol Biotechnol 2015; 99:9865-81. [DOI: 10.1007/s00253-015-6954-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/19/2015] [Accepted: 08/22/2015] [Indexed: 01/01/2023]
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39
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Miranda-Rojas S, Toro-Labbé A. Mechanistic insights into the dehalogenation reaction of fluoroacetate/fluoroacetic acid. J Chem Phys 2015; 142:194301. [PMID: 26001455 DOI: 10.1063/1.4920946] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Fluoroacetate is a toxic compound whose environmental accumulation may represent an important contamination problem, its elimination is therefore a challenging issue. Fluoroacetate dehalogenase catalyzes its degradation through a two step process initiated by an S(N)2 reaction in which the aspartate residue performs a nucleophilic attack on the carbon bonded to the fluorine; the second step is hydrolysis that releases the product as glycolate. In this paper, we present a study based on density functional theory calculations of the S(N)2 initiation reaction modeled through the interaction between the substrate and the propionate anion as the nucleophile. Results are analyzed within the framework of the reaction force and using the reaction electronic flux to identify and characterize the electronic activity that drives the reaction. Our results reveal that the selective protonation of the substrate catalyzes the reaction by decreasing the resistance of the structural and electronic reorganization needed to reach the transition state. Finally, the reaction energy is modulated by the degree of stabilization of the fluoride anion formed after the S(N)2 reaction. In this way, a site-induced partial protonation acts as a chemical switch in a key process that determines the output of the reaction.
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Affiliation(s)
- Sebastián Miranda-Rojas
- Chemical Processes and Catalysis (CPC), Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Avenida República 275, Santiago, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, Santiago, Chile
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40
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Tanaka S, Mochizuki Y, Komeiji Y, Okiyama Y, Fukuzawa K. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Phys Chem Chem Phys 2015; 16:10310-44. [PMID: 24740821 DOI: 10.1039/c4cp00316k] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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41
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Sudi IY, Shamsir MS, Jamaluddin H, Wahab RA, Huyop F. Interactions of non-natural halogenated substrates with D-specific dehalogenase (DehD) mutants using in silico studies. BIOTECHNOL BIOTEC EQ 2014; 28:949-957. [PMID: 26019583 PMCID: PMC4433833 DOI: 10.1080/13102818.2014.960663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 07/17/2014] [Indexed: 10/26/2022] Open
Abstract
The D-2-haloacid dehalogenase of D-specific dehalogenase (DehD) from Rhizobium sp. RC1 catalyses the hydrolytic dehalogenation of D-haloalkanoic acids, inverting the substrate-product configuration and thereby forming the corresponding L-hydroxyalkanoic acids. Our investigations were focused on DehD mutants: R134A and Y135A. We examined the possible interactions between these mutants with haloalkanoic acids and characterized the key catalytic residues in the wild-type dehalogenase, to design dehalogenase enzyme(s) with improved potential for dehalogenation of a wider range of substrates. Three natural substrates of wild-type DehD, specifically, monochloroacetate, monobromoacetate and D,L-2,3-dichloropropionate, and eight other non-natural haloalkanoic acids substrates of DehD, namely, L-2-chloropropionate; L-2-bromopropionate; 2,2-dichloropropionate; dichloroacetate; dibromoacetate; trichloroacetate; tribromoacetate; and 3-chloropropionate, were docked into the active site of the DehD mutants R134A and Y135A, which produced altered catalytic functions. The mutants interacted strongly with substrates that wild-type DehD does not interact with or degrade. The interaction was particularly enhanced with 3-chloropropionate, in addition to monobromoacetate, monochloroacetate and D,L-2,3-dichloropropionate. In summary, DehD variants R134A and Y135A demonstrated increased propensity for binding haloalkanoic acid and were non-stereospecific towards halogenated substrates. The improved characteristics in these mutants suggest that their functionality could be further exploited and harnessed in bioremediations and biotechnological applications.
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Affiliation(s)
- Ismaila Yada Sudi
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Mohd Shahir Shamsir
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Haryati Jamaluddin
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Fahrul Huyop
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
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42
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Skopelitou K, Georgakis N, Efrose R, Flemetakis E, Labrou NE. Sol–gel immobilization of haloalkane dehalogenase from Bradyrhizobium japonicum for the remediation 1,2-dibromoethane. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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43
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Hasan K, Gora A, Brezovsky J, Chaloupkova R, Moskalikova H, Fortova A, Nagata Y, Damborsky J, Prokop Z. The effect of a unique halide-stabilizing residue on the catalytic properties of haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58. FEBS J 2013; 280:3149-59. [PMID: 23490078 DOI: 10.1111/febs.12238] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/05/2013] [Accepted: 03/06/2013] [Indexed: 11/28/2022]
Abstract
Haloalkane dehalogenases catalyze the hydrolysis of carbon-halogen bonds in various chlorinated, brominated and iodinated compounds. These enzymes have a conserved pair of halide-stabilizing residues that are important in substrate binding and stabilization of the transition state and the halide ion product via hydrogen bonding. In all previously known haloalkane dehalogenases, these residues are either a pair of tryptophans or a tryptophan-asparagine pair. The newly-isolated haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 (EC 3.8.1.5) possesses a unique halide-stabilizing tyrosine residue, Y109, in place of the conventional tryptophan. A variant of DatA with the Y109W mutation was created and the effects of this mutation on the structure and catalytic properties of the enzyme were studied using spectroscopy and pre-steady-state kinetic experiments. Quantum mechanical and molecular dynamics calculations were used to obtain a detailed analysis of the hydrogen-bonding patterns within the active sites of the wild-type and the mutant, as well as of the stabilization of the ligands as the reaction proceeds. Fluorescence quenching experiments suggested that replacing the tyrosine with tryptophan improves halide binding by 3.7-fold, presumably as a result of the introduction of an additional hydrogen bond. Kinetic analysis revealed that the mutation affected the substrate specificity of the enzyme and reduced its K(0.5) for selected halogenated substrates by a factor of 2-4, without impacting the rate-determining hydrolytic step. We conclude that DatA is the first natural haloalkane dehalogenase that stabilizes its substrate in the active site using only a single hydrogen bond, which is a new paradigm in catalysis by this enzyme family.
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Affiliation(s)
- Khomaini Hasan
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
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Nikel PI, Pérez-Pantoja D, de Lorenzo V. Why are chlorinated pollutants so difficult to degrade aerobically? Redox stress limits 1,3-dichloroprop-1-ene metabolism by Pseudomonas pavonaceae. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120377. [PMID: 23479756 DOI: 10.1098/rstb.2012.0377] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chlorinated pollutants are hardly biodegradable under oxic conditions, but they can often be metabolized by anaerobic bacteria through organohalide respiration reactions. In an attempt to identify bottlenecks limiting aerobic catabolism of 1,3-dichloroprop-1-ene (1,3-DCP; a widely used organohalide) in Pseudomonas pavonaceae, the possible physiological restrictions for this process were surveyed. Flow cytometry and a bioluminescence reporter of metabolic state revealed that cells treated with 1,3-DCP experienced an intense stress that could be traced to the endogenous production of reactive oxygen species (ROS) during the metabolism of the compound. Cells exposed to 1,3-DCP also manifested increased levels of D-glucose-6-P 1-dehydrogenase activity (G6PDH, an enzyme key to the synthesis of reduced NADPH), observed under both glycolytic and gluconeogenic growth regimes. The increase in G6PDH activity, as well as cellular hydroperoxide levels, correlated with the generation of ROS. Additionally, the high G6PDH activity was paralleled by the accumulation of D-glucose-6-P, suggesting a metabolic flux shift that favours the production of NADPH. Thus, G6PDH and its cognate substrate seem to play an important role in P. pavonaceae under redox stress caused by 1,3-DCP, probably by increasing the rate of NADPH turnover. The data suggest that oxidative stress associated with the biodegradation of 1,3-DCP reflects a significant barrier for the evolution of aerobic pathways for chlorinated compounds, thereby allowing for the emergence of anaerobic counterparts.
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Affiliation(s)
- Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid 28049, Spain
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Bagherbaigi S, Gicana RG, Lamis RJ, Nemati M, Huyop F. Characterisation of Arthrobacter sp. S1 that can degrade α and β-haloalkanoic acids isolated from contaminated soil. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-012-0595-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Velazquez F, Peak-Chew SY, Fernández IS, Neumann CS, Kay RR. Identification of a eukaryotic reductive dechlorinase and characterization of its mechanism of action on its natural substrate. ACTA ACUST UNITED AC 2012; 18:1252-60. [PMID: 22035794 PMCID: PMC3205185 DOI: 10.1016/j.chembiol.2011.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/05/2011] [Accepted: 08/08/2011] [Indexed: 12/14/2022]
Abstract
Chlorinated compounds are important environmental pollutants whose biodegradation may be limited by inefficient dechlorinating enzymes. Dictyostelium amoebae produce a chlorinated alkyl phenone called DIF which induces stalk cell differentiation during their multicellular development. Here we describe the identification of DIF dechlorinase. DIF dechlorinase is active when expressed in bacteria, and activity is lost from Dictyostelium cells when its gene, drcA, is knocked out. It has a Km for DIF of 88 nM and Kcat of 6.7 s−1. DrcA is related to glutathione S-transferases, but with a key asparagine-to-cysteine substitution in the catalytic pocket. When this change is reversed, the enzyme reverts to a glutathione S-transferase, thus suggesting a catalytic mechanism. DrcA offers new possibilities for the rational design of bioremediation strategies.
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Affiliation(s)
- Francisco Velazquez
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK.
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Bachelor MA, Lu Y, Owens DM. L-3-Phosphoserine phosphatase (PSPH) regulates cutaneous squamous cell carcinoma proliferation independent of L-serine biosynthesis. J Dermatol Sci 2011; 63:164-72. [PMID: 21726982 DOI: 10.1016/j.jdermsci.2011.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/19/2011] [Accepted: 06/02/2011] [Indexed: 11/17/2022]
Abstract
BACKGROUND L-3-Phosphoserine phosphatase (PSPH) is a highly conserved and widely expressed member of the haloacid dehalogenase superfamily and the rate-limiting enzyme in l-serine biosynthesis. We previously found Psph expression to be uniquely upregulated in a α6β4 integrin transgenic mouse model that is predisposed to epidermal hyperproliferation and squamous cell carcinoma (SCC) formation implicating a role for Psph in epidermal homeostasis. OBJECTIVE We examined the status of PSPH in normal skin epidermis and skin tumors along with its sub-cellular localization in epidermal keratinocytes and its requirement for squamous cell carcinoma (SCC) proliferation. METHODS First, an immunohistochemical study was performed for PSPH in normal skin and skin cancer specimens and in cultured keratinocytes. Next, biochemical analyses were performed to confirm localization of PSPH and to identify candidate binding proteins. Finally, proliferation and apoptosis studies were performed in human SCC and normal keratinocytes, respectively, transduced with vectors encoding small hairpin RNAs targeting PSPH or overexpressing a phosphatase-deficient PSPH mutant. RESULTS PSPH is expressed throughout the proliferative layer of the epidermis and hair follicles in rodent and human skin and is highly induced in SCC. In keratinocytes, PSPH is a cytoplasmic protein that primarily localizes to endosomes and is present primarily as a homodimer. Knock down of PSPH dramatically diminished SCC cell proliferation and cyclin D1 levels in the presence of exogenous of l-serine production suggesting a non-canonical role for PSPH in epithelial carcinogenesis. CONCLUSIONS Psph is highly induced in proliferative normal keratinocytes and in skin tumors. PSPH appears to be critical for the proliferation of SCC cells; however, this phenomenon may not involve the phosphoserine metabolic pathway.
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Affiliation(s)
- Michael A Bachelor
- Department of Dermatology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
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Chan PWY, Yakunin AF, Edwards EA, Pai EF. Mapping the reaction coordinates of enzymatic defluorination. J Am Chem Soc 2011; 133:7461-8. [PMID: 21510690 DOI: 10.1021/ja200277d] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The carbon-fluorine bond is the strongest covalent bond in organic chemistry, yet fluoroacetate dehalogenases can readily hydrolyze this bond under mild physiological conditions. Elucidating the molecular basis of this rare biocatalytic activity will provide the fundamental chemical insights into how this formidable feat is achieved. Here, we present a series of high-resolution (1.15-1.80 Å) crystal structures of a fluoroacetate dehalogenase, capturing snapshots along the defluorination reaction: the free enzyme, enzyme-fluoroacetate Michaelis complex, glycolyl-enzyme covalent intermediate, and enzyme-product complex. We demonstrate that enzymatic defluorination requires a halide pocket that not only supplies three hydrogen bonds to stabilize the fluoride ion but also is finely tailored for the smaller fluorine halogen atom to establish selectivity toward fluorinated substrates. We have further uncovered dynamics near the active site which may play pivotal roles in enzymatic defluorination. These findings may ultimately lead to the development of novel defluorinases that will enable the biotransformation of more complex fluorinated organic compounds, which in turn will assist the synthesis, detoxification, biodegradation, disposal, recycling, and regulatory strategies for the growing markets of organofluorines across major industrial sectors.
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Affiliation(s)
- Peter W Y Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Lin C, Yang L, Xu G, Wu J. Biodegradation and metabolic pathway of β-chlorinated aliphatic acid in Bacillus sp. CGMCC no. 4196. Appl Microbiol Biotechnol 2011; 90:689-96. [PMID: 21210101 DOI: 10.1007/s00253-010-3081-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Revised: 12/17/2010] [Accepted: 12/19/2010] [Indexed: 10/18/2022]
Abstract
In this study, a bacterial Bacillus sp. CGMCC no. 4196 was isolated from mud. This strain exhibited the ability to degrade high concentration of 3-chloropropionate (3-CPA, 120 mM) or 3-chlorobutyrate (30 mM), but not chloroacetate or 2-chloropropionate (2-CPA). The growing cells, resting cells, and cell-free extracts from this bacterium had the capability of 3-CPA degradation. The results indicated that the optimum biocatalyst for 3-CPA biodegradation was the resting cells. The 3-CPA biodegradation pathway was further studied through the metabolites and critical enzymes analysis by HPLC, LC-MS, and colorimetric method. The results demonstrated that the metabolites of 3-CPA were 3-hydroxypropionic acid (3-HP) and malonic acid semialdehyde, and the critical enzymes were 3-CPA dehalogenase and 3-HP dehydroxygenase. Thus, the mechanism of the dehalogenase-catalyzed reaction was inferred as hydrolytic dehalogenation which was coenzyme A-independent and oxygen-independent. Finally, the pathway of β-chlorinated aliphatic acid biodegradation could be concluded as follows: the β-chlorinated acid is first hydrolytically dehalogenated to the β-hydroxyl aliphatic acid, and the hydroxyl aliphatic acid is oxidized to β-carbonyl aliphatic acid by β-hydroxy aliphatic acid dehydroxygenase. It is the first report that 3-HP was produced from 3-CPA by β-chlorinated aliphatic acid dehalogenase.
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Affiliation(s)
- Chunjiao Lin
- Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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Huang J, Xin Y, Cao X, Zhang W. Phylogenetic diversity and characterization of 2-haloacid degrading bacteria from the marine sponge Hymeniacidon perlevis. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-010-0636-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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