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de la Calle ME, Cabrera G, Linares-Pineda T, Cantero D, Molinillo JMG, Varela RM, Valle A, Bolívar J. Automatable downstream purification of the benzohydroxamic acid D-DIBOA from a biocatalytic synthesis. N Biotechnol 2022; 72:48-57. [PMID: 36155894 DOI: 10.1016/j.nbt.2022.09.001] [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: 04/28/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 12/14/2022]
Abstract
Herbicides play a vital role in agriculture, contributing to increased crop productivity by minimizing weed growth, but their low degradability presents a threat to the environment and human health. Allelochemicals, such as DIBOA (2,4-dihydroxy-(2H)-1,4-benzoxazin-3(4 H)-one), are secondary metabolites released by certain plants that affect the survival or growth of other organisms. Although these metabolites have an attractive potential for use as herbicides, their low natural production is a critical hurdle. Previously, the synthesis of the biologically active analog D-DIBOA (4-hydroxy-(2H)-1,4-benzoxazin-3(4H)-one) was achieved, using an engineered E. coli strain as a whole-cell biocatalyst, capable of transforming a precursor compound into D-DIBOA and exporting it into the culture medium, although it cannot be directly applied to crops. Here a chromatographic method to purify D-DIBOA from this cell culture medium without producing organic solvent wastes is described. The purification of D-DIBOA from a filtered culture medium to the pure compound could also be automated. Biological tests with the purified compound on weed models showed that it has virtually the same activity than the chemically synthesized D-DIBOA.
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Affiliation(s)
- Maria Elena de la Calle
- Department of Chemical Engineering and Food Technology, University of Cadiz, 11510 Puerto Real, Cadiz, Spain; Institute of Viticulture and Agri-Food Research (IVAGRO)-International Campus of Excellence (ceiA3), University of Cadiz, 11510 Puerto Real, Cadiz, Spain
| | - Gema Cabrera
- Department of Chemical Engineering and Food Technology, University of Cadiz, 11510 Puerto Real, Cadiz, Spain; Institute of Viticulture and Agri-Food Research (IVAGRO)-International Campus of Excellence (ceiA3), University of Cadiz, 11510 Puerto Real, Cadiz, Spain
| | - Teresa Linares-Pineda
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, University of Cadiz, 11510 Puerto Real, Cadiz, Spain; Institute of Biomolecules (INBIO), University of Cadiz, 11510 Puerto Real, Spain
| | - Domingo Cantero
- Department of Chemical Engineering and Food Technology, University of Cadiz, 11510 Puerto Real, Cadiz, Spain; Institute of Viticulture and Agri-Food Research (IVAGRO)-International Campus of Excellence (ceiA3), University of Cadiz, 11510 Puerto Real, Cadiz, Spain
| | - José M G Molinillo
- Department of Organic Chemistry, University of Cadiz, 11510 Puerto Real, Cadiz, Spain; Institute of Biomolecules (INBIO), University of Cadiz, 11510 Puerto Real, Spain
| | - Rosa M Varela
- Department of Organic Chemistry, University of Cadiz, 11510 Puerto Real, Cadiz, Spain; Institute of Biomolecules (INBIO), University of Cadiz, 11510 Puerto Real, Spain
| | - Antonio Valle
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, University of Cadiz, 11510 Puerto Real, Cadiz, Spain; Institute of Biomolecules (INBIO), University of Cadiz, 11510 Puerto Real, Spain
| | - Jorge Bolívar
- Department of Biomedicine, Biotechnology and Public Health-Biochemistry and Molecular Biology, University of Cadiz, 11510 Puerto Real, Cadiz, Spain; Institute of Biomolecules (INBIO), University of Cadiz, 11510 Puerto Real, Spain.
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Sellés Vidal L, Murray JW, Heap JT. Versatile selective evolutionary pressure using synthetic defect in universal metabolism. Nat Commun 2021; 12:6859. [PMID: 34824282 PMCID: PMC8616928 DOI: 10.1038/s41467-021-27266-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
The non-natural needs of industrial applications often require new or improved enzymes. The structures and properties of enzymes are difficult to predict or design de novo. Instead, semi-rational approaches mimicking evolution entail diversification of parent enzymes followed by evaluation of isolated variants. Artificial selection pressures coupling desired enzyme properties to cell growth could overcome this key bottleneck, but are usually narrow in scope. Here we show diverse enzymes using the ubiquitous cofactors nicotinamide adenine dinucleotide (NAD) or nicotinamide adenine dinucleotide phosphate (NADP) can substitute for defective NAD regeneration, representing a very broadly-applicable artificial selection. Inactivation of Escherichia coli genes required for anaerobic NAD regeneration causes a conditional growth defect. Cells are rescued by foreign enzymes connected to the metabolic network only via NAD or NADP, but only when their substrates are supplied. Using this principle, alcohol dehydrogenase, imine reductase and nitroreductase variants with desired selectivity modifications, and a high-performing isopropanol metabolic pathway, are isolated from libraries of millions of variants in single-round experiments with typical limited information to guide design.
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Affiliation(s)
- Lara Sellés Vidal
- grid.7445.20000 0001 2113 8111Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ UK ,grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - James W. Murray
- grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK
| | - John T. Heap
- grid.7445.20000 0001 2113 8111Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ UK ,grid.7445.20000 0001 2113 8111Department of Life Sciences, Imperial College London, London, SW7 2AZ UK ,grid.4563.40000 0004 1936 8868School of Life Sciences, The University of Nottingham, Biodiscovery Institute, University Park, Nottingham, NG7 2RD UK
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Thomas C, Gwenin CD. The Role of Nitroreductases in Resistance to Nitroimidazoles. BIOLOGY 2021; 10:388. [PMID: 34062712 PMCID: PMC8147198 DOI: 10.3390/biology10050388] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 01/14/2023]
Abstract
Antimicrobial resistance is a major challenge facing modern medicine, with an estimated 700,000 people dying annually and a global cost in excess of $100 trillion. This has led to an increased need to develop new, effective treatments. This review focuses on nitroimidazoles, which have seen a resurgence in interest due to their broad spectrum of activity against anaerobic Gram-negative and Gram-positive bacteria. The role of nitroreductases is to activate the antimicrobial by reducing the nitro group. A decrease in the activity of nitroreductases is associated with resistance. This review will discuss the resistance mechanisms of different disease organisms, including Mycobacterium tuberculosis, Helicobacter pylori and Staphylococcus aureus, and how these impact the effectiveness of specific nitroimidazoles. Perspectives in the field of nitroimidazole drug development are also summarised.
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Affiliation(s)
- Carol Thomas
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK;
| | - Christopher D. Gwenin
- Department of Chemistry, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou Industrial Park, Suzhou 215123, China
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Optimization of the Biocatalysis for D-DIBOA Synthesis Using a Quick and Sensitive New Spectrophotometric Quantification Method. Int J Mol Sci 2020; 21:ijms21228523. [PMID: 33198293 PMCID: PMC7697731 DOI: 10.3390/ijms21228523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 11/17/2022] Open
Abstract
D-DIBOA (4-hydroxy-(2H)-1,4-benzoxazin-3-(4H)-one) is an allelopathic-derived compound with interesting herbicidal, fungicidal, and insecticide properties whose production has been successfully achieved by biocatalysis using a genetically engineered Escherichia coli strain. However, improvement and scaling-up of this process are hampered by the current methodology for D-DIBOA quantification, which is based on high-performance liquid chromatographic (HPLC), a time-consuming technique that requires expensive equipment and the use of environmentally unsafe solvents. In this work, we established and validated a rapid, simple, and sensitive spectrophotometric method for the quantification of the D-DIBOA produced by whole-cell biocatalysis, with limits of detection and quantification of 0.0165 and 0.0501 µmol·mL−1 respectively. This analysis takes place in only a few seconds and can be carried out using 100 µL of the sample in a microtiter plate reader. We performed several whole-cell biocatalysis strategies to optimize the process by monitoring D-DIBOA production every hour to keep control of both precursor and D-DIBOA concentrations in the bioreactor. These experiments allowed increasing the D-DIBOA production from the previously reported 5.01 mM up to 7.17 mM (43% increase). This methodology will facilitate processes such as the optimization of the biocatalyst, the scaling up, and the downstream purification.
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