1
|
Petkowski JJ, Seager S, Bains W. Reasons why life on Earth rarely makes fluorine-containing compounds and their implications for the search for life beyond Earth. Sci Rep 2024; 14:15575. [PMID: 38971876 PMCID: PMC11227584 DOI: 10.1038/s41598-024-66265-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024] Open
Abstract
Life on Earth is known to rarely make fluorinated carbon compounds, as compared to other halocarbons. We quantify this rarity, based on our exhaustive natural products database curated from available literature. We build on explanations for the scarcity of fluorine chemistry in life on Earth, namely that the exclusion of the C-F bond stems from the unique physico-chemical properties of fluorine, predominantly its extreme electronegativity and strong hydration shell. We further show that the C-F bond is very hard to synthesize and when it is made by life its potential biological functions can be readily provided by alternative functional groups that are much less costly to incorporate into existing biochemistry. As a result, the overall evolutionary cost-to-benefit balance of incorporation of the C-F bond into the chemical repertoire of life is not favorable. We argue that the limitations of organofluorine chemistry are likely universal in that they do not exclusively apply to specifics of Earth's biochemistry. C-F bonds, therefore, will be rare in life beyond Earth no matter its chemical makeup.
Collapse
Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Faculty of Environmental Engineering, Wroclaw University of Science and Technology, 50-370, Wroclaw, Poland.
- JJ Scientific, Warsaw, Mazowieckie, Poland.
| | - Sara Seager
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - William Bains
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- School of Physics & Astronomy, Cardiff University, 4 The Parade, Cardiff, CF24 3AA, UK
- Rufus Scientific, Melbourn, Royston, Herts, UK
| |
Collapse
|
2
|
Dong S, Yan PF, Mezzari MP, Abriola LM, Pennell KD, Cápiro NL. Using Network Analysis and Predictive Functional Analysis to Explore the Fluorotelomer Biotransformation Potential of Soil Microbial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7480-7492. [PMID: 38639388 DOI: 10.1021/acs.est.4c00942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Microbial transformation of per- and polyfluoroalkyl substances (PFAS), including fluorotelomer-derived PFAS, by native microbial communities in the environment has been widely documented. However, few studies have identified the key microorganisms and their roles during the PFAS biotransformation processes. This study was undertaken to gain more insight into the structure and function of soil microbial communities that are relevant to PFAS biotransformation. We collected 16S rRNA gene sequencing data from 8:2 fluorotelomer alcohol and 6:2 fluorotelomer sulfonate biotransformation studies conducted in soil microcosms under various redox conditions. Through co-occurrence network analysis, several genera, including Variovorax, Rhodococcus, and Cupriavidus, were found to likely play important roles in the biotransformation of fluorotelomers. Additionally, a metagenomic prediction approach (PICRUSt2) identified functional genes, including 6-oxocyclohex-1-ene-carbonyl-CoA hydrolase, cyclohexa-1,5-dienecarbonyl-CoA hydratase, and a fluoride-proton antiporter gene, that may be involved in defluorination. This study pioneers the application of these bioinformatics tools in the analysis of PFAS biotransformation-related sequencing data. Our findings serve as a foundational reference for investigating enzymatic mechanisms of microbial defluorination that may facilitate the development of efficient microbial consortia and/or pure microbial strains for PFAS biotransformation.
Collapse
Affiliation(s)
- Sheng Dong
- Department of Biological and Environmental Engineering, Cornell University, 214 Riley-Robb Hall, 111 Wing Drive, Ithaca, New York 14853, United States
| | - Peng-Fei Yan
- Department of Biological and Environmental Engineering, Cornell University, 214 Riley-Robb Hall, 111 Wing Drive, Ithaca, New York 14853, United States
| | - Melissa P Mezzari
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Linda M Abriola
- School of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Kurt D Pennell
- School of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Natalie L Cápiro
- Department of Biological and Environmental Engineering, Cornell University, 214 Riley-Robb Hall, 111 Wing Drive, Ithaca, New York 14853, United States
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Pimviriyakul P, Chaiyen P. Formation and stabilization of C4a-hydroperoxy-FAD by the Arg/Asn pair in HadA monooxygenase. FEBS J 2023; 290:176-195. [PMID: 35942637 DOI: 10.1111/febs.16591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/25/2022] [Accepted: 08/08/2022] [Indexed: 01/14/2023]
Abstract
HadA monooxygenase catalyses the detoxification of halogenated phenols and nitrophenols via dehalogenation and denitration respectively. C4a-hydroperoxy-FAD is a key reactive intermediate wherein its formation, protonation and stabilization reflect enzyme efficiency. Herein, transient kinetics, site-directed mutagenesis and pH-dependent behaviours of HadA reaction were employed to identify key features stabilizing C4a-adducts in HadA. The formation of C4a-hydroperoxy-FAD is pH independent, whereas its decay and protonation of distal oxygen are associated with pKa values of 8.5 and 8.4 respectively. These values are correlated with product formation within a pH range of 7.6-9.1, indicating the importance of adduct stabilization to enzymatic efficiency. We identified Arg101 as a key residue for reduced FAD (FADH- ) binding and C4a-hydroperoxy-FAD formation due to the loss of these abilities as well as enzyme activity in HadAR101A and HadAR101Q . Mutations of the neighbouring Asn447 do not affect the rate of C4a-hydroperoxy-FAD formation; however, they impair FADH- binding. The disruption of Arg101/Asn447 hydrogen bond networking in HadAN447A increases the pKa value of C4a-hydroperoxy-FAD decay to 9.5; however, this pKa was not altered in HadAN447D (pKa of 8.5). Thus, Arg101/Asn447 pair should provide important interactions for FADH- binding and maintain the pKa associated with H2 O2 elimination from C4a-hydroperoxy-FAD in HadA. In the presence of substrate, the formation of C4a-hydroxy-FAD at the hydroxylation step is pH insensitive, and it dehydrates to form the oxidized FAD with pKa of 7.9. This structural feature might help elucidate how the reactive intermediate was stabilized in other flavin-dependent monooxygenases.
Collapse
Affiliation(s)
- Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| |
Collapse
|
5
|
Pimviriyakul P, Pholert P, Somjitt S, Choowongkomon K. Role of conserved arginine in
HadA
monooxygenase for
4‐nitrophenol
and
4‐chlorophenol
detoxification. Proteins 2022; 90:1291-1302. [DOI: 10.1002/prot.26312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/18/2022]
Affiliation(s)
- Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
| | - Patipan Pholert
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
| | - Supamas Somjitt
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science Kasetsart University Chatuchak Bangkok Thailand
| |
Collapse
|
6
|
Wang L, Peng R, Tian Y, Xu J, Wang B, Han H, Fu X, Gao J, Yao Q. Metabolic engineering of Escherichia coli for efficient degradation of 4-fluorophenol. AMB Express 2022; 12:55. [PMID: 35567640 PMCID: PMC9107566 DOI: 10.1186/s13568-022-01396-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/04/2022] [Indexed: 11/10/2022] Open
Abstract
As a kind of refractory organic pollutant, 4-fluorophenol (4-FP) can be degraded by only a few microorganisms with low efficiency because of the great electron-withdrawing ability of fluorine atoms. So it is necessary to artificially construct engineered strain to improve the degradation efficiency and meet the requirements of pollutant degradation. In this study, four genes (fpdA2, fpdB, fpdC, and fpdD) for 4-FP degradation from Arthrobacter sp. strain IF1 were optimized and synthesized and then reconstructed into Escherichia coli by a multi-monocistronic vector to obtain recombinant BL-fpd that could degrade 4-FP efficiently. Under optimized induction conditions (inducing the strain by 2 g/L L-arabinose and 1 mM IPTG at 37 ℃), BL-fpd could completely degrade 2 mM 4-FP, 4-chlorophenol, 4-bromophenol, and 4-nitrophenol into β-ketoadipate, which could be further metabolized by the bacteria. FpdA2 showed the highest activity towards 4-bromophenol. The strain could completely degrade 1 mM 4-FP in industrial wastewater within 3 h. This study provided a promising strain for the degradation of 4-FP and some other 4-substituted phenols. The construction technologies of multi-monocistronic expression vector may also be used to construct other organic pollutants degrading bacteria.
Collapse
Affiliation(s)
- Lijuan Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Rihe Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Yongsheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Jing Xu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Bo Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Hongjuan Han
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Xiaoyan Fu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
| | - Jianjie Gao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China.
| | - Quanhong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China.
| |
Collapse
|
7
|
Characterization of the 2,6-Dimethylphenol Monooxygenase MpdAB and Evaluation of Its Potential in Vitamin E Precursor Synthesis. Appl Environ Microbiol 2022; 88:e0011022. [PMID: 35380460 DOI: 10.1128/aem.00110-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2,6-Dimethylphenol (2,6-DMP) is a widely used chemical intermediate whose residue has been frequently detected in the environment, posing a threat to some aquatic organisms. Microbial degradation is an effective method to eliminate 2,6-DMP in nature. However, the genetic and biochemical mechanisms of 2,6-DMP metabolism remain unknown. Mycobacterium neoaurum B5-4 is a 2,6-DMP-degrading bacterium isolated in our previous study. Here, a 2,6-DMP degradation-deficient mutant of strain B5-4 was screened. Comparative genomic, transcriptomic, gene disruption, and genetic complementation data indicated that mpdA and mpdB are responsible for the initial step of 2,6-DMP degradation in M. neoaurum B5-4. MpdAB was predicted to be a two-component flavin-dependent monooxygenase system, which shows 32% and 36% identities with HsaAB from Mycobacterium tuberculosis CDC1551. The transcription of mpdA and mpdB was substantially increased upon exposure to 2,6-DMP. Nuclear magnetic resonance analysis showed that purified 6×His-MpdA and 6×His-MpdB hydroxylated 2,6-DMP and 2,3,6-trimethylphenol (2,3,6-TMP) at the para-position using NADH and flavin adenine dinucleotide (FAD) as cofactors. The apparent Km values of MpdAB for 2,6-DMP and 2,3,6-TMP were 0.12 ± 0.01 and 0.17 ± 0.01 mM, respectively, and the corresponding kcat/Km values were 4.02 and 2.84 s-1 mM-1, respectively. Since para-hydroxylated 2,3,6-TMP is a major precursor for vitamin E synthesis, the potential of MpdAB in vitamin E synthesis was preliminarily evaluated using whole-cell catalysis. Low expression levels of MpdA and 2,3,6-TMP cytotoxicity limited the efficiency of whole-cell catalysis. Together, this study reveals the genetic and biochemical basis for the initial step of 2,6-DMP biodegradation and provides candidate enzymes for vitamin E synthesis. IMPORTANCE Although the microbial degradation of the six isomers of dimethylphenol has been extensively studied, the genetic and biochemical mechanisms of 2,6-DMP degradation remain unclear. This study identified the genes responsible for the initial step in the 2,6-DMP catabolic pathway in M. neoaurum B5-4. Moreover, MpdAB also catalyzed the transformation of 2,3,6-TMP to 2,3,5-trimethylhydroquinone (2,3,5-TMHQ), a crucial step in vitamin E synthesis. Overall, this study provides candidate enzymes for both the bioremediation of 2,6-DMP contamination and the development of a green method to synthesize vitamin E.
Collapse
|
8
|
Bygd MD, Aukema KG, Richman JE, Wackett LP. Unexpected Mechanism of Biodegradation and Defluorination of 2,2-Difluoro-1,3-Benzodioxole by Pseudomonas putida F1. mBio 2021; 12:e0300121. [PMID: 34781746 PMCID: PMC8593668 DOI: 10.1128/mbio.03001-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Perfluorinated carbon atoms in a diether linkage are common in commercial anesthetics, drugs, fungicides, and insecticides. An important chemical group comprising perfluorodiethers is the 2,2-fluoro-1,3-benzodioxole (DFBD) moiety. The fluorine atoms stabilize the molecule by mitigating against metabolism by humans and microbes, as used in drugs and pesticides, respectively. Pseudomonas putida F1 catalyzed defluorination of DFBD at an initial rate of 2,100 nmol/h per mg cellular protein. This is orders of magnitude higher than previously reported microbial defluorination rates with multiply fluorinated carbon atoms. Defluorination rates declined after several hours, and the medium darkened. Significant defluorination activity was observed with cells grown on toluene but not l-arginine. Defluorination required only toluene dioxygenase. Pseudomonas and recombinant Escherichia coli cells expressing toluene dioxygenase oxidized DFBD to DFBD-4,5-dihydrodiol. The dihydrodiol could be oxidized to 4,5-dihydroxy-DFBD via the dihydrodiol dehydrogenase from P. putida F1. The dihydrodiol dehydrated with acid to yield a mixture of 4-hydroxy-DFBD and 5-hydroxy-DFBD. All those metabolites retained the difluoromethylene group; no fluoride or dark color was observed. The major route of DFBD-4,5-dihydrodiol decomposition produced fluoride and 1,2,3-trihydroxybenzene, or pyrogallol, and that was shown to be the source of the dark colors in the medium. A mechanism for DFBD-4,5-dihydrodiol transformation to two fluoride ions and pyrogallol is proposed. The Pseudomonas genome database and other databases revealed hundreds of bacteria with enzymes sharing high amino acid sequence identity to toluene dioxygenase from P. putida F1, suggesting the mechanism revealed here may apply to the defluorination of DFBD-containing compounds in the environment. IMPORTANCE There are more than 9,000 polyfluorinated compounds developed for commercial use, some negatively impacting human health, and they are generally considered to be resistant to biodegradation. Only a limited number of studies have identified microbes with enzymes sufficiently reactive to defluorinate difluoromethylene carbon groups. The present study examined one important group of commercial fluorinated chemicals and showed its rapid defluorination by a bacterium and its key enzyme, a Rieske dioxygenase. Rieske dioxygenases are common in environmental bacteria, and those closely resembling toluene dioxygenase from Pseudomonas putida F1 are candidates for biodegradative defluorination of the common 2,2-fluoro-1,3-benzodioxole (DFBD) moiety.
Collapse
Affiliation(s)
- Madison D. Bygd
- Microbial Engineering, University of Minnesota, St. Paul, Minnesota, USA
| | - Kelly G. Aukema
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Jack E. Richman
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Lawrence P. Wackett
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| |
Collapse
|
9
|
Maucourt B, Vuilleumier S, Bringel F. Transcriptional regulation of organohalide pollutant utilisation in bacteria. FEMS Microbiol Rev 2020; 44:189-207. [PMID: 32011697 DOI: 10.1093/femsre/fuaa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.
Collapse
Affiliation(s)
- Bruno Maucourt
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Stéphane Vuilleumier
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Françoise Bringel
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| |
Collapse
|
10
|
Biodiversity, isolation and genome analysis of sulfamethazine-degrading bacteria using high-throughput analysis. Bioprocess Biosyst Eng 2020; 43:1521-1531. [PMID: 32303845 DOI: 10.1007/s00449-020-02345-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/03/2020] [Indexed: 12/14/2022]
Abstract
Sulfamethazine (SM2) is one of the sulfonamide antibiotics that is frequently detected in aquatic environment. Given the complex structure of SM2 and its potential threat to the environment, it is necessary to determine the degradation behavior of high-concentration SM2. The mechanisms of community structure and diversity of activated sludge were analyzed. A novel SM2-degrading strain YL1 was isolated which can degrade SM2 with high concentration of 100 mg L-1. Strain YL1 was identified as Paenarthrobacter ureafaciens and there was also a significant increase in the genus during acclimation. Additional SM2 metabolic mechanisms and genomic information of YL1 were analyzed for further research. The succession of the community structure also investigated the effect of SM2 on the activated sludge. This result not only advances the current understanding of microbial ecology in activated sludge, but also has practical implications for the design and operation of the environmental bioprocesses for treatment of antimicrobial-bearing waste streams.
Collapse
|
11
|
Pongpamorn P, Watthaisong P, Pimviriyakul P, Jaruwat A, Lawan N, Chitnumsub P, Chaiyen P. Identification of a Hotspot Residue for Improving the Thermostability of a Flavin‐Dependent Monooxygenase. Chembiochem 2019; 20:3020-3031. [DOI: 10.1002/cbic.201900413] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Pornkanok Pongpamorn
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Pratchaya Watthaisong
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Panu Pimviriyakul
- Department of BiotechnologyFaculty of Engineering and Industrial TechnologySilpakorn University 6 Rajamankha Nai Road Nakornpathom 73000 Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Paholyothin Road Klong 1 Klong Luang Pathumthani 12120 Thailand
| | - Narin Lawan
- Department of ChemistryFaculty of ScienceChiang Mai University Chiang Mai 50200 Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Paholyothin Road Klong 1 Klong Luang Pathumthani 12120 Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| |
Collapse
|
12
|
Zhang H, Yu T, Wang Y, Li J, Wang G, Ma Y, Liu Y. 4-Chlorophenol Oxidation Depends on the Activation of an AraC-Type Transcriptional Regulator, CphR, in Rhodococcus sp. Strain YH-5B. Front Microbiol 2018; 9:2481. [PMID: 30405555 PMCID: PMC6205950 DOI: 10.3389/fmicb.2018.02481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/28/2018] [Indexed: 11/13/2022] Open
Abstract
4-Chlorophenol (4-CP) oxidation plays an essential role in the detoxification of 4-CP. However, oxidative regulation of 4-CP at the genetic and biochemical levels has not yet been studied. To explore the regulation mechanism of 4-CP oxidation, a novel gene cluster, cphRA2A1, involved in biodegradation of 4-CP was identified and cloned from Rhodococcus sp. strain YH-5B by genome walking. The sequence analysis showed that the cphRA2A1 gene cluster encoded an AraC-type transcriptional regulator and a two-component monooxygenase enzyme, while quantitative real-time PCR analysis further revealed that cphR was constitutively expressed and positively regulated the transcription of cphA2A1 genes in response to 4-CP or phenol, as evidenced by gene knockout and complementation experiments. Through the transcriptional fusion of the mutated cphA2A1 promoter with the lacZ gene, it was found that the CphR regulator binding sites had two 15-bp imperfect direct repeats (TGCA-N6-GGNTA) at -35 to -69 upstream of the cphA2A1 transcriptional start site. Notably, the sub-motifs at the -46 to -49 positions played a critical role in the appropriate interaction with the CphR dimer. In addition, it was confirmed that the monooxygenase subunits CphA1 and CphA2, which were purified by His-tag affinity chromatography, were able to catalyze the conversion of 4-CP to 4-chlorocatechol, suggesting that strain YH-5B could degrade 4-CP via the 4-chlorocatechol pathway. This study enhances our understanding of the genetic and biochemical diversity in the transcriptional regulation of 4-CP oxidation in Gram-positive bacteria.
Collapse
Affiliation(s)
- Hui Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Ting Yu
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Yiran Wang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Jie Li
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Guangli Wang
- College of Life Sciences, Huaibei Normal University, Huaibei, China
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Yingqun Ma
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
| | - Yu Liu
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
13
|
Ren L, Jia Y, Zhang R, Lin Z, Zhen Z, Hu H, Yan Y. Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1. Front Microbiol 2018; 9:2438. [PMID: 30364317 PMCID: PMC6193132 DOI: 10.3389/fmicb.2018.02438] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/24/2018] [Indexed: 01/11/2023] Open
Abstract
The genus Arthrobacter is ubiquitously distributed in different natural environments. Many xenobiotic-degrading Arthrobacter strains have been isolated and described; however, few have been systematically characterized with regard to multiple interrelated metabolic pathways and the genes that encode them. In this study, the biodegradability of seven aromatic compounds by Arthrobacter sp. YC-RL1 was investigated. Strain YC-RL1 could efficiently degrade p-xylene (PX), naphthalene, phenanthrene, biphenyl, p-nitrophenol (PNP), and bisphenol A (BPA) under both separated and mixed conditions. Based on the detected metabolic intermediates, metabolic pathways of naphthalene, biphenyl, PNP, and BPA were proposed, which indicated that strain YC-RL1 harbors systematic metabolic pathways toward aromatic compounds. Further, genomic analysis uncovered part of genes involved in the proposed pathways. Both intradiol and extradiol ring-cleavage dioxygenase genes were identified in the genome of strain YC-RL1. Meanwhile, gene clusters predicted to encode the degradation of biphenyl (bph), para-substituted phenols (npd) and protocatechuate (pca) were identified, and bphA1A2BCD was proposed to be a novel biphenyl-degrading gene cluster. The complete metabolic pathway of biphenyl was deduced via intermediates and functional gene analysis (bph and pca gene clusters). One of the these genes encoding ring-cleavage dioxygenase in bph gene cluster, a predicted 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) gene, was cloned and its activity was confirmed by heterologous expression. This work systematically illuminated the metabolic versatility of aromatic compounds in strain YC-RL1 via the combination of metabolites identification, genomics analysis and laboratory experiments. These results suggested that strain YC-RL1 might be a promising candidate for the bioremediation of aromatic compounds pollution sites.
Collapse
Affiliation(s)
- Lei Ren
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Jia
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Zhang
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, China
| | - Zhong Lin
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang, China
| | - Zhen Zhen
- Agricultural College, Guangdong Ocean University, Zhanjiang, China
| | - Hanqiao Hu
- Agricultural College, Guangdong Ocean University, Zhanjiang, China
| | - Yanchun Yan
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
14
|
Cho SY, Kwean OS, Yang JW, Cho W, Kwak S, Park S, Lim Y, Kim HS. Identification of the upstream 4-chlorophenol biodegradation pathway using a recombinant monooxygenase from Arthrobacter chlorophenolicus A6. BIORESOURCE TECHNOLOGY 2017; 245:1800-1807. [PMID: 28522197 DOI: 10.1016/j.biortech.2017.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 04/28/2017] [Accepted: 05/01/2017] [Indexed: 05/06/2023]
Abstract
This study aimed to clarify the initial 4-chlorophenol (4-CP) biodegradation pathway promoted by a two-component flavin-diffusible monooxygenase (TC-FDM) consisting of CphC-I and CphB contained in Arthrobacter chlorophenolicus A6 and the decomposition function of CphC-I. The TC-FDM genes were cloned from A. chlorophenolicus A6, and the corresponding enzymes were overexpressed. Since CphB was expressed in an insoluble form, Fre, a flavin reductase obtained from Escherichia coli, was used. These enzymes were purified using Ni2+-NTA resin. It was confirmed that TC-FDM catalyzes the oxidation of 4-CP and the sequential conversion of 4-CP to benzoquinone (BQN)→hydroquinone (HQN)→HQL. This indicated that CphC-I exhibits substrate specificity for 4-CP, BQN, and HQN. The activity of CphC-I for 4-CP was 63.22U/mg-protein, and the Michaelis-Menten kinetic parameters were vmax=0.21mM/min, KM=0.19mM, and kcat/KM=0.04mM-1min-1. These results would be useful for the development of a novel biochemical treatment technology for 4-CP and phenolic hydrocarbons.
Collapse
Affiliation(s)
- Su Yeon Cho
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Oh Sung Kwean
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jun Won Yang
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Wooyoun Cho
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Seonyeong Kwak
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sungyoon Park
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Yejee Lim
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Han S Kim
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| |
Collapse
|
15
|
Wang JP, Zhang WM, Chao HJ, Zhou NY. PnpM, a LysR-Type Transcriptional Regulator Activates the Hydroquinone Pathway in para-Nitrophenol Degradation in Pseudomonas sp. Strain WBC-3. Front Microbiol 2017; 8:1714. [PMID: 28959240 PMCID: PMC5603801 DOI: 10.3389/fmicb.2017.01714] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/24/2017] [Indexed: 11/17/2022] Open
Abstract
A LysR-type transcriptional regulator (LTTR), PnpR, has previously been shown to activate the transcription of operons pnpA, pnpB, and pnpCDEFG for para-nitrophenol (PNP) degradation in Pseudomonas sp. strain WBC-3. Further preliminary evidence suggested the possible presence of an LTTR additional binding site in the promoter region of pnpCDEFG. In this study, an additional LTTR PnpM, which shows 44% homology to PnpR, was determined to activate the expression of pnpCDEFG. Interestingly, a pnpM-deleted WBC-3 strain was unable to grow on PNP but accumulating hydroquinone (HQ), which is the catabolic product from PNP degradation by PnpAB and the substrate for PnpCD. Through electrophoretic mobility shift assays (EMSAs) and promoter activity detection, only PnpR was involved in the activation of pnpA and pnpB, but both PnpR and PnpM were involved in the activation of pnpCDEFG. DNase I footprinting analysis suggested that PnpR and PnpM shared the same DNA-binding regions of 27 bp in the pnpCDEFG promoter. In the presence of PNP, the protection region increased to 39 bp by PnpR and to 38 bp by PnpM. Our data suggested that both PnpR and PnpM were involved in activating pnpCDEFG expression, in which PNP rather than the substrate hydroquinone for PnpCD is the inducer. Thus, during the PNP catabolism in Pseudomonas sp. strain WBC-3, pnpA and pnpB operons for the initial two reactions were controlled by PnpR, while the third operon (pnpCDEFG) for HQ degradation was activated by PnpM and PnpR. This study builds upon our previous findings and shows that two LTTRs PnpR and PnpM are involved in the transcriptional activation of these three catabolic operons. Specifically, our identification that an LTTR, PnpM, regulates pnpCDEFG expression provides new insights in an intriguing regulation system of PNP catabolism that is controlled by two regulators.
Collapse
Affiliation(s)
- Jin-Pei Wang
- Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China.,University of Chinese Academy of SciencesBeijing, China
| | - Wen-Mao Zhang
- Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
| | - Hong-Jun Chao
- Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
| | - Ning-Yi Zhou
- Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China.,State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
| |
Collapse
|
16
|
Kang C, Yang JW, Cho W, Kwak S, Park S, Lim Y, Choe JW, Kim HS. Oxidative biodegradation of 4-chlorophenol by using recombinant monooxygenase cloned and overexpressed from Arthrobacter chlorophenolicus A6. BIORESOURCE TECHNOLOGY 2017; 240:123-129. [PMID: 28343861 DOI: 10.1016/j.biortech.2017.03.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 05/06/2023]
Abstract
In this study, cphC-I and cphB, encoding a putative two-component flavin-diffusible monooxygenase (TC-FDM) complex, were cloned from Arthrobacter chlorophenolicus A6. The corresponding enzymes were overexpressed to assess the feasibility of their utilization for the oxidative decomposition of 4-chlorophenol (4-CP). Soluble CphC-I was produced at a high level (∼50%), and subsequently purified. Since CphB was expressed in an insoluble form, a flavin reductase, Fre, cloned from Escherichia coli was used as an alternative reductase. CphC-I utilized cofactor FADH2, which was reduced by Fre for the hydroxylation of 4-CP. This recombinant enzyme complex exhibited a higher specific activity for the oxidation of 4-CP (45.34U/mg-protein) than that exhibited by CphC-I contained in cells (0.18U/mg-protein). The Michaelis-Menten kinetic parameters were determined as: vmax=223.3μM·min-1, KM=249.4μM, and kcat/KM=0.052min-1·μM-1. These results could be useful for the development of a new biochemical remediation technique based on enzymatic agents catalyzing the degradation of phenolic contaminants.
Collapse
Affiliation(s)
- Christina Kang
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jun Won Yang
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Wooyoun Cho
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Seonyeong Kwak
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sungyoon Park
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Yejee Lim
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jae Wan Choe
- Civil Engineering, Gwangju University, 277 Hyodeok-ro, Nam-gu, Gwanju 61743, Republic of Korea
| | - Han S Kim
- Environmental Engineering, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| |
Collapse
|
17
|
|
18
|
A mechanistic study on SMOB-ADP1: an NADH:flavin oxidoreductase of the two-component styrene monooxygenase of Acinetobacter baylyi ADP1. Arch Microbiol 2014; 196:829-45. [PMID: 25116410 DOI: 10.1007/s00203-014-1022-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/23/2014] [Accepted: 07/28/2014] [Indexed: 10/24/2022]
Abstract
Two styrene monooxygenase types, StyA/StyB and StyA1/StyA2B, have been described each consisting of an epoxidase and a reductase. A gene fusion which led to the chimeric reductase StyA2B and the occurrence in different phyla are major differences. Identification of SMOA/SMOB-ADP1 of Acinetobacter baylyi ADP1 may enlighten the gene fusion event since phylogenetic analysis indicated both proteins to be more related to StyA2B than to StyA/StyB. SMOB-ADP1 is classified like StyB and StyA2B as HpaC-like reductase. Substrate affinity and turnover number of the homo-dimer SMOB-ADP1 were determined for NADH (24 µM, 64 s(-1)) and FAD (4.4 µM, 56 s(-1)). SMOB-ADP1 catalysis follows a random sequential mechanism, and FAD fluorescence is quenched upon binding to SMOB-ADP1 (K d = 1.8 µM), which clearly distinguishes that reductase from StyB of Pseudomonas. In summary, this study confirmes made assumptions and provides phylogenetic and biochemical data for the differentiation of styrene monooxygenase-related flavin reductases.
Collapse
|
19
|
Qu Y, Shi S, Ma Q, Kong C, Zhou H, Zhang X, Zhou J. Multistep Conversion of para-Substituted Phenols by Phenol Hydroxylase and 2,3-Dihydroxybiphenyl 1,2-Dioxygenase. Appl Biochem Biotechnol 2013; 169:2064-75. [DOI: 10.1007/s12010-013-0112-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 01/14/2013] [Indexed: 10/27/2022]
|
20
|
Wells T, Ragauskas AJ. Biotechnological opportunities with the β-ketoadipate pathway. Trends Biotechnol 2012; 30:627-37. [DOI: 10.1016/j.tibtech.2012.09.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 09/24/2012] [Accepted: 09/26/2012] [Indexed: 01/18/2023]
|
21
|
Isolation and characterization of a Rhodococcus strain able to degrade 2-fluorophenol. Appl Microbiol Biotechnol 2011; 95:511-20. [DOI: 10.1007/s00253-011-3696-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Accepted: 10/31/2011] [Indexed: 10/15/2022]
|
22
|
Yamamoto K, Nishimura M, Kato DI, Takeo M, Negoro S. Identification and characterization of another 4-nitrophenol degradation gene cluster, nps, in Rhodococcus sp. strain PN1. J Biosci Bioeng 2011; 111:687-94. [PMID: 21396889 DOI: 10.1016/j.jbiosc.2011.01.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 01/13/2011] [Accepted: 01/28/2011] [Indexed: 11/15/2022]
Abstract
4-Nitrophenol (4-NP) is a toxic compound formed in soil by the hydrolysis of organophosphorous pesticides, such as parathion. We previously reported the presence of the 4-NP degradation gene cluster (nphRA1A2) in Rhodococcus sp. strain PN1, which encodes a two-component 4-NP hydroxylase system that oxidizes 4-NP into 4-nitrocatechol. In the current study, another gene cluster (npsC and npsRA2A1B) encoding a similar 4-NP hydroxylase system was cloned from strain PN1. The enzymes from this 4-NP hydroxylase system (NpsA1 and NpsA2) were purified as histidine-tagged (His-) proteins and then characterized. His-NpsA2 showed NADH/FAD oxidoreductase activity, and His-NpsA1 showed 4-NP oxidizing activity in the presence of His-NpsA2. In the 4-NP oxidation using the reconstituted enzyme system (His-NpsA1 and His-NpsA2), hydroquinone (35% of 4-NP disappeared) and hydroxyquinol (59% of 4-NP disappeared) were detected in the presence of ascorbic acid as a reducing reagent, suggesting that, without the reducing reagent, 4-NP was converted into their oxidized forms, 1,4-benzoquinone and 2-hydroxy-1,4-benzoquinone. In addition, in the cell extract of recombinant Escherichia coli expressing npsB, a typical spectral change showing conversion of hydroxyquinol into maleylacetate was observed. These results indicate that this nps gene cluster, in addition to the nph gene cluster, is also involved in 4-NP degradation in strain PN1.
Collapse
Affiliation(s)
- Kenta Yamamoto
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | | | | | | | | |
Collapse
|
23
|
Hasan SA, Ferreira MIM, Koetsier MJ, Arif MI, Janssen DB. Complete biodegradation of 4-fluorocinnamic acid by a consortium comprising Arthrobacter sp. strain G1 and Ralstonia sp. strain H1. Appl Environ Microbiol 2011; 77:572-9. [PMID: 21097599 PMCID: PMC3020533 DOI: 10.1128/aem.00393-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 11/08/2010] [Indexed: 11/20/2022] Open
Abstract
A consortium of the newly isolated bacterial strains Arthrobacter sp. strain G1 and Ralstonia sp. strain H1 utilized 4-fluorocinnamic acid for growth under aerobic conditions. Strain G1 converted 4-fluorocinnamic acid into 4-fluorobenzoic acid and used the two-carbon side chain for growth, with some formation of 4-fluoroacetophenone as a dead-end side product. In the presence of strain H1, complete mineralization of 4-fluorocinnamic acid and release of fluoride were obtained. Degradation of 4-fluorocinnamic acid by strain G1 occurred through a β-oxidation mechanism and started with the formation of 4-fluorocinnamoyl-coenzyme A (CoA), as indicated by the presence of 4-fluorocinnamoyl-CoA ligase. Enzymes for further transformation were detected in cell extract, i.e., 4-fluorocinnamoyl-CoA hydratase, 4-fluorophenyl-β-hydroxy propionyl-CoA dehydrogenase, and 4-fluorophenyl-β-keto propionyl-CoA thiolase. Degradation of 4-fluorobenzoic acid by strain H1 proceeded via 4-fluorocatechol, which was converted by an ortho-cleavage pathway.
Collapse
Affiliation(s)
- Syed A. Hasan
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Maria Isabel M. Ferreira
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Martijn J. Koetsier
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Muhammad I. Arif
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Dick B. Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| |
Collapse
|
24
|
Abstract
Investigations on diverse aspects of fluoro-organic compounds have rapidly increased during the past decades. Because natural sources of fluoro-organic compounds are extremely rare, the industrial synthesis of fluorinated organic compounds and production of fluorinated natural product derivatives have greatly expanded in recent years because of their increasing importance in the agrochemical and pharmaceutical industries. Due to structural complexity or instability, synthetic modification is often not possible, and various biofluorination strategies have been developed in recent years for applications in the anti-cancer, anti-viral and anti-infection fields. Despite the industrial importance of fluorinated compounds, there have been serious concerns worldwide over the levels and synthetic routes of certain fluorinated organic compounds, in particular perfluorinated chemicals (PFCs). PFCs are emerging and recalcitrant pollutants which are widely distributed in the environment and have been detected in humans and wildlife globally. PFCs have been demonstrated to be potentially carcinogenic, adversely affect the neuroendocrine and immune systems, and produce neurotoxicity, heptatotoxicity and endocrine disrupting effects in vertebrate animals. Here, we provide an overview of recent advances in our understanding of the biology of various fluoro-organic compounds and perspectives for new enzymes and metabolic pathways for bioremediation of these chemicals.
Collapse
Affiliation(s)
- Xiao-Jian Zhang
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | | | | |
Collapse
|