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Ali Rachedi S, Genest M, Mann S, Buisson D. Combinatory Library of Microorganisms in the Selection of Reductive Activity Applied to a Ketone Mixture: Unexpected Highlighting of an Enantioselective Oxidative Activity. Microorganisms 2023; 11:1415. [PMID: 37374917 DOI: 10.3390/microorganisms11061415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Biocatalytic processes are increasingly used in organic synthesis for the preparation of targeted molecules or the generation of molecular diversity. The search for the biocatalyst is often the bottleneck in the development of the process. We described a combinatorial approach for the selection of active strains from a library of microorganisms. In order to show the potential of the method we applied it to a mixture of substrates. We were able to select yeast strains capable of producing enantiopure alcohol from corresponding ketones with very few tests and highlight tandem reaction sequences involving several microorganisms. We demonstrate an interest in the kinetic study and the importance of incubation conditions. This approach is a promising tool for generating new products.
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Affiliation(s)
- Sofiane Ali Rachedi
- Unité Molécules de Communication et Adaptation des Microorganismes, Muséum National d'Histoire Naturelle, CNRS UMR 7245, CP54, 57 rue Cuvier (63 rue Buffon), 75005 Paris, France
| | - Maximillien Genest
- Unité Molécules de Communication et Adaptation des Microorganismes, Muséum National d'Histoire Naturelle, CNRS UMR 7245, CP54, 57 rue Cuvier (63 rue Buffon), 75005 Paris, France
| | - Stéphane Mann
- Unité Molécules de Communication et Adaptation des Microorganismes, Muséum National d'Histoire Naturelle, CNRS UMR 7245, CP54, 57 rue Cuvier (63 rue Buffon), 75005 Paris, France
| | - Didier Buisson
- Unité Molécules de Communication et Adaptation des Microorganismes, Muséum National d'Histoire Naturelle, CNRS UMR 7245, CP54, 57 rue Cuvier (63 rue Buffon), 75005 Paris, France
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Santos EDC, de Menezes LHS, Santos CS, Santana PVB, Soares GA, Tavares IMDC, Freitas JDS, de Souza-Motta CM, Bezerra JL, da Costa AM, Uetanabaro APT, Porto ALM, Franco M, de Oliveira JR. High-throughput screening for distinguishing nitrilases from nitrile hydratases in Aspergillus and application of a Box-Behnken design for the optimization of nitrilase. Biotechnol Appl Biochem 2021; 69:2081-2090. [PMID: 34617628 DOI: 10.1002/bab.2269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/28/2021] [Indexed: 11/11/2022]
Abstract
Nitrilases and nitrile hydratases/amidases hydrolyze nitriles into carboxylic acids and/or amides, which are used in industrial chemical processes. In the present study, 26 microorganisms, including yeasts and filamentous fungi, in a minimum solid mineral medium supplemented with glucose and phenylacetonitrile were screened to evaluate their biocatalytic potential. Of these microorganisms, five fungi of the genus Aspergillus were selected and subjected to colorimetry studies to evaluate the production and distinction of nitrilase and nitrile hydratase/amidase enzymes. Aspergillus parasiticus Speare 7967 and A. niger Tiegh. 8285 produced nitrilases and nitrile hydratase, respectively. Nitrilase optimization was performed using a Box-Behnken design (BBD) and fungus A. parasiticus Speare 7967 with phenylacetonitrile volume (μl), pH, and carbohydrate source (starch:glucose; g/g) as independent variables and nitrilase activity (U ml-1 ) as dependent variable. Maximum activity (2.97 × 10-3 U ml-1 ) was obtained at pH 5.5, 80 μl of phenylacetonitrile, and 15 g of glucose. A. parasiticus Speare 7967 showed promise in the biotransformation of nitriles to carboxylic acids.
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Affiliation(s)
- Edvan do Carmo Santos
- Department of Biological Sciences, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | | | - Carolline Silva Santos
- Department of Biological Sciences, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | | | | | | | - Janaina de Silva Freitas
- Department of Exact and Natural Sciences, State University of Southwest Bahia, Itapetinga, Bahia, Brazil
| | | | - José Luiz Bezerra
- Department of Biological Sciences, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | - Andréa Miura da Costa
- Department of Biological Sciences, State University of Santa Cruz, Ilhéus, Bahia, Brazil
| | | | | | - Marcelo Franco
- Department of Exact and Technological Sciences, State University of Santa Cruz, Ilhéus, Bahia, Brazil
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Yang WL, Dai ZL, Cheng X, Fan ZX, Jiang HY, Dai YJ. Biotransformation of insecticide flonicamid by Aminobacter sp. CGMCC 1.17253 via nitrile hydratase catalysed hydration pathway. J Appl Microbiol 2020; 130:1571-1581. [PMID: 33030814 DOI: 10.1111/jam.14880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/10/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022]
Abstract
AIMS This study evaluates flonicamid biotransformation ability of Aminobacter sp. CGMCC 1.17253 and the enzyme catalytic mechanism involved. METHODS AND RESULTS Flonicamid transformed by resting cells of Aminobacter sp. CGMCC 1.17253 was carried out. Aminobacter sp. CGMCC 1.17253 converts flonicamid into N-(4-trifluoromethylnicotinoyl) glycinamide (TFNG-AM). Aminobacter sp. CGMCC 1.17253 transforms 31·1% of the flonicamid in a 200 mg l-1 conversion solution in 96 h. Aminobacter sp. CGMCC 1.17253 was inoculated in soil, and 72·1% of flonicamid with a concentration of 0·21 μmol g-1 was transformed in 9 days. The recombinant Escherichia coli expressing Aminobacter sp. CGMCC 1.17253 nitrile hydratase (NHase) and purified NHase were tested for the flonicamid transformation ability, both of them acquired the ability to transform flonicamid into TFNG-AM. CONCLUSIONS Aminobacter sp. CGMCC 1.17253 transforms flonicamid into TFNG-AM via hydration pathway mediated by cobalt-containing NHase. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report that bacteria of genus Aminobacter has flonicamid-transforming ability. This study enhances our understanding of flonicamid-degrading mechanism. Aminobacter sp. CGMCC 1.17253 has the potential for bioremediation of flonicamid pollution.
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Affiliation(s)
- W L Yang
- 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, People's Republic of China
| | - Z L 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, People's Republic of China
| | - X Cheng
- 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, People's Republic of China
| | - Z X Fan
- 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, People's Republic of China
| | - H Y 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, People's Republic of China
| | - Y J 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, People's Republic of China
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Sahu R, Meghavarnam AK, Janakiraman S. A simple, efficient and rapid screening technique for differentiating nitrile hydratase and nitrilase producing bacteria. ACTA ACUST UNITED AC 2019; 24:e00396. [PMID: 31799145 PMCID: PMC6881679 DOI: 10.1016/j.btre.2019.e00396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 01/21/2023]
Abstract
A rapid dye based plate screening method for nitrile hydrolyzing enzymes. Method identifies the end products of nitrile hydrolyzing enzymes. The method differentiates between nitrile hydratase and nitrilase producing bacteria. A potential NHase producing bacterial strain was identified as Rhodococcus rhodochrous.
Nitrile hydrolyzing enzymes catalyze the hydration of nitrile compounds to corresponding amides and acids. Bacteria, isolated from soil samples were screened for nitrile hydrolyzing enzymes by simple dye based 96 well plate and nesslerization method. Bromothymol blue was used as an indicator for the detection of amides and acids based on colour change of the indicator dye from blue to dark green or yellow. The screening assay also differentiates between nitrile hydratase (NHase) and nitrilase producing bacteria. Among the 108 bacterial strains screened for enzyme activity, six strains were positive for NHase activity and eleven strains were positive for nitrilase activity based on their ability to degrade acrylonitrile into products. The strain showing maximum NHase activity in quantitative assay was identified as Rhodococcus rhodochrous. The modified method developed by us would be useful for rapid screening of nitrile degrading bacteria potent for acrylamide/acrylic acid production when acrylonitrile is supplied as substrate.
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Affiliation(s)
- Ruchi Sahu
- Department of Microbiology and Biotechnology, Bangalore University, 560056, Bangalore, Karnataka, India
| | | | - Savitha Janakiraman
- Department of Microbiology and Biotechnology, Bangalore University, 560056, Bangalore, Karnataka, India
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Yang WL, Guo LL, Dai ZL, Qin RC, Zhao YX, Dai YJ. Biodegradation of the Insecticide Flonicamid by Alcaligenes faecalis CGMCC 17553 via Hydrolysis and Hydration Pathways Mediated by Nitrilase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10032-10041. [PMID: 31419121 DOI: 10.1021/acs.jafc.9b04245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Flonicamid (N-cyanomethyl-4-trifluoromethylnicotinamide, FLO), a novel selective systemic pyridinecarboxamide insecticide, effectively controls hemipterous pests. However, microbial degradation of flonicamid, along with the enzymatic mechanism, has not been studied. Here, bacterial isolate PG13, which converts flonicamid into 4-(trifluoromethyl)nicotinol glycine (TFNG) and N-(4-trifluoromethylnicotinoyl)glycinamide (TFNG-AM), was isolated and identified as Alcaligenes faecalis CGMCC 17553. The genome of CGMCC 17553 contained five nitrilases but no nitrile hydratase, and recombinant Escherichia coli strains harboring CGMCC 17553 nitrilase gene nitA or nitD acquired the ability to degrade flonicamid. Purified NitA catalyzed flonicamid into both TFNG and TFNG-AM, indicating dual functionality, while NitD could only produce TFNG-AM. Three-dimensional homology modeling revealed that aromatic amino acid residues in the catalytic pocket affected nitrilase activity. These findings further our understanding of the enzymatic mechanism of flonicamid metabolism in the environment and may help develop a potential bioremediation agent for the elimination of flonicamid contamination.
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Affiliation(s)
- Wen-Long Yang
- 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
| | - Lei-Lei 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
| | - Zhi-Ling 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
| | - Ruo-Chen Qin
- 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
| | - 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
| | - 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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Oliveira KO, Silva AR, da Silva BF, Milagre HM, Milagre CD. Insights into the microbial degradation pathways of the ioxynil octanoate herbicide. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Fisk H, Xu Y, Westley C, Turner NJ, Micklefield J, Goodacre R. From Multistep Enzyme Monitoring to Whole-Cell Biotransformations: Development of Real-Time Ultraviolet Resonance Raman Spectroscopy. Anal Chem 2017; 89:12527-12532. [PMID: 29076721 DOI: 10.1021/acs.analchem.7b03742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Process analytical technologies (PAT) are used within industry to give real-time measurements of critical quality parameters, ultimately improving the quality by design (QbD) of the final product and reducing manufacturing costs. Spectroscopic and spectrophotometric methods are readily employed within PAT due to their ease of use, compatibility toward a range of sample types, robustness, and multiplexing capabilities. We have developed a UV resonance Raman (UVRR) spectroscopy approach to quantify industrially relevant biotransformations accurately, focusing on nitrile metabolizing enzymes: nitrile hydratase (NHase) and amidase versus nitrilase activity. Sensitive detection of the amide intermediate by UVRR spectroscopy enabled discrimination between the two nitrile-hydrolyzing pathways. Development of a flow-cell apparatus further exemplifies its suitability toward PAT measurements, incorporating in situ analysis within a closed system. Multivariate curve resolution-alternating least-squares (MCR-ALS) was applied to the UVRR spectra, as well as off-line HPLC measurements, to enable absolute quantification of substrate, intermediate, and product. Further application of hard modeling to MCR-ALS deconvolved concentration profiles enabled accurate kinetic determinations, thus removing the requirement for comparative off-line HPLC. Finally, successful quantitative measurements of in vivo activity using whole-cell biotransformations, where two Escherichia coli strains expressing either NHase (transforming benzonitrile to benzamide) or amidase (further conversion of benzamide to benzoic acid), illustrate the power, practicality, and sensitivity of this novel approach of multistep and, with further refinement, we believe, multiple micro-organism biotransformations.
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Affiliation(s)
- Heidi Fisk
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Chloe Westley
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicholas J Turner
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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Westley C, Fisk H, Xu Y, Hollywood KA, Carnell AJ, Micklefield J, Turner NJ, Goodacre R. Real-Time Monitoring of Enzyme-Catalysed Reactions using Deep UV Resonance Raman Spectroscopy. Chemistry 2017; 23:6983-6987. [PMID: 28370547 PMCID: PMC5488198 DOI: 10.1002/chem.201701388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Indexed: 01/23/2023]
Abstract
For enzyme-catalysed biotransformations, continuous in situ detection methods minimise the need for sample manipulation, ultimately leading to more accurate real-time kinetic determinations of substrate(s) and product(s). We have established for the first time an on-line, real-time quantitative approach to monitor simultaneously multiple biotransformations based on UV resonance Raman (UVRR) spectroscopy. To exemplify the generality and versatility of this approach, multiple substrates and enzyme systems were used involving nitrile hydratase (NHase) and xanthine oxidase (XO), both of which are of industrial and biological significance, and incorporate multistep enzymatic conversions. Multivariate data analysis of the UVRR spectra, involving multivariate curve resolution-alternating least squares (MCR-ALS), was employed to effect absolute quantification of substrate(s) and product(s); repeated benchmarking of UVRR combined with MCR-ALS by HPLC confirmed excellent reproducibility.
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Affiliation(s)
- Chloe Westley
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | - Heidi Fisk
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | - Yun Xu
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | - Katherine A. Hollywood
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | | | - Jason Micklefield
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | - Nicholas J. Turner
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
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de Carvalho CCCR. Whole cell biocatalysts: essential workers from Nature to the industry. Microb Biotechnol 2017; 10:250-263. [PMID: 27145540 PMCID: PMC5328830 DOI: 10.1111/1751-7915.12363] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 11/30/2022] Open
Abstract
Microorganisms have been exposed to a myriad of substrates and environmental conditions throughout evolution resulting in countless metabolites and enzymatic activities. Although mankind have been using these properties for centuries, we have only recently learned to control their production, to develop new biocatalysts with high stability and productivity and to improve their yields under new operational conditions. However, microbial cells still provide the best known environment for enzymes, preventing conformational changes in the protein structure in non-conventional medium and under harsh reaction conditions, while being able to efficiently regenerate necessary cofactors and to carry out cascades of reactions. Besides, a still unknown microbe is probably already producing a compound that will cure cancer, Alzeihmer's disease or kill the most resistant pathogen. In this review, the latest developments in screening desirable activities and improving production yields are discussed.
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Affiliation(s)
- Carla C. C. R. de Carvalho
- iBB‐Institute for Bioengineering and BiosciencesDepartment of BioengineeringInstituto Superior TécnicoUniversidade de LisboaAv. Rovisco PaisLisbon1049‐001Portugal
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