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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.
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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.
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Singha LP, Singha KM, Pandey P. Functionally coherent transcriptional responses of Jatropha curcas and Pseudomonas fragi for rhizosphere mediated degradation of pyrene. Sci Rep 2024; 14:1014. [PMID: 38200308 PMCID: PMC10781960 DOI: 10.1038/s41598-024-51581-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 01/07/2024] [Indexed: 01/12/2024] Open
Abstract
Pyrene is an extremely hazardous, carcinogenic polycyclic aromatic hydrocarbon (PAH). The plant-microbe interaction between Pseudomonas fragi DBC and Jatropha curcas was employed for biodegradation of pyrene and their transcriptional responses were compared. The genome of P. fragi DBC had genes for PAH degrading enzymes i.e. dioxygenases and dehydrogenases, along with root colonization (trpD, trpG, trpE and trpF), chemotaxis (flhF and flgD), stress adaptation (gshA, nuoHBEKNMG), and detoxification (algU and yfc). The transcriptional expression of catA and yfc that respectively code for catabolic enzyme (catechol-1, 2-dioxygnase) and glutathione-s-transferase for detoxification functions were quantitatively measured by qPCR. The catA was expressed in presence of artificial root exudate with or without pyrene, and glucose confirming the non-selective approach of bacteria, as desired. Pyrene induced 100-fold increase of yfc expression than catA, while there was no expression of yfc in absence of pyrene. The transcriptome of plant roots, in presence of pyrene, with or without P. fragi DBC inoculation was analysed. The P. fragi DBC could upregulate the genes for plant growth, induced the systemic acquired resistance and also ameliorated the stress response in Jatropha roots.
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Affiliation(s)
- L Paikhomba Singha
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
- Department of Microbiology, Central University of Rajasthan, Ajmer, Rajasthan, 305817, India
| | - K Malabika Singha
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India.
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Donoso-Piñol P, Briceño G, Evaristo JAM, Nogueira FCS, Leiva B, Lamilla C, Schalchli H, Diez MC. Metabolic Profiling and Comparative Proteomic Insight in Respect of Amidases during Iprodione Biodegradation. Microorganisms 2023; 11:2367. [PMID: 37894025 PMCID: PMC10608976 DOI: 10.3390/microorganisms11102367] [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: 08/08/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The fungicide iprodione (IPR) (3-(3,5-dichlorophenyl) N-isopropyl-2,4-dioxoimidazolidine-1-carboxamide) is a highly toxic compound. Although IPR has been restricted, it is still being applied in many places around the world, constituting an environmental risk. The biodegradation of IPR is an attractive option for reducing its residues. In this study, we isolated thirteen IPR-tolerant bacteria from a biopurification system designed to treat pesticides. A study of biodegradation using different strains was comparatively evaluated, and the best degradation rate of IPR was presented by Achromobacter sp. C1 with a half-life (T1/2) of 9 days. Based on a nano-LC-MS/MS analysis for the strains, proteins solely expressed in the IPR treatment were identified by highlighting the strain Achromobacter sp. C1, with 445 proteins primarily involved in the biosynthesis of secondary metabolites and microbial metabolism in diverse environments. Differentially expressed protein amidases were involved in six metabolic pathways. Interestingly, formamidase was inhibited while other cyclases, i.e., amidase and mandelamide hydrolase, were overexpressed, thereby minimizing the effect of IPR on the metabolism of strain C1. The dynamic changes in the protein profiles of bacteria that degrade IPR have been poorly studied; therefore, our results offer new insight into the metabolism of IPR-degrading microorganisms, with special attention paid to amidases.
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Affiliation(s)
- Pamela Donoso-Piñol
- Doctoral Program in Science of Natural Resources, University of La Frontera, Temuco 4780000, Chile; (P.D.-P.); (B.L.)
| | - Gabriela Briceño
- Department of Chemistry Science and Natural Resources, University of La Frontera, Temuco 4780000, Chile
- Biotechnological Research Centre Applied to the Environment (CIBAMA-BIOREN), University of La Frontera, Temuco 4780000, Chile; (C.L.); (H.S.)
| | - Joseph A. M. Evaristo
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 22775-000, Brazil; (J.A.M.E.); (F.C.S.N.)
| | - Fábio C. S. Nogueira
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 22775-000, Brazil; (J.A.M.E.); (F.C.S.N.)
| | - Barbara Leiva
- Doctoral Program in Science of Natural Resources, University of La Frontera, Temuco 4780000, Chile; (P.D.-P.); (B.L.)
- Biotechnological Research Centre Applied to the Environment (CIBAMA-BIOREN), University of La Frontera, Temuco 4780000, Chile; (C.L.); (H.S.)
| | - Claudio Lamilla
- Biotechnological Research Centre Applied to the Environment (CIBAMA-BIOREN), University of La Frontera, Temuco 4780000, Chile; (C.L.); (H.S.)
| | - Heidi Schalchli
- Biotechnological Research Centre Applied to the Environment (CIBAMA-BIOREN), University of La Frontera, Temuco 4780000, Chile; (C.L.); (H.S.)
| | - María Cristina Diez
- Biotechnological Research Centre Applied to the Environment (CIBAMA-BIOREN), University of La Frontera, Temuco 4780000, Chile; (C.L.); (H.S.)
- Department of Chemical Engineering, University of La Frontera, Temuco 4780000, Chile
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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: 0] [Impact Index Per Article: 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.
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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.
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Jiang H, Yuan P, Ding J, Wu H, Wang L, Chen K, Jiang N, Dai Y. Novel biodegradation pathway of insecticide flonicamid mediated by an amidase and its unusual substrate spectrum. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129952. [PMID: 36116312 DOI: 10.1016/j.jhazmat.2022.129952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/20/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
The insecticide flonicamid (FLO) and its main degradation intermediate 4-trifluoromethylnicotinamide (TFNA-AM) are hazardous to the environment and animals. Microbial transformation of FLO has been well studied, but no study has yet reported on TFNA-AM degradation by a microorganism. Here, Pseudomonas stutzeri CGMCC 22915 effectively degraded TFNA-AM to 5-trifluoromethylnicotinic acid (TFNA). P. stutzeri CGMCC 22915 degraded 60.0% of TFNA-AM (1154.44 μmol/L) within 6 h with a half-life of just 4.5 h. Moreover, P. stutzeri CGMCC 22915 significantly promoted TFNA-AM decomposition in surface water. The reaction was catalyzed by an amidase, PsAmiA. PsAmiA is encoded in a novel nitrile-converting enzyme gene cluster. The enzyme shared only 20-44% identities with previously characterized signature amidases. PsAmiA was successfully expressed in Escherichia coli and its enzymatic properties were investigated using TFNA-AM as the substrate. PsAmiA was more active toward amides without hydrophilic groups, and did not hydrolyze another amide metabolite of FLO, N-(4-trifluoromethylnicotinoyl)glycinamide (TFNG-AM), which is structurally very similar to TFNA-AM. Molecular docking of PsAmiA and TFNA-AM indicated that hydrophobic residues Leu148, Ala150, Ala195, Ile225, Trp341, Leu460, and Ile463 may affect its substrate spectrum. This study provides new insights of the environmental fate of FLO at the molecular level and the structure-function relationships of amidases.
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Affiliation(s)
- Huoyong 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.
| | - Panpan Yuan
- 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.
| | - Jianjun Ding
- 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.
| | - Hongkai Wu
- 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.
| | - Kexin 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.
| | - Nengdang 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.
| | - Yijun 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.
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Mugani R, El Khalloufi F, Redouane EM, Haida M, Zerrifi SEA, Campos A, Kasada M, Woodhouse J, Grossart HP, Vasconcelos V, Oudra B. Bacterioplankton Associated with Toxic Cyanobacteria Promote Pisum sativum (Pea) Growth and Nutritional Value through Positive Interactions. Microorganisms 2022; 10:microorganisms10081511. [PMID: 35893569 PMCID: PMC9394358 DOI: 10.3390/microorganisms10081511] [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: 07/05/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
Research on Plant Growth-Promoting Bacteria (PGPB) has focused much more on rhizospheric bacteria. However, PGPB associated with toxic cyanobacterial bloom (TCB) could enter the rhizosphere through irrigation water, helping plants such as Pisum sativum L. (pea) overcome oxidative stress induced by microcystin (MC) and improve plant growth and nutritional value. This study aimed to isolate bacteria associated with toxic cyanobacteria, test PGPB properties, and inoculate them as a consortium to pea seedlings irrigated with MC to investigate their role in plant protection as well as in improving growth and nutritional value. Two bacterioplankton isolates and one rhizosphere isolate were isolated and purified on a mineral salt medium supplemented with 1000 μg/L MC and identified via their 16S rRNA gene. The mixed strains were inoculated to pea seedlings in pots irrigated with 0, 50, and 100 μg/L MC. We measured the morphological and physiological parameters of pea plants at maturity and evaluated the efficiency of the plant’s enzymatic and non-enzymatic antioxidant responses to assess the role and contribution of PGPB. Both bacterioplankton isolates were identified as Starkeya sp., and the rhizobacterium was identified as Brevundimonas aurantiaca. MC addition significantly (p < 0.05) reduced all the growth parameters of the pea, i.e., total chlorophyll content, leaf quantum yield, stomatal conductance, carotenoids, and polyphenol contents, in an MC concentration-dependent manner, while bacterial presence positively affected all the measured parameters. In the MC treatment, the levels of the pea’s antioxidant traits, including SOD, CAT, POD, PPO, GST, and ascorbic acid, were increased in the sterile pots. In contrast, these levels were reduced with double and triple PGPB addition. Additionally, nutritional values such as sugars, proteins, and minerals (Ca and K) in pea fruits were reduced under MC exposure but increased with PGPB addition. Overall, in the presence of MC, PGPB seem to positively interact with pea plants and thus may constitute a natural alternative for soil fertilization when irrigated with cyanotoxin-contaminated water, increasing the yield and nutritional value of crops.
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Affiliation(s)
- Richard Mugani
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Av. Prince My Abdellah, P.O. Box 2390, Marrakech 40000, Morocco; (R.M.); (E.M.R.); (M.H.); (S.E.A.Z.); (B.O.)
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhuette 2, 14775 Stechlin, Germany; (M.K.); (J.W.); (H.-P.G.)
| | - Fatima El Khalloufi
- Natural Resources Engineering and Environmental Impacts Team, Multidisciplinary Research and Innovation Laboratory, Polydisciplinary Faculty of Khouribga, Sultan Moulay Slimane University of Beni Mellal, P.O. Box 145, Khouribga 25000, Morocco;
| | - El Mahdi Redouane
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Av. Prince My Abdellah, P.O. Box 2390, Marrakech 40000, Morocco; (R.M.); (E.M.R.); (M.H.); (S.E.A.Z.); (B.O.)
| | - Mohammed Haida
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Av. Prince My Abdellah, P.O. Box 2390, Marrakech 40000, Morocco; (R.M.); (E.M.R.); (M.H.); (S.E.A.Z.); (B.O.)
| | - Soukaina El Amrani Zerrifi
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Av. Prince My Abdellah, P.O. Box 2390, Marrakech 40000, Morocco; (R.M.); (E.M.R.); (M.H.); (S.E.A.Z.); (B.O.)
| | - Alexandre Campos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
| | - Minoru Kasada
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhuette 2, 14775 Stechlin, Germany; (M.K.); (J.W.); (H.-P.G.)
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Jason Woodhouse
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhuette 2, 14775 Stechlin, Germany; (M.K.); (J.W.); (H.-P.G.)
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhuette 2, 14775 Stechlin, Germany; (M.K.); (J.W.); (H.-P.G.)
- Institute for Biochemistry and Biology, University of Potsdam, Maulbeeralle 2, 14469 Potsdam, Germany
| | - Vitor Vasconcelos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: ; Tel.: +351-223-401-817
| | - Brahim Oudra
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Av. Prince My Abdellah, P.O. Box 2390, Marrakech 40000, Morocco; (R.M.); (E.M.R.); (M.H.); (S.E.A.Z.); (B.O.)
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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.
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Fuentes-Jaime J, Vargas-Suárez M, Cruz-Gómez MJ, Loza-Tavera H. Concerted action of extracellular and cytoplasmic esterase and urethane-cleaving activities during Impranil biodegradation by Alicycliphilus denitrificans BQ1. Biodegradation 2022; 33:389-406. [PMID: 35633408 DOI: 10.1007/s10532-022-09989-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022]
Abstract
The concerted action of commercial esterases, proteases and amidases has been demonstrated to be relevant in polyurethane (PU) degradation by in vitro experiments. However, the spatial and temporal dynamics of these activities during PU biodegradation by PU-degrading bacteria have not been addressed. Here, we examined the capability of Alicycliphilus denitrificans BQ1 to biodegrade the polyester (PS)-PU Impranil, analyzed the temporal and spatial coordination between the extracellular and cytoplasmic esterase and urethane-cleaving activities, and their independent and combined effects on Impranil biodegradation. A. denitrificans BQ1 grew in Impranil, and its clearing was correlated with the cleavage of ester and urethane groups since early times, with decrements of some Impranil compounds and the appearance of biodegradation products. While extracellular esterase was active at early times with its maximum at 18 h, urethanase appeared at this time and increased up to the end of the analysis (48 h), with the cytoplasmic activities behaving similarly but with lower levels than the extracellular ones. Both enzymatic activities exhibited distinct substrate specificity depending on their cellular localization and cultivation times, suggesting they cleave differentially located groups. As the urethane cleavage occurred since early times, when no urethane-cleaving activity was detected, different proteins should be acting at early and late times. In vitro experiments with independent or combined cellular protein fractions supported the previous deduction and confirmed the concerted action of extracellular and cytoplasmic esterase and urethane-cleaving activities. A two-stage process for Impranil degradation by A. denitrificans BQ1 is proposed.
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Affiliation(s)
- Jacqueline Fuentes-Jaime
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ave. Universidad 3000. Col. UNAM, 04510, Ciudad de México, México
| | - Martín Vargas-Suárez
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ave. Universidad 3000. Col. UNAM, 04510, Ciudad de México, México
| | - M Javier Cruz-Gómez
- Departamento de Ingeniería Química, Facultad de Química, Universidad Nacional Autónoma de México, Ave. Universidad 3000. Col. UNAM, 04510, Ciudad de México, México
| | - Herminia Loza-Tavera
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ave. Universidad 3000. Col. UNAM, 04510, Ciudad de México, México.
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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.
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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.
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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.
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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.
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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
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