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Liu B, Wang W, Qiu J, Huang X, Qiu S, Bao Y, Xu S, Ruan L, Ran T, He J. Crystal structures of herbicide-detoxifying esterase reveal a lid loop affecting substrate binding and activity. Nat Commun 2023; 14:4343. [PMID: 37468532 DOI: 10.1038/s41467-023-40103-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/11/2023] [Indexed: 07/21/2023] Open
Abstract
SulE, an esterase, which detoxifies a variety of sulfonylurea herbicides through de-esterification, provides an attractive approach to remove environmental sulfonylurea herbicides and develop herbicide-tolerant crops. Here, we determined the crystal structures of SulE and an activity improved mutant P44R. Structural analysis revealed that SulE is a dimer with spacious binding pocket accommodating the large sulfonylureas substrate. Particularly, SulE contains a protruding β hairpin with a lid loop covering the active site of the other subunit of the dimer. The lid loop participates in substrate recognition and binding. P44R mutation altered the lid loop flexibility, resulting in the sulfonylurea heterocyclic ring repositioning to a relative stable conformation thus leading to dramatically increased activity. Our work provides important insights into the molecular mechanism of SulE, and establish a solid foundation for further improving the enzyme activity to various sulfonylurea herbicides through rational design.
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Affiliation(s)
- Bin Liu
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Weiwu Wang
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xing Huang
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shenshen Qiu
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yixuan Bao
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Siqiong Xu
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Luyao Ruan
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingting Ran
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jian He
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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2
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Zeng J, He C, Guo J, Yuan L. Improvement of the Catalytic Activity of Thermoacidophilic Pullulan Hydrolase Type III by Error-Prone PCR Technology. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822030152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Malhotra H, Kaur S, Phale PS. Conserved Metabolic and Evolutionary Themes in Microbial Degradation of Carbamate Pesticides. Front Microbiol 2021; 12:648868. [PMID: 34305823 PMCID: PMC8292978 DOI: 10.3389/fmicb.2021.648868] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Carbamate pesticides are widely used as insecticides, nematicides, acaricides, herbicides and fungicides in the agriculture, food and public health sector. However, only a minor fraction of the applied quantity reaches the target organisms. The majority of it persists in the environment, impacting the non-target biota, leading to ecological disturbance. The toxicity of these compounds to biota is mediated through cholinergic and non-cholinergic routes, thereby making their clean-up cardinal. Microbes, specifically bacteria, have adapted to the presence of these compounds by evolving degradation pathways and thus play a major role in their removal from the biosphere. Over the past few decades, various genetic, metabolic and biochemical analyses exploring carbamate degradation in bacteria have revealed certain conserved themes in metabolic pathways like the enzymatic hydrolysis of the carbamate ester or amide linkage, funnelling of aryl carbamates into respective dihydroxy aromatic intermediates, C1 metabolism and nitrogen assimilation. Further, genomic and functional analyses have provided insights on mechanisms like horizontal gene transfer and enzyme promiscuity, which drive the evolution of degradation phenotype. Compartmentalisation of metabolic pathway enzymes serves as an additional strategy that further aids in optimising the degradation efficiency. This review highlights and discusses the conclusions drawn from various analyses over the past few decades; and provides a comprehensive view of the environmental fate, toxicity, metabolic routes, related genes and enzymes as well as evolutionary mechanisms associated with the degradation of widely employed carbamate pesticides. Additionally, various strategies like application of consortia for efficient degradation, metabolic engineering and adaptive laboratory evolution, which aid in improvising remediation efficiency and overcoming the challenges associated with in situ bioremediation are discussed.
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Affiliation(s)
- Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Sukhjeet Kaur
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Jiang W, Liu Y, Ke Z, Zhang L, Zhang M, Zhou Y, Wang H, Wu C, Qiu J, Hong Q. Substrate preference of carbamate hydrolase CehA reveals its environmental behavior. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123677. [PMID: 32835992 DOI: 10.1016/j.jhazmat.2020.123677] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
The cehA gene is the earliest reported and most widely found carbaryl hydrolase gene. CehA detoxifies carbaryl and other carbamate pesticides via de-esterification. Currently, there is no systematic research available on substrate preference or the mechanism of CehA action in different hosts. In this study, we found that CehA from different hosts is highly conserved, with more than 99% amino acid sequence similarity, and that transposable elements exist in both the upstream and downstream regions of cehA. By introducing point mutations into the cehA gene of Sphingobium sp. CFD-1, we obtained and heterologously expressed all reported CehA(CehAS) encoding genes. Assays to determine enzymatic properties and substrate profiles of CehAS showed that each CehA has a significant substrate preference for different carbamate insecticides. Specifically, CehA152Phe/Leu determines the catalytic preference for bicyclic carbamate substrates (carbofuran, carbaryl), while CehA494Thr/Ala and 570Thr/Ile determine the preference for monocyclic carbamate substrates (isoprocarb, propoxur) and linear carbamate substrates (oxamyl, aldicarb), respectively. Considering the existence of transposable elements in the flanking regions of cehA, we speculate that the cehA hosts may have acquired the hydrolysis ability, as well as substrate preference for carbamate pesticides, through horizontal gene transfer and genetic copying errors.
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Affiliation(s)
- Wankui Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yali Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Lu Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yidong Zhou
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Hui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Chenglong Wu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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Liu B, Wang H, Zhang K, Zhu J, He Q, He J. Improved Herbicide Resistance of 4-Hydroxyphenylpyruvate Dioxygenase from Sphingobium sp. TPM-19 through Directed Evolution. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:12365-12374. [PMID: 33105985 DOI: 10.1021/acs.jafc.0c05785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) has attracted extensive interest as a promising target for the genetic engineering of herbicide-resistant crops. However, naturally occurring HPPDs are generally very sensitive to HPPD inhibitors. In this study, random mutagenesis was performed to increase the HPPD inhibitors' resistance of Sphingobium sp. HPPD (SpHPPD). Two mutants, Q258M and Y333F, with improved resistance were obtained. Subsequently, a double-mutant (Q258M/Y333F) was generated through combined mutation. Q258M/Y333F exhibited the highest resistance to four HPPD inhibitors [topramezone, mesotrione, tembotrione, and diketonitrile (DKN)]. The enzyme fitness of Q258M/Y333F to topramezone, mesotrione, tembotrione, and DKN was increased by 4.0-, 4.1-, 4.2-, and 3.2-folds, respectively, in comparison with that of the wild-type. Molecular modeling and docking revealed that Q258M mutation leads to the decrease of enzyme-inhibitor-binding strength by breaking the hydrogen bond between the enzyme and the inhibitor, and Y333F mutation changes the conformational balance of the C-terminal helix H11, which hinders the binding of the inhibitor to the enzyme and thus would contribute to improved herbicide resistance. This study helps to further elucidate the structural basis for herbicide resistance and provides better genetic resources for the genetic engineering of herbicide-resistant crops.
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Affiliation(s)
- Bin Liu
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
| | - Haiyan Wang
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
| | - Kaiyun Zhang
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
| | - Jianchun Zhu
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
| | - Qin He
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
| | - Jian He
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P. R. China
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Serra-Mora P, Herráez-Hernández R, Campíns-Falcó P. Minimizing the impact of sample preparation on analytical results: In-tube solid-phase microextraction coupled on-line to nano-liquid chromatography for the monitoring of tribenuron methyl in environmental waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 721:137732. [PMID: 32172115 DOI: 10.1016/j.scitotenv.2020.137732] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/19/2020] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
The degradation kinetics and residual levels of the sulfonylurea herbicide tribenuron-methyl (TBM) in different environmental waters were studied using in tube-solid phase microextraction (IT-SPME) coupled on-line to nano-liquid chromatography (nanoLC) and UV diode array detection (DAD). This approach combines the high extraction efficiency of IT-SPME using polymeric coatings reinforced with metal oxide nanoparticles and the high sensitivity attainable by nanoLC, making possible the determination of TBM at low ppb levels (limit of detection, 0.25 ppb) without altering the sample matrix. The present study demonstrated that the preservation of the sample properties is essential to ensure accurate results at these concentration levels due to the high tendency of TBM to hydrolyze, particularly under the acidic conditions involved in most protocols used for sample treatment. The approach used in the present study was applied to evaluate the degradation of this herbicide under different conditions (UV radiation, pH), as well as to study the evolution of its concentration in different environmental waters, namely sea, river, ditch and transition waters. When the samples were exposed to identical conditions, significant differences in the degradation rate of TBM were found depending on the water matrix. The results obtained indicate that this herbicide can persist from several days to weeks depending on the type of water.
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Affiliation(s)
- P Serra-Mora
- MINTOTA Research Group, Departament de Química Analítica, Facultat de Química, Universitat de València, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - R Herráez-Hernández
- MINTOTA Research Group, Departament de Química Analítica, Facultat de Química, Universitat de València, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain.
| | - P Campíns-Falcó
- MINTOTA Research Group, Departament de Química Analítica, Facultat de Química, Universitat de València, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain.
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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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Zhang Z, Yang D, Wang J, Huo J, Zhang J. Studies on the interactions between nicosulfuron and degradation enzymes. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Jiang W, Gao Q, Zhang L, Wang H, Zhang M, Liu X, Zhou Y, Ke Z, Wu C, Qiu J, Hong Q. Identification of the key amino acid sites of the carbofuran hydrolase CehA from a newly isolated carbofuran-degrading strain Sphingbium sp. CFD-1. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 189:109938. [PMID: 31759739 DOI: 10.1016/j.ecoenv.2019.109938] [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: 07/31/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
A novel carbofuran-degrading strain CFD-1 was isolated and preliminarily identified as Sphingbium sp. This strain was able to utilize carbofuran as the sole carbon source for growth. The carbofuran hydrolase gene cehA was cloned from strain CFD-1 and expressed in Escherichia coli. CehA could hydrolyze carbamate pesticides including carbofuran and carbaryl efficiently, while it showed poor hydrolysis ability against isoprocarb, propoxur, oxamyl and aldicarb. CehA displayed maximal enzymatic activity at 40 °C and pH 7.0. The apparent Km and Kcat values of CehA for carbofuran were 133.22 ± 5.70 μM and 9.48 ± 0.89 s-1, respectively. The site-directed mutation experiment showed that His313, His315, His453 and His495 played important roles in the hydrolysis of carbofuran by CehA. Furthermore, the sequence of cehA is highly conserved among different carbofuran-degrading strains, and there are mobile elements around cehA, indicating that it may be transferred horizontally between different strains.
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Affiliation(s)
- Wankui Jiang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Qinqin Gao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Lu Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Hui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Mingliang Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Xiaoan Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Yidong Zhou
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Zhijian Ke
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Chenglong Wu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Jiguo Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Qing Hong
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
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Growth-coupled evolution of phosphoketolase to improve l-glutamate production by Corynebacterium glutamicum. Appl Microbiol Biotechnol 2019; 103:8413-8425. [DOI: 10.1007/s00253-019-10043-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/13/2019] [Accepted: 07/23/2019] [Indexed: 01/14/2023]
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