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Deng W, Takada Y, Nanasato Y, Kishida K, Stari L, Ohtsubo Y, Tabei Y, Watanabe M, Nagata Y. Transgenic Arabidopsis thaliana plants expressing bacterial γ-hexachlorocyclohexane dehydrochlorinase LinA. BMC Biotechnol 2024; 24:42. [PMID: 38898480 PMCID: PMC11186250 DOI: 10.1186/s12896-024-00867-0] [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: 02/25/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND γ-Hexachlorocyclohexane (γ-HCH), an organochlorine insecticide of anthropogenic origin, is a persistent organic pollutant (POP) that causes environmental pollution concerns worldwide. Although many γ-HCH-degrading bacterial strains are available, inoculating them directly into γ-HCH-contaminated soil is ineffective because of the low survival rate of the exogenous bacteria. Another strategy for the bioremediation of γ-HCH involves the use of transgenic plants expressing bacterial enzyme for γ-HCH degradation through phytoremediation. RESULTS We generated transgenic Arabidopsis thaliana expressing γ-HCH dehydrochlroninase LinA from bacterium Sphingobium japonicum strain UT26. Among the transgenic Arabidopsis T2 lines, we obtained one line (A5) that expressed and accumulated LinA well. The A5-derived T3 plants showed higher tolerance to γ-HCH than the non-transformant control plants, indicating that γ-HCH is toxic for Arabidopsis thaliana and that this effect is relieved by LinA expression. The crude extract of the A5 plants showed γ-HCH degradation activity, and metabolites of γ-HCH produced by the LinA reaction were detected in the assay solution, indicating that the A5 plants accumulated the active LinA protein. In some A5 lines, the whole plant absorbed and degraded more than 99% of γ-HCH (10 ppm) in the liquid medium within 36 h. CONCLUSION The transgenic Arabidopsis expressing active LinA absorbed and degraded γ-HCH in the liquid medium, indicating the high potential of LinA-expressing transgenic plants for the phytoremediation of environmental γ-HCH. This study marks a crucial step toward the practical use of transgenic plants for the phytoremediation of POPs.
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Affiliation(s)
- Wenhao Deng
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Yoshinobu Takada
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Yoshihiko Nanasato
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), Forest Research and Management Organization (FRMO), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Kouhei Kishida
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Leonardo Stari
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Yoshiyuki Ohtsubo
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Yutaka Tabei
- Faculty of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura-Machi, Ora-Gun, Gunma, 374-0193, Japan
| | - Masao Watanabe
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Yuji Nagata
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan.
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Yusuf Habibullah KO, Ito R, Stari L, Kishida K, Ohtsubo Y, Masai E, Fukuda M, Miyauchi K, Nagata Y. Degradation of DDT by γ-hexachlorocyclohexane dehydrochlorinase LinA. Biosci Biotechnol Biochem 2023; 88:123-130. [PMID: 37796901 DOI: 10.1093/bbb/zbad141] [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: 08/30/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023]
Abstract
1,1,1-Trichloro-2,2-bis(4-chlorophenyl)-ethane (DDT) is the first synthetic insecticide and one of the most widely used pesticides. The use of DDT has been banned, but it remains one of the most notorious environmental pollutants around the world. In this study, we found that γ-hexachlorocyclohexane (γ-HCH) dehydrochlorinase LinA from a γ-HCH-degrading bacterium, Sphingobium japonicum UT26, converts DDT to 1,1-dichloro-2,2-bis(4-chlorophenyl)-ethylene (DDE). Because of the weak DDT degradation activity of LinA, we could not detect such activity in UT26 cells expressing LinA constitutively. However, the linA-deletion mutant of UT26 harboring a plasmid for the expression of LinA, in which LinA was expressed at a higher level than UT26, showed the DDT degradation activity. This outcome highlights the potential for constructing DDT-degrading sphingomonad cells through elevated LinA expression.
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Affiliation(s)
| | - Ren Ito
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Leonardo Stari
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Kouhei Kishida
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yoshiyuki Ohtsubo
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Eiji Masai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Masao Fukuda
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Keisuke Miyauchi
- Department of Civil and Environmental Engineering, Faculty of Engineering, Tohoku Gakuin University, Sendai, Japan
| | - Yuji Nagata
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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Sun S, Wang Y, Xu C, Qiao C, Chen S, Zhao C, Liu Q, Zhang X. Reconstruction of microbiome and functionality accelerated crude oil biodegradation of 2,4-DCP-oil-contaminated soil systems using composite microbial agent B-Cl. JOURNAL OF HAZARDOUS MATERIALS 2023; 447:130808. [PMID: 36669400 DOI: 10.1016/j.jhazmat.2023.130808] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/02/2023] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Biodegradation is one of the safest and most economical methods for the elimination of toxic chlorophenols and crude oil from the environment. In this study, aerobic degradation of the aforementioned compounds by composite microbial agent B-Cl, which consisted of Bacillus B1 and B2 in a 3:2 ratio, was analyzed. The biodegradation mechanism of B-Cl was assessed based on whole genome sequencing, Fourier transform infrared spectroscopy and gas chromatographic analyses. B-Cl was most effective at reducing Cl- concentrations (65.17%) and crude oil biodegradation (59.18%) at 7 d, which was when the content of alkanes ≤ C30 showed the greatest decrease. Furthermore, adding B-Cl solution to soil significantly decreased the 2,4-DCP and oil content to below the detection limit and by 80.68%, respectively, and reconstructed of the soil microbial into a system containing more CPs-degrading (exaA, frmA, L-2-HAD, dehH, ALDH, catABE), aromatic compounds-degrading (pcaGH, catAE, benA-xylX, paaHF) and alkane- and fatty acid-degrading (alkB, atoB, fadANJ) microorganisms. Moreover, the presence of 2,4-DCP was the main hinder of the observed effects. This study demonstrates the importance of adding B-Cl solution to determine the interplay of CPs with microbes and accelerating oil degradation, which can be used for in-situ bioremediation of CPs and oil-contaminated soil.
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Affiliation(s)
- Shuo Sun
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao 266580, PR China
| | - Yaru Wang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao 266580, PR China
| | - Chenfei Xu
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao 266580, PR China
| | - Chenlu Qiao
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao 266580, PR China
| | - Shuiquan Chen
- College of Energy and Mining Engineering, Shandong University of Science and Technology, Qingdao 266590, PR China
| | - Chaocheng Zhao
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao 266580, PR China
| | - Qiyou Liu
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao 266580, PR China.
| | - Xiuxia Zhang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China; State Key Laboratory of Petroleum Pollution Control, Qingdao 266580, PR China
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Abstract
This study evaluated the efficiency of two biofilter systems, with and without biochar chambers installed, at degrading and removing HCH and its isomers in natural drainage water. The biochar biofilter proved to be 96% efficient at cleaning HCH and its transformation products from drainage water, a significant improvement over classic biofilter that remove, on average, 68% of HCH. Although iron- and sulfur-oxidizing bacteria, such as Gallionella and Sulfuricurvum, were dominant in the biochar bed outflows, they were absent in sediments, which were rich in Simplicispira, Rhodoluna, Rhodoferax, and Flavobacterium. The presence of functional genes involved in the biodegradation of HCH isomers and their byproducts was confirmed in both systems. The high effectiveness of the biochar biofilter displayed in this study should further encourage the use of biochar in water treatment solutions, e.g., for temporary water purification installations during the construction of other long-term wastewater treatment technologies, or even as final solutions at contaminated sites.
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Heeb NV, Hubeli J, Fleischmann T, Lienemann P, Nayyar N, Lal R, Kohler HPE. Transformation of ε-HBCD with the Sphingobium Indicum enzymes LinA1, LinA2 and LinATM, a triple mutant of LinA2. CHEMOSPHERE 2021; 267:129217. [PMID: 33321275 DOI: 10.1016/j.chemosphere.2020.129217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Hexabromocyclododecanes (HBCDs) were used as flame-retardants until their ban in 2013. Among the 16 stereoisomers known, ε-HBCD has the highest symmetry. This makes ε-HBCD an interesting substrate to study the selectivity of biotransformations. We expressed three LinA dehydrohalogenase enzymes in E. coli bacteria, two wild-type, originating from Sphingobium indicum B90A bacteria and LinATM, a triple mutant of LinA2, with mutations of L96C, F113Y and T133 M. These enzymes are involved in the hexachlorocyclohexane (HCH) metabolism, specifically of the insecticide γ-HCH (Lindane). We studied the reactivity of those eight HBCD stereoisomers found in technical HBCD. Furthermore, we compared kinetics and selectivity of these LinA variants with respect to ε-HBCD. LC-MS data indicate that all enzymes converted ε-HBCD to pentabromocyclododecenes (PBCDens). Transformations followed Michaelis-Menten kinetics. Rate constants kcat and enzyme specificities kcat/KM indicate that ε-HBCD conversion was fastest and most specific with LinA2. Only one PBCDen stereoisomer was formed by LinA2, while LinA1 and LinATM produced mixtures of two PBCDE enantiomers at three times lower rates than LinA2. In analogy to the biotransformation of (-)β-HBCD, with selective conversion of dibromides in R-S-configuration, we assume that 1E,5S,6R,9S,10R-PBCDen is the ε-HBCD transformation product from LinA2. Implementing three amino acids of the LinA1 substrate-binding site into LinA2 resulted in a triple mutant with similar kinetics and product specificity like LinA1. Thus, point-directed mutagenesis is an interesting tool to modify the substrate- and product-specificity of LinA enzymes and enlarge their scope to metabolize other halogenated persistent organic pollutants regulated under the Stockholm Convention.
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Affiliation(s)
- Norbert V Heeb
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland.
| | - Jasmin Hubeli
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland; ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820, Wädenswil, Switzerland; Current Address: Cantonal Pharmacy Zürich, Südstrasse 3, CH-8952, Schlieren, Switzerland
| | - Thomas Fleischmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Peter Lienemann
- ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820, Wädenswil, Switzerland
| | - Namita Nayyar
- Sri Venkateswara College, University of Delhi, Delhi, 1110021, India
| | - Rup Lal
- The Energy and Resources Institute, India Habitat Center, New Delhi, Delhi, 110003, India
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
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Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists. Sci Rep 2021; 11:3056. [PMID: 33542397 PMCID: PMC7862292 DOI: 10.1038/s41598-021-82660-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/22/2021] [Indexed: 12/01/2022] Open
Abstract
Hydroxybenzoic acids, like gallic acid and protocatechuic acid, are highly abundant natural compounds. In biotechnology, they serve as critical precursors for various molecules in heterologous production pathways, but a major bottleneck is these acids’ non-oxidative decarboxylation to hydroxybenzenes. Optimizing this step by pathway and enzyme engineering is tedious, partly because of the complicating cofactor dependencies of the commonly used prFMN-dependent decarboxylases. Here, we report the crystal structures (1.5–1.9 Å) of two homologous fungal decarboxylases, AGDC1 from Arxula adenivorans, and PPP2 from Madurella mycetomatis. Remarkably, both decarboxylases are cofactor independent and are superior to prFMN-dependent decarboxylases when heterologously expressed in Saccharomyces cerevisiae. The organization of their active site, together with mutational studies, suggests a novel decarboxylation mechanism that combines acid–base catalysis and transition state stabilization. Both enzymes are trimers, with a central potassium binding site. In each monomer, potassium introduces a local twist in a β-sheet close to the active site, which primes the critical H86-D40 dyad for catalysis. A conserved pair of tryptophans, W35 and W61, acts like a clamp that destabilizes the substrate by twisting its carboxyl group relative to the phenol moiety. These findings reveal AGDC1 and PPP2 as founding members of a so far overlooked group of cofactor independent decarboxylases and suggest strategies to engineer their unique chemistry for a wide variety of biotechnological applications.
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Sowińska A, Vasquez L, Żaczek S, Manna RN, Tuñón I, Dybala-Defratyka A. Seeking the Source of Catalytic Efficiency of Lindane Dehydrochlorinase, LinA. J Phys Chem B 2020; 124:10353-10364. [PMID: 33146535 PMCID: PMC7681783 DOI: 10.1021/acs.jpcb.0c08976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we present the results of an in-depth simulation study of LinA and its two variants. In our analysis, we combined the exploration of protein conformational dynamics with and without bound substrates (hexachlorocyclohexane (HCH) isomers) performed using molecular dynamics simulation followed by the extraction of the most frequently visited conformations and their characteristics with a detailed description of the interactions taking place in the active site between the respective HCH molecule and the first shell residues by using symmetry-adapted perturbation theory (SAPT) calculations. A detailed investigation of the conformational space of LinA substates has been accompanied by description of enzymatic catalytic steps carried out using a hybrid quantum mechanics/molecular mechanics (QM/MM) potential along with the computation of the potential of mean force (PMF) to estimate the free energy barriers for the studied transformations: dehydrochlorination of γ-, (-)-α-, and (+)-α-HCH by LinA-type I and -type II variants. The applied combination of computational techniques allowed us not only to characterize two LinA types but also to point to the most important differences between them and link their features to catalytic efficiency each of them possesses toward the respective ligand. More importantly it has been demonstrated that type I protein is more mobile, its active site has a larger volume, and the dehydrochlorination products are stabilized more strongly than in the case of type II enzyme, due to differences in the residues present in the active sites. Additionally, interaction energy calculations revealed very interesting patterns not predicted before but having the potential to be utilized in any attempts of improving LinA catalytic efficiency. On the basis of all these observations, LinA-type I protein seems to be more preorganized for the dehydrochlorination reaction it catalyzes than the type II variant.
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Affiliation(s)
- Agata Sowińska
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Luis Vasquez
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Szymon Żaczek
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Rabindra Nath Manna
- School Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Iñaki Tuñón
- Departamento de Quı́mica Fı́sica, Universitat de Valencia, 46100 Burjassot, Valencia Spain
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
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Vuksanovic N, Zhu X, Serrano DA, Siitonen V, Metsä-Ketelä M, Melançon CE, Silvaggi NR. Structural characterization of three noncanonical NTF2-like superfamily proteins: implications for polyketide biosynthesis. Acta Crystallogr F Struct Biol Commun 2020; 76:372-383. [PMID: 32744249 PMCID: PMC7397469 DOI: 10.1107/s2053230x20009814] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022] Open
Abstract
Proteins belonging to the NTF2-like superfamily are present in the biosynthetic pathways of numerous polyketide natural products, such as anthracyclins and benzoisochromanequinones. Some have been found to be bona fide polyketide cyclases, but many of them have roles that are currently unknown. Here, the X-ray crystal structures of three NTF2-like proteins of unknown function are reported: those of ActVI-ORFA from Streptomyces coelicolor A3(2) and its homologs Caci_6494, a protein from an uncharacterized biosynthetic cluster in Catenulispora acidiphila, and Aln2 from Streptomyces sp. CM020, a protein in the biosynthetic pathway of alnumycin. The presence of a solvent-accessible cavity and the conservation of the His/Asp dyad that is characteristic of many polyketide cyclases suggest a potential enzymatic role for these enzymes in polyketide biosynthesis.
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Affiliation(s)
- Nemanja Vuksanovic
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, WI 53211, USA
| | - Xuechen Zhu
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | - Dante A. Serrano
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, WI 53211, USA
| | - Vilja Siitonen
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Charles E. Melançon
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA
| | - Nicholas R. Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, WI 53211, USA
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Liu Y, Wu L, Kohli P, Kumar R, Stryhanyuk H, Nijenhuis I, Lal R, Richnow HH. Enantiomer and Carbon Isotope Fractionation of α-Hexachlorocyclohexane by Sphingobium indicum Strain B90A and the Corresponding Enzymes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:8715-8724. [PMID: 31266304 DOI: 10.1021/acs.est.9b01233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chiral organic contaminants, like α-hexachlorocyclohexane (α-HCH), showed isotope fractionation and enantiomer fractionation during biodegradation. This study aims to understand the correlation between these two processes. Initial tests of α-HCH degradation by six Sphingobium strains (with different LinA variants) were conducted. Results showed variable enantiomer selectivity over the time course. In contrast, constant enantiomer selectivity was observed in experiments employing (i) cell suspensions, (ii) crude extracts, or (iii) LinA1 and LinA2 enzymes of strain B90A for α-HCH degradation in enzyme activity assay buffer. The average value of enantioselectivity (ES) were -0.45 ± 0.03 (cell suspensions), -0.60 ± 0.05 (crude extracts), and 1 (LinA1) or -1 (LinA2). The average carbon isotope enrichment factors (εc) of (+)α- and (-)α-HCH were increased from cells suspensions (-6.3 ± 0.1‰ and -2.3 ± 0.03‰) over crude extracts (-7.7 ± 0.4‰ and -3.4 ± 0.02‰) to purified enzymes (-11.1 ± 0.3‰ and -3.8 ± 0.2‰). The variability of ES and the εc were discussed based on the effect of mass transport and degradation rates. Our study demonstrates that enantiomer and isotope fractionation of α-HCH are two independent processes and both are affected by underlying reactions of individual enzymes and mass transport to a different extent.
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Affiliation(s)
- Yaqing Liu
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research-UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Langping Wu
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research-UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Puneet Kohli
- Molecular Biology Laboratory, Department of Zoology , University of Delhi , Delhi - 110007 , India
| | - Roshan Kumar
- Molecular Biology Laboratory, Department of Zoology , University of Delhi , Delhi - 110007 , India
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research-UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research-UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology , University of Delhi , Delhi - 110007 , India
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research-UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
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Heeb NV, Schalles S, Lehner S, Schinkel L, Schilling I, Lienemann P, Bogdal C, Kohler HPE. Biotransformation of short-chain chlorinated paraffins (SCCPs) with LinA2: A HCH and HBCD converting bacterial dehydrohalogenase. CHEMOSPHERE 2019; 226:744-754. [PMID: 30965245 DOI: 10.1016/j.chemosphere.2019.03.169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/19/2019] [Accepted: 03/24/2019] [Indexed: 06/09/2023]
Abstract
Short-chain chlorinated paraffins (SCCPs) are polyhalogenated hydrocarbons as are hexachlorocyclohexanes (HCHs) and hexabromocyclododecanes (HBCDs). They all have been classified as persistent organic pollutants (POPs) under the UN Stockholm Convention. Per se such compounds are transformed slowly in the environment, transported over long distances and accumulate in biota. Several Sphingomonadacea strains isolated from HCH dump sites have evolved to express enzymes that can transform HCHs and HBCDs. We hypothesized that LinA2, a dehydrohalogenase expressed in such bacteria, may also transform CPs to chlorinated olefins (COs). Three mixtures of penta- to deca-chlorinated undecanes (C11), dodecanes (C12) and tridecanes (C13) were exposed to LinA2. High-resolution full-scan mass spectra (R∼8'000) of CPs and COs were obtained applying a soft ionization method, enhancing chloride-adduct [M+Cl]- formation. A mathematical deconvolution procedure was used to separate interfering spectra to verify that LinA2 indeed catalyzed the conversion of CPs to COs. About 20-40% of the material was transformed in 24 h, about 50-70% was converted in 200 h. A bimodal first-order kinetic model could describe transformations of reactive and persistent CPs. Under the given conditions reactive CPs (τ1/2 = 1.4-6.9 h) were converted 30 to 190-times faster than the persistent ones (τ1/2 = 150-260 h). Proportions of persistent isomers (pp) varied from 60 to 80%. Lower chlorinated homologues contained higher proportions of persistent isomers. In conclusion, SCCP mixtures contain both, material that is readily converted by LinA2, and persistent material that is not or only slowly transformed.
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Affiliation(s)
- Norbert V Heeb
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland.
| | - Simone Schalles
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland; RWTH, Aachen University, Institute for Environmental Sciences, Worringerweg 1, D-52074, Aachen, Germany; ETH, Swiss Federal Institute of Technology, Institute of Biogeochemistry and Pollutant Dynamic, Universitätsstrasse 16, CH-8092, Zurich, Switzerland
| | - Sandro Lehner
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland; ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820, Wädenswil, Switzerland
| | - Lena Schinkel
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland; ETH, Swiss Federal Institute of Technology, Institute of Chemical and Bioengineering, Vladimir-Prelog-Weg 1, CH-8093, Zurich, Switzerland
| | - Iris Schilling
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Peter Lienemann
- ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820, Wädenswil, Switzerland
| | - Christian Bogdal
- ETH, Swiss Federal Institute of Technology, Institute of Biogeochemistry and Pollutant Dynamic, Universitätsstrasse 16, CH-8092, Zurich, Switzerland; present address: FOR, Zurich Forensic Science Institute, Zeughausstrasse 11, CH-8004, Zurich, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
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11
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Lu Q, Qiu L, Yu L, Zhang S, de Toledo RA, Shim H, Wang S. Microbial transformation of chiral organohalides: Distribution, microorganisms and mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2019; 368:849-861. [PMID: 30772625 DOI: 10.1016/j.jhazmat.2019.01.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 05/27/2023]
Abstract
Chiral organohalides including dichlorodiphenyltrichloroethane (DDT), Hexabromocyclododecane (HBCD) and polychlorinated biphenyls (PCBs) raise a significant concern in the environmental occurrence, fate and ecotoxicology due to their enantioselective biological effects. This review provides a state-of-the-art overview on enantioselective microbial transformation of the chiral organohalides. We firstly summarized worldwide field assessments of chiral organohalides in a variety of environmental matrices, which suggested the pivotal role of microorganisms in enantioselective transformation of chiral organohalides. Then, laboratory studies provided experimental evidences to further link enantioselective attenuation of chiral organohalides to specific functional microorganisms and enzymes, revealing mechanistic insights into the enantioselective microbial transformation processes. Particularly, a few amino acid residues in the functional enzymes could play a key role in mediating the enantioselectivity at the molecular level. Finally, major challenges and further developments toward an in-depth understanding of the enantioselective microbial transformation of chiral organohalides are identified and discussed.
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Affiliation(s)
- Qihong Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, 510275 Guangzhou, China; Environmental Microbiome Research Center, Sun Yat-Sen University, 510275 Guangzhou, China
| | - Lan Qiu
- School of Environmental Science and Engineering, Sun Yat-Sen University, 510275 Guangzhou, China
| | - Ling Yu
- School of Environmental Science and Engineering, Sun Yat-Sen University, 510275 Guangzhou, China; Environmental Microbiome Research Center, Sun Yat-Sen University, 510275 Guangzhou, China
| | - Shangwei Zhang
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Renata Alves de Toledo
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, 999078 Macau SAR, China
| | - Hojae Shim
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, 999078 Macau SAR, China
| | - Shanquan Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, 510275 Guangzhou, China; Environmental Microbiome Research Center, Sun Yat-Sen University, 510275 Guangzhou, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, 510275 Guangzhou, China.
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12
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Abstract
Approaches to determine chlorine kinetic isotope effects (Cl-KIEs) on enzymatic dehalogenations are discussed and illustrated by representative examples. Three aspects are considered. First methodology for experimental measurement of Cl-KIEs, with stress being on FAB-IRMS technique developed in our laboratory, is described. Subsequently, we concentrate our discussion on the consequences of reaction complexity in the interpretation of experimental values, a problem especially important in cases of polychlorinated reactants. The most fruitful studies of enzymatic dehalogenations by Cl-KIEs require their theoretical evaluation, hence the computational focus of the second part of this chapter.
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13
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Heeb NV, Grubelnik A, Geueke B, Kohler HPE, Lienemann P. Biotransformation of hexabromocyclododecanes with hexachlorocyclohexane-transforming Sphingobium chinhatense strain IP26. CHEMOSPHERE 2017; 182:491-500. [PMID: 28521164 DOI: 10.1016/j.chemosphere.2017.05.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 06/07/2023]
Abstract
Bacterial evolution has resulted in the appearance of several Sphingomonadacea strains that gained the ability to metabolize hexachlorocyclohexanes (HCHs). HCHs have been widely used as pesticides but were banned under the Stockholm Convention on persistent organic pollutants (POPs) in 2009. Here we present evidence for bacterial transformation reactions of hexabromocyclododecanes (HBCDs), which are structurally related to HCHs. HBCDs were used as flame retardants. They are now also considered as POPs and their production and use is restricted since 2013. Racemic α-, β-, and γ-HBCDs and their mixture were exposed to Sphingobium chinhatense IP26 in resting cell assays in parallel to β-HCH. All HBCD stereoisomers were converted with (-)β-HBCD being the best and both α-HBCD enantiomers the poorest substrates. HBCD conversion rates were 27-430 times slower than that of β-HCH. Three generations of hydroxylated transformation products were observed, 7 pentabromocyclododecanol isomers (PeBCD-ols), 11 tetrabromocyclododecadiols (TeBCD-diols) and 3 tribromocyclododecatriols (TrBCD-triols). The conversion of (+)α-, (-)β- and (-)γ-HBCD was faster than those of their enantiomers. Therefore the respective enantiomeric excess increased to 3 ± 1%, 36 ± 1% and 6 ± 2% during 48 h of bacterial exposure. PeBCD-ols appeared first, followed by TeBCD-diols and TrBCD-triols indicating stepwise hydrolytic dehalogenation reactions. In conclusion, severe HCH pollution at geographically distinct dumpsites triggered bacterial evolution to express enzymes transforming such compounds. We used S. chinhatense IP26 bacteria to transform structurally related HBCDs, also regulated under the Stockholm Convention. Such bacteria might be useful for bioremediation but the toxicity of the numerous transformation products observed must be assessed in advance.
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Affiliation(s)
- Norbert V Heeb
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland.
| | - Andreas Grubelnik
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Advanced Analytical Technologies, Überlandstrasse 129, CH-8600, Dübendorf, Switzerland
| | - Birgit Geueke
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Peter Lienemann
- ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820, Wädenswil, Switzerland
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14
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Shrivastava N, Macwan AS, Kohler HPE, Kumar A. Important amino acid residues of hexachlorocyclohexane dehydrochlorinases (LinA) for enantioselective transformation of hexachlorocyclohexane isomers. Biodegradation 2017; 28:171-180. [PMID: 28251436 PMCID: PMC5422493 DOI: 10.1007/s10532-017-9786-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/22/2017] [Indexed: 11/25/2022]
Abstract
LinA-type1 and LinA-type2 are two well-characterized variants of the enzyme ‘hexachlorocyclohexane (HCH)-dehydrochlorinase’. They differ from each other at ten amino acid positions and exhibit differing enantioselectivity for the transformation of the (–) and (+) enantiomers of α-HCH. Amino acids responsible for this enantioselectivity, however, are not known. An in silico docking analysis identified four amino acids (K20, L96, A131, and T133) in LinA-type1 that could be involved in selective binding of the substrates. Experimental studies with constructed mutant enzymes revealed that a combined presence of three amino acid changes in LinA-type1, i.e. K20Q, L96C, and A131G, caused a reversal in its preference from the (–) to the (+) enantiomer of α-HCH. This preference was enhanced by the additional amino acid change T133 M. Presence of these four changes also caused the reversal of enantioselectivity of LinA-type1 for δ-HCH, and β-, γ-, and δ-pentachlorocyclohexens. Thus, the residues K20, L96, A131, and T133 in LinA-type1 and the residues Q20, C96, G131, and M133 in LinA-type 2 appear to be important determinants for the enantioselectivity of LinA enzymes.
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Affiliation(s)
- Nidhi Shrivastava
- Academy of Scientific and Innovative Research, New Delhi, India
- Environmental Biotechnology Section, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Ankit S Macwan
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Hans-Peter E Kohler
- Department of Environmental Microbiology, Swiss Federal Institute for Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
| | - Ashwani Kumar
- Academy of Scientific and Innovative Research, New Delhi, India
- Environmental Biotechnology Section, CSIR-Indian Institute of Toxicology Research, Lucknow, India
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15
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Nanasato Y, Namiki S, Oshima M, Moriuchi R, Konagaya KI, Seike N, Otani T, Nagata Y, Tsuda M, Tabei Y. Biodegradation of γ-hexachlorocyclohexane by transgenic hairy root cultures of Cucurbita moschata that accumulate recombinant bacterial LinA. PLANT CELL REPORTS 2016; 35:1963-1974. [PMID: 27295266 DOI: 10.1007/s00299-016-2011-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 06/04/2016] [Indexed: 06/06/2023]
Abstract
γ-HCH was successfully degraded using LinA-expressed transgenic hairy root cultures of Cucurbita moschata . Fusing an endoplasmic reticulum-targeting signal peptide to LinA was essential for stable accumulation in the hairy roots. The pesticide γ-hexachlorocyclohexane (γ-HCH) is a persistent organic pollutant (POP) that raises public health and environmental pollution concerns worldwide. Although several isolates of γ-HCH-degrading bacteria are available, inoculating them directly into γ-HCH-contaminated soil is ineffective because of the bacterial survival rate. Cucurbita species incorporate significant amounts of POPs from soils compared with other plant species. Here, we describe a novel bioremediation strategy that combines the bacterial degradation of γ-HCH and the efficient uptake of γ-HCH by Cucurbita species. We produced transgenic hairy root cultures of Cucurbita moschata that expressed recombinant bacterial linA, isolated from the bacterium Sphingobium japonicum UT26. The LinA protein was accumulated stably in the hairy root cultures by fusing an endoplasmic reticulum (ER)-targeting signal peptide to LinA. Then, we demonstrated that the cultures degraded more than 90 % of γ-HCH (1 ppm) overnight and produced the γ-HCH metabolite 1,2,4-trichlorobenzene, indicating that LinA degraded γ-HCH. These results indicate that the gene linA has high potential for phytoremediation of environmental γ-HCH.
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Affiliation(s)
- Yoshihiko Nanasato
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan.
| | - Sayuri Namiki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
- Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Masao Oshima
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Ryota Moriuchi
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi, 980-8577, Japan
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, Gifu, 501-1193, Japan
| | - Ken-Ichi Konagaya
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Nobuyasu Seike
- Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Takashi Otani
- Organochemicals Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yuji Nagata
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi, 980-8577, Japan
| | - Masataka Tsuda
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai, Miyagi, 980-8577, Japan
| | - Yutaka Tabei
- Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
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16
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Bhowmik S, Chiu HP, Jones DH, Chiu HJ, Miller MD, Xu Q, Farr CL, Ridlon JM, Wells JE, Elsliger MA, Wilson IA, Hylemon PB, Lesley SA. Structure and functional characterization of a bile acid 7α dehydratase BaiE in secondary bile acid synthesis. Proteins 2016; 84:316-31. [PMID: 26650892 DOI: 10.1002/prot.24971] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 11/12/2015] [Accepted: 11/30/2015] [Indexed: 01/10/2023]
Abstract
Conversion of the primary bile acids cholic acid (CA) and chenodeoxycholic acid (CDCA) to the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA) is performed by a few species of intestinal bacteria in the genus Clostridium through a multistep biochemical pathway that removes a 7α-hydroxyl group. The rate-determining enzyme in this pathway is bile acid 7α-dehydratase (baiE). In this study, crystal structures of apo-BaiE and its putative product-bound [3-oxo-Δ(4,6) -lithocholyl-Coenzyme A (CoA)] complex are reported. BaiE is a trimer with a twisted α + β barrel fold with similarity to the Nuclear Transport Factor 2 (NTF2) superfamily. Tyr30, Asp35, and His83 form a catalytic triad that is conserved across this family. Site-directed mutagenesis of BaiE from Clostridium scindens VPI 12708 confirm that these residues are essential for catalysis and also the importance of other conserved residues, Tyr54 and Arg146, which are involved in substrate binding and affect catalytic turnover. Steady-state kinetic studies reveal that the BaiE homologs are able to turn over 3-oxo-Δ(4) -bile acid and CoA-conjugated 3-oxo-Δ(4) -bile acid substrates with comparable efficiency questioning the role of CoA-conjugation in the bile acid metabolism pathway.
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Affiliation(s)
- Shiva Bhowmik
- Joint Center for Structural Genomics, (http://www.jcsg.org).,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037
| | - Hsien-Po Chiu
- Genomics Institute of Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California, 92121
| | - David H Jones
- Genomics Institute of Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California, 92121
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, (http://www.jcsg.org).,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 9, Menlo Park, California, 94025
| | - Mitchell D Miller
- Joint Center for Structural Genomics, (http://www.jcsg.org).,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 9, Menlo Park, California, 94025
| | - Qingping Xu
- Joint Center for Structural Genomics, (http://www.jcsg.org).,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 9, Menlo Park, California, 94025
| | - Carol L Farr
- Joint Center for Structural Genomics, (http://www.jcsg.org).,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037
| | - Jason M Ridlon
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, 23298.,McGuire VA Medical Center, Richmond, Virginia, 23298
| | - James E Wells
- USDA ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, (http://www.jcsg.org).,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037
| | - Ian A Wilson
- Joint Center for Structural Genomics, (http://www.jcsg.org).,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037
| | - Phillip B Hylemon
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, 23298.,McGuire VA Medical Center, Richmond, Virginia, 23298
| | - Scott A Lesley
- Joint Center for Structural Genomics, (http://www.jcsg.org).,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037.,Genomics Institute of Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California, 92121
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17
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Tang X, Zhang R, Zhang Q, Wang W. Dehydrochlorination mechanism of γ-hexachlorocyclohexane degraded by dehydrochlorinase LinA from Sphingomonas paucimobilis UT26. RSC Adv 2016. [DOI: 10.1039/c5ra21461k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The biotransformation pathway from γ-HCH to 1,3,4,6-TCDN catabolized by dehydrochlorinase LinA contains two discontinuous dehydrochlorination reactions and a conformational transition for the product of the first dehydrochlorination reaction.
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Affiliation(s)
- Xiaowen Tang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Ruiming Zhang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Qingzhu Zhang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Wenxing Wang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
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18
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Manna RN, Zinovjev K, Tuñón I, Dybala-Defratyka A. Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study. J Phys Chem B 2015; 119:15100-9. [DOI: 10.1021/acs.jpcb.5b07538] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rabindra Nath Manna
- Institute
of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
| | - Kirill Zinovjev
- Departament
de Química Física, Universitat de Valéncia, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat de Valéncia, 46100 Burjassot, Spain
| | - Agnieszka Dybala-Defratyka
- Institute
of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
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19
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Novel LinA type 3 δ-hexachlorocyclohexane dehydrochlorinase. Appl Environ Microbiol 2015; 81:7553-9. [PMID: 26296732 DOI: 10.1128/aem.01683-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/16/2015] [Indexed: 11/20/2022] Open
Abstract
LinA is the first enzyme of the microbial degradation pathway of a chlorinated insecticide, hexachlorocyclohexane (HCH), and mediates the dehydrochlorination of α-, γ-, and δ-HCH. Its two variants, LinA type 1 and LinA type 2, which differ at 10 out of 156 amino acid residues, have been described. Their activities for the metabolism of different HCH isomers differ considerably but overall are high for γ-HCH, moderate for α-HCH, low for δ-HCH, and lacking for β-HCH. Here, we describe the characterization of a new variant of this enzyme, LinA type 3, whose gene was identified from the metagenome of an HCH-contaminated soil sample. Its deduced primary structure in the region spanning amino acid residues 1 to 147 of the protein exhibits 17 and 12 differences from LinA type 1 and LinA type 2, respectively. In addition, the residues GIHFAPS, present at the region spanning residues 148 to 154 in both LinA type 1 and LinA type 2, are deleted in LinA type 3.The activity of LinA type 3 for the metabolism of δ-HCH is several orders of magnitude higher than that of LinA type 1 or LinA type 2 and can be useful for improvement of the metabolism of δ-HCH.
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20
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Pearce SL, Oakeshott JG, Pandey G. Insights into Ongoing Evolution of the Hexachlorocyclohexane Catabolic Pathway from Comparative Genomics of Ten Sphingomonadaceae Strains. G3 (BETHESDA, MD.) 2015; 5:1081-94. [PMID: 25850427 PMCID: PMC4478539 DOI: 10.1534/g3.114.015933] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/29/2015] [Indexed: 11/18/2022]
Abstract
Hexachlorocyclohexane (HCH), a synthetic organochloride, was first used as a broad-acre insecticide in the 1940s, and many HCH-degrading bacterial strains have been isolated from around the globe during the last 20 years. To date, the same degradation pathway (the lin pathway) has been implicated in all strains characterized, although the pathway has only been characterized intensively in two strains and for only a single HCH isomer. To further elucidate the evolution of the lin pathway, we have biochemically and genetically characterized three HCH-degrading strains from the Czech Republic and compared the genomes of these and seven other HCH-degrading bacterial strains. The three new strains each yielded a distinct set of metabolites during their degradation of HCH isomers. Variable assembly of the pathway is a common feature across the 10 genomes, eight of which (including all three Czech strains) were either missing key lin genes or containing duplicate copies of upstream lin genes (linA-F). The analysis also confirmed the important role of horizontal transfer mediated by insertion sequence IS6100 in the acquisition of the pathway, with a stronger association of IS6100 to the lin genes in the new strains. In one strain, a linA variant was identified that likely caused a novel degradation phenotype involving a shift in isomer preference. This study identifies a number of strains that are in the early stages of lin pathway acquisition and shows that the state of the pathway can explain the degradation patterns observed.
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Affiliation(s)
| | | | - Gunjan Pandey
- CSIRO Ecosystem Sciences, Acton, ACT-2601, Australia
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21
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Heeb NV, Wyss SA, Geueke B, Fleischmann T, Kohler HPE, Bernd Schweizer W, Moor H, Lienemann P. Stereochemistry of enzymatic transformations of (+)β- and (-)β-HBCD with LinA2--a HCH-degrading bacterial enzyme of Sphingobium indicum B90A. CHEMOSPHERE 2015; 122:70-78. [PMID: 25434265 DOI: 10.1016/j.chemosphere.2014.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 10/21/2014] [Accepted: 11/02/2014] [Indexed: 06/04/2023]
Abstract
LinA2, a bacterial enzyme expressed in various Sphingomonadaceae, catalyzes the elimination of HCl from hexachlorocyclohexanes (HCHs) and, as discussed here, the release of HBr from certain hexabromocyclododecanes (HBCDs). Both classes of compounds are persistent organic pollutants now regulated under the Stockholm Convention. LinA2 selectively catalyzes the transformation of β-HBCDs; other stereoisomers like α-, γ-, and δ-HBCDs are not converted. The transformation of (-)β-HBCD is considerably faster than that of its enantiomer. Here, we present the XRD crystal structure of 1E,5S,6S,9R,10S-pentabromocyclododecene (PBCDE) and demonstrate that its enantiomer with the 1E,5R,6R,9S,10R-configuration is the only metabolite formed during LinA2-catalyzed dehydrobromination of (-)β-HBCD. Formation of this product can be rationalized by HBr elimination at C5 and C6. A reasonable enzyme-substrate complex with the catalytic dyad His-73 and Asp-25 approaching the hydrogen at C6 and a cationic pocket of Lys-20, Try-42 and Arg-129 binding the leaving bromine at C5 was found from in silico docking experiments. A second PBCDE of yet unknown configuration was obtained from (+)β-HBCD. We predicted its stereochemistry to be 1E,5S,6S,9S,10R-PBCDE from docking experiments. The enzyme-substrate complex obtained from LinA2 and an activated conformation of (+)β-HBCD allows the HBr elimination at C9 and C10 leading to the predicted product. Both modeled enzyme-substrate complexes are in line with 1,2-diaxial HBr eliminations. In conclusion, LinA2, a bacterial enzyme of the HCH-degrading strain Sphingobium indicum B90A was able to stereoselectively convert β-HBCDs. Configurations of both PBCDE metabolites were predicted by molecular docking experiments and confirmed in one case by XRD data.
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Affiliation(s)
- Norbert V Heeb
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Analytical Chemistry, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland.
| | - Simon A Wyss
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Analytical Chemistry, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland; ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820 Wädenswil, Switzerland
| | - Birgit Geueke
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Thomas Fleischmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - W Bernd Schweizer
- ETH, Swiss Federal Institute of Technology, Laboratory for Organic Chemistry, Hönggerberg, CH-8093 Zürich, Switzerland
| | - Heidi Moor
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Analytical Chemistry, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland; ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820 Wädenswil, Switzerland
| | - Peter Lienemann
- ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820 Wädenswil, Switzerland
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22
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Heeb NV, Wyss SA, Geueke B, Fleischmann T, Kohler HPE, Lienemann P. LinA2, a HCH-converting bacterial enzyme that dehydrohalogenates HBCDs. CHEMOSPHERE 2014; 107:194-202. [PMID: 24444415 DOI: 10.1016/j.chemosphere.2013.12.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/28/2013] [Accepted: 12/11/2013] [Indexed: 06/03/2023]
Abstract
Hexabromocyclododecanes (HBCDs) and hexachlorocyclohexanes (HCHs) are lipophilic, polyhalogenated hydrocarbons with comparable stereochemistry. Bacterial evolution in HCH-contaminated soils resulted in the development of several Spingomonadaceae which express a series of HCH-converting enzymes. We showed that LinB, a haloalkane dehalogenase from Sphingobium indicum B90A, also transforms various HBCDs besides HCHs. Here we present evidence that LinA2, another dehalogenase from S. indicum also converts certain HBCDs to pentabromocyclododecenes (PBCDEs). Racemic mixtures of α-, β-, γ-HBCDs, a mixture of them, and δ-HBCD, a meso form, were exposed to LinA2. Substantial conversion of (-)β-HBCD was observed, but all other stereoisomers were not transformed significantly. The enantiomeric excess (EE) of β-HBCDs increased up to 60% in 32 h, whereas EE values of α- and γ-HBCDs were not affected. Substrate conversion and product formation were described with second-order kinetic models. One major (P1β) and possibly two minor (P2β, P3β) metabolites were detected. Respective mass spectra showed the characteristic isotope pattern of PBCDEs, the HBr elimination products of HBCDs. Michaelis-Menten parameters KM=0.47 ± 0.07 μM and vmax=0.17 ± 0.01 μmoll(-1)h(-1) were deduced from exposure data with varying enzyme/substrate ratios. LinA2 is more substrate specific than LinB, the latter converted all tested HBCDs, LinA2 only one. The widespread HCH pollution favored the selection and evolution of bacteria converting these compounds. We found that LinA2 and LinB, two of these HCH-converting enzymes expressed in S. indicum B90A, also dehalogenate HBCDs to lower brominated compounds, indicating that structural similarities of both classes of compounds are recognized at the level of substrate-protein interactions.
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Affiliation(s)
- Norbert V Heeb
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Analytical Chemistry, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland.
| | - Simon A Wyss
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Analytical Chemistry, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland; ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820 Wädenswil, Switzerland
| | - Birgit Geueke
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Thomas Fleischmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Hans-Peter E Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Peter Lienemann
- ZHAW, Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Reidbach, CH-8820 Wädenswil, Switzerland
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Hayes RP, Lewis KM, Xun L, Kang C. Catalytic mechanism of 5-chlorohydroxyhydroquinone dehydrochlorinase from the YCII superfamily of largely unknown function. J Biol Chem 2013; 288:28447-56. [PMID: 23955343 DOI: 10.1074/jbc.m113.499368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TftG, 5-chloro-2-hydroxyhydroquinone (5-CHQ) dehydrochlorinase, is involved in the biodegradation of 2,4,5-trichlorophenoxyacetate by Burkholderia phenoliruptrix AC1100. It belongs to the YCII superfamily, a group of proteins with largely unknown function. In this work, we utilized structural and functional studies, including the apo-form and 2,5-dihydroxybenzoquinone binary complex crystal structures, computational analysis, and site-directed mutagenesis, to determine the dehydrochlorination mechanism. The His-Asp dyad, which initiates catalysis, is strongly conserved in YCII-like proteins. In addition, other catalytically important residues such as Pro-76, which orients the His-Asp catalytic dyad; Arg-17 and Ser-56, which form an oxyanion hole; and Asp-9, which stabilizes the oxyanion hole, are among the most highly conserved residues across the YCII superfamily members. The comprehensive characterization of TftG helps not only for identifying effective mechanisms for chloroaromatic dechlorination but also for understanding the functions of YCII superfamily members, which we propose to be lyases.
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Enantioselective dehydrochlorination of δ-Hexachlorocyclohexane and δ-Pentachlorocyclohexene by LinA1 and LinA2 from Sphingobium indicum B90A. Appl Environ Microbiol 2013; 79:6180-3. [PMID: 23872559 DOI: 10.1128/aem.01770-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
δ-Hexachlorocyclohexane (δ-HCH), one of the prevalent isomers of technical HCH, was enantioselectively dehydrochlorinated by the dehydrochlorinases LinA1 and LinA2 from Sphingobium indicum B90A to the very same δ-pentachlorocyclohexene enantiomer. Racemic δ-pentachlorocyclohexene, however, was transformed with opposite enantioselectivities by the two enzymes. A transformation pathway based on an anti-1,2-elimination, followed by a syn-1,4-elimination and a subsequent syn-1,2-elimination is postulated.
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25
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Manna RN, Dybala-Defratyka A. Insights into the elimination mechanisms employed for the degradation of different hexachlorocyclohexane isomers using kinetic isotope effects and docking studies. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3163] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Rabindra Nath Manna
- Institute of Applied Radiation Chemistry, Faculty of Chemistry; Lodz University of Technology; Zeromskiego 116 Lodz Poland
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry; Lodz University of Technology; Zeromskiego 116 Lodz Poland
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26
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Yasui N, Takaoka Y, Nishio H, Nurputra DK, Sekiguchi K, Hamaguchi H, Kowa H, Maeda E, Sugano A, Miura K, Sakaeda T, Kanda F, Toda T. Molecular pathology of Sandhoff disease with p.Arg505Gln in HEXB: application of simulation analysis. J Hum Genet 2013; 58:611-7. [DOI: 10.1038/jhg.2013.68] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 05/15/2013] [Accepted: 05/19/2013] [Indexed: 11/09/2022]
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Roth C, Gröning JAD, Kaschabek SR, Schlömann M, Sträter N. Crystal structure and catalytic mechanism of chloromuconolactone dehalogenase ClcF from Rhodococcus opacus 1CP. Mol Microbiol 2013; 88:254-67. [PMID: 23421784 DOI: 10.1111/mmi.12182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2013] [Indexed: 11/30/2022]
Abstract
The actinobacterium Rhodococcus opacus 1CP possesses a so far unique variant of the modified 3-oxoadipate pathway for 3-chlorocatechol degradation. One important feature is the novel dehalogenase ClcF, which converts (4R,5S)-5-chloromuconolactone to E-dienelactone. ClcF is related to muconolactone isomerase (MLI, EC 5.3.3.4). The enzyme has a ferredoxin-type fold and forms a homodecamer of 52-symmetry, typical for the MLI family. The active site is formed by residues from two monomers. The complex structure of an E27A variant with bound substrate in conjunction with mutational studies indicate that E27 acts as the proton acceptor in a univalent single-base syn-dehydrohalogenation mechanism. Despite the evolutionary specialization of ClcF, the conserved active-site structures suggest that the proposed mechanism is representative for the MLI family. Furthermore, ClcF represents a novel type of dehalogenase based on an isomerase scaffold.
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Affiliation(s)
- Christian Roth
- Center for Biotechnology and Biomedicine, Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
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Macwan AS, Srivastava N, Javed S, Kumar A. Role of a repeated hexapeptide motif GIHFAP near C-terminus in assembly, stability, and activity of "HCH dehydrochlorinase LinA". Appl Biochem Biotechnol 2013; 169:1397-404. [PMID: 23315208 DOI: 10.1007/s12010-012-0035-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 12/10/2012] [Indexed: 11/28/2022]
Abstract
Enzyme "hexachlorocyclohexane (HCH) dehydrochlorinase LinA" mediates first step of aerobic microbial degradation of a chlorinated insecticide γ-HCH. The archetypal LinA-type1 consists of 156 amino acids that include a directly repeated hexapeptide motif GIHFAP at positions 141-146 and 148-153. Analysis of a series of LinA mutants, containing none, one, two, or three units of this repeated motif revealed that two units, as present in wild-type LinA, are required for its optimal activity and stability. Moreover, the presence of a bend in its secondary structure due to a proline residue that precedes the distal repeated unit contributes to enhanced LinA activity.
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Affiliation(s)
- Ankit S Macwan
- Environmental Biotechnology Section, Indian Institute of Toxicology Research (Council of Scientific and Industrial Research), Mahatma Gandhi Marg, Lucknow, 226001, India
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29
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Macwan AS, Kukshal V, Srivastava N, Javed S, Kumar A, Ramachandran R. Crystal structure of the hexachlorocyclohexane dehydrochlorinase (LinA-type2): mutational analysis, thermostability and enantioselectivity. PLoS One 2012; 7:e50373. [PMID: 23209726 PMCID: PMC3507683 DOI: 10.1371/journal.pone.0050373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 10/19/2012] [Indexed: 12/02/2022] Open
Abstract
Hexachlorocyclohexane dehydrochlorinase (LinA) mediates dehydrochlorination of γ-HCH to 1, 3, 4, 6-tetrachloro-1,4-cyclohexadiene that constitutes first step of the aerobic degradation pathway. We report the 3.5 Å crystal structure of a thermostable LinA-type2 protein, obtained from a soil metagenome, in the hexagonal space group P6(3)22 with unit cell parameters a = b = 162.5, c = 186.3 Å, respectively. The structure was solved by molecular replacement using the co-ordinates of LinA-type1 that exhibits mesophile-like properties. Structural comparison of LinA-type2 and -type1 proteins suggests that thermostability of LinA-type2 might partly arise due to presence of higher number of ionic interactions, along with 4% increase in the intersubunit buried surface area. Mutational analysis involving the differing residues between the -type1 and -type2 proteins, circular dichroism experiments and functional assays suggest that Q20 and G23 are determinants of stability for LinA-type2. It was earlier reported that LinA-type1 exhibits enantioselectivity for the (-) enantiomer of α-HCH. Contrastingly, we identified that -type2 protein prefers the (+) enantiomer of α-HCH. Structural analysis and molecular docking experiments suggest that changed residues K20Q, L96C and A131G, vicinal to the active site are probably responsible for the altered enantioselectivity of LinA-type2. Overall the study has identified features responsible for the thermostability and enantioselectivity of LinA-type2 that can be exploited for the design of variants for specific biotechnological applications.
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Affiliation(s)
- Ankit S. Macwan
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow, India
| | - Vandna Kukshal
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Chattar Manzil, Mahatma Gandhi Marg, Lucknow, India
| | - Nidhi Srivastava
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow, India
| | - Saleem Javed
- Department of Biochemistry, Hamdard University, New Delhi, India
| | - Ashwani Kumar
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Chattar Manzil, Mahatma Gandhi Marg, Lucknow, India
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30
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Heeb NV, Zindel D, Geueke B, Kohler HPE, Lienemann P. Biotransformation of Hexabromocyclododecanes (HBCDs) with LinB--an HCH-converting bacterial enzyme. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:6566-6574. [PMID: 22578084 DOI: 10.1021/es2046487] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Hexabromocyclododecanes (HBCDs) and hexachlorocyclohexanes (HCHs) are polyhalogenated hydrocarbons with similar stereochemistry. Both classes of compounds are considered biologically persistent and bioaccumulating pollutants. In 2009, the major HCH stereoisomers came under regulation of the Stockholm convention. Despite their persistence, HCHs are susceptible to bacterial biotransformations. Here we show that LinB, an HCH-converting haloalkane dehalogenase from Sphingobium indicum B90A, is also able to transform HBCDs. Racemic mixtures of α-, β-, and γ-HBCDs were exposed to LinB under various conditions. All stereoisomers were converted, but (-)α-, (+)β-, and (+)γ-HBCDs were transformed faster by LinB than their enantiomers. The enantiomeric excess increased to 8 ± 4%, 27 ± 1%, and 20 ± 2% in 32 h comparable to values of 7.1%, 27.0%, and 22.9% as obtained from respective kinetic models. Initially formed pentabromocyclododecanols (PBCDOHs) were further transformed to tetrabromocyclododecadiols (TBCDDOHs). At least, seven mono- and five dihydroxylated products were distinguished by LC-MS so far. The widespread occurrence of HCHs has led to the evolution of bacterial degradation pathways for such compounds. It remains to be shown if LinB-catalyzed HBCD transformations in vitro can also be observed in vivo, for example, in contaminated soils or in other words if such HBCD biotransformations are important environmental processes.
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Affiliation(s)
- Norbert V Heeb
- Laboratory for Analytical Chemistry, Swiss Federal Laboratories for Materials Testing and Research, Empa, Überlandstrasse 129, CH-8600 Dübendorf, Switzerland.
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31
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Isolation of a novel thermostable dehydrochlorinase (LinA) from a soil metagenome. 3 Biotech 2011; 1:193-198. [PMID: 22558537 PMCID: PMC3339611 DOI: 10.1007/s13205-011-0012-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 05/26/2011] [Indexed: 12/04/2022] Open
Abstract
Hexachlorocyclohexane dehydrochlorinase (LinA) mediates first step of aerobic degradation of a chlorinated insecticide γ-hexachlorocyclohexane (γ-HCH). In this study, we describe characterization of a novel variant (LinA-type2) that is distinct from reported LinAs and is substantially more thermostable than archetypal LinA-UT26. LinA-type2 remains active even after 8 h of incubation at 45 °C, when nearly 50% activity of LinA-UT26 is lost after incubation for 60 min at the same temperature. Circular dichroism analysis revealed that secondary structures of LinA-UT26 and LinA-type2 are similar, but their Tm was 45 and 65 °C, respectively. Thermostability of LinA-type2 makes it suitable for bioreactors where allowance for higher temperatures can be of advantage.
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Sharma P, Pandey R, Kumari K, Pandey G, Jackson CJ, Russell RJ, Oakeshott JG, Lal R. Kinetic and sequence-structure-function analysis of known LinA variants with different hexachlorocyclohexane isomers. PLoS One 2011; 6:e25128. [PMID: 21949868 PMCID: PMC3174995 DOI: 10.1371/journal.pone.0025128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 08/25/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Here we report specific activities of all seven naturally occurring LinA variants towards three different isomers, α, γ and δ, of a priority persistent pollutant, hexachlorocyclohexane (HCH). Sequence-structure-function differences contributing to the differences in their stereospecificity for α-, γ-, and δ-HCH and enantiospecificity for (+)- and (-)-α -HCH are also discussed. METHODOLOGY/PRINCIPAL FINDINGS Enzyme kinetic studies were performed with purified LinA variants. Models of LinA2(B90A) A110T, A111C, A110T/A111C and LinA1(B90A) were constructed using the FoldX computer algorithm. Turnover rates (min(-1)) showed that the LinAs exhibited differential substrate affinity amongst the four HCH isomers tested. α-HCH was found to be the most preferred substrate by all LinA's, followed by the γ and then δ isomer. CONCLUSIONS/SIGNIFICANCE The kinetic observations suggest that LinA-γ1-7 is the best variant for developing an enzyme-based bioremediation technology for HCH. The majority of the sequence variation in the various linA genes that have been isolated is not neutral, but alters the enantio- and stereoselectivity of the encoded proteins.
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Affiliation(s)
- Pooja Sharma
- Department of Zoology, University of Delhi, Delhi, India
| | | | - Kirti Kumari
- Department of Zoology, University of Delhi, Delhi, India
| | | | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | | | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India
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Russell RJ, Scott C, Jackson CJ, Pandey R, Pandey G, Taylor MC, Coppin CW, Liu JW, Oakeshott JG. The evolution of new enzyme function: lessons from xenobiotic metabolizing bacteria versus insecticide-resistant insects. Evol Appl 2011; 4:225-48. [PMID: 25567970 PMCID: PMC3352558 DOI: 10.1111/j.1752-4571.2010.00175.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 11/12/2010] [Indexed: 11/30/2022] Open
Abstract
Here, we compare the evolutionary routes by which bacteria and insects have evolved enzymatic processes for the degradation of four classes of synthetic chemical insecticide. For insects, the selective advantage of such degradative activities is survival on exposure to the insecticide, whereas for the bacteria the advantage is simply a matter of access to additional sources of nutrients. Nevertheless, bacteria have evolved highly efficient enzymes from a wide variety of enzyme families, whereas insects have relied upon generalist esterase-, cytochrome P450- and glutathione-S-transferase-dependent detoxification systems. Moreover, the mutant insect enzymes are less efficient kinetically and less diverged in sequence from their putative ancestors than their bacterial counterparts. This presumably reflects several advantages that bacteria have over insects in the acquisition of new enzymatic functions, such as a broad biochemical repertoire from which new functions can be evolved, large population sizes, high effective mutation rates, very short generation times and access to genetic diversity through horizontal gene transfer. Both the insect and bacterial systems support recent theory proposing that new biochemical functions often evolve from 'promiscuous' activities in existing enzymes, with subsequent mutations then enhancing those activities. Study of the insect enzymes will help in resistance management, while the bacterial enzymes are potential bioremediants of insecticide residues in a range of contaminated environments.
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Affiliation(s)
| | - Colin Scott
- CSIRO Ecosystem Sciences Canberra, ACT, Australia
| | | | - Rinku Pandey
- CSIRO Ecosystem Sciences Canberra, ACT, Australia
| | | | | | | | - Jian-Wei Liu
- CSIRO Ecosystem Sciences Canberra, ACT, Australia
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Brittain DRB, Pandey R, Kumari K, Sharma P, Pandey G, Lal R, Coote ML, Oakeshott JG, Jackson CJ. Competing SN2 and E2 reaction pathways for hexachlorocyclohexane degradation in the gas phase, solution and enzymes. Chem Commun (Camb) 2011; 47:976-8. [DOI: 10.1039/c0cc02925d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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