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Wahhab BH, Oyewusi HA, Wahab RA, Mohammad Hood MH, Abdul Hamid AA, Al-Nimer MS, Edbeib MF, Kaya Y, Huyop F. Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey. J Biomol Struct Dyn 2024; 42:1429-1442. [PMID: 37038649 DOI: 10.1080/07391102.2023.2199870] [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: 08/13/2022] [Accepted: 04/01/2023] [Indexed: 04/12/2023]
Abstract
This study presents the initial structural model of L-haloacid dehalogenase (DehLBHS1) from Bacillus megaterium BHS1, an alkalotolerant bacterium known for its ability to degrade halogenated environmental pollutants. The model provides insights into the structural features of DehLBHS1 and expands our understanding of the enzymatic mechanisms involved in the degradation of these hazardous pollutants. Key amino acid residues (Arg40, Phe59, Asn118, Asn176, and Trp178) in DehLBHS1 were identified to play critical roles in catalysis and molecular recognition of haloalkanoic acid, essential for efficient binding and transformation of haloalkanoic acid molecules. DehLBHS1 was modeled using I-TASSER, yielding a best TM-score of 0.986 and an RMSD of 0.53 Å. Validation of the model using PROCHECK revealed that 89.2% of the residues were located in the most favored region, providing confidence in its structural accuracy. Molecular docking simulations showed that the non-simulated DehLBHS1 preferred 2,2DCP over other substrates, forming one hydrogen bond with Arg40 and exhibiting a minimum energy of -2.5 kJ/mol. The simulated DehLBHS1 exhibited a minimum energy of -4.3 kJ/mol and formed four hydrogen bonds with Arg40, Asn176, Asp9, and Tyr11, further confirming the preference for 2,2DCP. Molecular dynamics simulations supported this preference, based on various metrics, including RMSD, RMSF, gyration, hydrogen bonding, and molecular distance. MM-PBSA calculations showed that the DehLBHS1-2,2-DCP complex had a markedly lower binding energy (-21.363 ± 1.26 kcal/mol) than the DehLBHS1-3CP complex (-14.327 ± 1.738 kcal/mol). This finding has important implications for the substrate specificity and catalytic function of DehLBHS1, particularly in the bioremediation of 2,2-DCP in contaminated alkaline environments. These results provide a detailed view of the molecular interactions between the enzyme and its substrate and may aid in the development of more efficient biocatalytic strategies for the degradation of halogenated compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Batool Hazim Wahhab
- Department of Microbiology, Faculty of Medicine, Al-Mustansiriyah University, Iraq
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
| | - Mohammad Hakim Mohammad Hood
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Marwan Salih Al-Nimer
- Department of Pharmacology, College of Medicine, University of Diyala, Baqubah, Iraq
| | - Mohamed Faraj Edbeib
- Department of Medical Laboratories, Faculty of Medical Technology, Bani Walid University, Libya
| | - Yilmaz Kaya
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Malaysia
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Łomża P, Krucoń T, Tabernacka A. Potential of Microbial Communities to Perform Dehalogenation Processes in Natural and Anthropogenically Modified Environments-A Metagenomic Study. Microorganisms 2023; 11:1702. [PMID: 37512875 PMCID: PMC10385969 DOI: 10.3390/microorganisms11071702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Halogenated organic compounds (HOCs) pose a serious problem for the environment. Many are highly toxic and accumulate both in soil and in organisms. Their biological transformation takes place by dehalogenation, in which the halogen substituents are detached from the carbon in the organic compound by enzymes produced by microorganisms. This increases the compounds' water solubility and bioavailability, reduces toxicity, and allows the resulting compound to become more susceptible to biodegradation. The microbial halogen cycle in soil is an important part of global dehalogenation processes. The aim of the study was to examine the potential of microbial communities inhabiting natural and anthropogenically modified environments to carry out the dehalogenation process. The potential of microorganisms was assessed by analyzing the metagenomes from a natural environment (forest soils) and from environments subjected to anthropopression (agricultural soil and sludge from wastewater treatment plants). Thirteen genes encoding enzymes with dehalogenase activity were identified in the metagenomes of both environments, among which, 2-haloacid dehalogenase and catechol 2,3-dioxygenase were the most abundant genes. Comparative analysis, based on comparing taxonomy, identified genes, total halogens content and content of DDT derivatives, demonstrated the ability of microorganisms to transform HOCs in both environments, indicating the presence of these compounds in the environment for a long period of time and the adaptive need to develop mechanisms for their detoxification. Metagenome analyses and comparative analyses indicate the genetic potential of microorganisms of both environments to carry out dehalogenation processes, including dehalogenation of anthropogenic HOCs.
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Affiliation(s)
- Pola Łomża
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
| | - Tomasz Krucoń
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, 1 Miecznikowa Street, 02-089 Warsaw, Poland
| | - Agnieszka Tabernacka
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
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Isolation and Characterization of a Novel Bacterium from the Marine Environment for Trichloroacetic Acid Bioremediation. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10134593] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Halogenated compounds are an important class of environmental pollutants that are widely used in industrial chemicals such as solvents, herbicides, and pesticides. Many studies have been carried out to explore the biodegradation of these chemicals. Trichloroacetic acid (TCA) is one of the main halogenated compounds that are carcinogenic to humans and animals. The bacterium was isolated from the northern coastline of Johor Strait. In this study, the ability of strain MH2 to biodegrade TCA was evaluated by a growth experiment and dehalogenase enzyme assay. The growth profile of the isolated strain was examined. The doubling time for L. boronitolerans MH2 was found to be 32 h. The release of chloride ion in the degradation process was measured at 0.33 × 10−3 ± 0.03 mol∙L−1 after 96 h when the growth curve had reached its maximum within the late bacterial exponential phase. The results showed that the strain had a promising ability to degrade TCA by producing dehalogenase enzyme when cell-free extracts were prepared from growth on TCA as the sole carbon source with enzyme-specific activity, 1.1 ± 0.05 µmolCl−min−1∙mg−1 protein. Furthermore, the morphological, and biochemical aspects of the isolated bacterium were studied to identify and characterize the strain. The morphological observation of the isolated bacterium was seen to be a rod-shaped, Gram-positive, motile, heterotrophic, and spore-forming bacterium. The amplification of the 16S rRNA and gene analysis results indicated that the isolated bacterium had 98% similarity to Lysinibacillus boronitolerans. The morphological and biochemical tests supported the 16S rRNA gene amplification. To the best of the authors’ knowledge, this is the first reported case of this genus of bacteria to degrade this type of halogenated compound.
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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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Satpathy R, Konkimalla VB, Ratha J. In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin. Adv Bioinformatics 2016; 2016:8701201. [PMID: 26880911 PMCID: PMC4736600 DOI: 10.1155/2016/8701201] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 11/17/2022] Open
Abstract
2-Haloalkanoic acid dehalogenase enzymes have broad range of applications, starting from bioremediation to chemical synthesis of useful compounds that are widely distributed in fungi and bacteria. In the present study, a total of 81 full-length protein sequences of 2-haloalkanoic acid dehalogenase from bacteria and fungi were retrieved from NCBI database. Sequence analysis such as multiple sequence alignment (MSA), conserved motif identification, computation of amino acid composition, and phylogenetic tree construction were performed on these primary sequences. From MSA analysis, it was observed that the sequences share conserved lysine (K) and aspartate (D) residues in them. Also, phylogenetic tree indicated a subcluster comprised of both fungal and bacterial species. Due to nonavailability of experimental 3D structure for fungal 2-haloalkanoic acid dehalogenase in the PDB, molecular modelling study was performed for both fungal and bacterial sources of enzymes present in the subcluster. Further structural analysis revealed a common evolutionary topology shared between both fungal and bacterial enzymes. Studies on the buried amino acids showed highly conserved Leu and Ser in the core, despite variation in their amino acid percentage. Additionally, a surface exposed tryptophan was conserved in all of these selected models.
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Affiliation(s)
- Raghunath Satpathy
- School of Life Science, Sambalpur University, Jyoti Vihar, Burla, Odisha 768019, India
| | - V. B. Konkimalla
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Odisha 751005, India
| | - Jagnyeswar Ratha
- School of Life Science, Sambalpur University, Jyoti Vihar, Burla, Odisha 768019, India
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Sudi IY, Hamid AAA, Shamsir MS, Jamaluddin H, Wahab RA, Huyop F. Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward d- and l-2-chloropropionate. BIOTECHNOL BIOTEC EQ 2014; 28:608-615. [PMID: 26740767 PMCID: PMC4684057 DOI: 10.1080/13102818.2014.937907] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/06/2014] [Indexed: 11/15/2022] Open
Abstract
Halogenated compounds are recalcitrant environmental pollutants prevalent in agricultural fields, waste waters and industrial by-products, but they can be degraded by dehalogenase-containing microbes. Notably, 2-haloalkanoic acid dehalogenases are employed to resolve optically active chloropropionates, as exemplified by the d-specific dehalogenase from Rhizobium sp. RCI (DehD), which acts on d-2-chloropropionate but not on its l-enantiomer. The catalytic residues of this dehalogenase responsible for its affinity toward d-2-chloropropionate have not been experimentally determined, although its three-dimensional crystal structure has been solved. For this study, we performed in silico docking and molecular dynamic simulations of complexes formed by this dehalogenase and d- or l-2-chloropropionate. Arg134 of the enzyme plays the key role in the stereospecific binding and Arg16 is in a position that would allow it to activate a water molecule for hydrolytic attack on the d-2-chloropropionate chiral carbon for release of the halide ion to yield l-2-hydroxypropionate. We propose that within the DehD active site, the NH group of Arg134 can form a hydrogen bond with the carboxylate of d-2-chloropropionate with a strength of ∼4 kcal/mol that may act as an acid–base catalyst, whereas, when l-2-chloropropionate is present, this bond cannot be formed. The significance of the present work is vital for rational design of this dehalogenase in order to confirm the involvement of Arg16 and Arg134 residues implicated in hydrolysis and binding of d-2-chloropropionate in the active site of d-specific dehalogenase from Rhizobium sp. RC1.
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Affiliation(s)
- Ismaila Yada Sudi
- Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | | | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Haryati Jamaluddin
- Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | | | - Fahrul Huyop
- Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
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Affiliation(s)
- Fahrul Huyop
- Universiti Teknologi Malaysia, Faculty of Biosciences and Bioengineering, Johor, Malaysia
| | - Ismaila Yada Sudi
- Universiti Teknologi Malaysia, Faculty of Biosciences and Bioengineering, Johor, Malaysia
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Schober M, Faber K. Inverting hydrolases and their use in enantioconvergent biotransformations. Trends Biotechnol 2013; 31:468-78. [PMID: 23809848 PMCID: PMC3725421 DOI: 10.1016/j.tibtech.2013.05.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/14/2013] [Accepted: 05/14/2013] [Indexed: 01/23/2023]
Abstract
Enantioconvergent processes overcome the 50%-yield limits of kinetic resolution. Inverting enzymes are key catalysts for enantioconvergent processes. Enzyme engineering provided improved variants of inverting enzymes.
Owing to the more abundant occurrence of racemic compounds compared to prochiral or meso forms, most enantiomerically pure products are obtained via racemate resolution. This review summarizes (chemo)enzymatic enantioconvergent processes based on the use of hydrolytic enzymes, which are able to invert a stereocenter during catalysis that can overcome the 50%-yield limitation of kinetic resolution. Recent developments are presented in the fields of inverting or retaining sulfatases, epoxide hydrolases and dehalogenases, which allow the production of secondary alcohols or vicinal diols at a 100% theoretical yield from a racemate via enantioconvergent processes.
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Affiliation(s)
- Markus Schober
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Liang B, Cheng HY, Kong DY, Gao SH, Sun F, Cui D, Kong FY, Zhou AJ, Liu WZ, Ren NQ, Wu WM, Wang AJ, Lee DJ. Accelerated reduction of chlorinated nitroaromatic antibiotic chloramphenicol by biocathode. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:5353-5361. [PMID: 23607616 DOI: 10.1021/es400933h] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Chlorinated nitroaromatic antibiotic chloramphenicol (CAP) is a priority pollutant in wastewaters. A fed-batch bioelectrochemical system (BES) with biocathode with applied voltage of 0.5 V (served as extracellular electron donor) and glucose as intracellular electron donor was applied to reduce CAP to amine product (AMCl2). The biocathode BES converted 87.1 ± 4.2% of 32 mg/L CAP in 4 h, and the removal efficiency reached 96.0 ± 0.9% within 24 h. Conversely, the removal efficiency of CAP in BES with an abiotic cathode was only 73.0 ± 3.2% after 24 h. When the biocathode was disconnected (no electrochemical reaction but in the presence of microbial activities), the CAP removal rate was dropped to 62.0% of that with biocathode BES. Acetylation of one hydroxyl of CAP was noted exclusive in the biocatalyzed process, while toxic intermediates, hydroxylamino (HOAM), and nitroso (NO), from CAP reduction were observed only in the abiotic cathode BES. Electrochemical hydrodechlorination and dehalogenase were responsible for dechlorination of AMCl2 to AMCl in abiotic and microbial cathode BES, respectively. The cyclic voltammetry (CV) highlighted higher peak currents and lower overpotentials for CAP reduction at the biocathode compared with abiotic cathode. With the biocathode BES, antibacterial activity of CAP was completely removed and nitro group reduction combined with dechlorination reaction enhanced detoxication efficiency of CAP. The CAP cathodic transformation pathway was proposed based on intermediates analysis. Bacterial community analysis indicated that the dominate bacteria on the biocathode were belonging to α, β, and γ-Proteobacteria. The biocathode BES could serve as a potential treatment process for CAP-containing wastewater.
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Affiliation(s)
- Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090, P R China
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Bagherbaigi S, Gicana RG, Lamis RJ, Nemati M, Huyop F. Characterisation of Arthrobacter sp. S1 that can degrade α and β-haloalkanoic acids isolated from contaminated soil. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-012-0595-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Koudelakova T, Bidmanova S, Dvorak P, Pavelka A, Chaloupkova R, Prokop Z, Damborsky J. Haloalkane dehalogenases: Biotechnological applications. Biotechnol J 2012; 8:32-45. [DOI: 10.1002/biot.201100486] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 06/30/2012] [Accepted: 07/20/2012] [Indexed: 12/21/2022]
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Liang B, Jiang J, Zhang J, Zhao Y, Li S. Horizontal transfer of dehalogenase genes involved in the catalysis of chlorinated compounds: evidence and ecological role. Crit Rev Microbiol 2011; 38:95-110. [DOI: 10.3109/1040841x.2011.618114] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Wang G, Liang B, Li F, Li S. Recent advances in the biodegradation of chlorothalonil. Curr Microbiol 2011; 63:450-7. [PMID: 21879378 DOI: 10.1007/s00284-011-0001-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 08/15/2011] [Indexed: 11/25/2022]
Abstract
Chlorothalonil (TPN; 2,4,5,6-tetrachloroisophthalonitrile) has been widely used as a broad-spectrum chlorinated aromatic fungicide and its application resulted in global pollution commonly detected in the diverse ecosystems. Recently, microbial degradation of TPN has been studied extensively as an effective and environmental-friendly method to reduce TPN residue levels in the environment. This review summarizes the current knowledge of recent developments in the biodegradation of TPN. Diverse pure culture strains capable of degrading TPN were widely distributed among Proteobacteria and several metabolic pathways of TPN biotransformation were discovered. The two key genes (glutathione S-transferase and chlorothalonil hydrolytic dehalogenase coding gene) responsible for the conversion of TPN and recent findings for future practical bioremediation of TPN-contaminated ecosystem are also discussed.
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Affiliation(s)
- Guangli Wang
- Department of Microbiology, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, People's Republic of China
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Facilitation of bacterial adaptation to chlorothalonil-contaminated sites by horizontal transfer of the chlorothalonil hydrolytic dehalogenase gene. Appl Environ Microbiol 2011; 77:4268-72. [PMID: 21498744 DOI: 10.1128/aem.02457-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Horizontal transfer of the chlorothalonil hydrolytic dehalogenase gene (chd) is proposed based on the high conservation of the chd gene and its close association with a novel insertion sequence, ISOcsp1, in 16 isolated chlorothalonil-dechlorinating strains belonging to eight different genera. The ecological role of horizontal gene transfer is assumed to facilitate bacterial adaptation to chlorothalonil-contaminated sites, through detoxification of chlorothalonil to less toxic 2,4,5-trichloro-6-hydroxybenzene-1,3-dicarbonitrile.
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Wang G, Li R, Li S, Jiang J. A novel hydrolytic dehalogenase for the chlorinated aromatic compound chlorothalonil. J Bacteriol 2010; 192:2737-45. [PMID: 20363940 PMCID: PMC2876492 DOI: 10.1128/jb.01547-09] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 03/25/2010] [Indexed: 11/20/2022] Open
Abstract
Dehalogenases play key roles in the detoxification of halogenated aromatics. Interestingly, only one hydrolytic dehalogenase for halogenated aromatics, 4-chlorobenzoyl-coenzyme A (CoA) dehalogenase, has been reported. Here, we characterize another novel hydrolytic dehalogenase for a halogenated aromatic compound from the 2,4,5,6-tetrachloroisophthalonitrile (chlorothalonil)-degrading strain of Pseudomonas sp. CTN-3, which we have named Chd. Chd catalyzes a hydroxyl substitution at the 4-chlorine atom of chlorothalonil. The metabolite of the Chd dehalogenation, 4-hydroxy-trichloroisophthalonitrile, was identified by reverse-phase high-performance liquid chromatography (HPLC), tandem mass spectrometry (MS/MS), and nuclear magnetic resonance (NMR). Chd dehalogenates chlorothalonil under anaerobic and aerobic conditions and does not require the presence of cofactors such as CoA and ATP. Chd contains a putative conserved domain of the metallo-beta-lactamase superfamily and shows the highest identity with several metallohydrolases (24 to 29%). Chd is a monomer (36 kDa), and the isoelectric point (pI) of Chd is estimated to be 4.13. Chd has a dissociation constant (K(m)) of 0.112 mM and an overall catalytic rate (k(cat)) of 207 s(-1) for chlorothalonil. Chd is completely inhibited by 1,10-phenanthroline, diethyl pyrocarbonate, and N-bromosuccinic acid. Site-directed mutagenesis of Chd revealed that histidines 128 and 157, serine 126, aspartates 45, 130 and 184, and tryptophan 241 were essential for the dehalogenase activity. Chd differs from other reported hydrolytic dehalogenases based on the analysis of amino acid sequences and catalytic mechanisms. This study provides an excellent dehalogenase candidate for mechanistic study of hydrolytic dehalogenation of halogenated aromatic compound.
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Affiliation(s)
- Guangli Wang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, Jiangsu Province, People's Republic of China
| | - Rong Li
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, Jiangsu Province, People's Republic of China
| | - Shunpeng Li
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, Jiangsu Province, People's Republic of China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, Jiangsu Province, People's Republic of China
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Liang B, Li R, Jiang D, Sun J, Qiu J, Zhao Y, Li S, Jiang J. Hydrolytic Dechlorination of Chlorothalonil by Ochrobactrum sp. CTN-11 Isolated from a Chlorothalonil-Contaminated Soil. Curr Microbiol 2010; 61:226-33. [DOI: 10.1007/s00284-010-9603-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 01/26/2010] [Indexed: 10/19/2022]
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Aerobic biodegradation of the brominated flame retardants, dibromoneopentyl glycol and tribromoneopentyl alcohol. Biodegradation 2009; 20:621-7. [DOI: 10.1007/s10532-009-9249-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Accepted: 01/20/2009] [Indexed: 10/21/2022]
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Higgins TP, Hope SJ, Effendi AJ, Dawson S, Dancer BN. Biochemical and molecular characterisation of the 2,3-dichloro-1-propanol dehalogenase and stereospecific haloalkanoic dehalogenases from a versatile Agrobacterium sp. Biodegradation 2005; 16:485-92. [PMID: 15865161 DOI: 10.1007/s10532-004-5670-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We previously reported the presence of both haloalcohol and haloalkanoate dehalogenase activity in the Agrobacterium sp. strain NHG3. The versatile nature of the organism led us to further characterise the genetic basis of these dehalogenation activities. Cloning and sequencing of the haloalcohol dehalogenase and subsequent analysis suggested that it was part of a highly conserved catabolic gene cluster. Characterisation of the haloalkanoate dehalogenase enzyme revealed the presence of two stereospecific enzymes with a narrow substrate range which acted on D-2-chloropropionic and L-2-chloropropionoic acid, respectively. Cloning and sequencing indicated that the two genes were separated by 87 bp of non-coding DNA and were preceded by a putative transporter gene 66 bp upstream of the D-specific enzyme.
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Affiliation(s)
- Timothy P Higgins
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3TL, UK.
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Heath E, Brown WA, Jensen SR, Bratty MP. Biodegradation of chlorinated alkanes and their commercial mixtures by Pseudomonas sp. strain 273. J Ind Microbiol Biotechnol 2004; 33:197-207. [PMID: 16491365 DOI: 10.1007/s10295-004-0186-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2004] [Accepted: 09/29/2004] [Indexed: 11/28/2022]
Abstract
The biodegradation of chlorinated alkanes was studied under oxic conditions with the objective of identifying favorable and unfavorable intramolecular chlorination sequences with respect to the enzymes studied. Several dehalogenating bacterial strains were screened for their ability to degrade middle-chain polychlorinated alkanes as well as a commercial mixture. Of the organisms tested, the most promising was Pseudomonas sp. strain 273, which possesses an oxygenolytic dehalogenase. The effects of carbon chain length (C(6)-C(16)), halogen position, and overall chlorine content (14-61% w/w) were examined using both commercially available compounds and molecules synthesized in our laboratory. The effects of co-substrates, solvents, and inducing agents were also studied. The results with pure chlorinated alkanes showed that the relative positions of the chlorine atoms strongly influenced the total amount of dehalogenation achieved. The greatest dehalogenation yields were associated with terminally chlorinated alkanes. The alpha- and alpha,omega-chlorinated compounds yielded similar results. Vicinal chlorination had the most dramatic impact on degradation. When present on both ends or at the center of the molecule, no dehalogenation was detected. Although partial dehalogenation of 1,2-dichlorodecane was observed, it was likely due to a combination of beta-oxidation and an abiotic mechanism. Cereclor S52 was appreciably dehalogenated in shake flasks only when 1,10-dichlorodecane was present as a co-substrate and after increasing the oil surface area through mechanical emulsification, demonstrating the importance of abiotic factors in degrading commercial polychlorinated alkane mixtures.
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Affiliation(s)
- Ester Heath
- Department of Environmental Sciences, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
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21
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Singh BK, Kuhad RC, Singh A, Tripathi KK, Ghosh PK. Microbial degradation of the pesticide lindane (gamma-hexachlorocyclohexane). ADVANCES IN APPLIED MICROBIOLOGY 2003; 47:269-98. [PMID: 12876800 DOI: 10.1016/s0065-2164(00)47007-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- B K Singh
- Department of Microbiology, University of Delhi, New Delhi 110021, India
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22
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Otyepka M, Damborský J. Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains. Protein Sci 2002; 11:1206-17. [PMID: 11967377 PMCID: PMC2373552 DOI: 10.1110/ps3830102] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
One-nanosecond molecular dynamics trajectories of three haloalkane dehalogenases (DhlA, LinB, and DhaA) are compared. The main domain was rigid in all three dehalogenases, whereas the substrate specificity-modulating cap domains showed considerably higher mobility. The functionally relevant motions were spread over the entire cap domain in DhlA, whereas they were more localized in LinB and DhaA. The highest amplitude of essential motions of DhlA was noted in the alpha4'-helix-loop-alpha4-helix region, formerly proposed to participate in the large conformation change needed for product release. The highest amplitude of essential motions of LinB and DhaA was observed in the random coil before helix 4, linking two domains of these proteins. This flexibility is the consequence of the modular composition of haloalkane dehalogenases. Two members of the catalytic triad, that is, the nucleophile and the base, showed a very high level of rigidity in all three dehalogenases. This rigidity is essential for their function. One of the halide-stabilizing residues, important for the catalysis, shows significantly higher flexibility in DhlA compared with LinB and DhaA. Enhanced flexibility may be required for destabilization of the electrostatic interactions during the release of the halide ion from the deeply buried active site of DhlA. The exchange of water molecules between the enzyme active site and bulk solvent was very different among the three dehalogenases. The differences could be related to the flexibility of the cap domains and to the number of entrance tunnels.
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Affiliation(s)
- Michal Otyepka
- Department of Inorganic and Physical Chemistry, Faculty of Science, Palacky University, 771 46 Olomouc, Czech Republic
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23
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Song B, Palleroni NJ, Häggblom MM. Isolation and characterization of diverse halobenzoate-degrading denitrifying bacteria from soils and sediments. Appl Environ Microbiol 2000; 66:3446-53. [PMID: 10919805 PMCID: PMC92169 DOI: 10.1128/aem.66.8.3446-3453.2000] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Denitrifying bacteria capable of degrading halobenzoates were isolated from various geographical and ecological sites. The strains were isolated after initial enrichment on one of the monofluoro-, monochloro-, or monobromo-benzoate isomers with nitrate as an electron acceptor, yielding a total of 33 strains isolated from the different halobenzoate-utilizing enrichment cultures. Each isolate could grow on the selected halobenzoate with nitrate as the terminal electron acceptor. The isolates obtained on 2-fluorobenzoate could use 2-fluorobenzoate under both aerobic and denitrifying conditions, but did not degrade other halobenzoates. In contrast, the 4-fluorobenzoate isolates degraded 4-fluorobenzoate under denitrifying conditions only, but utilized 2-fluorobenzoate under both aerobic and denitrifying conditions. The strains isolated on either 3-chlorobenzoate or 3-bromobenzoate could use 3-chlorobenzoate, 3-bromobenzoate, and 2- and 4-fluorobenzoates under denitrifying conditions. The isolates were identified and classified on the basis of 16S rRNA gene sequence analysis and their cellular fatty acid profiles. They were placed in nine genera belonging to either the alpha-, beta-, or gamma-branch of the Proteobacteria, namely, Acidovorax, Azoarcus, Bradyrhizobium, Ochrobactrum, Paracoccus, Pseudomonas, Mesorhizobium, Ensifer, and Thauera. These results indicate that the ability to utilize different halobenzoates under denitrifying conditions is ubiquitously distributed in the Proteobacteria and that these bacteria are widely distributed in soils and sediments.
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Affiliation(s)
- B Song
- Department of Biochemistry and Microbiology and Biotechnology Center for Agriculture and the Environment, Cook College, Rutgers University, New Brunswick, NJ 08901-8525, USA
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24
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Damborský J, Koca J. Analysis of the reaction mechanism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons. PROTEIN ENGINEERING 1999; 12:989-98. [PMID: 10585505 DOI: 10.1093/protein/12.11.989] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Haloalkane dehalogenases catalyse environmentally important dehalogenation reactions. These microbial enzymes represent objects of interest for protein engineering studies, attempting to improve their catalytic efficiency or broaden their substrate specificity towards environmental pollutants. This paper presents the results of a comparative study of haloalkane dehalogenases originating from different organisms. Protein sequences and the models of tertiary structures of haloalkane dehalogenases were compared to investigate the protein fold, reaction mechanism and substrate specificity of these enzymes. Haloalkane dehalogenases contain the structural motifs of alpha/beta-hydrolases and epoxidases within their sequences. They contain a catalytic triad with two different topological arrangements. The presence of a structurally conserved oxyanion hole suggests the two-step reaction mechanism previously described for haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. The differences in substrate specificity of haloalkane dehalogenases originating from different species might be related to the size and geometry of an active site and its entrance and the efficiency of the transition state and halide ion stabilization by active site residues. Structurally conserved motifs identified within the sequences can be used for the design of specific primers for the experimental screening of haloalkane dehalogenases. Those amino acids which were predicted to be functionally important represent possible targets for future site-directed mutagenesis experiments.
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Affiliation(s)
- J Damborský
- Laboratory of Biomolecular Structure and Dynamics, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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25
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Abstract
In the recent past, the development of dehalogenating enzymes for industrial biocatalysis has been limited, but significant advances have been made. Three classes of enzymes have received attention and development: halalkanoic acid dehalogenases (EC 3.8.1.2), hydrogen-halide lyases (EC 4.5.1), and haloalkane dehalogenases (EC 3.8.1). Applications range from the manufacture of chiral intermediates, to recycling of chlorinated byproducts from chemical manufacturing, and selective treatment of process waste streams.
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Affiliation(s)
- P E Swanson
- The Dow Chemical Company, Corporate Research and Development, Building 1707, Midland, MI 48674, USA.
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26
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Hill KE, Marchesi JR, Weightman AJ. Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families. J Bacteriol 1999; 181:2535-47. [PMID: 10198020 PMCID: PMC93682 DOI: 10.1128/jb.181.8.2535-2547.1999] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dehalogenases are key enzymes in the metabolism of halo-organic compounds. This paper describes a systematic approach to the isolation and molecular analysis of two families of bacterial alpha-halocarboxylic acid (alphaHA) dehalogenase genes, called group I and group II deh genes. The two families are evolutionarily unrelated and together represent almost all of the alphaHA deh genes described to date. We report the design and evaluation of degenerate PCR primer pairs for the separate amplification and isolation of group I and II deh genes. Amino acid sequences derived from 10 of 11 group I deh partial gene products of new and previously reported bacterial isolates showed conservation of five residues previously identified as essential for activity. The exception, DehD from a Rhizobium sp., had only two of these five residues. Group II deh gene sequences were amplified from 54 newly isolated strains, and seven of these sequences were cloned and fully characterized. Group II dehalogenases were stereoselective, dechlorinating L- but not D-2-chloropropionic acid, and derived amino acid sequences for all of the genes except dehII degrees P11 showed conservation of previously identified essential residues. Molecular analysis of the two deh families highlighted four subdivisions in each, which were supported by high bootstrap values in phylogenetic trees and by enzyme structure-function considerations. Group I deh genes included two putative cryptic or silent genes, dehI degrees PP3 and dehI degrees 17a, produced by different organisms. Group II deh genes included two cryptic genes and an active gene, dehIIPP3, that can be switched off and on. All alphaHA-degrading bacteria so far described were Proteobacteria, a result that may be explained by limitations either in the host range for deh genes or in isolation methods.
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Affiliation(s)
- K E Hill
- Cardiff School of Biosciences, Cardiff University, Cardiff, CF1 3TL, Wales, United Kingdom
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27
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Benning MM, Wesenberg G, Liu R, Taylor KL, Dunaway-Mariano D, Holden HM. The three-dimensional structure of 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. Strain CBS-3. J Biol Chem 1998; 273:33572-9. [PMID: 9837940 DOI: 10.1074/jbc.273.50.33572] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The soil-dwelling microbe, Pseudomonas sp. strain CBS-3, has attracted recent attention due to its ability to survive on 4-chlorobenzoate as its sole carbon source. The biochemical pathway by which this organism converts 4-chlorobenzoate to 4-hydroxybenzoate consists of three enzymes: 4-chlorobenzoyl-CoA ligase, 4-chlorobenzoyl-CoA dehalogenase, and 4-hydroxybenzoyl-CoA thioesterase. Here we describe the three-dimensional structure of the thioesterase determined to 2.0-A resolution. Each subunit of the homotetramer is characterized by a five-stranded anti-parallel beta-sheet and three major alpha-helices. While previous amino acid sequence analyses failed to reveal any similarity between this thioesterase and other known proteins, the results from this study clearly demonstrate that the molecular architecture of 4-hydroxybenzoyl-CoA thioesterase is topologically equivalent to that observed for beta-hydroxydecanoyl thiol ester dehydrase from Escherichia coli. On the basis of the structural similarity between these two enzymes, the active site of the thioesterase has been identified and a catalytic mechanism proposed.
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Affiliation(s)
- M M Benning
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin- Madison, Madison, Wisconsin 53705, USA
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28
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Allpress JD, Gowland PC. Dehalogenases: environmental defence mechanism and model of enzyme evolution. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0307-4412(98)00090-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Wischnak C, Löffler FE, Li J, Urbance JW, Müller R. Pseudomonas sp. strain 273, an aerobic alpha, omega-dichloroalkaneDegrading bacterium. Appl Environ Microbiol 1998; 64:3507-11. [PMID: 9726906 PMCID: PMC106756 DOI: 10.1128/aem.64.9.3507-3511.1998] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A gram-negative, aerobic bacterium was isolated from soil; this bacterium grew in 50% (vol/vol) suspensions of 1,10-dichlorodecane (1,10-DCD) as the sole source of carbon and energy. Phenotypic and small-subunit ribosomal RNA characterizations identified the organism, designated strain 273, as a member of the genus Pseudomonas. After induction with 1,10-DCD, Pseudomonas sp. strain 273 released stoichiometric amounts of chloride from C5 to C12 alpha, omega-dichloroalkanes in the presence of oxygen. No dehalogenation occurred under anaerobic conditions. The best substrates for dehalogenation and growth were C9 to C12 chloroalkanes. The isolate also grew with nonhalogenated aliphatic compounds, and decane-grown cells dechlorinated 1,10-DCD without a lag phase. In addition, cells grown on decane dechlorinated 1,10-DCD in the presence of chloramphenicol, indicating that the 1,10-DCD-dechlorinating enzyme system was also induced by decane. Other known alkane-degrading Pseudomonas species did not grow with 1,10-DCD as a carbon source. Dechlorination of 1,10-DCD was demonstrated in cell extracts of Pseudomonas sp. strain 273. Cell-free activity was strictly oxygen dependent, and NADH stimulated dechlorination, whereas EDTA had an inhibitory effect.
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Affiliation(s)
- C Wischnak
- Arbeitsbereich Biotechnologie II, Technische Universität Hamburg-Harburg, D-21071 Hamburg, Germany
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30
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31
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Assis HM, Sallis PJ, Bull AT, Hardman DJ. Biochemical characterization of a haloalcohol dehalogenase from Arthrobacter erithii H10a. Enzyme Microb Technol 1998; 22:568-74. [PMID: 9621448 DOI: 10.1016/s0141-0229(97)00254-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Arthrobacter erithii H10a possesses two enzymes capable of catalyzing the dehalogenation of vicinal halohydrins which have been designated as dehalogenases DehA and DehC. The DehA dehalogenase demonstrated greater activity toward 1,3-dichloro-2-propanol (1,3-DCP) while the DehC dehalogenase showed higher activity toward 3-chloro-1,2-propanediol (3-CPD) and brominated alcohols. The DehA dehalogenase was composed of two non-identical subunits (relative molecular mass of 31.5 and 34 kDa) which probably associate with other proteins to form a large catalytically active protein of 200 kDa. The two subunits were purified and the amino acid sequence of their tryptic digests determined. The DehA enzyme catalyzed the conversion of vicinal halohydrins to epoxides and the reverse reaction in the presence of an excess of halogen. This enzyme had maximum activity at 50 degrees C and a broad pH optimum over the range 8.5-10.5. The apparent K(m) and Vmax values for dehalogenation of 1,3-DCP and 3-CPD were 0.105 mM and 223 mumol min-1 mg-1; and 2.366 mM and 1.742 mumol min-1 mg-1, respectively. The enzyme was inhibited by 2-chloroacetic acid (MCA) and 2,2-dichloroacetic acid (DCA). The inhibition pattern suggested a mixed type inhibition which was predominantly uncompetitive. Amino acid modification experiments demonstrated that one or more cysteine and arginine residues are likely to be involved in catalysis or play an important role in the maintenance of the enzyme structure. The characteristics of the DehA enzyme are compared to those of previously reported haloalcohol dehalogenases and discussed in terms of diversity of this type of dehalogenase.
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Affiliation(s)
- H M Assis
- Research School of Biosciences, University of Kent, Canterbury, United Kingdom
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Nagata Y, Miyauchi K, Damborsky J, Manova K, Ansorgova A, Takagi M. Purification and characterization of a haloalkane dehalogenase of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26. Appl Environ Microbiol 1997; 63:3707-10. [PMID: 9293022 PMCID: PMC168677 DOI: 10.1128/aem.63.9.3707-3710.1997] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The linB gene product (LinB), 1,3,4,6-tetrachloro-1,4-cyclohexadiene halidohydrolase, which is involved in the degradation of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis UT26 (Y. Nagata, T. Nariya, R. Ohtomo, M. Fukuda, K. Yano, and M. Takagi, J. Bacteriol. 175:6403-6410, 1993), was overproduced in E. coli and purified to homogeneity. The molecular mass of LinB was deduced to be 30 kDa by gel filtration chromatography and 32 kDa by electrophoresis on sodium dodecyl sulfate-polyacrylamide gel, indicating that LiuB is a monomeric enzyme. The optimal pH for activity was 8.2. Not only monochloroalkanes (C3 to C10) but also dichloroalkanes, bromoalkanes, and chlorinated allphatic alcohols were good substrates for LinB, suggesting that LinB shares properties with another haloalkane dehalogenase, DhlA (S. Keuning, D.B. Janssen, and B. Witholt, J. Bacteriol. 163:635-639, 1985), which shows significant similarity to LinB in primary structure (D. B. Janssen, F. Pries, J. van der Ploeg, B. Kazemier, P. Terpstra, and B. Witholt, J. Bacteriol. 171:6791-6799, 1989) but not in substrate specificity. Principal component analysis of substrate activities of various haloalkane dehalogenases suggested that LinB probably constitutes a new substrate specificity class within this group of enzymes.
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Affiliation(s)
- Y Nagata
- Department of Biotechnology, University of Tokyo, Japan.
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33
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Zheng YJ, Bruice TC. On the Dehalogenation Mechanism of 4-Chlorobenzoyl CoA by 4-Chlorobenzoyl CoA Dehalogenase: Insights from Study Based on the Nonenzymatic Reaction. J Am Chem Soc 1997. [DOI: 10.1021/ja970114j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ya-Jun Zheng
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Thomas C. Bruice
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
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Diez A, Prieto M, Alvarez M, Bautista J, Puyet A, Pertierra G. Purification and properties of a high-affinity L-2-haloacid dehalogenase from Azotabacter sp. strain RC26. Lett Appl Microbiol 1996. [DOI: 10.1111/j.1472-765x.1996.tb00189.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Brokamp A, Happe B, Schmidt FR. Cloning and nucleotide sequence of a D,L-haloalkanoic acid dehalogenase encoding gene from Alcaligenes xylosoxidans ssp. denitrificans ABIV. Biodegradation 1996; 7:383-96. [PMID: 9144969 DOI: 10.1007/bf00056422] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have cloned DNA fragments of plasmid pFL40 from Alcaligenes xylosoxidans ssp. denitrificans ABIV encoding a D,L-2-haloalkanoic acid halidohydrolase (DhlIV). A 6.5-kb EcoRI/SalI-fragment with inducible expression of the halidohydrolase was cloned in Pseudomonas fluorescens and Escherichia coli. A 1.9-kb HindII-fragment demonstrated expression of the dehalogenase only due to the presence of the promoter from the pUC vector in Escherichia coli. The nucleotide sequence of this DNA-fragment was determined. It had an open reading frame coding for 296 amino acid residues (molecular weight of 32783 D). The dhlIV gene showed sequence homology to a short segment of a D-specific dehalogenase (hadD) from Pseudomonas putida AJ1, but not to any other known DNA sequences. Restriction enzyme patterns indicated similarity between dhlIV and the D,L- isomer specific dehl dehalogenase gene from Pseudomonas putida PP3. There are some indications from restriction enzyme patterns and initial sequencing data, that a gene encoding a sigma 54-dependent activator protein, similar to the dehRI regulatory gene from Pseudomonas putida PP3 is located upstream of dhlIV. In contrast to DehI, dehalogenation of D- or L-chloropropionic acid by the DhlIV-protein leads to lactic acid of inverted configuration.
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Affiliation(s)
- A Brokamp
- Department of Microbiology, University Gesamthochschule Kassel, Germany
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36
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Slater JH, Bull AT, Hardman DJ. Microbial dehalogenation of halogenated alkanoic acids, alcohols and alkanes. Adv Microb Physiol 1996; 38:133-76. [PMID: 8922120 DOI: 10.1016/s0065-2911(08)60157-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- J H Slater
- Molecular Ecology Research Unit, School of Pure and Applied Biology, University of Wales, Cardiff, UK
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