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Snajdarova K, Marques SM, Damborsky J, Bednar D, Marek M. Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum. Acta Crystallogr D Struct Biol 2023; 79:956-970. [PMID: 37860958 PMCID: PMC10619424 DOI: 10.1107/s2059798323006642] [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] [Received: 05/31/2023] [Accepted: 07/31/2023] [Indexed: 10/21/2023] Open
Abstract
Haloalkane dehalogenases (HLDs) are a family of α/β-hydrolase fold enzymes that employ SN2 nucleophilic substitution to cleave the carbon-halogen bond in diverse chemical structures, the biological role of which is still poorly understood. Atomic-level knowledge of both the inner organization and supramolecular complexation of HLDs is thus crucial to understand their catalytic and noncatalytic functions. Here, crystallographic structures of the (S)-enantioselective haloalkane dehalogenase DmmarA from the waterborne pathogenic microbe Mycobacterium marinum were determined at 1.6 and 1.85 Å resolution. The structures show a canonical αβα-sandwich HLD fold with several unusual structural features. Mechanistically, the atypical composition of the proton-relay catalytic triad (aspartate-histidine-aspartate) and uncommon active-site pocket reveal the molecular specificities of a catalytic apparatus that exhibits a rare (S)-enantiopreference. Additionally, the structures reveal a previously unobserved mode of symmetric homodimerization, which is predominantly mediated through unusual L5-to-L5 loop interactions. This homodimeric association in solution is confirmed experimentally by data obtained from small-angle X-ray scattering. Utilizing the newly determined structures of DmmarA, molecular modelling techniques were employed to elucidate the underlying mechanism behind its uncommon enantioselectivity. The (S)-preference can be attributed to the presence of a distinct binding pocket and variance in the activation barrier for nucleophilic substitution.
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Affiliation(s)
- Karolina Snajdarova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Building A13, 625 00 Brno, Czech Republic
| | - Sérgio M. Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Building A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Building A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Building A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Martin Marek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Building A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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2
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Chmelova K, Gao T, Polak M, Schenkmayerova A, Croll TI, Shaikh TR, Skarupova J, Chaloupkova R, Diederichs K, Read RJ, Damborsky J, Novacek J, Marek M. Multimeric structure of a subfamily III haloalkane dehalogenase-like enzyme solved by combination of cryo-EM and x-ray crystallography. Protein Sci 2023; 32:e4751. [PMID: 37574754 PMCID: PMC10503415 DOI: 10.1002/pro.4751] [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] [Received: 05/08/2023] [Revised: 07/25/2023] [Accepted: 08/08/2023] [Indexed: 08/15/2023]
Abstract
Haloalkane dehalogenase (HLD) enzymes employ an SN 2 nucleophilic substitution mechanism to erase halogen substituents in diverse organohalogen compounds. Subfamily I and II HLDs are well-characterized enzymes, but the mode and purpose of multimerization of subfamily III HLDs are unknown. Here we probe the structural organization of DhmeA, a subfamily III HLD-like enzyme from the archaeon Haloferax mediterranei, by combining cryo-electron microscopy (cryo-EM) and x-ray crystallography. We show that full-length wild-type DhmeA forms diverse quaternary structures, ranging from small oligomers to large supramolecular ring-like assemblies of various sizes and symmetries. We optimized sample preparation steps, enabling three-dimensional reconstructions of an oligomeric species by single-particle cryo-EM. Moreover, we engineered a crystallizable mutant (DhmeAΔGG ) that provided diffraction-quality crystals. The 3.3 Å crystal structure reveals that DhmeAΔGG forms a ring-like 20-mer structure with outer and inner diameter of ~200 and ~80 Å, respectively. An enzyme homodimer represents a basic repeating building unit of the crystallographic ring. Three assembly interfaces (dimerization, tetramerization, and multimerization) were identified to form the supramolecular ring that displays a negatively charged exterior, while its interior part harboring catalytic sites is positively charged. Localization and exposure of catalytic machineries suggest a possible processing of large negatively charged macromolecular substrates.
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Affiliation(s)
- Klaudia Chmelova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrnoCzech Republic
| | - Tadeja Gao
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrnoCzech Republic
| | - Martin Polak
- Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Andrea Schenkmayerova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrnoCzech Republic
| | - Tristan I. Croll
- Department of Hematology, Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - Tanvir R. Shaikh
- Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
- Institute of NeuropathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Jana Skarupova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrnoCzech Republic
| | - Kay Diederichs
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Randy J. Read
- Department of Hematology, Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrnoCzech Republic
| | - Jiri Novacek
- Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Martin Marek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrnoCzech Republic
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3
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Parchemin C, Raviglione D, Mejait A, Sasal P, Faliex E, Clerissi C, Tapissier-Bontemps N. Antibacterial Activities and Life Cycle Stages of Asparagopsis armata: Implications of the Metabolome and Microbiome. Mar Drugs 2023; 21:363. [PMID: 37367688 DOI: 10.3390/md21060363] [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: 05/02/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023] Open
Abstract
The red alga Asparagopsis armata is a species with a haplodiplophasic life cycle alternating between morphologically distinct stages. The species is known for its various biological activities linked to the production of halogenated compounds, which are described as having several roles for the algae such as the control of epiphytic bacterial communities. Several studies have reported differences in targeted halogenated compounds (using gas chromatography-mass spectrometry analysis (GC-MS)) and antibacterial activities between the tetrasporophyte and the gametophyte stages. To enlarge this picture, we analysed the metabolome (using liquid chromatography-mass spectrometry (LC-MS)), the antibacterial activity and the bacterial communities associated with several stages of the life cycle of A. armata: gametophytes, tetrasporophytes and female gametophytes with developed cystocarps. Our results revealed that the relative abundance of several halogenated molecules including dibromoacetic acid and some more halogenated molecules fluctuated depending on the different stages of the algae. The antibacterial activity of the tetrasporophyte extract was significantly higher than that of the extracts of the other two stages. Several highly halogenated compounds, which discriminate algal stages, were identified as candidate molecules responsible for the observed variation in antibacterial activity. The tetrasporophyte also harboured a significantly higher specific bacterial diversity, which is associated with a different bacterial community composition than the other two stages. This study provides elements that could help in understanding the processes that take place throughout the life cycle of A. armata with different potential energy investments between the development of reproductive elements, the production of halogenated molecules and the dynamics of bacterial communities.
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Affiliation(s)
- Christelle Parchemin
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Delphine Raviglione
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Anouar Mejait
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Pierre Sasal
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Elisabeth Faliex
- Centre de Formation et de Recherche sur les Environnements Méditerranéens (CEFREM), UMR 5110 UPVD-CNRS, Université de Perpignan-Via Domitia, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Camille Clerissi
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
| | - Nathalie Tapissier-Bontemps
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Ecole Pratique des Hautes Etudes (EPHE), Université PSL, UPVD, CNRS, UAR 3278, 52 Av. Paul Alduy, CEDEX, 66860 Perpignan, France
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4
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Wu SC, Chang BS, Li YY. Effect of the coexistence of endosulfan on the lindane biodegradation by Novosphingobium barchaimii and microbial enrichment cultures. CHEMOSPHERE 2022; 297:134063. [PMID: 35192855 DOI: 10.1016/j.chemosphere.2022.134063] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/30/2022] [Accepted: 02/18/2022] [Indexed: 05/06/2023]
Abstract
Organochlorine pesticides, especially lindane and endosulfan, have been demonstrated to be both biodegradable and frequently coexistent, but their inhibitory effect has never been studied. In this study, we investigated the effect of endosulfan coexistence on lindane degradation to a lindane-degrading isolate, Novosphingobium barchaimii strain LL02, and mixed enrichment cultures from two different inocula. Our results of the lindane degradation batch experiments demonstrated that endosulfan concentration above 20 mg L-1 causes significant inhibition to the lindane degradation efficiency of the strain LL02. Besides, the acidic conditions at pH 5.0 to 6.0 further decreased its lindane degradation rate constants by 57% compared to the neutral and alkaline conditions. For the mixed microbial cultures, the lindane degradation efficiency in the lindane/endosulfan co-contamination conditions decreased by 35.7%-50.7% compared to the lindane alone conditions. From our 16S rRNA amplicon sequencing results through the PacBio platform, most of the predominant bacteria in the lindane-enriched cultures were depressed in the lindane/endosulfan-enriched cultures. Moreover, bacteria of Burkholderia australis, Chujaibacter soli, Flavitalea flava, and one Rhodanobacteraceae bacterium were relatively highly abundant in the co-contamination enrichment cultures, suggesting their potential for lindane degradation under the endosulfan stress. Our results demonstrated that endosulfan coexistence causes inhibitory impacts on lindane biodegradation toward both lindane-degrading bacteria and mixed microbial cultures. The coexistence of multiple organochlorine pesticides on the biodegradation efficiencies should be carefully considered when applying bioremediation to remove organochlorine pesticide contamination.
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Affiliation(s)
- Siang Chen Wu
- Department of Environmental Engineering, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan.
| | - Bo-Sheng Chang
- Department of Environmental Engineering, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
| | - Yu-Ying Li
- Department of Environmental Engineering, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
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5
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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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Mazur A, Prudnikova T, Grinkevich P, Mesters JR, Mrazova D, Chaloupkova R, Damborsky J, Kuty M, Kolenko P, Kuta Smatanova I. The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:347-356. [PMID: 33645538 DOI: 10.1107/s2059798321000486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/13/2021] [Indexed: 11/10/2022]
Abstract
Haloalkane dehalogenases (EC 3.8.1.5) are microbial enzymes that catalyse the hydrolytic conversion of halogenated compounds, resulting in a halide ion, a proton and an alcohol. These enzymes are used in industrial biocatalysis, bioremediation and biosensing of environmental pollutants or for molecular tagging in cell biology. The novel haloalkane dehalogenase DpaA described here was isolated from the psychrophilic and halophilic bacterium Paraglaciecola agarilytica NO2, which was found in marine sediment collected from the East Sea near Korea. Gel-filtration experiments and size-exclusion chromatography provided information about the dimeric composition of the enzyme in solution. The DpaA enzyme was crystallized using the sitting-drop vapour-diffusion method, yielding rod-like crystals that diffracted X-rays to 2.0 Å resolution. Diffraction data analysis revealed a case of merohedral twinning, and subsequent structure modelling and refinement resulted in a tetrameric model of DpaA, highlighting an uncommon multimeric nature for a protein belonging to haloalkane dehalogenase subfamily I.
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Affiliation(s)
- Andrii Mazur
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Tatyana Prudnikova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Pavel Grinkevich
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Jeroen R Mesters
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Daria Mrazova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Kuty
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Petr Kolenko
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, 115 19 Prague, Czech Republic
| | - Ivana Kuta Smatanova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
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Oyewusi HA, Wahab RA, Huyop F. Dehalogenase-producing halophiles and their potential role in bioremediation. MARINE POLLUTION BULLETIN 2020; 160:111603. [PMID: 32919122 DOI: 10.1016/j.marpolbul.2020.111603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/21/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
This review aims to briefly describe the potential role of dehalogenase-producing halophilic bacteria in decontamination of organohalide pollutants. Hypersaline habitats pose challenges to life because of low water activity (water content) and is considered as the largest and ultimate sink for pollutants due to naturally and anthropogenic activities in which a substantial amount of ecological contaminants are organohalides. Several such environments appear to host and support substantial diversity of extremely halophilic and halotolerant bacteria as well as halophilic archaea. Biodegradation of several toxic inorganic and organic compounds in both aerobic and anaerobic conditions are carried out by halophilic microbes. Therefore, remediation of polluted marine/hypersaline environments are the main scorching issues in the field of biotechnology. Although many microbial species are reported as effective pollutants degrader, but little has been isolated from marine/hypersaline environments. Therefore, more novel microbial species with dehalogenase-producing ability are still desired.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, PMB, 5351, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia.
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8
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Aslan‐Üzel AS, Beier A, Kovář D, Cziegler C, Padhi SK, Schuiten ED, Dörr M, Böttcher D, Hollmann F, Rudroff F, Mihovilovic MD, Buryška T, Damborský J, Prokop Z, Badenhorst CPS, Bornscheuer UT. An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation. ChemCatChem 2020; 12:2032-2039. [PMID: 32362951 PMCID: PMC7188320 DOI: 10.1002/cctc.201901891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/16/2019] [Indexed: 12/31/2022]
Abstract
Halide assays are important for the study of enzymatic dehalogenation, a topic of great industrial and scientific importance. Here we describe the development of a very sensitive halide assay that can detect less than a picomole of bromide ions, making it very useful for quantifying enzymatic dehalogenation products. Halides are oxidised under mild conditions using the vanadium-dependent chloroperoxidase from Curvularia inaequalis, forming hypohalous acids that are detected using aminophenyl fluorescein. The assay is up to three orders of magnitude more sensitive than currently available alternatives, with detection limits of 20 nM for bromide and 1 μM for chloride and iodide. We demonstrate that the assay can be used to determine specific activities of dehalogenases and validate this by comparison to a well-established GC-MS method. This new assay will facilitate the identification and characterisation of novel dehalogenases and may also be of interest to those studying other halide-producing enzymes.
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Affiliation(s)
- Aşkın S. Aslan‐Üzel
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Andy Beier
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - David Kovář
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Clemens Cziegler
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | - Santosh K. Padhi
- Biocatalysis and Enzyme Engineering Laboratory Department of Biochemistry School of Life SciencesUniversity of HyderabadGachibowli500046India
| | - Eva D. Schuiten
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Mark Dörr
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Dominique Böttcher
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Frank Hollmann
- Department of BiotechnologyDelft University of TechnologyDelft2629 HZ (TheNetherlands
| | - Florian Rudroff
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | | | - Tomáš Buryška
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
| | - Jiří Damborský
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Zbyněk Prokop
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
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9
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Akcay K, Kaya Y. Isolation, characterization and molecular identification of a halotolerant Bacillus megaterium CTBmeg1 able to grow on halogenated compounds. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1631717] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Kazim Akcay
- Agricultural Biotechnology Department, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Yilmaz Kaya
- Agricultural Biotechnology Department, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
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10
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Ferrandi EE, Sayer C, De Rose SA, Guazzelli E, Marchesi C, Saneei V, Isupov MN, Littlechild JA, Monti D. New Thermophilic α/β Class Epoxide Hydrolases Found in Metagenomes From Hot Environments. Front Bioeng Biotechnol 2018; 6:144. [PMID: 30386778 PMCID: PMC6198070 DOI: 10.3389/fbioe.2018.00144] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/21/2018] [Indexed: 12/21/2022] Open
Abstract
Two novel epoxide hydrolases (EHs), Sibe-EH and CH65-EH, were identified in the metagenomes of samples collected in hot springs in Russia and China, respectively. The two α/β hydrolase superfamily fold enzymes were cloned, over-expressed in Escherichia coli, purified and characterized. The new EHs were active toward a broad range of substrates, and in particular, Sibe-EH was excellent in the desymmetrization of cis-2,3-epoxybutane producing the (2R,3R)-diol product with ee exceeding 99%. Interestingly these enzymes also hydrolyse (4R)-limonene-1,2-epoxide with Sibe-EH being specific for the trans isomer. The Sibe-EH is a monomer in solution whereas the CH65-EH is a dimer. Both enzymes showed high melting temperatures with the CH65-EH being the highest at 85°C retaining 80% of its initial activity after 3 h thermal treatment at 70°C making it the most thermal tolerant wild type epoxide hydrolase described. The Sibe-EH and CH65-EH have been crystallized and their structures determined to high resolution, 1.6 and 1.4 Å, respectively. The CH65-EH enzyme forms a dimer via its cap domains with different relative orientation of the monomers compared to previously described EHs. The entrance to the active site cavity is located in a different position in CH65-EH and Sibe-EH in relation to other known bacterial and mammalian EHs.
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Affiliation(s)
| | - Christopher Sayer
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Simone Antonio De Rose
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Elisa Guazzelli
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy
| | - Carlotta Marchesi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy
| | - Vahid Saneei
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Daniela Monti
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy
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11
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Christenson JK, Robinson SL, Engel TA, Richman JE, Kim AN, Wackett LP. OleB from Bacterial Hydrocarbon Biosynthesis Is a β-Lactone Decarboxylase That Shares Key Features with Haloalkane Dehalogenases. Biochemistry 2017; 56:5278-5287. [PMID: 28872321 DOI: 10.1021/acs.biochem.7b00667] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
OleB is an α/β-hydrolase found in bacteria that biosynthesize long-chain olefinic hydrocarbons, but its function has remained obscure. We report that OleB from the Gram-negative bacterium Xanthomonas campestris performs an unprecedented β-lactone decarboxylation reaction, to complete cis-olefin biosynthesis. OleB reactions monitored by 1H nuclear magnetic resonance spectroscopy revealed a selectivity for decarboxylating cis-β-lactones and no discernible activity with trans-β-lactones, consistent with the known configuration of pathway intermediates. Protein sequence analyses showed OleB proteins were most related to haloalkane dehalogenases (HLDs) and retained the canonical Asp-His-Asp catalytic triad of HLDs. Unexpectedly, it was determined that an understudied subfamily, denoted as HLD-III, is comprised mostly of OleB proteins encoded within oleABCD gene clusters, suggesting a misannotation. OleB from X. campestris showed very low dehalogenase activity only against haloalkane substrates with long alkyl chains. A haloalkane substrate mimic alkylated wild-type X. campestris OleB but not OleBD114A, implicating this residue as the active site nucleophile as in HLDs. A sequence-divergent OleB, found as part of a natural OleBC fusion and classified as an HLD-III, from the Gram-positive bacterium Micrococcus luteus was demonstrated to have the same activity, stereochemical preference, and dependence on the proposed Asp nucleophile. H218O studies with M. luteus OleBC suggested that the canonical alkyl-enzyme intermediate of HLDs is hydrolyzed differently by OleB enzymes, as 18O is not incorporated into the nucleophilic aspartic acid. This work defines a previously unrecognized reaction in nature, functionally identifies some HLD-III enzymes as β-lactone decarboxylases, and posits an enzymatic mechanism of β-lactone decarboxylation.
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Affiliation(s)
- James K Christenson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States.,Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Serina L Robinson
- Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States.,Department of Microbiology and Immunology, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Tiffany A Engel
- Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Jack E Richman
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States.,Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - An N Kim
- Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Larry P Wackett
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States.,Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States.,Microbial and Plant Genomics Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
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Kotik M, Vanacek P, Kunka A, Prokop Z, Damborsky J. Metagenome-derived haloalkane dehalogenases with novel catalytic properties. Appl Microbiol Biotechnol 2017; 101:6385-6397. [PMID: 28674849 DOI: 10.1007/s00253-017-8393-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 06/11/2017] [Accepted: 06/13/2017] [Indexed: 01/30/2023]
Abstract
Haloalkane dehalogenases (HLDs) are environmentally relevant enzymes cleaving a carbon-halogen bond in a wide range of halogenated pollutants. PCR with degenerate primers and genome-walking was used for the retrieval of four HLD-encoding genes from groundwater-derived environmental DNA. Using specific primers and the environmental DNA as a template, we succeeded in generating additional amplicons, resulting altogether in three clusters of sequences with each cluster comprising 8-13 closely related putative HLD-encoding genes. A phylogenetic analysis of the translated genes revealed that three HLDs are members of the HLD-I subfamily, whereas one gene encodes an enzyme from the subfamily HLD-II. Two metagenome-derived HLDs, eHLD-B and eHLD-C, each from a different subfamily, were heterologously produced in active form, purified and characterized in terms of their thermostability, pH and temperature optimum, quaternary structure, substrate specificity towards 30 halogenated compounds, and enantioselectivity. eHLD-B and eHLD-C showed striking differences in their activities, substrate preferences, and tolerance to temperature. Profound differences were also determined in the enantiopreference and enantioselectivity of these enzymes towards selected substrates. Comparing our data with those of known HLDs revealed that eHLD-C exhibits a unique combination of high thermostability, high activity, and an unusually broad pH optimum, which covers the entire range of pH 5.5-8.9. Moreover, a so far unreported high thermostability for HLDs was determined for this enzyme at pH values lower than 6.0. Thus, eHLD-C represents an attractive and novel biocatalyst for biotechnological applications.
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Affiliation(s)
- Michael Kotik
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Pavel Vanacek
- Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic, Brno, Czech Republic
| | - Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic, Brno, Czech Republic.
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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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15
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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: 249] [Impact Index Per Article: 35.6] [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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Nikolaivits E, Dimarogona M, Fokialakis N, Topakas E. Marine-Derived Biocatalysts: Importance, Accessing, and Application in Aromatic Pollutant Bioremediation. Front Microbiol 2017; 8:265. [PMID: 28265269 PMCID: PMC5316534 DOI: 10.3389/fmicb.2017.00265] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 02/07/2017] [Indexed: 12/31/2022] Open
Abstract
The aim of the present review is to highlight the potential use of marine biocatalysts (whole cells or enzymes) as an alternative bioprocess for the degradation of aromatic pollutants. Firstly, information about the characteristics of the still underexplored marine environment and the available scientific tools used to access novel marine-derived biocatalysts is provided. Marine-derived enzymes, such as dioxygenases and dehalogenases, and the involved catalytic mechanisms for the degradation of aromatic and halogenated compounds, are presented, with the purpose of underpinning their potential use in bioremediation. Emphasis is given on persistent organic pollutants (POPs) that are organic compounds with significant impact on health and environment due to their resistance in degradation. POPs bioaccumulate mainly in the fatty tissue of living organisms, therefore current efforts are mostly focused on the restriction of their use and production, since their removal is still unclear. A brief description of the guidelines and criteria that render a pollutant POP is given, as well as their potential biodegradation by marine microorganisms by surveying recent developments in this rather unexplored field.
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Affiliation(s)
- Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Maria Dimarogona
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens Athens, Greece
| | - Nikolas Fokialakis
- Division of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, University of Athens Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens Athens, Greece
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Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World J Microbiol Biotechnol 2016; 32:135. [PMID: 27344438 DOI: 10.1007/s11274-016-2081-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.
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18
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Unno T, Kim J, Kim Y, Nguyen SG, Guevarra RB, Kim GP, Lee JH, Sadowsky MJ. Influence of seawater intrusion on microbial communities in groundwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 532:337-343. [PMID: 26081736 DOI: 10.1016/j.scitotenv.2015.05.111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 05/20/2015] [Accepted: 05/24/2015] [Indexed: 06/04/2023]
Abstract
Groundwater is the sole source of potable water on Jeju Island in the Republic of (South) Korea. Groundwater is also used for irrigation and industrial purposes, and it is severely impacted by seawater intrusion in coastal areas. Consequently, monitoring the intrusion of seawater into groundwater on Jeju is very important for health and environmental reasons. A number of studies have used hydrological models to predict the deterioration of groundwater quality caused by seawater intrusion. However, there is conflicting evidence of intrusion due to complicated environmental influences on groundwater quality. Here we investigated the use of next generation sequencing (NGS)-based microbial community analysis as a way to monitor groundwater quality and detect seawater intrusion. Pristine groundwater, groundwater from three coastal areas, and seawater were compared. Analysis of the distribution of bacterial species clearly indicated that the high and low salinity groundwater differed significantly with respect to microbial composition. While members of the family Parvularculaceae were only identified in high salinity water samples, a greater percentage of the phylum Actinobacteria was predominantly observed in pristine groundwater. In addition, we identified 48 shared operational taxonomic units (OTUs) with seawater, among which the high salinity groundwater sample shared a greater number of bacterial species with seawater (6.7%). In contrast, other groundwater samples shared less than 0.5%. Our results suggest that NGS-based microbial community analysis of groundwater may be a useful tool for monitoring groundwater quality and detect seawater intrusion. This technology may also provide additional insights in understanding hydrological dynamics.
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Affiliation(s)
- Tatsuya Unno
- Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju 690-756, Republic of Korea.
| | - Jungman Kim
- Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju 690-756, Republic of Korea
| | - Yumi Kim
- Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju 690-756, Republic of Korea
| | - Son G Nguyen
- Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju 690-756, Republic of Korea; Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi, Viet Nam
| | - Robin B Guevarra
- Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju 690-756, Republic of Korea
| | - Gee Pyo Kim
- Jeju Water Resources Headquarters, Jeju 695-962, Republic of Korea
| | - Ji-Hoon Lee
- Department of Bioenvironmental Chemistry, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | - Michael J Sadowsky
- Department of Soil, Water, and Climate, BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, United States
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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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21
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Yarrowia lipolytica NCIM 3589, a tropical marine yeast, degrades bromoalkanes by an initial hydrolytic dehalogenation step. Biodegradation 2015; 26:127-38. [DOI: 10.1007/s10532-015-9721-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/10/2015] [Indexed: 10/24/2022]
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