1
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Liu M, Li S. Nitrile biosynthesis in nature: how and why? Nat Prod Rep 2024; 41:649-671. [PMID: 38193577 DOI: 10.1039/d3np00028a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Covering: up to the end of 2023Natural nitriles comprise a small set of secondary metabolites which however show intriguing chemical and functional diversity. Various patterns of nitrile biosynthesis can be seen in animals, plants, and microorganisms with the characteristics of both evolutionary divergence and convergence. These specialized compounds play important roles in nitrogen metabolism, chemical defense against herbivores, predators and pathogens, and inter- and/or intraspecies communications. Here we review the naturally occurring nitrile-forming pathways from a biochemical perspective and discuss the biological and ecological functions conferred by diversified nitrile biosyntheses in different organisms. Elucidation of the mechanisms and evolutionary trajectories of nitrile biosynthesis underpins better understandings of nitrile-related biology, chemistry, and ecology and will ultimately benefit the development of desirable nitrile-forming biocatalysts for practical applications.
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Affiliation(s)
- Mingyu Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
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2
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Křístková B, Martínková L, Rucká L, Kotik M, Kulik N, Rädisch R, Winkler M, Pátek M. Immobilization of aldoxime dehydratases on metal affinity resins and use of the immobilized catalysts for the synthesis of nitriles important in fragrance industry. J Biotechnol 2024; 384:12-19. [PMID: 38373531 DOI: 10.1016/j.jbiotec.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Nitriles have a wide range of uses as building blocks, solvents, and alternative fuels, but also as intermediates and components of flavors and fragrances. The enzymatic synthesis of nitriles by aldoxime dehydratase (Oxd) is an emerging process with significant advantages over conventional approaches. Here we focus on the immobilization of His-tagged Oxds on metal affinity resins, an approach that has not been used previously for these enzymes. The potential of the immobilized Oxd was demonstrated for the synthesis of phenylacetonitrile (PAN) and E-cinnamonitrile, compounds applicable in the fragrance industry. A comparison of Talon and Ni-NTA resins showed that Ni-NTA with its higher binding capacity was more suitable for the immobilization of Oxd. Immobilized Oxds were prepared from purified enzymes (OxdFv from Fusarium vanettenii and OxdBr1 from Bradyrhizobium sp.) or the corresponding cell-free extracts. The immobilization of cell-free extracts reduced time and cost of the catalyst production. The immobilized OxdBr1 was superior in terms of recyclability (22 cycles) in the synthesis of PAN from 15 mM E/Z-phenylacetaldoxime at pH 7.0 and 30 °C (100% conversion, 61% isolated yield after product purification). The volumetric and catalyst productivity was 10.5 g/L/h and 48.3 g/g of immobilized protein, respectively.
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Affiliation(s)
- Barbora Křístková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic; Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technická 5, Prague CZ-166 28, Czech Republic
| | - Ludmila Martínková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic.
| | - Lenka Rucká
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic
| | - Michael Kotik
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic
| | - Natalia Kulik
- Laboratory of Photosynthesis, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Novohradská 237, Třeboň CZ-37981, Czech Republic
| | - Robert Rädisch
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, Prague CZ-128 44, Czech Republic
| | - Margit Winkler
- Institute of Molecular Biotechnology, Faculty of Technical Chemistry, Chemical and Process Engineering, Biotechnology, Graz University of Technology, Petersgasse 14, Graz A-8010, Austria; Austrian Center of Industrial Biotechnology GmbH, Krenngasse 37, Graz A-8010, Austria
| | - Miroslav Pátek
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Prague CZ-142 00, Czech Republic
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3
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Yamaguchi T, Asano Y. Nitrile-synthesizing enzymes and biocatalytic synthesis of volatile nitrile compounds: A review. J Biotechnol 2024; 384:20-28. [PMID: 38395363 DOI: 10.1016/j.jbiotec.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Nitriles (R-CN) comprise a broad group of chemicals industrially produced and used in fine chemicals, pharmaceuticals, and bulk applications, polymer chemistry, solvents, etc. Nitriles are important starting materials for producing carboxylic acids, amides, amines, and several other compounds. In addition, some volatile nitriles have been evaluated for their potential as ingredients in fragrance and flavor formulations. However, many nitrile synthesis methods have drawbacks, such as drastic reaction conditions, limited substrate scope, lack of readily available reagents, poor yields, and long reaction times. In contrast to chemical synthesis, biocatalytic approaches using enzymes can produce nitriles without harsh conditions, such as high temperatures and pressures, or toxic compounds. In this review, we summarize the nitrile-synthesizing enzymes from microorganisms, plants, and animals. Furthermore, we introduce several examples of biocatalytic synthesis of volatile nitrile compounds, particularly those using aldoxime dehydratase.
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Affiliation(s)
- Takuya Yamaguchi
- Biotechnology Research Center and Department of Biotechnology, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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4
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Křístková B, Rädisch R, Kulik N, Horvat M, Rucká L, Grulich M, Rudroff F, Kádek A, Pátek M, Winkler M, Martínková L. Scanning aldoxime dehydratase sequence space and characterization of a new aldoxime dehydratase from Fusarium vanettenii. Enzyme Microb Technol 2023; 164:110187. [PMID: 36610228 DOI: 10.1016/j.enzmictec.2022.110187] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/30/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
The aim of this work was to map the sequence space of aldoxime dehydratases (Oxds) as enzymes with great potential for nitrile synthesis. Microbes contain an abundance of putative Oxds but fewer than ten Oxds were characterized in total and only two in fungi. In this work, we prepared and characterized a new Oxd (protein gb|EEU37245.1 named OxdFv) from Fusarium vanettenii 77-13-4. OxdFv is distant from the characterized Oxds with a maximum of 36% identity. Moreover, the canonical Oxd catalytic triad RSH is replaced by R141-E187-E303 in OxdFv. R141A and E187A mutants did not show significant activities, but mutant E303A showed a comparable activity as the wild-type enzyme. According to native mass spectrometry, OxdFv contained almost 1 mol of heme per 1 mol of protein, and was composed of approximately 88% monomer (41.8 kDa) and 12% dimer. A major advantage of this enzyme is its considerable activity under aerobic conditions (25.0 ± 4.3 U/mg for E,Z-phenylacetaldoxime at pH 9.0 and 55 °C). Addition of sodium dithionite (reducing agent) and Fe2+ was required for this activity. OxdFv favored (aryl)aliphatic aldoximes over aromatic aldoximes. Substrate docking in the homology model of OxdFv showed a similar substrate specificity. We conclude that OxdFv is the first characterized Oxd of the REE type.
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Affiliation(s)
- Barbora Křístková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic; Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague, Czech Republic
| | - Robert Rädisch
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic; Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Viničná 5, CZ-128 44 Prague, Czech Republic
| | - Natalia Kulik
- Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, CZ-373 33 Nové Hrady, Czech Republic
| | - Melissa Horvat
- Institute of Molecular Biotechnology, Faculty of Technical Chemistry, Chemical and Process Engineering, Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Lenka Rucká
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
| | - Michal Grulich
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9/OC-163, A-1060 Vienna, Austria
| | - Alan Kádek
- Laboratory of Structural Biology and Cell Signaling, BIOCEV - Institute of Microbiology, Czech Academy of Sciences, Průmyslová 595, CZ-252 50 Vestec, Czech Republic; Leibniz Institute of Virology (LIV), Martinistraße 52, D-20251 Hamburg, Germany; European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany
| | - Miroslav Pátek
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
| | - Margit Winkler
- Institute of Molecular Biotechnology, Faculty of Technical Chemistry, Chemical and Process Engineering, Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria; Austrian Center of Industrial Biotechnology GmbH, Krenngasse 37, A-8010 Graz, Austria
| | - Ludmila Martínková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic.
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Gao H, Chen JY, Peng Z, Feng L, Tung CH, Wang W. Bioinspired Iron-Catalyzed Dehydration of Aldoximes to Nitriles: A General N-O Redox-Cleavage Method. J Org Chem 2022; 87:10848-10857. [PMID: 35914249 DOI: 10.1021/acs.joc.2c01122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inspired by OxdA that operates biocatalytic aldoxime dehydration, we have developed an efficient iron catalyst, Cp*Fe(1,2-Cy2PC6H4O) (1), which rapidly converts various aliphatic and aromatic aldoximes to nitriles with release of H2O at room temperature. The catalysis involves redox activation of the N-O bond by a 1e- transfer from the iron catalyst to the oxime. Such redox-mediated N-O cleavage was demonstrated by the isolation of a ferrous iminato intermediate from the reaction of the ketoxime substrate. This iron-catalyzed acceptorless dehydration approach represents a general method for the preparation of nitriles, and it also delivers salicylonitriles by catalyzing the Kemp elimination reaction.
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Affiliation(s)
- Hongjie Gao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Jia-Yi Chen
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zhiqiang Peng
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lei Feng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Chen-Ho Tung
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Wenguang Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.,College of Chemistry, Beijing Normal University, Beijing 100875, China
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6
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Rädisch R, Pátek M, Křístková B, Winkler M, Křen V, Martínková L. Metabolism of Aldoximes and Nitriles in Plant-Associated Bacteria and Its Potential in Plant-Bacteria Interactions. Microorganisms 2022; 10:549. [PMID: 35336124 PMCID: PMC8955678 DOI: 10.3390/microorganisms10030549] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/22/2022] Open
Abstract
In plants, aldoximes per se act as defense compounds and are precursors of complex defense compounds such as cyanogenic glucosides and glucosinolates. Bacteria rarely produce aldoximes, but some are able to transform them by aldoxime dehydratase (Oxd), followed by nitrilase (NLase) or nitrile hydratase (NHase) catalyzed transformations. Oxds are often encoded together with NLases or NHases in a single operon, forming the aldoxime-nitrile pathway. Previous reviews have largely focused on the use of Oxds and NLases or NHases in organic synthesis. In contrast, the focus of this review is on the contribution of these enzymes to plant-bacteria interactions. Therefore, we summarize the substrate specificities of the enzymes for plant compounds. We also analyze the taxonomic and ecological distribution of the enzymes. In addition, we discuss their importance in selected plant symbionts. The data show that Oxds, NLases, and NHases are abundant in Actinobacteria and Proteobacteria. The enzymes seem to be important for breaking through plant defenses and utilizing oximes or nitriles as nutrients. They may also contribute, e.g., to the synthesis of the phytohormone indole-3-acetic acid. We conclude that the bacterial and plant metabolism of aldoximes and nitriles may interfere in several ways. However, further in vitro and in vivo studies are needed to better understand this underexplored aspect of plant-bacteria interactions.
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Affiliation(s)
- Robert Rädisch
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
- Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Viničná 5, CZ-128 44 Prague, Czech Republic
| | - Miroslav Pátek
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
| | - Barbora Křístková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
- Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, CZ-166 28 Prague, Czech Republic
| | - Margit Winkler
- Institute of Molecular Biotechnology, Faculty of Technical Chemistry, Chemical and Process Engineering, Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
- Austrian Center of Industrial Biotechnology GmbH, Krenngasse 37, A-8010 Graz, Austria
| | - Vladimír Křen
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
| | - Ludmila Martínková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20 Prague, Czech Republic
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7
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Protein engineering of the aldoxime dehydratase from Bacillus sp. OxB-1 based on a rational sequence alignment approach. Sci Rep 2021; 11:14316. [PMID: 34253740 PMCID: PMC8275659 DOI: 10.1038/s41598-021-92749-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 06/08/2021] [Indexed: 12/31/2022] Open
Abstract
Recently, the program INTMSAlign_HiSol for identifying aggregation hotspots in proteins only requiring secondary structure data was introduced. We explored the utility of this program further and applied it for engineering of the aldoxime dehydratase from Bacillus sp. OxB-1. Towards this end, the effect of inverting the hydropathy at selected positions of the amino acid sequence on the enzymatic activity was studied leading to 60% of our constructed variants, which showed improved activity. In part, this activity increase can be rationalised by an improved heme incorporation of the variants. For example, a single mutation gave a 1.8 fold increased enzymatic activity and 30% improved absolute heme incorporation.
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8
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Chen K, Wang Z, Ding K, Chen Y, Asano Y. Recent progress on discovery and research of aldoxime dehydratases. GREEN SYNTHESIS AND CATALYSIS 2021. [DOI: 10.1016/j.gresc.2021.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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9
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Hinzmann A, Betke T, Asano Y, Gröger H. Synthetic Processes toward Nitriles without the Use of Cyanide: A Biocatalytic Concept Based on Dehydration of Aldoximes in Water. Chemistry 2021; 27:5313-5321. [PMID: 33112445 PMCID: PMC8049032 DOI: 10.1002/chem.202001647] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/22/2020] [Indexed: 11/29/2022]
Abstract
While belonging to the most fundamental functional groups, nitriles represent a class of compound that still raises challenges in terms of an efficient, cost‐effective, general and, at the same time, sustainable way for their synthesis. Complementing existing chemical routes, recently a cyanide‐free enzymatic process technology based on the use of an aldoxime dehydratase (Oxd) as a biocatalyst component has been developed and successfully applied for the synthesis of a range of nitrile products. In these biotransformations, the Oxd enzymes catalyze the dehydration of aldoximes as readily available substrates to the nitrile products. Herein, these developments with such enzymes are summarized, with a strong focus on synthetic applications. It is demonstrated that this biocatalytic technology has the potential to “cross the bridge” between the production of fine chemicals and pharmaceuticals, on one hand, and bulk and commodity chemicals, on the other.
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Affiliation(s)
- Alessa Hinzmann
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Tobias Betke
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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10
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Choi JE, Shinoda S, Inoue R, Zheng D, Gröger H, Asano Y. Cyanide-free synthesis of an aromatic nitrile from a biorenewable-based aldoxime: Development and application of a recombinant aldoxime dehydratase as a biocatalyst. BIOCATAL BIOTRANSFOR 2019. [DOI: 10.1080/10242422.2019.1591376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Ji Eun Choi
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Bielefeld, Germany
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Japan
| | - Suguru Shinoda
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Japan
| | - Risa Inoue
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Japan
| | - Daijun Zheng
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Japan
| | - Harald Gröger
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Japan
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11
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Hinzmann A, Glinski S, Worm M, Gröger H. Enzymatic Synthesis of Aliphatic Nitriles at a Substrate Loading of up to 1.4 kg/L: A Biocatalytic Record Achieved with a Heme Protein. J Org Chem 2019; 84:4867-4872. [PMID: 30844280 DOI: 10.1021/acs.joc.9b00184] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A biocatalytic approach toward linear aliphatic nitriles being widely used as industrial bulk chemicals has been developed that runs at high substrate loadings of up to 1.4 kg/L as demonstrated for the synthesis of n-octanenitrile. This substrate loading is one of the highest ever reported in biocatalysis and to best of our knowledge the highest obtained for a water-immiscible product in aqueous medium. It is noteworthy that the biotransformation at such a high substrate loading was achieved by means of a metalloprotein bearing an iron-containing heme subunit in the active site. In detail, an aldoxime dehydratase from Bacillus sp. OxB-1 was used as a biocatalyst for a dehydration of aldoximes as readily available starting materials due to their easy preparation from aliphatic aldehydes through spontaneous condensation with hydroxylamine as bulk chemical. Excellent conversions toward the nitriles in the two-phase system were achieved and the products are easily separated from the reaction mixture without the need for further purification. Aliphatic nitriles are used in industry as solvents and intermediates for the production of surfactants and life sciences products.
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Affiliation(s)
- Alessa Hinzmann
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry , Bielefeld University , Universitätsstrase 25 , 33615 Bielefeld , Germany
| | - Sylvia Glinski
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry , Bielefeld University , Universitätsstrase 25 , 33615 Bielefeld , Germany
| | - Marion Worm
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry , Bielefeld University , Universitätsstrase 25 , 33615 Bielefeld , Germany
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry , Bielefeld University , Universitätsstrase 25 , 33615 Bielefeld , Germany
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12
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Plass C, Hinzmann A, Terhorst M, Brauer W, Oike K, Yavuzer H, Asano Y, Vorholt AJ, Betke T, Gröger H. Approaching Bulk Chemical Nitriles from Alkenes: A Hydrogen Cyanide-Free Approach through a Combination of Hydroformylation and Biocatalysis. ACS Catal 2019. [DOI: 10.1021/acscatal.8b05062] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carmen Plass
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Alessa Hinzmann
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Michael Terhorst
- Chair of Technical Chemistry, Faculty of Bio- and Chemistry Engineering, Technical University Dortmund, Emil-Figge-Straße 66, 44227 Dortmund, Germany
| | - Waldemar Brauer
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Keiko Oike
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Hilmi Yavuzer
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Andreas J. Vorholt
- Department of Molecular Catalysis, Group Multiphase Catalysis, MPI for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Tobias Betke
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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13
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Betke T, Maier M, Gruber-Wölfler H, Gröger H. Biocatalytic production of adiponitrile and related aliphatic linear α,ω-dinitriles. Nat Commun 2018; 9:5112. [PMID: 30504854 PMCID: PMC6269433 DOI: 10.1038/s41467-018-07434-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/01/2018] [Indexed: 11/29/2022] Open
Abstract
Linear α,ω-dinitriles are important precursors for the polymer industry. Most prominently, adiponitrile is produced on an annual scale of ca. 1 million tons. However, a drawback of today’s dominating process is the need for large amounts of highly toxic hydrogen cyanide. In this contribution, an alternative approach towards such linear dinitriles is presented based on dehydration of readily available α,ω-dialdoximes at ambient conditions by means of aldoxime dehydratases. In contrast to existing production routes this biocatalytic route enables a highly regio- and chemoselective approach towards dinitriles without the use of hydrogen cyanide or harsh reaction conditions. In addition, a selective synthesis of adiponitrile with substrate loadings of up to 100 g/L and high yields of up to 80% was achieved. Furthermore, a lab scale process on liter scale leading to > 99% conversion at 50 g/L underlines the potential and robustness of this method for technical applicability. Typically, preparation of the polymer precursors α,ω-dinitriles requires hydrogen cyanide. Here, the authors use aldoxime hydratase to produce adiponitrile and related aliphatic linear dinitriles under ambient conditions starting from readily available substrates without needing hydrogen cyanide.
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Affiliation(s)
- Tobias Betke
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Manuel Maier
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13/III, 8010, Graz, Austria
| | - Heidrun Gruber-Wölfler
- Institute of Process and Particle Engineering, Graz University of Technology, Inffeldgasse 13/III, 8010, Graz, Austria
| | - Harald Gröger
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany.
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Overproduction and characterization of the first enzyme of a new aldoxime dehydratase family in Bradyrhizobium sp. Int J Biol Macromol 2018; 115:746-753. [PMID: 29698761 DOI: 10.1016/j.ijbiomac.2018.04.103] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 11/23/2022]
Abstract
Almost 100 genes within the genus Bradyrhizobium are known to potentially encode aldoxime dehydratases (Oxds), but none of the corresponding proteins have been characterized yet. Aldoximes are natural substances involved in plant defense and auxin synthesis, and Oxds are components of enzymatic cascades enabling bacteria to transform, utilize and detoxify them. The aim of this work was to characterize a representative of the highly conserved Oxds in Bradyrhizobium spp. which include both plant symbionts and members of the soil communities. The selected oxd gene from Bradyrhizobium sp. LTSPM299 was expressed in Escherichia coli, and the corresponding gene product (OxdBr1; GenBank: WP_044589203) was obtained as an N-His6-tagged protein (monomer, 40.7 kDa) with 30-47% identity to Oxds characterized previously. OxdBr1 was most stable at pH ca. 7.0-8.0 and at up to 30 °C. As substrates, the enzyme acted on (aryl)aliphatic aldoximes such as E/Z-phenylacetaldoxime, E/Z-2-phenylpropionaldoxime, E/Z-3-phenylpropionaldoxime, E/Z-indole-3-acetaldoxime, E/Z-propionaldoxime, E/Z-butyraldoxime, E/Z-valeraldoxime and E/Z-isovaleraldoxime. Some of the reaction products of OxdBr1 are substrates of nitrilases occurring in the same genus. Regions upstream of the oxd gene contained genes encoding a putative aliphatic nitrilase and its transcriptional activator, indicating the participation of OxdBr1 in the metabolic route from aldoximes to carboxylic acids.
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Betke T, Higuchi J, Rommelmann P, Oike K, Nomura T, Kato Y, Asano Y, Gröger H. Biocatalytic Synthesis of Nitriles through Dehydration of Aldoximes: The Substrate Scope of Aldoxime Dehydratases. Chembiochem 2018; 19:768-779. [PMID: 29333684 DOI: 10.1002/cbic.201700571] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Indexed: 11/05/2022]
Abstract
Nitriles, which are mostly needed and produced by the chemical industry, play a major role in various industry segments, ranging from high-volume, low-price sectors, such as polymers, to low-volume, high-price sectors, such as chiral pharma drugs. A common industrial technology for nitrile production is ammoxidation as a gas-phase reaction at high temperature. Further popular approaches are substitution or addition reactions with hydrogen cyanide or derivatives thereof. A major drawback, however, is the very high toxicity of cyanide. Recently, as a synthetic alternative, a novel enzymatic approach towards nitriles has been developed with aldoxime dehydratases, which are capable of converting an aldoxime in one step through dehydration into nitriles. Because the aldoxime substrates are easily accessible, this route is of high interest for synthetic purposes. However, whenever a novel method is developed for organic synthesis, it raises the question of substrate scope as one of the key criteria for application as a "synthetic platform technology". Thus, the scope of this review is to give an overview of the current state of the substrate scope of this enzymatic method for synthesizing nitriles with aldoxime dehydratases. As a recently emerging enzyme class, a range of substrates has already been studied so far, comprising nonchiral and chiral aldoximes. This enzyme class of aldoxime dehydratases shows a broad substrate tolerance and accepts aliphatic and aromatic aldoximes, as well as arylaliphatic aldoximes. Furthermore, aldoximes with a stereogenic center are also recognized and high enantioselectivities are found for 2-arylpropylaldoximes, in particular. It is further noteworthy that the enantiopreference depends on the E and Z isomers. Thus, opposite enantiomers are accessible from the same racemic aldehyde and the same enzyme.
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Affiliation(s)
- Tobias Betke
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany.,Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Jun Higuchi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Philipp Rommelmann
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Keiko Oike
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
| | - Taiji Nomura
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuo Kato
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Harald Gröger
- Chair of Organic Chemistry I, Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
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Nitrile Metabolizing Enzymes in Biocatalysis and Biotransformation. Appl Biochem Biotechnol 2018; 185:925-946. [DOI: 10.1007/s12010-018-2705-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/19/2018] [Indexed: 11/26/2022]
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Sørensen M, Neilson EHJ, Møller BL. Oximes: Unrecognized Chameleons in General and Specialized Plant Metabolism. MOLECULAR PLANT 2018; 11:95-117. [PMID: 29275165 DOI: 10.1016/j.molp.2017.12.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 05/19/2023]
Abstract
Oximes (R1R2C=NOH) are nitrogen-containing chemical constituents that are formed in species representing all kingdoms of life. In plants, oximes are positioned at important metabolic bifurcation points between general and specialized metabolism. The majority of plant oximes are amino acid-derived metabolites formed by the action of a cytochrome P450 from the CYP79 family. Auxin, cyanogenic glucosides, glucosinolates, and a number of other bioactive specialized metabolites including volatiles are produced from oximes. Oximes with the E configuration have high biological activity compared with Z-oximes. Oximes or their derivatives have been demonstrated or proposed to play roles in growth regulation, plant defense, pollinator attraction, and plant communication with the surrounding environment. In addition, oxime-derived products may serve as quenchers of reactive oxygen species and storage compounds for reduced nitrogen that may be released on demand by the activation of endogenous turnover pathways. As highly bioactive molecules, chemically synthesized oximes have found versatile uses in many sectors of society, especially in the agro- and medical sectors. This review provides an update on the structural diversity, occurrence, and biosynthesis of oximes in plants and discusses their role as key players in plant general and specialized metabolism.
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Affiliation(s)
- Mette Sørensen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark
| | - Elizabeth H J Neilson
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; VILLUM Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark.
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18
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Dooley-Cullinane TM, O’Reilly C, Coffey L. Real-time PCR detection of aldoxime dehydratase genes in nitrile-degrading microorganisms. Antonie van Leeuwenhoek 2016; 110:271-279. [DOI: 10.1007/s10482-016-0786-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/11/2016] [Indexed: 11/30/2022]
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19
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Yew SM, Chan CL, Kuan CS, Toh YF, Ngeow YF, Na SL, Lee KW, Hoh CC, Yee WY, Ng KP. The genome of newly classified Ochroconis mirabilis: Insights into fungal adaptation to different living conditions. BMC Genomics 2016; 17:91. [PMID: 26842951 PMCID: PMC4738786 DOI: 10.1186/s12864-016-2409-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/21/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Ochroconis mirabilis, a recently introduced water-borne dematiaceous fungus, is occasionally isolated from human skin lesions and nails. We identified an isolate of O. mirabilis from a skin scraping with morphological and molecular studies. Its genome was then sequenced and analysed for genetic features related to classification and biological characteristics. RESULTS UM 578 was identified as O. mirabilis based on morphology and internal transcribed spacer (ITS)-based phylogeny. The 34.61 Mb assembled genome with 13,435 predicted genes showed less efficiency of this isolate in plant cell wall degradation. Results from the peptidase comparison analysis with reported keratin-degrading peptidases from dermatophytes suggest that UM 578 is very unlikely to be utilising these peptidases to survive in the host. Nevertheless, we have identified peptidases from M10A, M12A and S33 families that may allow UM 578 to invade its host via extracellular matrix and collagen degradation. Furthermore, the lipases in UM 578 may have a role in supporting the fungus in host invasion. This fungus has the potential ability to synthesise melanin via the 1,8-dihydroxynaphthalene (DHN)-melanin pathway and to produce mycotoxins. The mating ability of this fungus was also inspected in this study and a mating type gene containing alpha domain was identified. This fungus is likely to produce taurine that is required in osmoregulation. The expanded gene family encoding the taurine catabolism dioxygenase TauD/TdfA domain suggests the utilisation of taurine under sulfate starvation. The expanded glutathione-S-transferase domains and RTA1-like protein families indicate the selection of genes in UM 578 towards adaptation in hostile environments. CONCLUSIONS The genomic analysis of O. mirabilis UM 578 provides a better understanding of fungal survival tactics in different habitats.
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Affiliation(s)
- Su Mei Yew
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Chai Ling Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Chee Sian Kuan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yue Fen Toh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yun Fong Ngeow
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Bandar Sungai Long, 43000, Kajang, Selangor Darul Ehsan, Malaysia.
| | - Shiang Ling Na
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kok Wei Lee
- Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor Darul Ehsan, Malaysia.
| | - Chee-Choong Hoh
- Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor Darul Ehsan, Malaysia.
| | - Wai-Yan Yee
- Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor Darul Ehsan, Malaysia.
| | - Kee Peng Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Maheshwari DK, Dheeman S, Agarwal M. Phytohormone-Producing PGPR for Sustainable Agriculture. BACTERIAL METABOLITES IN SUSTAINABLE AGROECOSYSTEM 2015. [DOI: 10.1007/978-3-319-24654-3_7] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Duca D, Lorv J, Patten CL, Rose D, Glick BR. Indole-3-acetic acid in plant-microbe interactions. Antonie van Leeuwenhoek 2014; 106:85-125. [PMID: 24445491 DOI: 10.1007/s10482-013-0095-y] [Citation(s) in RCA: 325] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/07/2013] [Indexed: 01/04/2023]
Abstract
Indole-3-acetic acid (IAA) is an important phytohormone with the capacity to control plant development in both beneficial and deleterious ways. The ability to synthesize IAA is an attribute that many bacteria including both plant growth-promoters and phytopathogens possess. There are three main pathways through which IAA is synthesized; the indole-3-pyruvic acid, indole-3-acetamide and indole-3-acetonitrile pathways. This chapter reviews the factors that effect the production of this phytohormone, the role of IAA in bacterial physiology and in plant-microbe interactions including phytostimulation and phytopathogenesis.
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Affiliation(s)
- Daiana Duca
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada,
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22
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Liao RZ, Thiel W. Why Is the Oxidation State of Iron Crucial for the Activity of Heme-Dependent Aldoxime Dehydratase? A QM/MM Study. J Phys Chem B 2012; 116:9396-408. [DOI: 10.1021/jp305510c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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23
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Pan XL, Cui FC, Liu W, Liu JY. QM/MM Study on the Catalytic Mechanism of Heme-Containing Aliphatic Aldoxime Dehydratase. J Phys Chem B 2012; 116:5689-93. [DOI: 10.1021/jp302114d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiao-Liang Pan
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Feng-Chao Cui
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Wei Liu
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Jing-Yao Liu
- State Key Laboratory of Theoretical
and Computational
Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
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Pedras MSC, Minic Z, Thongbam PD, Bhaskar V, Montaut S. Indolyl-3-acetaldoxime dehydratase from the phytopathogenic fungus Sclerotinia sclerotiorum: purification, characterization, and substrate specificity. PHYTOCHEMISTRY 2010; 71:1952-1962. [PMID: 21036375 DOI: 10.1016/j.phytochem.2010.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 09/27/2010] [Accepted: 10/04/2010] [Indexed: 05/30/2023]
Abstract
The purification and characterization of indolyl-3-acetaldoxime dehydratase produced by the plant fungal pathogen Sclerotinia sclerotiorum is described. The substrate specificity indicates that it is an indolyl-3-acetaldoxime dehydratase (IAD, EC 4.99.1.6), which catalyzes transformation of indolyl-3-acetaldoxime to indolyl-3-acetonitrile. The enzyme showed Michaelis-Menten kinetics and had an apparent molecular mass of 44 kDa. The amino acid sequence of IAD, determined using LC-ESI-MS/MS, identified it as the protein SS1G_01653 from S. sclerotiorum. IADSs was highly homologous (84% amino acid identity) to the hypothetical protein BC1G_14775 from Botryotinia fuckeliana B05.10. In addition, similarity to the phenylacetaldoxime dehydratases from Gibberella zeae (33% amino acid identity) and Bacillus sp. (20% amino acid identity) was noted. The specific activity of IADSs increased about 17-fold upon addition of Na(2)S(2)O(4) under anaerobic conditions, but in the absence of Na(2)S(2)O(4) no significant change was observed, whether aerobic or anaerobic conditions were used. As with other aldoxime dehydratases isolated from microbes, the role of IADSs in fungal plant pathogens is not clear, but given its substrate specificity, it appears unlikely that IADSs is a general xenobiotic detoxifying enzyme.
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Affiliation(s)
- M Soledade C Pedras
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK, Canada S7N 5C9.
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Coffey L, Owens E, Tambling K, O'Neill D, O'Connor L, O'Reilly C. Real-time PCR detection of Fe-type nitrile hydratase genes from environmental isolates suggests horizontal gene transfer between multiple genera. Antonie van Leeuwenhoek 2010; 98:455-63. [PMID: 20502965 DOI: 10.1007/s10482-010-9459-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 05/14/2010] [Indexed: 11/25/2022]
Abstract
Nitriles are widespread in the environment as a result of biological and industrial activity. Nitrile hydratases catalyse the hydration of nitriles to the corresponding amide and are often associated with amidases, which catalyze the conversion of amides to the corresponding acids. Nitrile hydratases have potential as biocatalysts in bioremediation and biotransformation applications, and several successful examples demonstrate the advantages. In this work a real-time PCR assay was designed for the detection of Fe-type nitrile hydratase genes from environmental isolates purified from nitrile-enriched soils and seaweeds. Specific PCR primers were also designed for amplification and sequencing of the genes. Identical or highly homologous nitrile hydratase genes were detected from isolates of numerous genera from geographically diverse sites, as were numerous novel genes. The genes were also detected from isolates of genera not previously reported to harbour nitrile hydratases. The results provide further evidence that many bacteria have acquired the genes via horizontal gene transfer. The real-time PCR assay should prove useful in searching for nitrile hydratases that could have novel substrate specificities and therefore potential in industrial applications.
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Affiliation(s)
- Lee Coffey
- Pharmaceutical & Molecular Biotechnology Research Centre, Chemical & Life Sciences Department, Waterford Institute of Technology, Ireland.
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Transcriptional regulation of the nitrile hydratase gene cluster in Pseudomonas chlororaphis B23. J Bacteriol 2008; 190:4210-7. [PMID: 18408036 DOI: 10.1128/jb.00061-08] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An enormous amount of nitrile hydratase (NHase) is inducibly produced by Pseudomonas chlororaphis B23 after addition of methacrylamide as the sole nitrogen source to a medium. The expression pattern of the P. chlororaphis B23 NHase gene cluster in response to addition of methacrylamide to the medium was investigated. Recently, we reported that the NHase gene cluster comprises seven genes (oxdA, amiA, nhpA, nhpB, nhpC, nhpS, and acsA). Sequence analysis of the 1.5-kb region upstream of the oxdA gene revealed the presence of a 936-bp open reading frame (designated nhpR), which should encode a protein with a molecular mass of 35,098. The deduced amino acid sequence of the nhpR product showed similarity to the sequences of transcriptional regulators belonging to the XylS/AraC family. Although the transcription of the eight genes (nhpR, oxdA, amiA, nhpABC, nhpS, and acsA) in the NHase gene cluster was induced significantly in the P. chlororaphis B23 wild-type strain after addition of methacrylamide to the medium, transcription of these genes in the nhpR disruptant was not induced, demonstrating that nhpR codes for a positive transcriptional regulator in the NHase gene cluster. A reverse transcription-PCR experiment revealed that five genes (oxdA, amiA, nhpA, nhpB, and nhpC) are cotranscribed, as are two other genes (nhpS and acsA). The transcription start sites for nhpR, oxdA, nhpA, and nhpS were mapped by primer extension analysis, and putative -12 and -24 sigma(54)-type promoter binding sites were identified. NhpR was found to be the first transcriptional regulator of NHase belonging to the XylS/AraC family.
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Kelly DR, Baker SC, King DS, de Silva DS, Lord G, Taylor JP. Studies of nitrile oxide cycloadditions, and the phenolic oxidative coupling of vanillin aldoxime by Geobacillus sp. DDS012 from Italian rye grass silage. Org Biomol Chem 2008; 6:787-96. [PMID: 18264580 DOI: 10.1039/b716915a] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
During studies directed towards the discovery of nitrile hydrolysing enzymes from thermophiles, vanillin aldoxime was incubated with the thermophilic organism, Geobacillus sp. DDS012 isolated from Italian rye grass (Lolium multiflorum) silage. The predominant product was a dihydro-dimer, which could only be characterised by LC-MS. This was initially imagined to be the product of cycloaddition of vanillin aldoxime with the corresponding nitrile oxide, but preparation of the supposed adduct and model studies excluded this possibility. The rate constant for the second order dimerisation of 4-O-acetyl vanillin nitrile oxide was measured (1.21 x 10(-4) M(-1) s(-1), 0.413 M, 25 degrees C) and the (13)C-NMR signal for the nitrile oxide carbon was observed (delta(C) 34.4, br. t (1)J(13)C,(14)N circa 50 Hz). Treatment of vanillin aldoxime with potassium persulfate and iron sulfate gave material with the same LC-MS properties as the natural product, which is therefore identified as 5,5'-dehydro-di-(vanillin aldoxime) 1d formed by phenolic oxidative coupling.
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Affiliation(s)
- David R Kelly
- The Tatem Laboratories, School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.
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Kato Y, Tsuda T, Asano Y. Purification and partial characterization of N-hydroxy-l-phenylalanine decarboxylase/oxidase from Bacillus sp. strain OxB-1, an enzyme involved in aldoxime biosynthesis in the “aldoxime–nitrile pathway”. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:856-65. [PMID: 17544345 DOI: 10.1016/j.bbapap.2007.04.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 03/27/2007] [Accepted: 04/25/2007] [Indexed: 11/22/2022]
Abstract
An enzyme that catalyzes the conversion of N-hydroxy-l-phenylalanine to phenylacetaldoxime was shown to be present in the Z-phenylacetaldoxime-degrading bacterium, Bacillus sp. strain OxB-1. The aldoxime-forming enzyme, which is induced by L-phenylalanine, was purified 8,050-fold to apparent homogeneity with a yield of 15.2%. The enzyme has a subunit M(r) of about 86,000. The enzyme converts N-hydroxy-L-phenylalanine (K(m) 0.99 mM) to only one geometrical isomer, namely Z-phenylacetaldoxime. Relatively large amounts of pyridoxal 5'-phosphate (PLP) are required to be present in the reaction mixture because PLP reacts non-enzymatically with the N-hydroxy amino acid substrate to form a nitrone. Several characteristics of the enzyme were compared with those of other PLP-dependent aromatic amino acid-converting enzymes described in the literature. The enzyme is tentatively named "N-hydroxy-L-phenylalanine decarboxylase/oxidase". Finally, the possible biosynthesis and metabolism of phenylacetaldoxime in Bacillus sp. strain OxB-1 is discussed.
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Affiliation(s)
- Yasuo Kato
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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