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Faridy N, Torabi E, Pourbabaee AA, Osdaghi E, Talebi K. Efficacy of novel bacterial consortia in degrading fipronil and thiobencarb in paddy soil: a survey for community structure and metabolic pathways. Front Microbiol 2024; 15:1366951. [PMID: 38812693 PMCID: PMC11133635 DOI: 10.3389/fmicb.2024.1366951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 04/22/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction Fipronil (FIP) and thiobencarb (THIO) represent widely utilized pesticides in paddy fields, presenting environmental challenges that necessitate effective remediation approaches. Despite the recognized need, exploring bacterial consortia efficiently degrading FIP and THIO remains limited. Methods This study isolated three unique bacterial consortia-FD, TD, and MD-demonstrating the capability to degrade FIP, THIO, and an FIP + THIO mixture within a 10-day timeframe. Furthermore, the bioaugmentation abilities of the selected consortia were evaluated in paddy soils under various conditions. Results Sequencing results shed light on the consortia's composition, revealing a diverse bacterial population prominently featuring Azospirillum, Ochrobactrum, Sphingobium, and Sphingomonas genera. All consortia efficiently degraded pesticides at 800 µg/mL concentrations, primarily through oxidative and hydrolytic processes. This metabolic activity yields more hydrophilic metabolites, including 4-(Trifluoromethyl)-phenol and 1,4-Benzenediol, 2-methyl-, for FIP, and carbamothioic acid, diethyl-, S-ethyl ester, and Benzenecarbothioic acid, S-methyl ester for THIO. Soil bioaugmentation tests highlight the consortia's effectiveness, showcasing accelerated degradation of FIP and THIO-individually or in a mixture-by 1.3 to 13-fold. These assessments encompass diverse soil moisture levels (20 and 100% v/v), pesticide concentrations (15 and 150 µg/g), and sterile conditions (sterile and non-sterile soils). Discussion This study offers an understanding of bacterial communities adept at degrading FIP and THIO, introducing FD, TD, and MD consortia as promising contenders for bioremediation endeavors.
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Affiliation(s)
- Nastaran Faridy
- Department of Plant Protection, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ehssan Torabi
- Department of Plant Protection, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ahmad Ali Pourbabaee
- Department of Soil Science, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ebrahim Osdaghi
- Department of Plant Protection, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Khalil Talebi
- Department of Plant Protection, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
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Duc HD, Oanh NT, Khanh NTM. Thiobencarb Degradation by Pseudomonas sp. Th1 and Cupriavidus oxalaticus Th2 Isolated from Soil. Curr Microbiol 2023; 80:342. [PMID: 37725172 DOI: 10.1007/s00284-023-03456-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023]
Abstract
Thiobencarb has been extensively applied for weed control, resulting in severe environmental problems. In this study, thiobencarb degradation in liquid media and in soil by two bacterial strains, Pseudomonas sp. Th1 and Cupriavidus oxalaticus Th2, was investigated. Both bacterial isolates utilized the compound as a sole carbon, nitrogen and sulfur source. The utilization rates of thiobencarb by Pseudomonas sp. Th1 and C. oxalaticus Th2 in a liquid mineral medium were 1.02 ± 0.11 and 0.80 ± 0.07 µM/h at 100 µM, respectively. The determination of degradation and bacterial growth rates kinetics showed that the rates for pure thiobencarb followed the Michaelis-Menten model; meanwhile, the rates for thiobencarb in a commercial herbicide fitted well with the Edwards model. Their degradation by the mixed culture of both strains reduced the accumulation of intermediate products, including S-4-chlorobenzyl ethylthiocarbamate and 4-chlorobenzyl mercaptan, in media. The degradation by the mixed culture of these bacteria immobilized in rice straw was significantly higher than those of their free counterparts when determining in a packed bed bioreactor (P < 0.05). In addition, the inoculation of the mixed bacterial culture in soil significantly enhanced the degradation performance for both thiobencarb and propanil in a commercial herbicide. This study elucidates the differences in biodegradation of pure thiobencarb and thiobencarb in an herbicide.
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Affiliation(s)
- Ha Danh Duc
- Dong Thap University, 783 Pham Huu Lau Street, Cao Lanh City, Dong Thap Province, Vietnam.
| | - Nguyen Thi Oanh
- Dong Thap University, 783 Pham Huu Lau Street, Cao Lanh City, Dong Thap Province, Vietnam.
| | - Nguyen Thi Mai Khanh
- Can Tho University of Technology, 256 Nguyen Van Cu Street, An Hoa Ward, Ninh Kieu District, Can Tho City, Vietnam
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Yu Y, Huang J, Jin L, Yu M, Yu X, Zhu X, Sun J, Zhu L. Translocation and metabolism of tricresyl phosphate in rice and microbiome system: Isomer-specific processes and overlooked metabolites. ENVIRONMENT INTERNATIONAL 2023; 172:107793. [PMID: 36739853 DOI: 10.1016/j.envint.2023.107793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Tricresyl phosphate (TCP) is extensively used organophosphorus flame retardants and plasticizers that posed risks to organisms and human beings. In this study, the translocation and biotransformation behavior of isomers tri-p-cresyl phosphate (TpCP), tri-m-cresyl phosphate (TmCP), and tri-o-cresyl phosphate (ToCP) in rice and rhizosphere microbiome was explored by hydroponic exposure. TpCP and TmCP were found more liable to be translocated acropetally, compared with ToCP, although they have same molecular weight and similar Kow. Rhizosphere microbiome named microbial consortium GY could reduce the uptake of TpCP, TmCP, and ToCP in rice tissues, and promote rice growth. New metabolites were successfully identified in rice and microbiome, including hydrolysis, hydroxylated, methylated, demethylated, methoxylated, and glucuronide- products. The methylation, demethylation, methoxylation, and glycosylation pathways of TCP isomers were observed for the first time in organisms. What is more important is that the demethylation of TCPs could be an important and overlooked source of triphenyl phosphate (TPHP), which broke the traditional understanding of the only manmade source of toxic TPHP in the environment. Active members of the microbial consortium GY during degradation were revealed and metagenomic analysis indicated that most of active populations contained TCP-degrading genes. It is noteworthy that the strains and function genes in microbial consortium GY that responsible for TCP isomers' transformation were different. These results can improve our understanding of the translocation and transformation of organic pollutant isomers in plants and rhizosphere microbiome.
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Affiliation(s)
- Yuanyuan Yu
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Jiahui Huang
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Ling Jin
- Department of Civil and Environmental Engineering and Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong
| | - Miao Yu
- The Jackson Laboratory For Genomic Medicine 10 Discovery Dr, Farmington, CT 06032, USA
| | - Xiaolong Yu
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Xifen Zhu
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Jianteng Sun
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China.
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Duc HD. Anaerobic degradation of thiobencarb by mixed culture of isolated bacteria. FEMS Microbiol Lett 2023; 370:6912244. [PMID: 36521844 DOI: 10.1093/femsle/fnac123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/22/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Thiobencarb is a highly effective thiocarbamate herbicide frequently used in rice fields globally. In this study, three bacterial strains (Dechloromonas sp. Th1, Thauera sp. Th2, and Azoarcus sp. Th3) isolated from immobilized biomass were analyzed for thiobencarb degradation under anaerobic conditions, with nitrate serving as an electron acceptor. The experimental results showed that thiobencarb was transformed by Dechloromonas sp. Th1 and Thauera sp. Th2 to produce high concentrations of metabolites in a mineral medium. Dechloromonas sp. Th1 dechlorinated the herbicide to benzyl mercaptan, which was then degraded by Thauera sp. Th2 and Azoarcus sp. Th3. Azoarcus sp. Th3 effectively degraded intermediates, i.e. 4-chlorobenzyl alcohol, 4-chlorobenzoic acid, and benzoic acid, produced from the degradation by Dechloromonas sp. Th1 and Thauera sp. Th2. The cross-feeding, nutrient sharing, and cooperation of all isolates in the degradation process decreased the concentrations of intermediate products. The determination of the degradation kinetics showed that the utilization in the exponential phase of the mixed bacteria was consistent with the Michaelis-Menten model, with a maximum degradation rate of 1.56 ± 0.16 µM day-1. This study showed the degradation mechanisms in bacteria and the synergistic process in the degradation of thiobencarb and its metabolites.
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Affiliation(s)
- Ha Danh Duc
- Dong Thap University, 783 Pham Huu Lau Street, Cao Lanh City, Dong Thap Province, 81100, Viet Nam
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Cheng M, Chen D, Parales RE, Jiang J. Oxygenases as Powerful Weapons in the Microbial Degradation of Pesticides. Annu Rev Microbiol 2022; 76:325-348. [PMID: 35650666 DOI: 10.1146/annurev-micro-041320-091758] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oxygenases, which catalyze the reductive activation of O2 and incorporation of oxygen atoms into substrates, are widely distributed in aerobes. They function by switching the redox states of essential cofactors that include flavin, heme iron, Rieske non-heme iron, and Fe(II)/α-ketoglutarate. This review summarizes the catalytic features of flavin-dependent monooxygenases, heme iron-dependent cytochrome P450 monooxygenases, Rieske non-heme iron-dependent oxygenases, Fe(II)/α-ketoglutarate-dependent dioxygenases, and ring-cleavage dioxygenases, which are commonly involved in pesticide degradation. Heteroatom release (hydroxylation-coupled hetero group release), aromatic/heterocyclic ring hydroxylation to form ring-cleavage substrates, and ring cleavage are the main chemical fates of pesticides catalyzed by these oxygenases. The diversity of oxygenases, specificities for electron transport components, and potential applications of oxygenases are also discussed. This article summarizes our current understanding of the catalytic mechanisms of oxygenases and a framework for distinguishing the roles of oxygenases in pesticide degradation. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Minggen Cheng
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
| | - Dian Chen
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA
| | - Jiandong Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs and Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China;
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Ito K. Mechanisms of aerobic dechlorination of hexachlorobenzene and pentachlorophenol by Nocardioides sp. PD653. JOURNAL OF PESTICIDE SCIENCE 2021; 46:373-381. [PMID: 34908898 PMCID: PMC8640678 DOI: 10.1584/jpestics.j21-04] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/31/2021] [Indexed: 06/14/2023]
Abstract
We sought to elucidate the mechanisms underlying the aerobic dechlorination of the persistent organic pollutants hexachlorobenzene (HCB) and pentachlorophenol (PCP). We performed genomic and heterologous expression analyses of dehalogenase genes in Nocardioides sp. PD653, the first bacterium found to be capable of mineralizing HCB via PCP under aerobic conditions. The hcbA1A2A3 and hcbB1B2B3 genes, which were involved in catalysing the aerobic dechlorination of HCB and PCP, respectively, were identified and characterized; they were classified as members of the two-component flavin-diffusible monooxygenase family. This was subsequently verified by biochemical analysis; aerobic dechlorination activity was successfully reconstituted in vitro in the presence of flavin, NADH, the flavin reductase HcbA3, and the HCB monooxygenase HcbA1. These findings will contribute to the implementation of in situ bioremediation of HCB- or PCP-contaminated sites, as well as to a better understanding of bacterial evolution apropos their ability to degrade heavily chlorinated anthropogenic compounds under aerobic conditions.
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Affiliation(s)
- Koji Ito
- National Agriculture and Food Research Organization, Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba-city, Ibaraki 305–8604, Japan
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The Operon Encoding Hydrolytic Dehalogenation of 4-Chlorobenzoate Is Transcriptionally Regulated by the TetR-Type Repressor FcbR and Its Ligand 4-Chlorobenzoyl Coenzyme A. Appl Environ Microbiol 2021; 87:AEM.02652-20. [PMID: 33397703 DOI: 10.1128/aem.02652-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/22/2020] [Indexed: 12/24/2022] Open
Abstract
The bacterial hydrolytic dehalogenation of 4-chlorobenzoate (4CBA) is a coenzyme A (CoA)-activation-type catabolic pathway that is usually a common part of the microbial mineralization of chlorinated aromatic compounds. Previous studies have shown that the transport and dehalogenation genes for 4CBA are typically clustered as an fcbBAT1T2T3C operon and inducibly expressed in response to 4CBA. However, the associated molecular mechanism remains unknown. In this study, a gene (fcbR) adjacent to the fcb operon was predicted to encode a TetR-type transcriptional regulator in Comamonas sediminis strain CD-2. The fcbR knockout strain exhibited constitutive expression of the fcb cluster. In the host Escherichia coli, the expression of the Pfcb -fused green fluorescent protein (gfp) reporter was repressed by the introduction of the fcbR gene, and genetic studies combining various catabolic genes suggest that the ligand for FcbR may be an intermediate metabolite. Purified FcbR could bind to the Pfcb DNA probe in vitro, and the metabolite 4-chlorobenzyl-CoA (4CBA-CoA) prevented FcbR binding to the P fcb DNA probe. Isothermal titration calorimetry (ITC) measurements showed that 4CBA-CoA could bind to FcbR at a 1:1 molar ratio. DNase I footprinting showed that FcbR protected a 42-bp DNA motif (5'-GGAAATCAATAGGTCCATAGAAAATCTATTGACTAATCGAAT-3') that consists of two sequence repeats containing four pseudopalindromic sequences (5'-TCNATNGA-3'). This binding motif overlaps with the -35 box of Pfcb and was proposed to prevent the binding of RNA polymerase. This study characterizes a transcriptional repressor of the fcb operon, together with its ligand, thus identifying halogenated benzoyl-CoA as belonging to the class of ligands of transcriptional regulators.IMPORTANCE The bacterial hydrolytic dehalogenation of 4CBA is a special CoA-activation-type catabolic pathway that plays an important role in the biodegradation of polychlorinated biphenyls and some herbicides. With genetic and biochemical approaches, the present study identified the transcriptional repressor and its cognate effector of a 4CBA hydrolytic dehalogenation operon. This work extends halogenated benzoyl-CoA as a new member of CoA-derived effector compounds that mediate allosteric regulation of transcriptional regulators.
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Pileggi M, Pileggi SA, Sadowsky MJ. Herbicide bioremediation: from strains to bacterial communities. Heliyon 2020; 6:e05767. [PMID: 33392402 PMCID: PMC7773584 DOI: 10.1016/j.heliyon.2020.e05767] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/23/2020] [Accepted: 12/15/2020] [Indexed: 01/12/2023] Open
Abstract
There is high demand for herbicides based on the necessity to increase crop production to satisfy world-wide demands. Nevertheless, there are negative impacts of herbicide use, manifesting as selection for resistant weeds, production of toxic metabolites from partial degradation of herbicides, changes in soil microbial communities and biogeochemical cycles, alterations in plant nutrition and soil fertility, and persistent environmental contamination. Some herbicides damage non-target microorganisms via directed interference with host metabolism and via oxidative stress mechanisms. For these reasons, it is necessary to identify sustainable, efficient methods to mitigate these environmental liabilities. Before the degradation process can be initiated by microbial enzymes and metabolic pathways, microorganisms need to tolerate the oxidative stresses caused by the herbicides themselves. This can be achieved via a complex system of enzymatic and non-enzymatic antioxidative stress systems. Many of these response systems are not herbicide specific, but rather triggered by a variety of substances. Collectively, these nonspecific response systems enhance the survival and fitness potential of microorganisms. Biodegradation studies and remediation approaches have relied on individually selected strains to effectively remediate herbicides in the environment. Nevertheless, it has been shown that microbial communication systems that modulate social relationships and metabolic pathways inside biofilm structures among microorganisms are complex; therefore, use of isolated strains for xenobiotic degradation needs to be enhanced using a community-based approach with biodegradation pathway integration. Bioremediation efforts can use omics-based technologies to gain a deeper understanding of the molecular complexes of bacterial communities to achieve to more efficient elimination of xenobiotics. With this knowledge, the possibility of altering microbial communities is increased to improve the potential for bioremediation without causing other environmental impacts not anticipated by simpler approaches. The understanding of microbial community dynamics in free-living microbiota and those present in complex communities and in biofilms is paramount to achieving these objectives. It is also essential that non-developed countries, which are major food producers and consumers of pesticides, have access to these techniques to achieve sustainable production, without causing impacts through unknown side effects.
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Affiliation(s)
- Marcos Pileggi
- Laboratory of Environmental Microbiology, Biological Science and Health Institute, Department of Structural and Molecular Biology, and Genetics, State University of Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Sônia A.V. Pileggi
- Laboratory of Environmental Microbiology, Biological Science and Health Institute, Department of Structural and Molecular Biology, and Genetics, State University of Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Michael J. Sadowsky
- The Biotechnology Institute, Department of Soil, Water, and Climate, Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
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Zhang L, Hu Q, Liu B, Li F, Jiang JD. Characterization of a Linuron-Specific Amidohydrolase from the Newly Isolated Bacterium Sphingobium sp. Strain SMB. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4335-4345. [PMID: 32207940 DOI: 10.1021/acs.jafc.0c00597] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The phenylurea herbicide linuron is globally used and has caused considerable concern because it leads to environmental pollution. In this study, a highly efficient linuron-transforming strain Sphingobium sp. SMB was isolated, and a gene (lahB) responsible for the hydrolysis of linuron to 3,4-dichloroaniline and N,O-dimethylhydroxylamine was cloned from the genome of strain SMB. The lahB gene encodes an amidohydrolase, which shares 20-53% identity with other biochemically characterized amidohydrolases, except for the newly reported linuron hydrolase Phh (75%). The optimal conditions for the hydrolysis of linuron by LahB were determined to be pH 7.0 and 30 °C, and the Km value of LahB for linuron was 37.3 ± 1.2 μM. Although LahB and Phh shared relatively high identity, LahB exhibited a narrow substrate spectrum (specific for linuron) compared to Phh (active for linuron, diuron, chlortoluron, etc.). Sequence analysis and site-directed mutagenesis revealed that Ala261 of Phh was the key amino acid residue affecting the substrate specificity. Our study provides a new amidohydrolase for the specific hydrolysis of linuron.
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Affiliation(s)
- Long Zhang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
- College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Qiang Hu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Bin Liu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Feng Li
- College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
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Liu S, Du MZ, Wen QF, Kang J, Dong C, Xiong L, Huang J, Guo FB. Comprehensive exploration of the enzymes catalysing oxygen-involved reactions and COGs relevant to bacterial oxygen utilization. Environ Microbiol 2018; 20:3836-3850. [PMID: 30187624 DOI: 10.1111/1462-2920.14399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/31/2018] [Indexed: 12/12/2022]
Abstract
To better understand the mechanisms of bacterial adaptation in oxygen environments, we explored the aerobic living-associated genes in bacteria by comparing Clusters of Orthologous Groups of proteins' (COGs) frequencies and gene expression analyses and 38 COGs were detected at significantly higher frequencies (p-value less than 1e-6) in aerobes than in anaerobes. Differential expression analyses between two conditions further narrowed the prediction to 27 aerobe-specific COGs. Then, we annotated the enzymes associated with these COGs. Literature review revealed that 14 COGs contained enzymes catalysing oxygen-involved reactions or products involved in aerobic pathways, suggesting their important roles for survival in aerobic environments. Additionally, protein-protein interaction analyses and step length comparisons of metabolic networks suggested that the other 13 COGs may function relevantly with the 14 enzymes-corresponding COGs, indicating that these genes may be highly associated with oxygen utilization. Phylogenetic and evolutionary analyses showed that the 27 COGs did not have similar trees, and all suffered purifying selection pressures. The divergent times of species containing or lacking aerobic COGs validated that the appearing time of oxygen-utilizing gene was approximately 2.80 Gyr ago. In addition to help better understand oxygen adaption, our method may be extended to identify genes relevant to other living environments.
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Affiliation(s)
- Shuo Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Meng-Ze Du
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Qing-Feng Wen
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Juanjuan Kang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Chuan Dong
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Lifeng Xiong
- Department of Microbiology, University of Hong Kong, Special Administrative Region, Hong Kong, 999077, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
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Roles of Two Glutathione-Dependent 3,6-Dichlorogentisate Dehalogenases in Rhizorhabdus dicambivorans Ndbn-20 in the Catabolism of the Herbicide Dicamba. Appl Environ Microbiol 2018; 84:AEM.00623-18. [PMID: 29934333 DOI: 10.1128/aem.00623-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/18/2018] [Indexed: 11/20/2022] Open
Abstract
The herbicide dicamba is initially demethylated to 3,6-dichlorosalicylate (3,6-DCSA) in Rhizorhabdus dicambivorans Ndbn-20 and is subsequently 5-hydroxylated to 3,6-dichlorogentisate (3,6-DCGA). In the present study, two glutathione-dependent 3,6-DCGA dehalogenases, DsmH1 and DsmH2, were identified in strain Ndbn-20. DsmH2 shared a low identity (only 31%) with the tetrachlorohydroquinone (TCHQ) dehalogenase PcpC from Sphingobium chlorophenolicum ATCC 39723, while DsmH1 shared a high identity (79%) with PcpC. In the phylogenetic tree of related glutathione S-transferases (GSTs), DsmH1 and DsmH2, together with PcpC and the 2,5-dichlorohydroquinone dehalogenase LinD, formed a separate clade. DsmH1 and DsmH2 were synthesized in Escherichia coli BL21 and purified as His-tagged enzymes. Both enzymes required glutathione (GSH) as a cofactor and could 6-dechlorinate 3,6-DCGA to 3-chlorogentisate in vitro DsmH2 had a significantly higher catalytic efficiency toward 3,6-DCGA than DsmH1. Transcription and disruption analysis revealed that DsmH2 but not DsmH1 was responsible for the 6-dechlorination of 3,6-DCGA in strain Ndbn-20 in vivo Furthermore, we propose a novel eta class of GSTs to accommodate the four bacterial dehalogenases PcpC, LinD, DsmH1, and DsmH2.IMPORTANCE Dicamba is an important herbicide, and its use and leakage into the environment have dramatically increased since the large-scale planting of genetically modified (GM) dicamba-resistant crops in 2015. However, the complete catabolic pathway of dicamba has remained unknown, which limits ecotoxicological studies of this herbicide. Our previous study revealed that 3,6-DCGA was an intermediate of dicamba degradation in strain Ndbn-20. In this study, we identified two glutathione-dependent 3,6-DCGA dehalogenases, DsmH1 and DsmH2, and demonstrated that DsmH2 is physiologically responsible for the 6-dechlorination of 3,6-DCGA in strain Ndbn-20. GSTs play an important role in the detoxification and degradation of a variety of endogenous and exogenous toxic compounds. On the basis of their sequence identities, phylogenetic status, and functions, the four bacterial GSH-dependent dehalogenases (PcpC, LinD, DsmH1, and DsmH2) were reclassified as a new eta class of GSTs. This study helps us to elucidate the microbial catabolism of dicamba and enhances our understanding of the diversity and functions of GSTs.
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Ito K, Takagi K, Matsushima Y, Iwasaki A, Tanaka N, Kanesaki Y, Martin-Laurent Martin-Laurent FF, Igimi S. Identification of the novel hcbB operon catalyzing the dechlorination of pentachlorophenol in the Gram-positive bacterium Nocardioides sp. strain PD653. JOURNAL OF PESTICIDE SCIENCE 2018; 43:124-131. [PMID: 30363388 PMCID: PMC6173144 DOI: 10.1584/jpestics.d17-089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
While pcp genes are well known in Gram-negative bacteria to code for the enzymes responsible for pentachlorophenol (C6HCl5O; PCP) degradation, little is known about PCP-degrading genes in Gram-positive bacteria. Here we describe a novel gene operon possibly responsible for catalyzing the degradation of PCP in the Gram-positive bacterium Nocardioides sp. strain PD653, which is capable of mineralizing hexachlorobenzene (C6Cl6; HCB) via PCP. Transcriptome analysis based on RNA-Seq revealed overexpressed genes in strain PD653 following exposure to HCB. Based on in silico annotation, three open reading frames (ORFs) were selected as biodegrading enzyme candidates. Recombinant E. coli cells expressing candidate genes degraded approximately 9.4 µmol L-1 PCP in 2 hr. Therefore, we designated these genes as hcbB1, hcbB2, and hcbB3. Interestingly, PCP-degrading activity was recorded when hcbB3 was coexpressed with hcbB1 or hcbB2, and the function of HcbB3 was expected to be similar to chlorophenol 4-monooxygenase (TftD).
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Affiliation(s)
- Koji Ito
- Department of Agricultural Chemistry, Tokyo University of Agriculture
- Hazardous Chemicals Division, Institute for Agro-Environmental Sciences, NARO
| | - Kazuhiro Takagi
- Department of Agricultural Chemistry, Tokyo University of Agriculture
- Hazardous Chemicals Division, Institute for Agro-Environmental Sciences, NARO
- To whom correspondence should be addressed. E-mail:
| | | | - Akio Iwasaki
- Juntendo Medical Technology Innovation Center, Juntendo University
| | - Naoto Tanaka
- Department of Molecular Microbiology, Tokyo University of Agriculture
| | - Yu Kanesaki
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture
| | | | - Shizunobu Igimi
- Department of Agricultural Chemistry, Tokyo University of Agriculture
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