1
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Verma S, Singh A, Kumar P, Singla J. In-silico characterization of a hypothetical protein of Sulfobacillus sp. hq2 for degradation of phthalate diesters. Int J Biol Macromol 2024; 280:136006. [PMID: 39326604 DOI: 10.1016/j.ijbiomac.2024.136006] [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: 08/24/2024] [Revised: 09/19/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Phthalate plasticizers are hazardous compounds capable of causing endocrine disruption, cancers, and developmental disorders. Phthalate diesters are commonly used plasticizers in plastic products (PVC pipes) that leach out into the environment due to changes in temperature, pressure, and pH, posing harmful effects on different life forms. Bioremediation of phthalate diesters utilizing bacterial esterase has been recognized as an efficient approach but few effective esterases capable of degrading a wide range of phthalate diesters have been identified. Further, the thermostability of these esterases is a highly desirable property for their applications in diverse in-situ conditions. In this present in-silico study a hypothetical protein (POB10642.1) as a high-potential esterase from a thermostable strain of Sulfobacillus sp. hq2 has been characterized. Analysis revealed a significant sequence identity of 42.67 % and structural similarity (RMSD 0.557) with known phthalate diester degrading EstS1 esterase and a high Tm range of 55-66 °C. Structural analysis revealed the presence of two cavities on the surface mediating toward the catalytic site forming a catalytic tunnel. The enzyme POB10642.1 has significant molecular docking binding energies in the range of -5.4 to -7.5 kcal/mol with several phthalate diesters, including Diethyl phthalate, Dipropyl phthalate, Dibutyl phthalate, Dipentyl phthalate, Dihexyl phthalate, Benzyl butyl phthalate, Dicyclohexyl phthalate, and Bis(2-ethylhexyl) phthalate. High stability of binding during 100 ns molecular dynamics simulations revealed efficient and stable binding of the enzyme with a wide range of phthalate diesters at its active site, demonstrating the ability of the identified esterase to interact with and degrade diverse phthalate diesters. Therefore, POB10642.1 esterase can be an efficient candidate to be utilized in the development of enzyme-based bioremediation technologies to reduce the toxic levels of phthalate diesters.
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Affiliation(s)
- Shalja Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India
| | - Anika Singh
- Montfort School, Roorkee 24766, Uttarakhand, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
| | - Jitin Singla
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee 247667, Uttarakhand, India.
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2
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Zhang K, Zhou H, Ke J, Feng H, Lu C, Chen S, Liu A. Biodegradation of phthalic acid esters (PAEs) by Janthinobacterium sp. strain E1 under stress conditions. J GEN APPL MICROBIOL 2024; 70:n/a. [PMID: 38220211 DOI: 10.2323/jgam.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Phthalates esters (PAEs) are a kind of polymeric material additives widely been added into plastics to improve products' flexibility. It can easily cause environmental pollution which are hazards to public health. In this study, we isolated an efficient PAEs degrading strain, Janthinobacterium sp. E1, and determined its degradation effect of di-2-ethylhexyl phthalate (DEHP) under stress conditions. Strain E1 showed an obvious advantage in pollutants degradation under various environmental stress conditions. Degradation halo clearly occurred around the colony of strain E1 on agar plate supplemented with triglyceride. Strain E1's esterase is a constitutively expressed intracellular enzyme. The esterase purified from strain E1 showed a higher catalytic effect on short-chain PAEs than long-chain PAEs. The input of DEHP, DBP (dibutyl phthalate) and DMP (dimethyl phthalate) into the tested soil did not change the species composition of soil prokaryotic community, but altered the dominant species in specific environmental conditions. And the community diversity and richness decreased to a certain extent. However, the diversity and richness of the microbial community were improved after the contaminated soil was treated with the strain E1. Our results also suggested that strain E1 exhibited a tremendous potential in environmental bioremediation in the real environment, which provides a new insight into the elimination of the pollutants contamination in the urban environment.
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Affiliation(s)
- Kailu Zhang
- College of Life Sciences, Anhui Normal University
| | - Hui Zhou
- College of Life Sciences, Anhui Normal University
| | - Juntao Ke
- College of Life Sciences, Anhui Normal University
| | - Hongli Feng
- College of Life Sciences, Anhui Normal University
| | - Cunlong Lu
- College of Life Sciences, Anhui Normal University
| | | | - Aimin Liu
- College of Life Sciences, Anhui Normal University
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3
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Lin Z, Wu W, Yang C, Yang G, Wu W, Wei T, Huang F, Li H, Ren L, Liang Y, Zhang D, Li Z, Zhen Z. Mechanisms of biochar assisted di-2-ethylhexyl phthalate (DEHP) biodegradation in tomato rhizosphere by metabolic and metagenomic analysis. CHEMOSPHERE 2024; 353:141520. [PMID: 38395368 DOI: 10.1016/j.chemosphere.2024.141520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
The intensive accumulation of di-2-ethylhexyl phthalate (DEHP) in agricultural soils has resulted in severe environmental pollution that endangers ecosystem and human health. Biochar is an eco-friendly material that can help in accelerating organic pollutant degradation; nevertheless, its roles in enhancing DEHP removal in rhizosphere remain unclear. This work investigated the impacts of biochar dosage (0%-2.0%) on DEHP degradation performance in tomato rhizosphere by comprehensively exploring the change in DEHP metabolites, bacterial communities and DEHP-degrading genes. Our results showed a significant increase of rhizosphere pH, organic matter and humus by biochar amendment, which achieved a satisfactorily higher DEHP removal efficiency, maximally 77.53% in treatments with 1.0% of biochar. Biochar addition also remarkably changed rhizosphere bacterial communities by enriching some potential DEHP degraders of Nocardioides, Sphingomonas, Bradyrhizobium and Rhodanobacter. The abundance of genes encoding key enzymes (hydrolase, esterase and cytochrome P450) and DEHP-degrading genes (pht3, pht4, pht5, benC-xylZ and benD-xylL) were increased after biochar amendment, leading to the change in DEHP degradation metabolism, primarily from benzoic acid pathway to protocatechuic acid pathway. Our findings evidenced that biochar amendment could accelerate DEHP degradation by altering rhizosphere soil physicochemical variables, bacterial community composition and metabolic genes, providing clues for the mechanisms of biochar-assisted DEHP degradation in organic contaminated farmland soils.
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Affiliation(s)
- Zhong Lin
- Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, PR China; Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, 518108, PR China
| | - Weijian Wu
- Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Changhong Yang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Guiqiong Yang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Weilong Wu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Ting Wei
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Fengcheng Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Huijun Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Yanqiu Liang
- Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang, 524088, PR China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Zhe Li
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, PR China.
| | - Zhen Zhen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China.
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4
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Lai J, Huang H, Lin M, Xu Y, Li X, Sun B. Enzyme catalyzes ester bond synthesis and hydrolysis: The key step for sustainable usage of plastics. Front Microbiol 2023; 13:1113705. [PMID: 36713200 PMCID: PMC9878459 DOI: 10.3389/fmicb.2022.1113705] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Petro-plastic wastes cause serious environmental contamination that require effective solutions. Developing alternatives to petro-plastics and exploring feasible degrading methods are two solving routes. Bio-plastics like polyhydroxyalkanoates (PHAs), polylactic acid (PLA), polycaprolactone (PCL), poly (butylene succinate) (PBS), poly (ethylene furanoate) s (PEFs) and poly (ethylene succinate) (PES) have emerged as promising alternatives. Meanwhile, biodegradation plays important roles in recycling plastics (e.g., bio-plastics PHAs, PLA, PCL, PBS, PEFs and PES) and petro-plastics poly (ethylene terephthalate) (PET) and plasticizers in plastics (e.g., phthalate esters, PAEs). All these bio- and petro-materials show structure similarity by connecting monomers through ester bond. Thus, this review focused on bio-plastics and summarized the sequences and structures of the microbial enzymes catalyzing ester-bond synthesis. Most of these synthetic enzymes belonged to α/β-hydrolases with conserved serine catalytic active site and catalyzed the polymerization of monomers by forming ester bond. For enzymatic plastic degradation, enzymes about PHAs, PBS, PCL, PEFs, PES and PET were discussed, and most of the enzymes also belonged to the α/β hydrolases with a catalytic active residue serine, and nucleophilically attacked the ester bond of substrate to generate the cleavage of plastic backbone. Enzymes hydrolysis of the representative plasticizer PAEs were divided into three types (I, II, and III). Type I enzymes hydrolyzed only one ester-bond of PAEs, type II enzymes catalyzed the ester-bond of mono-ester phthalates, and type III enzymes hydrolyzed di-ester bonds of PAEs. Divergences of catalytic mechanisms among these enzymes were still unclear. This review provided references for producing bio-plastics, and degrading or recycling of bio- and petro-plastics from an enzymatic point of view.
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Affiliation(s)
- Jinghui Lai
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Huiqin Huang
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Mengwei Lin
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Youqiang Xu
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
| | - Xiuting Li
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, China
| | - Baoguo Sun
- Key Laboratory of Brewing Microbiology and Enzymatic Molecular Engineering of China General Chamber of Commence, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, China
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5
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Bhattacharyya M, Basu S, Dhar R, Dutta TK. Phthalate hydrolase: distribution, diversity and molecular evolution. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:333-346. [PMID: 34816599 DOI: 10.1111/1758-2229.13028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 05/12/2023]
Abstract
The alpha/beta-fold superfamily of hydrolases is rapidly becoming one of the largest groups of structurally related enzymes with diverse catalytic functions. In this superfamily of enzymes, esterase deserves special attention because of their wide distribution in biological systems and importance towards environmental and industrial applications. Among various esterases, phthalate hydrolases are the key alpha/beta enzymes involved in the metabolism of structurally diverse estrogenic phthalic acid esters, ubiquitously distributed synthetic chemicals, used as plasticizer in plastic manufacturing processes. Although they vary both at the sequence and functional levels, these hydrolases use a similar acid-base-nucleophile catalytic mechanism to catalyse reactions on structurally different substrates. The current review attempts to present insights on phthalate hydrolases, describing their sources, structural diversities, phylogenetic affiliations and catalytically different types or classes of enzymes, categorized as diesterase, monoesterase and diesterase-monoesterase, capable of hydrolysing phthalate diester, phthalate monoester and both respectively. Furthermore, available information on in silico analyses and site-directed mutagenesis studies revealing structure-function integrity and altered enzyme kinetics have been highlighted along with the possible scenario of their evolution at the molecular level.
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Affiliation(s)
| | - Suman Basu
- Department of Microbiology, Bose Institute, Kolkata, West Bengal, India
| | - Rinita Dhar
- Department of Microbiology, Bose Institute, Kolkata, West Bengal, India
| | - Tapan K Dutta
- Department of Microbiology, Bose Institute, Kolkata, West Bengal, India
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6
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Zhao Z, Liu C, Xu Q, Ahmad S, Zhang H, Pang Y, Aikemu A, Liu Y, Yan H. Characterization and genomic analysis of an efficient dibutyl phthalate degrading bacterium Microbacterium sp. USTB-Y. World J Microbiol Biotechnol 2021; 37:212. [PMID: 34738191 DOI: 10.1007/s11274-021-03181-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022]
Abstract
A promising bacterial strain for biodegrading dibutyl phthalate (DBP) was successfully isolated from activated sludge and characterized as a potential novel Microbacterium sp. USTB-Y based on 16S rRNA sequence analysis and whole genome average nucleotide identity (ANI). Initial DBP of 50 mg/L could be completely biodegraded by USTB-Y both in mineral salt medium and in DBP artificially contaminated soil within 12 h at the optimal culture conditions of pH 7.5 and 30 ℃, which indicates that USTB-Y has a strong ability in DBP biodegradation. Phthalic acid (PA) was identified as the end-product of DBP biodegraded by USTB-Y using GC/MS. The draft genome of USTB-Y was sequenced by Illumina NovaSeq and 29 and 188 genes encoding for putative esterase/carboxylesterase and hydrolase/alpha/beta hydrolase were annotated based on NR (non redundant protein sequence database) analysis, respectively. Gene3781 and gene3780 from strain USTB-Y showed 100% identity with dpeH and mpeH from Microbacterium sp. PAE-1. But no phthalate catabolic gene (pht) cluster was found in the genome of strain USTB-Y. The results in the present study are valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs biodegrading Microbacterium sp. strains.
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Affiliation(s)
- Zhenzhen Zhao
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Chao Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Qianqian Xu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Shahbaz Ahmad
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Haiyang Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yu Pang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Abudumukeyiti Aikemu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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7
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Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments. mSystems 2021; 6:e0035821. [PMID: 34100638 PMCID: PMC8269228 DOI: 10.1128/msystems.00358-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Di-(2-ethylhexyl) phthalate (DEHP) is the most widely used plasticizer worldwide, with an annual global production of more than 8 million tons. Because of its improper disposal, endocrine-disrupting DEHP often accumulates in estuarine sediments in industrialized countries at submillimolar levels, resulting in adverse effects on both ecosystems and human beings. The microbial degraders and biodegradation pathways of DEHP in O2-limited estuarine sediments remain elusive. Here, we employed an integrated meta-omics approach to identify the DEHP degradation pathway and major degraders in this ecosystem. Estuarine sediments were treated with DEHP or its derived metabolites, o-phthalic acid and benzoic acid. The rate of DEHP degradation in denitrifying mesocosms was two times slower than that of o-phthalic acid, suggesting that side chain hydrolysis of DEHP is the rate-limiting step of anaerobic DEHP degradation. On the basis of microbial community structures, functional gene expression, and metabolite profile analysis, we proposed that DEHP biodegradation in estuarine sediments is mainly achieved through synergistic networks between denitrifying proteobacteria. Acidovorax and Sedimenticola are the major degraders of DEHP side chains; the resulting o-phthalic acid is mainly degraded by Aestuariibacter through the UbiD-dependent benzoyl coenzyme A (benzoyl-CoA) pathway. We isolated and characterized Acidovorax sp. strain 210-6 and its extracellular hydrolase, which hydrolyzes both alkyl side chains of DEHP. Interestingly, genes encoding DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase and phthaloyl-CoA decarboxylase—key enzymes for side chain hydrolysis and o-phthalic acid degradation, respectively—are flanked by transposases in these proteobacterial genomes, indicating that DEHP degradation capacity is likely transferred horizontally in microbial communities. IMPORTANCE Xenobiotic phthalate esters (PAEs) have been produced on a considerably large scale for only 70 years. The occurrence of endocrine-disrupting di-(2-ethylhexyl) phthalate (DEHP) in environments has raised public concern, and estuarine sediments are major DEHP reservoirs. Our multi-omics analyses indicated that complete DEHP degradation in O2-limited estuarine sediments depends on synergistic microbial networks between diverse denitrifying proteobacteria and uncultured candidates. Our data also suggested that the side chain hydrolysis of DEHP, rather than o-phthalic acid activation, is the rate-limiting step in DEHP biodegradation within O2-limited estuarine sediments. Therefore, deciphering the bacterial ecophysiology and related biochemical mechanisms can help facilitate the practice of bioremediation in O2-limited environments. Furthermore, the DEHP hydrolase genes of active DEHP degraders can be used as molecular markers to monitor environmental DEHP degradation. Finally, future studies on the directed evolution of identified DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase would bring a more catalytically efficient DEHP/MEHP hydrolase into practice.
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Chen F, Li X, Dong Y, Li J, Li Y, Li H, Chen L, Zhou M, Hou H. Biodegradation of phthalic acid esters (PAEs) by Cupriavidus oxalaticus strain E3 isolated from sediment and characterization of monoester hydrolases. CHEMOSPHERE 2021; 266:129061. [PMID: 33310526 DOI: 10.1016/j.chemosphere.2020.129061] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/03/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
Phthalic acid esters (PAEs) are teratogenic and carcinogenic and mainly metabolized by microorganisms in sediment. A novel strain, Cupriavidus oxalaticus strain E3, was isolated and characterized from sediment for PAEs degradation. The transformation of dibutyl phthalate (DBP) and bis(2-ethylhexyl) phthalate (DEHP) as the sole carbon source by strain E3 was systematically studied in the darkness through the kinetic studies and analysis of intermediates. After the initial lag pause of 5 h-8 h, the strain efficiently degraded 87.4%-94.4% of DBP and 82.5%-85.6% of DEHP at an initial amount of each phthalate of 200 mg/L after 60 h of incubation. The biodegradation rate of DBP and DEHP followed a first-order kinetic model, and degradation rate constants (k) of them by E3 were 1.37 and 0.86 d-1, respectively. Gas chromatography-mass spectrometry (GC-MS) results revealed that the tentative PAEs degradation pathway, included the transformation from PAEs to phthalic acid (PA) and the complete mineralization of PA. In the phase of PAEs to PA, DBP with short sides reduced the chain length via hydrolyzation, and DEHP with long sides reduced the chain length via hydrolyzation and β-oxidation. The 3D model of monoester hydrolase from C. oxalaticus was predicted and used for docking with mono-2-ethylhexyl phthalate (MEHP) and mono-n-butyl phthalate (MBP). The docking results showed that the conserved catalytic triplet structure (Ser140, His284, and Asp254) acted as active sites and participated in degrading PMEs. This study provided novel insights into the mechanisms of PAEs degradation at a molecular level and widened the scope of functional bacteria by isolating strain E3.
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Affiliation(s)
- Fangyuan Chen
- School of Resource and Environmental Science, Wuhan University, Wuhan, 430079, Hubei, China
| | - Xuli Li
- School of Resource and Environmental Science, Wuhan University, Wuhan, 430079, Hubei, China
| | - Yiqie Dong
- School of Resource and Environmental Science, Wuhan University, Wuhan, 430079, Hubei, China
| | - Jiahao Li
- School of Resource and Environmental Science, Wuhan University, Wuhan, 430079, Hubei, China
| | - Yixin Li
- School of Resource and Environmental Science, Wuhan University, Wuhan, 430079, Hubei, China
| | - He Li
- School of Resource and Environmental Science, Wuhan University, Wuhan, 430079, Hubei, China
| | - Lei Chen
- School of Resource and Environmental Science, Wuhan University, Wuhan, 430079, Hubei, China
| | - Min Zhou
- School of Resource and Environmental Science, Wuhan University, Wuhan, 430079, Hubei, China.
| | - Haobo Hou
- School of Resource and Environmental Science, Wuhan University, Wuhan, 430079, Hubei, China; Zhaoqing (Wuhan University) Environmental Technology Research Institute, Zhaoqing, 526200, Guangdong, China.
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9
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Xu Y, Liu X, Zhao J, Huang H, Wu M, Li X, Li W, Sun X, Sun B. An efficient phthalate ester-degrading Bacillus subtilis: Degradation kinetics, metabolic pathway, and catalytic mechanism of the key enzyme. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 273:116461. [PMID: 33485001 DOI: 10.1016/j.envpol.2021.116461] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Phthalate ester pollution in the environment and food chain is frequently reported. Microbial treatment is a green and efficient method for solving this problem. The isolation and systematic investigation of microorganisms generally recognized as safe (GRAS) will provide useful resources. A GRAS Bacillus subtilis strain, BJQ0005, was isolated from Baijiu fermentation starter and efficiently degraded phthalate esters (PAEs). The half-lives for di-isobutyl phthalate, di-butyl phthalate and di-(2-ethylhexyl) phthalate were 3.93, 4.28, and 25.49 h, respectively, from the initial amount of 10 mg per 10 mL reaction mixture, which are records using wild-type strains. Genome sequencing and metabolic intermediate analysis generated the whole metabolic pathway. Eighteen enzymes from the α/β hydrolase family were expressed. Enzymes GTW28_09400 and GTW28_13725 were capable of single ester bond hydrolysis of PAEs, while GTW28_17760 hydrolyzed di-ester bonds of PAEs. Using molecular docking, a possible mechanism affecting enzymatic ester bond hydrolysis of mono-butyl phthalate was proposed of GTW28_17760. The carboxyl group generated by the first hydrolysis step interacted with histidine in the catalytic active center, which negatively affected enzymatic hydrolysis. Isolation and systematic investigation of the PAE degradation characteristics of B. subtilis will promote the green and safe treatment of PAEs in the environment and food industry.
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Affiliation(s)
- Youqiang Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China; Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing, 100048, China
| | - Xiao Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Jingrong Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Huiqin Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Mengqin Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Xiuting Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China; Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing, 100048, China.
| | - Weiwei Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Xiaotao Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China; Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, 100048, China
| | - Baoguo Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China; Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, 100048, China; Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing, 100048, China
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10
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Lu M, Jiang W, Gao Q, Zhang M, Hong Q. Degradation of dibutyl phthalate (DBP) by a bacterial consortium and characterization of two novel esterases capable of hydrolyzing PAEs sequentially. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 195:110517. [PMID: 32220793 DOI: 10.1016/j.ecoenv.2020.110517] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Phthalate esters (PAEs), a class of toxic anthropogenic compounds, have been predominantly used as additives or plasticizers, and great concern and interests have been raised regarding its environmental behavior and degradation mechanism. In the present study, a bacterial consortium consisting of Microbacterium sp. PAE-1 and Pandoraea sp. PAE-2 was isolated by the enrichment method, which could degrade dibutyl phthalate (DBP) completely by biochemical cooperation. DBP was converted to phthalic acid (PA) via monobutyl phthalate (MBP) by two sequential hydrolysis steps in strain PAE-1, and then PA was further degraded by strain PAE-2. Strain PAE-1 could hydrolyze many dialkyl Phthalate esters (PAEs) including dimethyl, diethyl, dibutyl, dipentyl, benzyl butyl, dihexyl, di-(2-ethyhexyl) and their corresponding monoalkyl PAEs. Two esterase genes named dpeH and mpeH, located in the same transcription unit, were cloned from strain PAE-1 by the shotgun method and heterologously expressed in Escherichia. coli (DE3). The Km and kcat values of DpeH for DBP were 9.60 ± 0.97 μM and (2.72 ± 0.06) × 106 s-1, while those of MpeH for MBP were 18.61 ± 2.00 μM and (5.83 ± 1.00) × 105 s-1, respectively. DpeH could only hydrolyze dialkyl PAEs to the corresponding monoalkyl PAEs, which were then hydrolyzed to PA by MpeH. DpeH shares the highest similarity (53%) with an alpha/beta hydrolase from Microbacterium sp. MED-G48 and MpeH shows only 25% identity with a secreted lipase from Trichophyton benhamiae CBS 112371, indicating that DpeH and MpeH are two novel hydrolases against PAEs.
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Affiliation(s)
- Meiyu Lu
- Key Lab of Microbiological Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China
| | - Wankui Jiang
- Key Lab of Microbiological Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China
| | - Qinqin Gao
- Key Lab of Microbiological Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China
| | - Mingliang Zhang
- Key Lab of Microbiological Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China
| | - Qing Hong
- Key Lab of Microbiological Agricultural Environment, Ministry of Agriculture, College of Life Science, Nanjing Agriculture University, Nanjing, 210095, People's Republic of China.
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11
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Huang L, Meng D, Tian Q, Yang S, Deng H, Guan Z, Cai Y, Liao X. Characterization of a novel carboxylesterase from Bacillus velezensis SYBC H47 and its application in degradation of phthalate esters. J Biosci Bioeng 2020; 129:588-594. [DOI: 10.1016/j.jbiosc.2019.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/17/2019] [Accepted: 11/01/2019] [Indexed: 10/25/2022]
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12
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Sarkar J, Dutta A, Pal Chowdhury P, Chakraborty J, Dutta TK. Characterization of a novel family VIII esterase EstM2 from soil metagenome capable of hydrolyzing estrogenic phthalates. Microb Cell Fact 2020; 19:77. [PMID: 32209105 PMCID: PMC7092541 DOI: 10.1186/s12934-020-01336-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbes are rich sources of enzymes and esterases are one of the most important classes of enzymes because of their potential for application in the field of food, agriculture, pharmaceuticals and bioremediation. Due to limitations in their cultivation, only a small fraction of the complex microbial communities can be cultured from natural habitats. Thus to explore the catalytic potential of uncultured organisms, the metagenomic approach has turned out to be an effective alternative method for direct mining of enzymes of interest. Based on activity-based screening method, an esterase-positive clone was obtained from metagenomic libraries. RESULTS Functional screening of a soil metagenomic fosmid library, followed by transposon mutagenesis led to the identification of a 1179 bp esterase gene, estM2, that encodes a 392 amino acids long protein (EstM2) with a translated molecular weight of 43.12 kDa. Overproduction, purification and biochemical characterization of the recombinant protein demonstrated carboxylesterase activity towards short-chain fatty acyl esters with optimal activity for p-nitrophenyl butyrate at pH 8.0 and 37 °C. Amino acid sequence analysis and subsequent phylogenetic analysis suggested that EstM2 belongs to the family VIII esterases that bear modest similarities to class C β-lactamases. EstM2 possessed the conserved S-x-x-K motif of class C β-lactamases but did not exhibit β-lactamase activity. Guided by molecular docking analysis, EstM2 was shown to hydrolyze a wide range of di- and monoesters of alkyl-, aryl- and benzyl-substituted phthalates. Thus, EstM2 displays an atypical hydrolytic potential of biotechnological significance within family VIII esterases. CONCLUSIONS This study has led to the discovery of a new member of family VIII esterases. To the best of our knowledge, this is the first phthalate hydrolase (EstM2), isolated from a soil metagenomic library that belongs to a family possessing β-lactamase like catalytic triad. Based on its catalytic potential towards hydrolysis of both phthalate diesters and phthalate monoesters, this enzyme may find use to counter the growing pollution caused by phthalate-based plasticizers in diverse geological environment and in other aspects of biotechnological applications.
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Affiliation(s)
- Jayita Sarkar
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Arindam Dutta
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Piyali Pal Chowdhury
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Joydeep Chakraborty
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Tapan K Dutta
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India.
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13
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Qiu J, Zhang Y, Shi Y, Jiang J, Wu S, Li L, Shao Y, Xin Z. Identification and characterization of a novel phthalate-degrading hydrolase from a soil metagenomic library. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 190:110148. [PMID: 31911388 DOI: 10.1016/j.ecoenv.2019.110148] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/27/2019] [Accepted: 12/28/2019] [Indexed: 06/10/2023]
Abstract
Phthalate esters have raised public concerns owing to their effects on the environment and human health. We identified a novel phthalate-degrading hydrolase, EstJ6, from a metagenomic library using function-driven screening. Phylogenetic analysis indicated that EstJ6 is a member of family IV esterases. EstJ6 hydrolyzed various dialkyl and monoalkyl phthalate esters, and exhibited high hydrolytic activity (128 U/mg) toward dibutyl phthalate at 40 °C and pH 7.5. EstJ6 hydrolyzed not only common phthalate esters with simple side chains but also diethylhexyl phthalate and monoethylhexyl phthalate, which have complex and long side chains. Site-directed mutagenesis indicated that the catalytic triad residues of EstJ6 consists of Ser146, Glu240, and His270. EstJ6 is therefore a promising biodegradation enzyme, and our study illustrates the advantages of a metagenomic approach in identifying enzyme-coding genes for agricultural, food, and biotechnological applications.
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Affiliation(s)
- Jiarong Qiu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yueqi Zhang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yaning Shi
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Junwei Jiang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Shenglu Wu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Longxiang Li
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yuting Shao
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Zhihong Xin
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, PR China.
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14
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Huang H, Zhang XY, Chen TL, Zhao YL, Xu DS, Bai YP. Biodegradation of Structurally Diverse Phthalate Esters by a Newly Identified Esterase with Catalytic Activity toward Di(2-ethylhexyl) Phthalate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8548-8558. [PMID: 31266305 DOI: 10.1021/acs.jafc.9b02655] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Herein, we report a double enzyme system to degrade 12 phthalate esters (PAEs), particularly bulky PAEs, such as the widely used bis(2-ethylhexyl) phthalate (DEHP), in a one-pot cascade process. A PAE-degrading bacterium, Gordonia sp. strain 5F, was isolated from soil polluted with plastic waste. From this strain, a novel esterase (GoEst15) and a mono(2-ethylhexyl) phthalate hydrolase (GoEstM1) were identified by homology-based cloning. GoEst15 showed broad substrate specificity, hydrolyzing DEHP and 10 other PAEs to monoalkyl phthalates, which were further degraded by GoEstM1 to phthalic acid. GoEst15 and GoEstM1 were heterologously coexpressed in Escherichia coli BL21 (DE3), which could then completely degrade 12 PAEs (5 mM), within 1 and 24 h for small and bulky substrates, respectively. To our knowledge, GoEst15 is the first DEHP hydrolase with a known protein sequence, which will enable protein engineering to enhance its catalytic performance in the future.
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Affiliation(s)
- Han Huang
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , People's Republic of China
| | - Xiao-Yan Zhang
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , People's Republic of China
| | - Tian-Lei Chen
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , People's Republic of China
| | - Yu-Lian Zhao
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , People's Republic of China
| | - Dian-Sheng Xu
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , People's Republic of China
| | - Yun-Peng Bai
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , People's Republic of China
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15
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Duan X, Jiang Z, Liu Y, Yan Q, Xiang M, Yang S. High-level expression of codon-optimized Thielavia terrestris cutinase suitable for ester biosynthesis and biodegradation. Int J Biol Macromol 2019; 135:768-775. [DOI: 10.1016/j.ijbiomac.2019.05.173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 10/26/2022]
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16
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Nahurira R, Wang J, Yan Y, Jia Y, Fan S, Khokhar I, Eltoukhy A. In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2. AMB Express 2019; 9:21. [PMID: 30715639 PMCID: PMC6362181 DOI: 10.1186/s13568-019-0733-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 01/03/2019] [Indexed: 12/29/2022] Open
Abstract
Members of genus Gordonia are known to degrade various xenobitics and produce secondary metabolites. The genome of a halotorelant phthalic acid ester (PAEs) degrading actinobacterium Gordonia alkanivorans strain YC-RL2 was sequenced using Biosciences RS II platform and Single Molecular Real-Time (SMRT) technology. The reads were assembled de novo by hierarchical genome assembly process (HGAP) algorithm version 2. Genes were annotated by NCBI Prokaryotic Genome Annotation Pipeline. The generated genome sequence was 4,979,656 bp with an average G+C content of 67.45%. Calculation of ANI confirmed previous classification that strain YC-RL2 is G. alkanivorans. The sequences were searched against KEGG and COG databases; 3132 CDSs were assigned to COG families and 1808 CDSs were predicted to be involved in 111 pathways. 95 of the KEGG annotated genes were predicted to be involved in the degradation of xenobiotics. A phthalate degradation operon could not be identified in the genome indicating that strain YC-RL2 possesses a novel way of phthalate degradation. A total of 203 and 22 CDSs were annotated as esterase/hydrolase and dioxygenase genes respectively. A total of 53 biosynthetic gene clusters (BGCs) were predicted by antiSMASH (antibiotics & Secondary Metabolite Analysis Shell) bacterial version 4.0. The genome also contained putative genes for heavy metal metabolism. The strain could tolerate 1 mM of Cd2+, Co2+, Cu2+, Ni2+, Zn2+, Mn2+ and Pb2+ ions. These results show that strain YC-RL2 has a great potential to degrade various xenobiotics in different environments and will provide a rich genetic resource for further biotechnological and remediation studies.
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Affiliation(s)
- Ruth Nahurira
- Biological Laboratory, Department of Biology, Graduate School of Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Junhuan Wang
- Biological Laboratory, Department of Biology, Graduate School of Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Yanchun Yan
- Biological Laboratory, Department of Biology, Graduate School of Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Yang Jia
- Biological Laboratory, Department of Biology, Graduate School of Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Shuanghu Fan
- Biological Laboratory, Department of Biology, Graduate School of Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Ibatsam Khokhar
- Biological Laboratory, Department of Biology, Graduate School of Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Adel Eltoukhy
- Biological Laboratory, Department of Biology, Graduate School of Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
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17
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Zhu F, Zhu C, Doyle E, Liu H, Zhou D, Gao J. Fate of di (2‑ethylhexyl) phthalate in different soils and associated bacterial community changes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:460-469. [PMID: 29754081 DOI: 10.1016/j.scitotenv.2018.05.055] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 06/08/2023]
Abstract
Di (2‑ethylhexyl) phthalate (DEHP) is a ubiquitous organic pollutant, which has caused considerable pollution in arable soils. In this study, the relationship between DEHP degradation potential and soil properties in 12 agricultural soils (S1-S12) was examined in a microcosm based experiment. Six of these soils were then selected to monitor patterns in bacterial community responses. It was found that DEHP degradation was positively correlated with bacterial counts in the original soils, suggesting a key role for bacteria in degradation. However, DEHP metabolism did not always lead to complete degradation. Its monoester metabolite, mono (2‑ethylhexyl) phthalate (MEHP), was present at appreciable levels in the two acidic soils (S1 and S2) during the incubation period of 35 days. Based on high-throughput sequencing data, we observed a greater impact of DEHP contamination on bacterial community structure in acidic soils than in the other soils. Nocardioides, Ramlibacter and unclassified Sphingomonadaceae were enriched in the two near-neutral soils where degradation was highest (S4 and S7), suggesting that these organisms might be efficient degraders. The relative abundance of Tumibacillus was greatly reduced in 50% of the six soils examined, demonstrating a high sensitivity to DEHP contamination. Furthermore, putative organic-matter decomposing bacteria (including Tumebacillus and other bacteria taxa such as members from Micromonosporaceae) were greatly reduced in the two acidic soils (S1 and S2), possibly due to the accumulation of MEHP. These results suggest a crucial role of soil acidity in determining the fate and impact of DEHP in soil ecosystems, which deserves further investigation. This work contributes to a better understanding of the environmental behavior of DEHP in soil and should facilitate the development of appropriate remediation technologies.
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Affiliation(s)
- Fengxiao Zhu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Changyin Zhu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Evelyn Doyle
- Environmental Microbiology Group, School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hailong Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Dongmei Zhou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Juan Gao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
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18
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Fan S, Wang J, Yan Y, Wang J, Jia Y. Excellent Degradation Performance of a Versatile Phthalic Acid Esters-Degrading Bacterium and Catalytic Mechanism of Monoalkyl Phthalate Hydrolase. Int J Mol Sci 2018; 19:ijms19092803. [PMID: 30231475 PMCID: PMC6164851 DOI: 10.3390/ijms19092803] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/05/2018] [Accepted: 09/08/2018] [Indexed: 12/03/2022] Open
Abstract
Despites lots of characterized microorganisms that are capable of degrading phthalic acid esters (PAEs), there are few isolated strains with high activity towards PAEs under a broad range of environmental conditions. In this study, Gordonia sp. YC-JH1 had advantages over its counterparts in terms of di(2-ethylhexyl) phthalate (DEHP) degradation performance. It possessed an excellent degradation ability in the range of 20–50 °C, pH 5.0–12.0, or 0–8% NaCl with the optimal degradation condition 40 °C and pH 10.0. Therefore, strain YC-JH1 appeared suitable for bioremediation application at various conditions. Metabolites analysis revealed that DEHP was sequentially hydrolyzed by strain YC-JH1 to mono(2-ethylhexyl) phthalate (MEHP) and phthalic acid (PA). The hydrolase MphG1 from strain YC-JH1 hydrolyzed monoethyl phthalate (MEP), mono-n-butyl phthalate (MBP), mono-n-hexyl phthalate (MHP), and MEHP to PA. According to molecular docking and molecular dynamics simulation between MphG1 and monoalkyl phthalates (MAPs), some key residues were detected, including the catalytic triad (S125-H291-D259) and the residues R126 and F54 potentially binding substrates. The mutation of these residues accounted for the reduced activity. Together, the mechanism of MphG1 catalyzing MAPs was elucidated, and would shed insights into catalytic mechanism of more hydrolases.
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Affiliation(s)
- Shuanghu Fan
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Junhuan Wang
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Yanchun Yan
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jiayi Wang
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Yang Jia
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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19
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Fan S, Wang J, Li K, Yang T, Jia Y, Zhao B, Yan Y. Complete genome sequence of Gordonia sp. YC-JH1, a bacterium efficiently degrading a wide range of phthalic acid esters. J Biotechnol 2018; 279:55-60. [DOI: 10.1016/j.jbiotec.2018.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/29/2018] [Accepted: 05/09/2018] [Indexed: 02/05/2023]
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20
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Bacteria-mediated phthalic acid esters degradation and related molecular mechanisms. Appl Microbiol Biotechnol 2017; 102:1085-1096. [DOI: 10.1007/s00253-017-8687-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/30/2017] [Accepted: 11/30/2017] [Indexed: 10/18/2022]
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21
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Singh N, Dalal V, Mahto JK, Kumar P. Biodegradation of phthalic acid esters (PAEs) and in silico structural characterization of mono-2-ethylhexyl phthalate (MEHP) hydrolase on the basis of close structural homolog. JOURNAL OF HAZARDOUS MATERIALS 2017; 338:11-22. [PMID: 28531656 DOI: 10.1016/j.jhazmat.2017.04.055] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 05/27/2023]
Abstract
Three bacterial strains capable of degrading phthalates namely Pseudomonas sp. PKDM2, Pseudomonas sp. PKDE1 and Pseudomonas sp. PKDE2 were isolated and characterized for their degradative potential. These strains efficiently degraded 77.4%-84.4% of DMP, 75.0%-75.7% of DEP and 71.7%-74.7% of DEHP, initial amount of each phthalate is 500mgL-1 of each phthalate, after 44h of incubation. GC-MS results reveal the tentative DEHP degradation pathway, where hydrolases mediate the breakdown of DEHP to phthalic acid (PA) via an intermediate MEHP. MEHP hydrolase is a serine hydrolase which is involved in the reduction of the MEHP to PA. The predicted 3D model of MEHP hydrolase from Pseudomonas mosselii was docked with phthalate monoesters (PMEs) such as MEHP, mono-n-hexyl phthalate (MHP), mono-n-butyl phthalate (MBP) and mono-n-ethyl phthalate (MEP), respectively. Docking results show the distance between the carbonyl carbon of respective phthalate monoester and the hydroxyl group of catalytic serine lies in the range of 2.9 to 3.3Å, which is similar to the ES complex of other serine hydrolases. This structural study highlights the interaction and the role of catalytic residues of MEHP hydrolase involved in the biodegradation of PMEs to phthalate.
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Affiliation(s)
- Neha Singh
- Department of Biotechnology, Indian Institute of Technology, Roorkee, 247667, India
| | - Vikram Dalal
- Department of Biotechnology, Indian Institute of Technology, Roorkee, 247667, India
| | - Jai Krishna Mahto
- Department of Biotechnology, Indian Institute of Technology, Roorkee, 247667, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology, Roorkee, 247667, India.
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