1
|
Zhou X, Huang J, Xu S, Cheng H, Liu B, Huang J, Liu J, Pan D, Wu X. Novel Bifunctional Amidase Catalyzing the Degradation of Propanil and Aryloxyphenoxypropionate Herbicides in Rhodococcus sp. C-1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18067-18077. [PMID: 39082634 DOI: 10.1021/acs.jafc.4c02268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Propanil residues can contaminate habitats where microbial degradation is predominant. In this study, an efficient propanil-degrading strain C-1 was isolated from paddy and identified as Rhodococcus sp. It can completely degrade 10 μg/L-150 mg/L propanil within 0.33-10 h via the hydrolysis of the amide bond, forming 3,4-dichloroaniline. A novel bifunctional amidase, PamC, was identified in strain C-1. PamC can catalyze the hydrolysis of the amide bond of propanil to produce 3,4-dichloroaniline as well as the hydrolysis of the ester bonds of aryloxyphenoxypropionate herbicides (APPHs, clodinafop-propargyl, cyhalofop-butyl, fenoxaprop-p-ethyl, fluazifop-p-butyl, haloxyfop-p-methyl, and quizalofop-p-ethyl) to form aryloxyphenoxypropionic acids. Molecular docking and site-directed mutagenesis confirmed that the catalytic triad Lys82-Ser157-Ser181 was the active center for PamC to hydrolyze propanil and cyhalofop-butyl. This study presents a novel bifunctional amidase with capabilities for both amide and ester bond hydrolysis and enhances our understanding of the molecular mechanisms underlying the degradation of propanil and APPHs.
Collapse
Affiliation(s)
- Xiaoyu Zhou
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Jinjin Huang
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Shiwei Xu
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Huan Cheng
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Bin Liu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Junwei Huang
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Junwei Liu
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Dandan Pan
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Xiangwei Wu
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| |
Collapse
|
2
|
Lavrov KV, Shemyakina AO, Grechishnikova EG, Gerasimova TV, Kalinina TI, Novikov AD, Leonova TE, Ryabchenko LE, Bayburdov TA, Yanenko AS. A new concept of biocatalytic synthesis of acrylic monomers for obtaining water-soluble acrylic heteropolymers. Metab Eng Commun 2024; 18:e00231. [PMID: 38222043 PMCID: PMC10787234 DOI: 10.1016/j.mec.2023.e00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/03/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024] Open
Abstract
Rhodococcus strains were designed as model biocatalysts (BCs) for the production of acrylic acid and mixtures of acrylic monomers consisting of acrylamide, acrylic acid, and N-alkylacrylamide (N-isopropylacrylamide). To obtain BC strains, we used, among other approaches, adaptive laboratory evolution (ALE), based on the use of the metabolic pathway of amide utilization. Whole genome sequencing of the strains obtained after ALE, as well as subsequent targeted gene disruption, identified candidate genes for three new amidases that are promising for the development of BCs for the production of acrylic acid from acrylamide. New BCs had two types of amidase activities, acrylamide-hydrolyzing and acrylamide-transferring, and by varying the ratio of these activities in BCs, it is possible to influence the ratio of monomers in the resulting mixtures. Based on these strains, a prototype of a new technological concept for the biocatalytic synthesis of acrylic monomers was developed for the production of water-soluble acrylic heteropolymers containing valuable N-alkylacrylamide units. In addition to the possibility of obtaining mixtures of different compositions, the advantages of the concept are a single starting reagent (acrylamide), more unification of processes (all processes are based on the same type of biocatalyst), and potentially greater safety for personnel and the environment compared to existing chemical technologies.
Collapse
Affiliation(s)
- Konstantin V. Lavrov
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Anna O. Shemyakina
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Elena G. Grechishnikova
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Tatyana V. Gerasimova
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Tatyana I. Kalinina
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Andrey D. Novikov
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Tatyana E. Leonova
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Ludmila E. Ryabchenko
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| | - Telman A. Bayburdov
- Saratov Chemical Plant of Acrylic Polymers “AKRYPOL”, 410059, Saratov, Russia
| | - Alexander S. Yanenko
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, 123182, Akademika Kurchatova pl. 1, Moscow, Russia
| |
Collapse
|
3
|
Mao Z, Song M, Zhao R, Liu Y, Zhu Y, Liu X, Liang H, Zhang H, Wu X, Wang G, Li F, Zhang L. Characterization of two novel hydrolases from Sphingopyxis sp. DBS4 for enantioselective degradation of chiral herbicide diclofop-methyl. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133967. [PMID: 38457978 DOI: 10.1016/j.jhazmat.2024.133967] [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: 11/21/2023] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Diclofop-methyl, an aryloxyphenoxypropionate (AOPP) herbicide, is a chiral compound with two enantiomers. Microbial detoxification and degradation of various enantiomers is garnering immense research attention. However, enantioselective catabolism of diclofop-methyl has been rarely explored, especially at the molecular level. This study cloned two novel hydrolase genes (dcmA and dcmH) in Sphingopyxis sp. DBS4, and characterized them for diclofop-methyl degradation. DcmA, a member of the amidase superfamily, exhibits 26.1-45.9% identity with functional amidases. Conversely, DcmH corresponded to the DUF3089 domain-containing protein family (a family with unknown function), sharing no significant similarity with other biochemically characterized proteins. DcmA exhibited a broad spectrum of substrates, with preferential hydrolyzation of (R)-(+)-diclofop-methyl, (R)-(+)-quizalofop-ethyl, and (R)-(+)-haloxyfop-methyl. DcmH also preferred (R)-(+)-quizalofop-ethyl and (R)-(+)-haloxyfop-methyl degradation while displaying no apparent enantioselective activity towards diclofop-methyl. Using site-directed mutagenesis and molecular docking, it was determined that Ser175 was the fundamental residue influencing DcmA's activity against the two enantiomers of diclofop-methyl. For the degradation of AOPP herbicides, DcmA is an enantioselective amidase that has never been reported in research. This study provided novel hydrolyzing enzyme resources for the remediation of diclofop-methyl in the environment and deepened the understanding of enantioselective degradation of chiral AOPP herbicides mediated by microbes.
Collapse
Affiliation(s)
- Zhenbo Mao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Man Song
- College of Chemistry and Materials Science, Huaibei Normal University, 235000 Huaibei, China
| | - Ruiqi Zhao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Yuan Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Yumeng Zhu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Xinyu Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Hailong Liang
- Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Huijun Zhang
- Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Xiaomin Wu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Guangli Wang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Feng Li
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China
| | - Long Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, 235000 Huaibei, China; Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, 235000 Huaibei, China.
| |
Collapse
|
4
|
Ganjoo A, Babu V. Recombinant Amidases: Recent Insights and its Applications in the Production of Industrially Important Fine Chemicals. Mol Biotechnol 2024:10.1007/s12033-024-01123-8. [PMID: 38598092 DOI: 10.1007/s12033-024-01123-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/27/2024] [Indexed: 04/11/2024]
Abstract
The current research for the synthesis of industrially important fine chemicals is more inclined towards developing enzyme-based processes. The biotransformation reactions wherein microbial cells/enzymes are used, have become essential in making the process efficient, green, and economical. Amongst industrially important enzymes, amidase is one of the most versatile tools in biocatalysis and biotransformation reactions. It shows broad substrate specificity and sturdy functional characteristics because of its promiscuous nature. Further, advancement in the area led to the development of amidase recombinant systems, which are developed using biotechnology and enzyme engineering tools. Additionally, recombinant amidases may be instrumental in commercializing the synthesis of fine chemicals such as hydroxamic acids that have a significant pharmaceutical market. Hence, the present review focuses on highlighting and assimilating the tools and techniques used in developing recombinant systems followed by their applications.
Collapse
Affiliation(s)
- Ananta Ganjoo
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vikash Babu
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
5
|
Sun S, Chen W, Peng K, Chen X, Chen J. Characterization of a novel amidohydrolase with promiscuous esterase activity from a soil metagenomic library and its application in degradation of amide herbicides. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:20970-20982. [PMID: 38383926 PMCID: PMC10948491 DOI: 10.1007/s11356-024-32362-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/03/2024] [Indexed: 02/23/2024]
Abstract
Amide herbicides have been extensively used worldwide and have received substantial attention due to their adverse environmental effects. Here, a novel amidohydrolase gene was identified from a soil metagenomic library using diethyl terephthalate (DET) as a screening substrate. The recombinant enzyme, AmiH52, was heterologously expressed in Escherichia coli and later purified and characterized, with the highest activity occurring at 40 ℃ and pH 8.0. AmiH52 was demonstrated to have both esterase and amidohydrolase activities, which exhibited highly specific activity for p-nitrophenyl butyrate (2669 U/mg) and degrading activity against several amide herbicides. In particular, it displayed the strongest activity against propanil, with a high degradation rate of 84% at 8 h. A GC-MS analysis revealed that propanil was transformed into 3,4-dichloroaniline (3,4-DCA) during this degradation. The molecular interactions and binding stability were then analyzed by molecular docking and molecular dynamics simulation, which revealed that several key amino acid residues, including Tyr164, Trp66, Ala59, Val283, Arg58, His33, His191, and His226, are involved in the specific interactions with propanil. This study provides a function-driven screening method for amide herbicide hydrolase from the metagenomic libraries and a promising propanil-degrading enzyme (AmiH52) for potential applications in environmental remediation.
Collapse
Affiliation(s)
- Shengwei Sun
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Wanqi Chen
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Kailin Peng
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xueyingzi Chen
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
- Department of Materials, Loughborough University, Loughborough, LE11 3TU, UK.
| |
Collapse
|
6
|
Zhang L, Yao G, Mao Z, Song M, Zhao R, Zhang X, Chen C, Zhang H, Liu Y, Wang G, Li F, Wu X. Experimental and computational approaches to characterize a novel amidase that initiates the biodegradation of the herbicide propanil in Bosea sp. P5. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131155. [PMID: 36893600 DOI: 10.1016/j.jhazmat.2023.131155] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
The herbicide propanil and its major metabolite 3,4-dichloroaniline (3,4-DCA) are difficult to biodegrade and pose great health and environmental risks. However, studies on the sole or synergistic mineralization of propanil by pure cultured strains are limited. A two-strain consortium (Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34), obtained from a swep-mineralizing enrichment culture that can synergistically mineralize propanil, has been previously reported. Here, another propanil degradation strain, Bosea sp. P5, was successfully isolated from the same enrichment culture. A novel amidase, PsaA, responsible for initial propanil degradation, was identified from strain P5. PsaA shared low sequence identity (24.0-39.7 %) with other biochemically characterized amidases. PsaA exhibited optimal activity at 30 °C and pH 7.5 and had kcat and Km values of 5.7 s-1 and 125 μM, respectively. PsaA could convert the herbicide propanil to 3,4-DCA but exhibited no activity toward other herbicide structural analogs. This catalytic specificity was explained by using propanil and swep as substrates and then analyzed by molecular docking, molecular dynamics simulation and thermodynamic calculations, which revealed that Tyr138 is the key residue that affects the substrate spectrum of PsaA. This is the first propanil amidase with a narrow substrate spectrum identified, providing new insights into the catalytic mechanism of amidase in propanil hydrolysis.
Collapse
Affiliation(s)
- Long Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China; Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China.
| | - Gui Yao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Zhenbo Mao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Man Song
- College of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Ruiqi Zhao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Xiaochun Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China; School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Chun Chen
- Institute of Biomedicine, Jinan University, Guangzhou, 510632, PR China
| | - Huijun Zhang
- Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Yuan Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Guangli Wang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Feng Li
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Xiaomin Wu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China.
| |
Collapse
|
7
|
Yu Z, Gu W, Yang Y, Li X, Li X, Li T, Wang J, Su Z, Li X, Dai Y, Xu M, Zhang H. Whole-Genome Sequencing of a Chlorimuron-Ethyl-Degrading Strain: Chenggangzhangella methanolivorans CHL1 and Its Degrading Enzymes. Microbiol Spectr 2022; 10:e0182222. [PMID: 35861510 PMCID: PMC9430300 DOI: 10.1128/spectrum.01822-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/01/2022] [Indexed: 11/20/2022] Open
Abstract
Chlorimuron-ethyl is a commonly used sulfonylurea herbicide, and its long-term residues cause serious environmental problems. Biodegradation of chlorimuron-ethyl is effective and feasible, and many degrading strains have been obtained, but still, the genes and enzymes involved in this degradation are often unclear. In this study, whole-genome sequencing was performed on chlorimuron-ethyl-degrading strain, Chenggangzhangella methanolivorans CHL1. The complete genome of strain CHL1 contains one circular chromosome of 5,542,510 bp and a G+C content of 68.17 mol%. Three genes, sulE, pnbA, and gst, were predicted to be involved in the degradation of chlorimuron-ethyl, and this was confirmed by gene knockout and gene complementation experiments. The three genes were cloned and expressed in Escherichia coli BL21 (DE3) to allow for the evaluation of the catalytic activities of the respective enzymes. The glutathione-S-transferase (GST) catalyzes the cleavage of the sulfonylurea bridge of chlorimuron-ethyl, and the esterases, PnbA and SulE, both de-esterify it. This study identifies three key functional genes of strain CHL1 that are involved in the degradation of chlorimuron-ethyl and also provides new approaches by which to construct engineered bacteria for the bioremediation of environments polluted with sulfonylurea herbicides. IMPORTANCE Chlorimuron-ethyl is a commonly used sulfonylurea herbicide, worldwide. However, its residues in soil and water have a potent toxicity toward sensitive crops and other organisms, such as microbes and aquatic algae, and this causes serious problems for the environment. Microbial degradation has been demonstrated to be a feasible and promising strategy by which to eliminate xenobiotics from the environment. Many chlorimuron-ethyl-degrading microorganisms have been reported, but few studies have investigated the genes and enzymes that are involved in the degradation. In this work, two esterase-encoding genes (sulE, pnbA) and a glutathione-S-transferase-encoding gene (gst) responsible for the detoxification of chlorimuron-ethyl by strain Chenggangzhangella methanolivorans CHL1 were identified, then cloned and expressed in Escherichia coli BL21 (DE3). These key chlorimuron-ethyl-degrading enzymes are candidates for the construction of engineered bacteria to degrade this pesticide and enrich the resources for bioremediating environments polluted with sulfonylurea herbicides.
Collapse
Affiliation(s)
- Zhixiong Yu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wu Gu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xiang Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Tingting Li
- Shenyang Research Institute of Chemical Industry, Shenyang, China
| | - Jian Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Zhencheng Su
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yumeng Dai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingkai Xu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| |
Collapse
|
8
|
The Novel Amidase PcnH Initiates the Degradation of Phenazine-1-Carboxamide in Sphingomonas histidinilytica DS-9. Appl Environ Microbiol 2022; 88:e0054322. [PMID: 35579476 PMCID: PMC9195955 DOI: 10.1128/aem.00543-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Phenazines are an important class of secondary metabolites and are primarily named for their heterocyclic phenazine cores, including phenazine-1-carboxylic acid (PCA) and its derivatives, such as phenazine-1-carboxamide (PCN) and pyocyanin (PYO). Although several genes involved in the degradation of PCA and PYO have been reported so far, the genetic foundations of PCN degradation remain unknown. In this study, a PCN-degrading bacterial strain, Sphingomonas histidinilytica DS-9, was isolated. The gene pcnH, encoding a novel amidase responsible for the initial step of PCN degradation, was cloned by genome comparison and subsequent experimental validation. PcnH catalyzed the hydrolysis of the amide bond of PCN to produce PCA, which shared low identity (only 26 to 33%) with reported amidases. The Km and kcat values of PcnH for PCN were 33.22 ± 5.70 μM and 18.71 ± 0.52 s-1, respectively. PcnH has an Asp-Lys-Cys motif, which is conserved among amidases of the isochorismate hydrolase-like (IHL) superfamily. The replacement of Asp37, Lys128, and Cys163 with alanine in PcnH led to the complete loss of enzymatic activity. Furthermore, the genes pcaA1A2A3A4 and pcnD were found to encode PCA 1,2-dioxygenase and 1,2-dihydroxyphenazine (2OHPC) dioxygenase, which were responsible for the subsequent degradation steps of PCN. The PCN-degradative genes were highly conserved in some bacteria of the genus Sphingomonas, with slight variations in the sequence identities. IMPORTANCE Phenazines have been widely acknowledged as a natural antibiotic for more than 150 years, but their degradation mechanisms are still not completely elucidated. Compared with the studies on the degradation mechanism of PCA and PYO, little is known regarding PCN degradation by far. Previous studies have speculated that its initial degradation step may be catalyzed by an amidase, but no further studies have been conducted. This study identified a novel amidase, PcnH, that catalyzed the hydrolysis of PCN to PCA. In addition, the PCA 1,2-dioxygenase PcaA1A2A3A4 and 2OHPC dioxygenase PcnD were also found to be involved in the subsequent degradation steps of PCN in S. histidinilytica DS-9. And the genes responsible for PCN catabolism are highly conserved in some strains of Sphingomonas. These results deepen our understanding of the PCN degradation mechanism.
Collapse
|
9
|
Li C, Sun Y, Sun G, Zang H, Sun S, Zhao X, Hou N, Li D. An amidase and a novel phenol hydroxylase catalyze the degradation of the antibacterial agent triclocarban by Rhodococcus rhodochrous. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128444. [PMID: 35183828 DOI: 10.1016/j.jhazmat.2022.128444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/29/2022] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
Triclocarban (TCC) is an emerging and intractable environmental contaminant due to its hydrophobicity and chemical stability. However, the antibacterial property of TCC limits its biodegradation, and only the functional enzyme TccA involved in TCC degradation has been characterized to date. In this study, we report a highly efficient TCC-degrading bacterium, Rhodococcus rhodochrous BX2, that could degrade and mineralize TCC (10 mg/L) by 76.8% and 56.5%, respectively, within 5 days. Subsequently, the TCC biodegradation pathway was predicted based on the detection of metabolites using modern mass spectrometry techniques. Furthermore, an amidase (TccS) and a novel phenol hydroxylase (PHIND) encoded by the tccS and PHIND genes, respectively, were identified by genomic and transcriptomic analyses of strain BX2, and these enzymes were further unequivocally proven to be the key enzymes responsible for the metabolism of TCC and its intermediate 4-chloroaniline (4-CA) by using a combination of heterologous expression and gene knockout. Our results shed new light on the mechanism of TCC biodegradation and better utilization of microbes to remediate TCC contamination.
Collapse
Affiliation(s)
- Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
| | - Yueling Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
| | - Guanjun Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
| | - Shanshan Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
| | - Xinyue Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
| | - Ning Hou
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
| | - Dapeng Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, PR China.
| |
Collapse
|
10
|
Zhao YX, Guo L, Wang L, Jiang ND, Chen KX, Dai YJ. Biodegradation of the pyridinecarboxamide insecticide flonicamid by Microvirga flocculans and characterization of two novel amidases involved. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 220:112384. [PMID: 34091185 DOI: 10.1016/j.ecoenv.2021.112384] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/11/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
Flonicamid (N-cyanomethyl-4-trifluoromethylnicotinamide, FLO) is a new type of pyridinecarboxamide insecticide that exhibits particularly good efficacy in pest control. However, the extensive use of FLO in agricultural production poses environmental risks. Hence, its environmental behavior and degradation mechanism have received increasing attention. Microvirga flocculans CGMCC 1.16731 rapidly degrades FLO to produce the intermediate N-(4-trifluoromethylnicotinoyl) glycinamide (TFNG-AM) and the end acid metabolite 4-(trifluoromethyl) nicotinol glycine (TFNG). This bioconversion is mediated by the nitrile hydratase/amidase system; however, the amidase that is responsible for the conversion of TFNG-AM to TFNG has not yet been reported. Here, gene cloning, overexpression in Escherichia coli and characterization of pure enzymes showed that two amidases-AmiA and AmiB-hydrolyzed TFNG-AM to TFNG. AmiA and AmiB showed only 20-30% identity to experimentally characterized amidase signature family members, and represent novel amidases. Compared with AmiA, AmiB was more sensitive to silver and copper ions but more resistant to organic solvents. Both enzymes demonstrated good pH tolerance and exhibited broad amide substrate specificity. Homology modeling suggested that residues Asp191 and Ser195 may strongly affect the catalytic activity of AmiA and AmiB, respectively. The present study furthers our understanding of the enzymatic mechanisms of biodegradation of nitrile-containing insecticides and may aid in the development of a bioremediation agent for FLO.
Collapse
Affiliation(s)
- Yun-Xiu Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Ling Guo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Li Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Neng-Dang Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Ke-Xin Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| | - Yi-Jun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
| |
Collapse
|
11
|
Xi L, Tan W, Li J, Qu J, Liu J. Cloning and characterization of a novel thermostable amidase, Xam, from Xinfangfangia sp. DLY26. Biotechnol Lett 2021; 43:1395-1402. [PMID: 33811594 DOI: 10.1007/s10529-021-03124-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 03/26/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Identification and characterization of a novel thermostable amidase (Xam) with wide pH tolerance and broad-spectrum substrate specificity. RESULTS Xam was identified from non-thermophilic Xinfangfangia sp. DLY26 and its acyl transfer activity was investigated. Recombinant Xam was optimally active at 60 °C and pH 9.0. The enzyme had a half life of 18 h at 55 °C and maintained more than 60 % of its maximum activity in the range of pH 3.0-11.0. Additionally, Xam exhibited broad substrate specificity towards aliphatic, aromatic, and heterocyclic amides. CONCLUSIONS These unique properties make Xam a promising biocatalyst for production of important hydroxamic acids at elevated temperatures.
Collapse
Affiliation(s)
- Lijun Xi
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Wenfei Tan
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jing Li
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jianbo Qu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jianguo Liu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
| |
Collapse
|
12
|
Carbamate C-N Hydrolase Gene ameH Responsible for the Detoxification Step of Methomyl Degradation in Aminobacter aminovorans Strain MDW-2. Appl Environ Microbiol 2020; 87:AEM.02005-20. [PMID: 33097501 DOI: 10.1128/aem.02005-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
Methomyl {bis[1-methylthioacetaldehyde-O-(N-methylcarbamoyl)oximino]sulfide} is a highly toxic oxime carbamate insecticide. Several methomyl-degrading microorganisms have been reported so far, but the role of specific enzymes and genes in this process is still unexplored. In this study, a protein annotated as a carbamate C-N hydrolase was identified in the methomyl-degrading strain Aminobacter aminovorans MDW-2, and the encoding gene was termed ameH A comparative analysis between the mass fingerprints of AmeH and deduced proteins of the strain MDW-2 genome revealed AmeH to be a key enzyme of the detoxification step of methomyl degradation. The results also demonstrated that AmeH was a functional homodimer with a subunit molecular mass of approximately 34 kDa and shared the highest identity (27%) with the putative formamidase from Schizosaccharomyces pombe ATCC 24843. AmeH displayed maximal enzymatic activity at 50°C and pH 8.5. Km and k cat of AmeH for methomyl were 87.5 μM and 345.2 s-1, respectively, and catalytic efficiency (k cat/Km ) was 3.9 μM-1 s-1 Phylogenetic analysis revealed AmeH to be a member of the FmdA_AmdA superfamily. Additionally, five key amino acid residues (162, 164, 191, 193, and 207) of AmeH were identified by amino acid variations.IMPORTANCE Based on the structural characteristic, carbamate insecticides can be classified into oxime carbamates (methomyl, aldicarb, oxamyl, etc.) and N-methyl carbamates (carbaryl, carbofuran, isoprocarb, etc.). So far, research on the degradation of carbamate pesticides has mainly focused on the detoxification step and hydrolysis of their carbamate bond. Several genes, such as cehA, mcbA, cahA, and mcd, and their encoding enzymes have also been reported to be involved in the detoxification step. However, none of these enzymes can hydrolyze methomyl. In this study, a carbamate C-N hydrolase gene, ameH, responsible for the detoxification step of methomyl in strain MDW-2 was cloned and the key amino acid sites of AmeH were investigated. These findings provide insight into the microbial degradation mechanism of methomyl.
Collapse
|
13
|
González-Magaña A, Sainz-Polo MÁ, Pretre G, Çapuni R, Lucas M, Altuna J, Montánchez I, Fucini P, Albesa-Jové D. Structural insights into Pseudomonas aeruginosaType six secretion system exported effector 8. J Struct Biol 2020; 212:107651. [PMID: 33096229 DOI: 10.1016/j.jsb.2020.107651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Recent reports indicate that the Type six secretion system exported effector 8 (Tse8) is a cytoactive effector secreted by the Type VI secretion system (T6SS) of the human pathogen Pseudomonas aeruginosa. The T6SS is a nanomachine that assembles inside of the bacteria and injects effectors/toxins into target cells, providing a fitness advantage over competing bacteria and facilitating host colonisation. Here we present the first crystal structure of Tse8 revealing that it conserves the architecture of the catalytic triad Lys84-transSer162-Ser186 that characterises members of the Amidase Signature superfamily. Furthermore, using binding affinity experiments, we show that the interaction of phenylmethylsulfonyl fluoride (PMSF) to Tse8 is dependent on the putative catalytic residue Ser186, providing support for its nucleophilic reactivity. This work thus demonstrates that Tse8 belongs to the Amidase Signature (AS) superfamily. Furthermore, it highlights Tse8 similarity to two family members: the Stenotrophomonas maltophilia Peptide Amidase and the Glutamyl-tRNAGln amidotransferase subunit A from Staphylococcus aureus.
Collapse
Affiliation(s)
- Amaia González-Magaña
- Instituto Biofisika (UPV/EHU, CSIC), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, University of the Basque Country, 48940 Leioa, Spain
| | - M Ángela Sainz-Polo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Gabriela Pretre
- Instituto Biofisika (UPV/EHU, CSIC), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, University of the Basque Country, 48940 Leioa, Spain
| | - Retina Çapuni
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - María Lucas
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria. Santander, 39011 Cantabria, Spain
| | - Jon Altuna
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Itxaso Montánchez
- Departamento de Inmunología, Microbiología y Parasitología, University of the Basque Country, 48940 Leioa, Spain
| | - Paola Fucini
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - David Albesa-Jové
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
| |
Collapse
|
14
|
Du Q, Zhang X, Pan X, Zhang H, Yang YS, Liu J, Jiao Q. A novel strategy for efficient chemoenzymatic synthesis of D-glutamine using recombinant Escherichia coli cells. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
15
|
Tan W, Liu J, Li Z, Xu Z, Xin W, Xi L. Cloning, expression and biochemical characterization of a novel amidase from Thauera sinica K11. Protein Expr Purif 2020; 177:105751. [PMID: 32931916 DOI: 10.1016/j.pep.2020.105751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/14/2020] [Accepted: 09/10/2020] [Indexed: 11/17/2022]
Abstract
A novel amidase (TAM) was identified and cloned from the genome of Thauera sinica K11. The recombinant protein was purified to homogeneity by one-step affinity chromatography for up to 26.4-fold with a yield of 38.1%. Gel filtration chromatography and SDS-PAGE revealed that the enzyme was a tetramer with a subunit of approximately 37.5 kDa. The amidase exhibited the maximum acyl transfer activity at 45 °C and pH 7.0, and it was highly stable over a wide pH range of 6.0-11.0. Inhibition of enzyme activity was observed in the presence of metal ions, thiol reagents and organic solvents. TAM showed a broad substrate spectrum toward aliphatic, aromatic and heterocyclic amides. For linear aliphatic monoamides, the acyl transfer activity of TAM was decreased with the extension of the carbon chain length, and thus the highest activity of 228.2 U/mg was obtained when formamide was used as substrate. This distinct selectivity of amidase to linear aliphatic monoamides expanded the findings of signature amidases to substrate specificity.
Collapse
Affiliation(s)
- Wenfei Tan
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jianguo Liu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
| | - Ziyi Li
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Zhenzhen Xu
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Wen Xin
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Lijun Xi
- Centre for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
| |
Collapse
|
16
|
Wu Z, Liu C, Zhang Z, Zheng R, Zheng Y. Amidase as a versatile tool in amide-bond cleavage: From molecular features to biotechnological applications. Biotechnol Adv 2020; 43:107574. [PMID: 32512219 DOI: 10.1016/j.biotechadv.2020.107574] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/27/2022]
Abstract
Amidases (EC 3. 5. 1. X) are versatile biocatalysts for synthesis of chiral carboxylic acids, α-amino acids and amides due to their hydrolytic and acyl transfer activity towards the C-N linkages. They have been extensively exploited and studied during the past years for their high specific activity and excellent enantioselectivity involved in various biotechnological applications in pharmaceutical and agrochemical industries. Additionally, they have attracted considerable attentions in biodegradation and bioremediation owing to environmental pressures. Motivated by industrial demands, crystallographic investigations and catalytic mechanisms of amidases based on structural biology have witnessed a dramatic promotion in the last two decades. The protein structures showed that different types of amidases have their typical stuctural elements, such as the conserved AS domains in signature amidases and the typical architecture of metal-associated active sites in acetamidase/formamidase family amidases. This review provides an overview of recent research advances in various amidases, with a focus on their structural basis of phylogenetics, substrate specificities and catalytic mechanisms as well as their biotechnological applications. As more crystal structures of amidases are determined, the structure/function relationships of these enzymes will also be further elucidated, which will facilitate molecular engineering and design of amidases to meet industrial requirements.
Collapse
Affiliation(s)
- Zheming Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Changfeng Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhaoyu Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Renchao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| |
Collapse
|
17
|
Mineralization of the herbicide swep by a two-strain consortium and characterization of a new amidase for hydrolyzing swep. Microb Cell Fact 2020; 19:4. [PMID: 31910844 PMCID: PMC6945715 DOI: 10.1186/s12934-020-1276-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 01/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Swep is an excellent carbamate herbicide that kills weeds by interfering with metabolic processes and inhibiting cell division at the growth point. Due to the large amount of use, swep residues in soil and water not only cause environmental pollution but also accumulate through the food chain, ultimately pose a threat to human health. This herbicide is degraded in soil mainly by microbial activity, but no studies on the biotransformation of swep have been reported. RESULTS In this study, a consortium consisting of two bacterial strains, Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34, was enriched from a contaminated soil sample and shown to be capable of mineralizing swep. Swep was first transformed by Comamonas sp. SWP-3 to the intermediate 3,4-dichloroaniline (3,4-DCA), after which 3,4-DCA was mineralized by Alicycliphilus sp. PH-34. An amidase gene, designated as ppa, responsible for the transformation of swep into 3,4-DCA was cloned from strain SWP-3. The expressed Ppa protein efficiently hydrolyzed swep and a number of other structural analogues, such as propanil, chlorpropham and propham. Ppa shared less than 50% identity with previously reported arylamidases and displayed maximal activity at 30 °C and pH 8.6. Gly449 and Val266 were confirmed by sequential error prone PCR to be the key catalytic sites for Ppa in the conversion of swep. CONCLUSIONS These results provide additional microbial resources for the potential remediation of swep-contaminated sites and add new insights into the catalytic mechanism of amidase in the hydrolysis of swep.
Collapse
|
18
|
Mei X, Wu C, Zhao J, Yan T, Jiang P. Community Structure of Bacteria Associated With Drifting Sargassum horneri, the Causative Species of Golden Tide in the Yellow Sea. Front Microbiol 2019; 10:1192. [PMID: 31191503 PMCID: PMC6546727 DOI: 10.3389/fmicb.2019.01192] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/10/2019] [Indexed: 01/28/2023] Open
Abstract
Golden tides dominated by Sargassum spp. are occurring at an accelerated rate worldwide. In China, Sargassum has started to bloom in the Yellow Sea and led to tremendous economic losses, but the underlying biological causes and mechanisms are still unclear. Although algae-associated bacteria were suggested to play crucial roles in algal blooms, the profiles of bacteria associated with drifting Sargassum remain unexplored. In this study, the community structures and functions of Sargassum-associated bacteria were analyzed using the high-throughput sequencing data of the V5–V7 hypervariable region of the 16S rRNA gene. Molecular identification revealed that the golden tide analyzed in the Yellow Sea was dominated by a single species, Sargassum horneri. They were a healthy brown color nearshore but were yellow offshore with significantly decreased chlorophyll contents (P < 0.01), which indicates that yellow S. horneri was under physiological stress. The structural and functional analyses of bacterial communities indicated that the drifting S. horneri had an obvious selectivity on their associated bacteria against surrounding seawater. Although the bacterial communities phylogenetically differed between brown and yellow S. horneri (P < 0.01), their dominant functions were all nitrogen and iron transporters, which strongly indicates microbial contribution to blooming of the algal host. For the first time, potential epiphytic and endophytic bacteria associated with Sargassum were independently analyzed by a modified co-vortex method with silica sand. We showed that the composition of dominant endophytes, mainly Bacillus and Propionibacterium, was relatively consistent regardless of host status, whereas the epiphytic operational taxonomic units (OTUs) greatly varied in response to weakness of host status; however, dominant functions were consistent at elevated intensities, which might protect the host from stress related to nitrogen or iron deficiency. Thus, we propose that host physiological status at different intensities of functional demands, which were related to variable environmental conditions, may be a critical factor that influences the assembly of epiphytic bacterial communities. This study provided new insight into the structure and potential functions of associated bacteria with golden tide blooms.
Collapse
Affiliation(s)
- Xiangyuan Mei
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chunhui Wu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jin Zhao
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Tian Yan
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Peng Jiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| |
Collapse
|
19
|
Sun L, Gao X, Chen W, Huang K, Bai N, Lyu W, Liu H. Characterization of the Propham Biodegradation Pathway in Starkeya sp. Strain YW6 and Cloning of a Novel Amidase Gene mmH. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:4193-4199. [PMID: 30864436 DOI: 10.1021/acs.jafc.8b06928] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We previously isolated a monocrotophos-degrading strain Starkeya sp. YW6, which could also degrade propham. Here, we show that strain YW6 metabolizes propham via a pathway in which propham is initially hydrolyzed to aniline and then converted to catechol, which is then oxidized via an ortho-cleavage pathway. The novel amidase gene mmH was cloned from strain YW6 and expressed in Escherichia coli BL21(DE3). MmH, which exhibits aryl acylamidase activity, was purified for enzymatic analysis. Bioinformatic analysis confirmed that MmH belongs to the amidase signature (AS) enzyme family and shares 26-50% identity with several AS family members. MmH (molecular mass of 53 kDa) was most active at 40 °C and pH 8.0 and showed high activity toward propham, with Kcat and Km values of 33.4 s-1 and 16.9 μM, respectively. These characteristics make MmH suitable for novel amide biosynthesis and environmental remediation.
Collapse
Affiliation(s)
- Lina Sun
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERCLA) , Shanghai 201403 , People's Republic of China
| | - Xinhua Gao
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Environmental Protection Monitoring Station of Shanghai , Shanghai 201403 , People's Republic of China
| | - Wei Chen
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Key Laboratory of Horticultural Technology , Shanghai 201403 , People's Republic of China
| | - Kaihua Huang
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Environmental Protection Monitoring Station of Shanghai , Shanghai 201403 , People's Republic of China
| | - Naling Bai
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Agricultural Environment and Farmland Conservation Experiment Station of Ministry of Agriculture , Shanghai 201403 , People's Republic of China
| | - Weiguang Lyu
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERCLA) , Shanghai 201403 , People's Republic of China
- Shanghai Agricultural Environment and Farmland Conservation Experiment Station of Ministry of Agriculture , Shanghai 201403 , People's Republic of China
| | - Hongming Liu
- Institute of Molecular Biology and Biotechnology , Anhui Normal University , Wuhu , Anhui 241000 , People's Republic of China
| |
Collapse
|
20
|
Zhang L, Hu Q, Hang P, Zhou X, Jiang J. Characterization of an arylamidase from a newly isolated propanil-transforming strain of Ochrobactrum sp. PP-2. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 167:122-129. [PMID: 30317116 DOI: 10.1016/j.ecoenv.2018.09.127] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/16/2018] [Accepted: 09/30/2018] [Indexed: 06/08/2023]
Abstract
Propanil, one of the most extensively used post-emergent contact herbicides, has also been reported to have adverse effect on environmental safety. A bacterial strain of Ochrobactrum sp. PP-2, which was capable of transforming propanil, was isolated from a propanil-contaminated soil collected from a chemical factory. An arylamidase gene mah responsible for transforming propanil to 3,4-dichloroaniline (3,4-DCA) was cloned from strain PP-2 by shotgun method and subsequently confirmed by function expression. The arylamidase Mah shares low amino acid sequence identity (27-50%) with other biochemically characterized amidases and shows less than 30% identities to other reported propanil hydrolytic enzymes. Mah was most active at pH 8 and 35 °C. Mah had a remarkable activity toward propanil (Km = 6.3 ± 1.2 µM), showing the highest affinity efficiency for propanil as compared with other reported propanil hydrolytic enzymes. Our study also provides a new arylamidase for the hydrolysis of propanil.
Collapse
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, People's Republic of 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, People's Republic of China
| | - Ping Hang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Xiyi Zhou
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, People's Republic of China.
| |
Collapse
|
21
|
An Amidase Gene, ipaH, Is Responsible for the Initial Step in the Iprodione Degradation Pathway of Paenarthrobacter sp. Strain YJN-5. Appl Environ Microbiol 2018; 84:AEM.01150-18. [PMID: 30054359 DOI: 10.1128/aem.01150-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 07/20/2018] [Indexed: 11/20/2022] Open
Abstract
Iprodione [3-(3,5-dichlorophenyl) N-isopropyl-2,4-dioxoimidazolidine-1-carboxamide] is a highly effective broad-spectrum dicarboxamide fungicide. Several bacteria with iprodione-degrading capabilities have been reported; however, the enzymes and genes involved in this process have not been characterized. In this study, an iprodione-degrading strain, Paenarthrobacter sp. strain YJN-5, was isolated and characterized. Strain YJN-5 degraded iprodione through the typical pathway, with hydrolysis of its N-1 amide bond to N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine as the initial step. The ipaH gene, encoding a novel amidase responsible for this step, was cloned from strain YJN-5 by the shotgun method. IpaH shares the highest similarity (40%) with an indoleacetamide hydrolase (IAHH) from Bradyrhizobium diazoefficiens USDA 110. IpaH displayed maximal enzymatic activity at 35°C and pH 7.5, and it was not a metalloamidase. The kcat and Km of IpaH against iprodione were 22.42 s-1 and 7.33 μM, respectively, and the catalytic efficiency value (kcat/Km ) was 3.09 μM-1 s-1 IpaH has a Ser-Ser-Lys motif, which is conserved among members of the amidase signature family. The replacement of Lys82, Ser157, and Ser181 with alanine in IpaH led to the complete loss of enzymatic activity. Furthermore, strain YJN-5M lost the ability to degrade iprodione, suggesting that ipaH is the only gene responsible for the initial iprodione degradation step. The ipaH gene could also be amplified from another previously reported iprodione-degrading strain, Microbacterium sp. strain YJN-G. The sequence similarity between the two IpaHs at the amino acid level was 98%, indicating that conservation of IpaH exists in different strains.IMPORTANCE Iprodione is a widely used dicarboxamide fungicide, and its residue has been frequently detected in the environment. The U.S. Environmental Protection Agency has classified iprodione as moderately toxic to small animals and a probable carcinogen to humans. Bacterial degradation of iprodione has been widely investigated. Previous studies demonstrate that hydrolysis of its N-1 amide bond is the initial step in the typical bacterial degradation pathway of iprodione; however, enzymes or genes involved in iprodione degradation have yet to be reported. In this study, a novel ipaH gene encoding an amidase responsible for the initial degradation step of iprodione in Paenarthrobacter sp. strain YJN-5 was cloned. In addition, the characteristics and key amino acid sites of IpaH were investigated. These findings enhance our understanding of the microbial degradation mechanism of iprodione.
Collapse
|
22
|
Zheng RC, Jin JQ, Wu ZM, Tang XL, Jin LQ, Zheng YG. Biocatalytic hydrolysis of chlorinated nicotinamides by a superior AS family amidase and its application in enzymatic production of 2-chloronicotinic acid. Bioorg Chem 2018; 76:81-87. [DOI: 10.1016/j.bioorg.2017.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/05/2017] [Accepted: 11/06/2017] [Indexed: 12/17/2022]
|
23
|
Efficient biodegradation of dihalogenated benzonitrile herbicides by recombinant Escherichia coli harboring nitrile hydratase-amidase pathway. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.05.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
24
|
Bhatia RK, Bhatia SK, Mehta PK, Bhalla TC. Bio-statistical enhancement of acyl transfer activity of amidase for biotransformation of N-substituted aromatic amides. J GEN APPL MICROBIOL 2017; 62:90-7. [PMID: 27118077 DOI: 10.2323/jgam.62.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Abstract
Acyl transfer activity (ATA) of amidase transfers an acyl group of different amides to hydroxylamine to form the corresponding hydroxamic acid. Bacterial isolate BR-1 was isolated from cyanogenic plant Cirsium vulgare rhizosphere and identified as Pseudomonas putida BR-1 by 16S rDNA sequencing. This organism exhibited high ATA for the biotransformation of N-substituted aromatic amide to the corresponding hydroxamic acid. Optimization of media, tryptone (0.6%), inducer, pH 8.5, and a growth temperature 25°C for 56 h, resulted in a 7-fold increase in ATA. Further, Response Surface Methodology (RSM) and multiple feeding approach (20 mM after 14 h) of inducer led to a 29% enhancement of ATA from this organism. The half life (t1/2) of this enzyme at 50°C and 60°C was 3 h and 1 h, respectively. The ATA of amidase of Pseudomonas putida BR-1 makes it a potential candidate for the production of a variety of N-substituted aromatic hydroxamic acid.
Collapse
|
25
|
Santoshkumar M, Ismailsab M, Nayak AS, Mashetty SB, Karegoudar T. Purification and characterization of amidase from Paracoccus sp. SKG: Utilization of amidase-inhibited whole cells for bioconversion of acrylonitrile to acrylamide. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
26
|
Yun H, Liang B, Qiu J, Zhang L, Zhao Y, Jiang J, Wang A. Functional Characterization of a Novel Amidase Involved in Biotransformation of Triclocarban and its Dehalogenated Congeners in Ochrobactrum sp. TCC-2. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:291-300. [PMID: 27966913 DOI: 10.1021/acs.est.6b04885] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Haloaromatic antimicrobial triclocarban (3,4,4'-trichlorocarbanilide, TCC) is a refractory contaminant which is frequently detected in various aquatic and sediment environments globally. However, few TCC-degrading communities or pure cultures have been documented, and functional enzymes involved in TCC biodegradation hitherto have not yet been characterized. In this study, a bacterial strain, Ochrobactrum sp. TCC-2, capable of degrading TCC under both aerobic and anaerobic conditions was isolated from a sediment sample. A novel amidase gene (tccA), responsible for the hydrolysis of the two amide bonds of TCC and its dehalogenated congeners 4,4'-dichlorocarbanilide (DCC) and carbanilide (NCC) to more biodegradable chloroaniline or aniline products, was cloned and characterized. TccA shares low amino acid sequence identity (27 to 38%) with other biochemically characterized amidases and contains the conserved catalytic triad (Ser-Ser-Lys) of the amidase signature enzyme family. TccA was stable over a pH range of 5.0 to 10.0 and at temperatures lower than 60 °C, and it was constitutively expressed in strain TCC-2. In contrast to the halogenated TCC and DCC, the nonchlorinated NCC was the preferred substrate for TccA. TccA also had hydrolysis activity to a broad spectrum of amide bonds in herbicides, insecticides, and chemical intermediates. The constitutive expression and broad substrate spectrum of TccA suggested strain TCC-2 may be potentially useful for bioremediation applications.
Collapse
Affiliation(s)
- Hui Yun
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing, 100085, China
- University of Chinese Academy of Sciences , Beijing, China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing, 100085, China
| | - Jiguo Qiu
- Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University , 210095, Nanjing, China
| | - Long Zhang
- Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University , 210095, Nanjing, China
| | - Youkang Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology , Harbin, 150090, China
| | - Jiandong Jiang
- Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University , 210095, Nanjing, China
| | - Aijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing, 100085, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology , Harbin, 150090, China
| |
Collapse
|
27
|
Identification and characterization of a novel amidase signature family amidase from Parvibaculum lavamentivorans ZJB14001. Protein Expr Purif 2017; 129:60-68. [DOI: 10.1016/j.pep.2016.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/08/2016] [Accepted: 09/13/2016] [Indexed: 11/17/2022]
|
28
|
Identification and characterization of a thermostable and cobalt-dependent amidase from Burkholderia phytofirmans ZJB-15079 for efficient synthesis of (R)-3,3,3-trifluoro-2-hydroxy-2-methylpropionic acid. Appl Microbiol Biotechnol 2016; 101:1953-1964. [DOI: 10.1007/s00253-016-7921-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/20/2016] [Accepted: 10/05/2016] [Indexed: 10/20/2022]
|
29
|
Ruan LT, Zheng RC, Zheng YG. Mining and characterization of two amidase signature family amidases from Brevibacterium epidermidis ZJB-07021 by an efficient genome mining approach. Protein Expr Purif 2016; 126:16-25. [DOI: 10.1016/j.pep.2016.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 11/28/2022]
|
30
|
Ruan LT, Zheng RC, Zheng YG. A novel amidase from Brevibacterium epidermidis ZJB-07021: gene cloning, refolding and application in butyrylhydroxamic acid synthesis. ACTA ACUST UNITED AC 2016; 43:1071-83. [DOI: 10.1007/s10295-016-1786-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 05/21/2016] [Indexed: 10/21/2022]
Abstract
Abstract
A novel amidase gene (bami) was cloned from Brevibacterium epidermidis ZJB-07021 by combination of degenerate PCR and high-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR). The deduced amino acid sequence showed low identity (≤55 %) with other reported amidases. The bami gene was overexpressed in Escherichia coli, and the resultant inclusion bodies were refolded and purified to homogeneity with a recovery of 22.6 %. Bami exhibited a broad substrate spectrum towards aliphatic, aromatic and heterocyclic amides, and showed the highest acyl transfer activity towards butyramide with specific activity of 1331.0 ± 24.0 U mg−1. Kinetic analysis demonstrated that purified Bami exhibited high catalytic efficiency (414.9 mM−1 s−1) for acyl transfer of butyramide, with turnover number (K cat) of 3569.0 s−1. Key parameters including pH, substrate/co-substrate concentration, reaction temperature and catalyst loading were investigated and the Bami showed maximum acyl transfer activity at 50 °C, pH 7.5. Enzymatic catalysis of 200 mM butyramide with 15 μg mL−1 purified Bami was completed in 15 min with a BHA yield of 88.1 % under optimized conditions. The results demonstrated the great potential of Bami for the production of a variety of hydroxamic acids.
Collapse
Affiliation(s)
- Li-Tao Ruan
- grid.469325.f 000000041761325X Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.469325.f 000000041761325X Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| | - Ren-Chao Zheng
- grid.469325.f 000000041761325X Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.469325.f 000000041761325X Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| | - Yu-Guo Zheng
- grid.469325.f 000000041761325X Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.469325.f 000000041761325X Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| |
Collapse
|
31
|
Mishra P, Kaur S, Sharma AN, Jolly RS. Characterization of an Indole-3-Acetamide Hydrolase from Alcaligenes faecalis subsp. parafaecalis and Its Application in Efficient Preparation of Both Enantiomers of Chiral Building Block 2,3-Dihydro-1,4-Benzodioxin-2-Carboxylic Acid. PLoS One 2016; 11:e0159009. [PMID: 27391673 PMCID: PMC4938524 DOI: 10.1371/journal.pone.0159009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/25/2016] [Indexed: 11/19/2022] Open
Abstract
Both the enantiomers of 2,3-dihydro-1,4-benzodioxin-2-carboxylic acid are valuable chiral synthons for enantiospecific synthesis of therapeutic agents such as (S)-doxazosin mesylate, WB 4101, MKC 242, 2,3-dihydro-2-hydroxymethyl-1,4-benzodioxin, and N-[2,4-oxo-1,3-thiazolidin-3-yl]-2,3-dihydro-1,4-benzodioxin-2-carboxamide. Pharmaceutical applications require these enantiomers in optically pure form. However, currently available methods suffer from one drawback or other, such as low efficiency, uncommon and not so easily accessible chiral resolving agent and less than optimal enantiomeric purity. Our interest in finding a biocatalyst for efficient production of enantiomerically pure 2,3-dihydro-1,4-benzodioxin-2-carboxylic acid lead us to discover an amidase activity from Alcaligenes faecalis subsp. parafaecalis, which was able to kinetically resolve 2,3-dihydro-1,4-benzodioxin-2-carboxyamide with E value of >200. Thus, at about 50% conversion, (R)-2,3-dihydro-1,4-benzodioxin-2-carboxylic acid was produced in >99% e.e. The remaining amide had (S)-configuration and 99% e.e. The amide and acid were easily separated by aqueous (alkaline)-organic two phase extraction method. The same amidase was able to catalyse, albeit at much lower rate the hydrolysis of (S)-amide to (S)-acid without loss of e.e. The amidase activity was identified as indole-3-acetamide hydrolase (IaaH). IaaH is known to catalyse conversion of indole-3-acetamide (IAM) to indole-3-acetic acid (IAA), which is phytohormone of auxin class and is widespread among plants and bacteria that inhabit plant rhizosphere. IaaH exhibited high activity for 2,3-dihydro-1,4-benzodioxin-2-carboxamide, which was about 65% compared to its natural substrate, indole-3-acetamide. The natural substrate for IaaH indole-3-acetamide shared, at least in part a similar bicyclic structure with 2,3-dihydro-1,4-benzodioxin-2-carboxamide, which may account for high activity of enzyme towards this un-natural substrate. To the best of our knowledge this is the first application of IaaH in production of industrially important molecules.
Collapse
Affiliation(s)
- Pradeep Mishra
- Department of Bioorganic Chemistry, CSIR-Institute of Microbial Technology, Sector 39, Chandigarh, India
| | - Suneet Kaur
- Department of Bioorganic Chemistry, CSIR-Institute of Microbial Technology, Sector 39, Chandigarh, India
| | - Amar Nath Sharma
- Department of Bioorganic Chemistry, CSIR-Institute of Microbial Technology, Sector 39, Chandigarh, India
| | - Ravinder S. Jolly
- Department of Bioorganic Chemistry, CSIR-Institute of Microbial Technology, Sector 39, Chandigarh, India
- * E-mail:
| |
Collapse
|
32
|
Wu ZM, Zheng RC, Zheng YG. Exploitation and characterization of three versatile amidase super family members from Delftia tsuruhatensis ZJB-05174. Enzyme Microb Technol 2016; 86:93-102. [DOI: 10.1016/j.enzmictec.2016.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/01/2016] [Accepted: 02/09/2016] [Indexed: 10/22/2022]
|
33
|
Guo FM, Wu JP, Yang LR, Xu G. Soluble and functional expression of a recombinant enantioselective amidase from Klebsiella oxytoca KCTC 1686 in Escherichia coli and its biochemical characterization. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
34
|
Zhao B, Hua X, Wang F, Dong W, Li Z, Yang Y, Cui Z, Wang M. Biodegradation of propyzamide by Comamonas testosteroni W1 and cloning of the propyzamide hydrolase gene camH. BIORESOURCE TECHNOLOGY 2015; 179:144-149. [PMID: 25541381 DOI: 10.1016/j.biortech.2014.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/02/2014] [Accepted: 12/04/2014] [Indexed: 06/04/2023]
Abstract
Propyzamide is a widely used benzamide herbicide for controlling weeds in lettuce, soybeans, cotton and other crops. An efficient propyzamide-degrading strain W1 was firstly isolated from activated sludge and identified as Comamonas testosteroni. A metabolite of propyzamide by strain W1 was firstly identified. The novel gene camH encoding a hydrolase that catalyzed the amide bond cleavage of propyzamide was cloned from strain W1. The gene contained an open reading frame of 1452 bp, the deduced amino acid sequence showed low identity with other amidases. The recombinant enzyme CamH was expressed in Escherichia coli BL21 and purified. CamH displayed the highest activity at 30°C and pH 8.0 with propyzamide as the substrate. These results provide important knowledge on the fate of propyzamide in the biodegradation, and elucidate the biodegradation mechanism of propyzamide by the strain W1.
Collapse
Affiliation(s)
- Baiping Zhao
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Xiude Hua
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Fei Wang
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; College of Bioscience and Bioengineering, Jiangxi Agriculture University, Nanchang 330045, China
| | - Weiliang Dong
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhoukun Li
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Yang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Zhongli Cui
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Minghua Wang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China.
| |
Collapse
|
35
|
Bhatia RK, Bhatia SK, Kumar V, Bhalla TC. Bi-substrate Kinetic Analysis of Acyl Transfer Activity of Purified Amidase from Pseudomonas putida BR-1. Catal Letters 2015. [DOI: 10.1007/s10562-014-1467-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
36
|
Simultaneous purification of nitrile hydratase and amidase of Alcaligenes sp. MTCC 10674. 3 Biotech 2014; 4:375-381. [PMID: 28324474 PMCID: PMC4145624 DOI: 10.1007/s13205-013-0163-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 08/12/2013] [Indexed: 10/31/2022] Open
Abstract
Alcaligenes sp. MTCC 10674 has a bienzymatic system for the hydrolysis of nitriles. The nitrile hydratase and amidase have been purified simultaneously to homogeneity using a combination of (NH)4SO4 precipitation, ion exchange chromatography and gel permeation chromatography. Nitrile hydratase and amidase have molecular weight of 47 and 114 kDa, respectively and exist as heterodimer. Optimum temperatures for maximum activity of nitrile hydratase and amidase were 15 °C (2.4 U/mg protein) and 45 °C (2.3 U/mg protein), respectively. Nitrile hydratase showed maximum 7.8 U/mg protein at 50 mM acrylonitrile and amidase has 9.2 U/mg protein at 25 mM propionamide. Nitrile hydratase has Vmax 10 μmol/min/mg and Km 40 mM, while amidase has Vmax 12.5 μmol/min/mg and Km 45.5 mM, respectively. Heavy metal ions Hg2+, Ag+, Pb2+ and Cu2+ were strong inhibitors of nitrile hydratase and amidase activity.
Collapse
|
37
|
Nitrilase superfamily aryl acylamidase from the halotolerant mangrove Streptomyces sp. 211726. Appl Microbiol Biotechnol 2014; 98:8583-90. [DOI: 10.1007/s00253-014-5762-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 10/25/2022]
|
38
|
Purification of an amide hydrolase DamH from Delftia sp. T3-6 and its gene cloning, expression, and biochemical characterization. Appl Microbiol Biotechnol 2014; 98:7491-9. [DOI: 10.1007/s00253-014-5710-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 03/17/2014] [Indexed: 11/26/2022]
|
39
|
Purification and characterization of a thermostable aliphatic amidase from the hyperthermophilic archaeon Pyrococcus yayanosii CH1. Extremophiles 2014; 18:429-40. [PMID: 24430467 DOI: 10.1007/s00792-014-0628-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 01/02/2014] [Indexed: 10/25/2022]
Abstract
Amidases catalyze the hydrolysis of amides to free carboxylic acids and ammonia. Hyperthermophilic archaea are a natural reservoir of various types of thermostable enzymes. Here, we report the purification and characterization of an amidase from Pyrococcus yayanosii CH1, the first representative of a strict-piezophilic hyperthermophilic archaeon that originated from a deep-sea hydrothermal vent. An open reading frame that encoded a putative member of the nitrilase protein superfamily was identified. We cloned and overexpressed amiE in Escherichia coli C41 (DE3). The purified AmiE enzyme displayed maximal activity at 85 °C and pH 6.0 (NaH2PO4-Na2HPO4) with acetamide as the substrate and showed activity over the pH range of 4-8 and the temperature range of 4-95 °C. AmiE is a dimer and active on many aliphatic amide substrates, such as formamide, acetamide, hexanamide, acrylamide, and L-glutamine. Enzyme activity was induced by 1 mM Ca(2+), 1 mM Al(3+), and 1-10 mM Mg(2+), but strongly inhibited by Zn(2+), Cu(2+), Ni(2+), and Fe(3+). The presence of acetone and ethanol significantly decreased the enzymatic activity. Neither 5% methanol nor 5% isopropanol had any significant effect on AmiE activity (99 and 96% retained, respectively). AmiE displayed amidase activity although it showed high sequence homology (78% identity) with the known nitrilase from Pyrococcus abyssi. AmiE is the most characterized archaeal thermostable amidase in the nitrilase superfamily. The thermostability and pH-stability of AmiE will attract further studies on its potential industrial applications.
Collapse
|
40
|
Guo Y, Chen S, Su L, Wu J, Chen J. Cloning, expression, and characterization of polyamidase from Nocardia farcinica and its application to polyamide modification. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0189-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
41
|
An isobutyronitrile-induced bienzymatic system of Alcaligenes sp. MTCC 10674 and its application in the synthesis of α-hydroxyisobutyric acid. Bioprocess Biosyst Eng 2012; 36:613-25. [DOI: 10.1007/s00449-012-0817-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 08/20/2012] [Indexed: 12/06/2022]
|
42
|
Cloning of a novel arylamidase gene from Paracoccus sp. strain FLN-7 that hydrolyzes amide pesticides. Appl Environ Microbiol 2012; 78:4848-55. [PMID: 22544249 DOI: 10.1128/aem.00320-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial isolate Paracoccus sp. strain FLN-7 hydrolyzes amide pesticides such as diflubenzuron, propanil, chlorpropham, and dimethoate through amide bond cleavage. A gene, ampA, encoding a novel arylamidase that catalyzes the amide bond cleavage in the amide pesticides was cloned from the strain. ampA contains a 1,395-bp open reading frame that encodes a 465-amino-acid protein. AmpA was expressed in Escherichia coli BL21 and homogenously purified using Ni-nitrilotriacetic acid affinity chromatography. AmpA is a homodimer with an isoelectric point of 5.4. AmpA displays maximum enzymatic activity at 40°C and a pH of between 7.5 and 8.0, and it is very stable at pHs ranging from 5.5 to 10.0 and at temperatures up to 50°C. AmpA efficiently hydrolyzes a variety of secondary amine compounds such as propanil, 4-acetaminophenol, propham, chlorpropham, dimethoate, and omethoate. The most suitable substrate is propanil, with K(m) and k(cat) values of 29.5 μM and 49.2 s(-1), respectively. The benzoylurea insecticides (diflubenzuron and hexaflumuron) are also hydrolyzed but at low efficiencies. No cofactor is needed for the hydrolysis activity. AmpA shares low identities with reported arylamidases (less than 23%), forms a distinct lineage from closely related arylamidases in the phylogenetic tree, and has different biochemical characteristics and catalytic kinetics with related arylamidases. The results in the present study suggest that AmpA is a good candidate for the study of the mechanism for amide pesticide hydrolysis, genetic engineering of amide herbicide-resistant crops, and bioremediation of amide pesticide-contaminated environments.
Collapse
|