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Kunkle DE, Skaar EP. Moving metals: How microbes deliver metal cofactors to metalloproteins. Mol Microbiol 2023; 120:547-554. [PMID: 37408317 PMCID: PMC10592388 DOI: 10.1111/mmi.15117] [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: 02/13/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 07/07/2023]
Abstract
First row d-block metal ions serve as vital cofactors for numerous essential enzymes and are therefore required nutrients for all forms of life. Despite this requirement, excess free transition metals are toxic. Free metal ions participate in the production of noxious reactive oxygen species and mis-metalate metalloproteins, rendering enzymes catalytically inactive. Thus, bacteria require systems to ensure metalloproteins are properly loaded with cognate metal ions to maintain protein function, while avoiding metal-mediated cellular toxicity. In this perspective we summarize the current mechanistic understanding of bacterial metallocenter maturation with specific emphasis on metallochaperones; a group of specialized proteins that both shield metal ions from inadvertent reactions and distribute them to cognate target metalloproteins. We highlight several recent advances in the field that have implicated new classes of proteins in the distribution of metal ions within bacterial proteins, while speculating on the future of the field of bacterial metallobiology.
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Affiliation(s)
- Dillon E. Kunkle
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
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2
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Moraes MI, Iglesias C, Teixeira IS, Milagre HM, Giordano SR, Milagre CD. Biotransformations of nitriles mediated by in vivo nitrile hydratase of Rhodococcus erythropolis ATCC 4277 heterologously expressed in E. Coli. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2022.100760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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3
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Merging enzymes with chemocatalysis for amide bond synthesis. Nat Commun 2022; 13:380. [PMID: 35046426 PMCID: PMC8770729 DOI: 10.1038/s41467-022-28005-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/16/2021] [Indexed: 01/03/2023] Open
Abstract
Amides are one of the most fundamental chemical bonds in nature. In addition to proteins and other metabolites, many valuable synthetic products comprise amide bonds. Despite this, there is a need for more sustainable amide synthesis. Herein, we report an integrated next generation multi-catalytic system, merging nitrile hydratase enzymes with a Cu-catalysed N-arylation reaction in a single reaction vessel, for the construction of ubiquitous amide bonds. This synergistic one-pot combination of chemo- and biocatalysis provides an amide bond disconnection to precursors, that are orthogonal to those in classical amide synthesis, obviating the need for protecting groups and delivering amides in a manner unachievable using existing catalytic regimes. Our integrated approach also affords broad scope, very high (molar) substrate loading, and has excellent functional group tolerance, telescoping routes to natural product derivatives, drug molecules, and challenging chiral amides under environmentally friendly conditions at scale. Proteins, other metabolites and many valuable synthetic products contain amide bonds and there is a need for more sustainable amide synthesis routes. Here the authors show an integrated next generation multi-catalytic system, merging nitrile hydratase enzymes with a Cu-catalysed N-arylation reaction in a single reaction vessel, for the construction of ubiquitous amide bonds.
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4
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Lankathilaka KPW, Bennett B, Holz RC. The Fe-type nitrile hydratase from Rhodococcus equi TG328-2 forms an alpha-activator protein complex. J Biol Inorg Chem 2020; 25:903-911. [DOI: 10.1007/s00775-020-01806-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
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Guo L, Cheng X, Jiang HY, Dai YJ. Maturation Mechanism of Nitrile Hydratase From Streptomyces canus CGMCC 13662 and Its Structural Character. Front Microbiol 2020; 11:1419. [PMID: 32670250 PMCID: PMC7329996 DOI: 10.3389/fmicb.2020.01419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/02/2020] [Indexed: 11/13/2022] Open
Abstract
Nitrile hydratases have received significant interest both in the large-scale industrial production of acrylamide and nicotinamide, and the remediation of environmental contamination with nitrile-containing pollutants. Almost all known nitrile hydratases include an α-subunit (AnhA) and β-subunit (AnhB), and a specific activator protein is crucial for their maturation and catalytic activity. Many studies exist on nitrile hydratase characteristics and applications, but few have reported their metal insertion and post-translational maturation mechanism. In this study, we investigated the cobalt insertion and maturation mechanism of nitrile hydratase from Streptomyces canus CGMCC 13662 (ScNHase) bearing three subunits (AnhD, AnhE, and AnhA). ScNHase subunits were purified, and the cobalt content and nitrile hydratase activity of the ScNHase subunits were detected. We discovered that cobalt could insert into the cobalt-free AnhA of ScNHase in the absence of activator protein under reduction agent DL-dithiothreitol (DTT) environment. AnhD not only performed the function of AnhB of NHase, but also acted as a metal ion chaperone and self-subunit swapping chaperone, while AnhE did not act as similar performance. A cobalt direct-insertion under reduction condition coordinated self-subunit swapping mechanism is responsible for ScNHase post-translational maturation. Molecular docking of ScNHase and substrates suggested that the substrate specificity of ScNHase was correlated with its structure. ScNHase had a weak hydrophobic interaction with IAN through protein-ligand interaction analysis and, therefore, had no affinity with indole-3-acetonitrile (IAN). The post-translational maturation mechanism and structure characteristics of ScNHase could help guide research on the environmental remediation of nitrile-containing waste contamination and three-subunit nitrile hydratase.
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Affiliation(s)
- 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, China
| | - Xi 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, China
| | - Huo-Yong 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, 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, China
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Jiao S, Li F, Yu H, Shen Z. Advances in acrylamide bioproduction catalyzed with Rhodococcus cells harboring nitrile hydratase. Appl Microbiol Biotechnol 2019; 104:1001-1012. [DOI: 10.1007/s00253-019-10284-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 01/10/2023]
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Lankathilaka KPW, Stein N, Holz RC, Bennett B. Cellular maturation of an iron-type nitrile hydratase interrogated using EPR spectroscopy. J Biol Inorg Chem 2019; 24:1105-1113. [PMID: 31549242 DOI: 10.1007/s00775-019-01720-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/13/2019] [Indexed: 11/24/2022]
Abstract
Nitrile hydratase (NHase) is a non-heme iron-containing enzyme that has applications in commodity chemical synthesis, pharmaceutical intermediate synthesis, and reclamation of nitrile-(bromoxynil) contaminated land. Mechanistic study of the enzyme has been complicated by the expression of multiple overlapping Fe(III) EPR signals. The individual signals were recently assigned to distinct chemical species with the assistance of DFT calculations. Here, the origins and evolution of the EPR signals from cells overexpressing the enzyme were investigated, with the aims of optimizing the preparation of homogeneous samples of NHase for study and investigating the application of E. coli overexpressing the enzyme for "green" chemistry. It was revealed that nitrile hydratase forms two sets of inactive complexes in vivo over time. One is due to reversible complexation with endogenous carboxylic acids, while the second is due to irreversibly inactivating oxidation of an essential cysteine sulfenic acid. It was shown that the homogeneity of preparations can be improved by employing an anaerobic protocol. The ability of the substrates acrylonitrile and acetonitrile to be taken up by cells and hydrated to the corresponding amides by NHase was demonstrated by EPR identification of the product complexes of NHase in intact cells. The inhibitors butyric acid and butane boronic acid were also taken up by E. coli and formed complexes with NHase in vivo, indicating that care must be taken with environmental variables when attempting microbially assisted synthesis and reclamation.
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Affiliation(s)
| | - Natalia Stein
- Department of Physics, Marquette University, 1420 W. Clybourn St., Milwaukee, WI, 53233, USA
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI, 53226, USA
| | - Richard C Holz
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA.
- Department of Chemistry, Colorado School of Mines, Golden, CO, 80401, USA.
| | - Brian Bennett
- Department of Physics, Marquette University, 1420 W. Clybourn St., Milwaukee, WI, 53233, USA.
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8
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Advances in cloning, structural and bioremediation aspects of nitrile hydratases. Mol Biol Rep 2019; 46:4661-4673. [DOI: 10.1007/s11033-019-04811-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/10/2019] [Indexed: 01/09/2023]
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9
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Guo L, Fang WW, Guo LL, Yao CF, Zhao YX, Ge F, Dai YJ. Biodegradation of the Neonicotinoid Insecticide Acetamiprid by Actinomycetes Streptomyces canus CGMCC 13662 and Characterization of the Novel Nitrile Hydratase Involved. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5922-5931. [PMID: 31067049 DOI: 10.1021/acs.jafc.8b06513] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Neonicotinoid insecticide pollution in soil and water poses serious environmental risks. Microbial biodegradation is an important neonicotinoid insecticide degradation pathway in the environment. In this study, 70.0% of the acetamiprid in a 200 mg/L solution was degraded by actinomycetes Streptomyces canus CGMCC 13662 (isolated from soil) in 48 h, and the acetamiprid degradation half-life was 27.7 h. Acetamiprid was degraded to IM-1-2 (( E)-1-(1-(((6-chloropyridin-3-yl)methyl)(methyl) amino)ethylidene)urea) through hydrolysis of the cyanoimine moiety. Gene cloning and overexpression indicated that a novel nitrile hydratase with three unusual subunits (AnhD, AnhE, and AnhA) without accessory protein mediated IM-1-2 formation. The purified nitrile hydratase responsible for degrading acetamiprid had a Km of 5.85 mmol/L and a Vmax of 15.99 U/mg. A homology model suggested that AnhD-Glu56 and AnhE-His21 play important roles in the catalytic efficiency of the nitrile hydratase. S. canus CGMCC 13662 could be used to remediate environments contaminated with acetamiprid.
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Affiliation(s)
- 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
| | - Wen-Wan Fang
- 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
| | - Chuan-Fei Yao
- 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
| | - Feng Ge
- Ministry of Environmental Protection , Nanjing Institute of Environmental Sciences , Nanjing 210042 , 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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Yu H, Jiao S, Wang M, Liang Y, Tang L. Biodegradation of Nitriles by Rhodococcus. BIOLOGY OF RHODOCOCCUS 2019. [DOI: 10.1007/978-3-030-11461-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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11
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Pei X, Wang J, Wu Y, Zhen X, Tang M, Wang Q, Wang A. Evidence for the participation of an extra α-helix at β-subunit surface in the thermal stability of Co-type nitrile hydratase. Appl Microbiol Biotechnol 2018; 102:7891-7900. [DOI: 10.1007/s00253-018-9191-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 12/23/2022]
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12
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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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Stein N, Gumataotao N, Hajnas N, Wu R, Wasantha Lankathilaka KP, Bornscheuer UT, Liu D, Fiedler AT, Holz RC, Bennett B. Multiple States of Nitrile Hydratase from Rhodococcus equi TG328-2: Structural and Mechanistic Insights from Electron Paramagnetic Resonance and Density Functional Theory Studies. Biochemistry 2017; 56:3068-3077. [PMID: 28520398 PMCID: PMC5821057 DOI: 10.1021/acs.biochem.6b00876] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-type nitrile hydratases (NHases) contain an Fe(III) ion coordinated in a characteristic "claw setting" by an axial cysteine thiolate, two equatorial peptide nitrogens, the sulfur atoms of equatorial cysteine-sulfenic and cysteine-sulfinic acids, and an axial water/hydroxyl moiety. The cysteine-sulfenic acid is susceptible to oxidation, and the enzyme is traditionally prepared using butyric acid as an oxidative protectant. The as-prepared enzyme exhibits a complex electron paramagnetic resonance (EPR) spectrum due to multiple low-spin (S = 1/2) Fe(III) species. Four distinct signals can be assigned to the resting active state, the active state bound to butyric acid, an oxidized Fe(III)-bis(sulfinic acid) form, and an oxidized complex with butyric acid. A combination of comparison with earlier work, development of methods to elicit individual signals, and design and application of a novel density functional theory method for reproducing g tensors to unprecedentedly high precision was used to assign the signals. These species account for the previously reported EPR spectra from Fe-NHases, including spectra observed upon addition of substrates. Completely new EPR signals were observed upon addition of inhibitory boronic acids, and the distinctive g1 features of these signals were replicated in the steady state with the slow substrate acetonitrile. This latter signal constitutes the first EPR signal from a catalytic intermediate of NHase and is assigned to a key intermediate in the proposed catalytic cycle. Earlier, apparently contradictory, electron nuclear double resonance reports are reconsidered in the context of this work.
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Affiliation(s)
- Natalia Stein
- Department of Physics, Marquette University, 540 North 15th Street, Milwaukee, Wisconsin 53233, United States
| | - Natalie Gumataotao
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Natalia Hajnas
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Rui Wu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - K. P. Wasantha Lankathilaka
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Uwe T. Bornscheuer
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Adam T. Fiedler
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Richard C. Holz
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Brian Bennett
- Department of Physics, Marquette University, 540 North 15th Street, Milwaukee, Wisconsin 53233, United States
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Pei X, Yang Z, Wang A, Yang L, Wu J. Identification and functional analysis of the activator gene involved in the biosynthesis of Co-type nitrile hydratase from Aurantimonas manganoxydans. J Biotechnol 2017; 251:38-46. [DOI: 10.1016/j.jbiotec.2017.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/05/2017] [Accepted: 03/14/2017] [Indexed: 11/15/2022]
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Pratush A, Seth A, Bhalla TC. Expression of nitrile hydratase gene of mutant 4D strain of Rhodococcus rhodochrous PA 34 in Pichia pastoris. BIOCATAL BIOTRANSFOR 2016. [DOI: 10.1080/10242422.2016.1247831] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Amit Pratush
- Department of Bioengineering, School of life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,
| | - Amit Seth
- Department of Bioengineering, Shoolini University of Biotechnology and management Sciences, Solan, India, and
| | - Tek Chand Bhalla
- Department of Biotechnology, Himachal Pradesh University, Shimla, India
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The iron-type nitrile hydratase activator protein is a GTPase. Biochem J 2016; 474:247-258. [PMID: 27807009 DOI: 10.1042/bcj20160884] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/27/2016] [Accepted: 11/02/2016] [Indexed: 01/01/2023]
Abstract
The Fe-type nitrile hydratase activator protein from Rhodococcus equi TG328-2 (ReNHase TG328-2) was successfully expressed and purified. Sequence analysis and homology modeling suggest that it is a G3E P-loop guanosine triphosphatase (GTPase) within the COG0523 subfamily. Kinetic studies revealed that the Fe-type activator protein is capable of hydrolyzing GTP to GDP with a kcat value of 1.2 × 10-3 s-1 and a Km value of 40 μM in the presence of 5 mM MgCl2 in 50 mM 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid at a pH of 8.0. The addition of divalent metal ions, such as Co(II), which binds to the ReNHase TG328-2 activator protein with a Kd of 2.9 μM, accelerated the rate of GTP hydrolysis, suggesting that GTP hydrolysis is potentially connected to the proposed metal chaperone function of the ReNHase TG328-2 activator protein. Circular dichroism data reveal a significant conformational change upon the addition of GTP, which may be linked to the interconnectivity of the cofactor binding sites, resulting in an activator protein that can be recognized and can bind to the NHase α-subunit. A combination of these data establishes, for the first time, that the ReNHase TG328-2 activator protein falls into the COG0523 subfamily of G3E P-loop GTPases, many of which play a role in metal homeostasis processes.
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Guo FM, Wu JP, Yang LR, Xu G. Overexpression of a nitrile hydratase from Klebsiella oxytoca KCTC 1686 in Escherichia coli and its biochemical characterization. BIOTECHNOL BIOPROC E 2016. [DOI: 10.1007/s12257-015-0370-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Sun SL, Lu TQ, Yang WL, Guo JJ, Rui X, Mao SY, Zhou LY, Dai YJ. Characterization of a versatile nitrile hydratase of the neonicotinoid thiacloprid-degrading bacterium Ensifer meliloti CGMCC 7333. RSC Adv 2016. [DOI: 10.1039/c5ra27966f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The nitrogen-fixing bacterium Ensifer meliloti CGMCC 7333 and its nitrile hydratase (NHase) degrade the neonicotinoid insecticides, thiacloprid (THI) and acetamiprid (ACE), to their corresponding amide metabolites.
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Affiliation(s)
- Shi-Lei Sun
- 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
| | - Tian-Qi Lu
- 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
| | - 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
| | - Jing-Jing 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
| | - Xue Rui
- 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
| | - Shi-Yun Mao
- 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
| | - Ling-Yan Zhou
- 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
| | - 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
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Gong JS, Shi JS, Lu ZM, Li H, Zhou ZM, Xu ZH. Nitrile-converting enzymes as a tool to improve biocatalysis in organic synthesis: recent insights and promises. Crit Rev Biotechnol 2015; 37:69-81. [DOI: 10.3109/07388551.2015.1120704] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Pei X, Wang Q, Meng L, Li J, Yang Z, Yin X, Yang L, Chen S, Wu J. Chaperones-assisted soluble expression and maturation of recombinant Co-type nitrile hydratase in Escherichia coli to avoid the need for a low induction temperature. J Biotechnol 2015; 203:9-16. [PMID: 25796588 DOI: 10.1016/j.jbiotec.2015.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 03/03/2015] [Accepted: 03/07/2015] [Indexed: 11/28/2022]
Abstract
Nitrile hydratase (NHase) is an important industrial enzyme that biosynthesizes high-value amides. However, most of NHases expressed in Escherichia coli easily aggregate to inactive inclusion bodies unless the induction temperature is reduced to approximately 20°C. The NHase from Aurantimonas manganoxydans has been functionally expressed in E. coli, and exhibits considerable potential for the production of nicotinamide in industrial application. In this study, the effects of chaperones including GroEL/ES, Dnak/J-GrpE and trigger factor on the expression of the recombinant Co-type NHase were investigated. The results indicate that three chaperones can significantly promote the active expression of the recombinant NHase at 30°C. The total NHase activities reached to 263 and 155U/ml in shake flasks when the NHase was co-expressed with GroEL/ES and DnaK/J-GrpE, which were 52- and 31-fold higher than the observed activities without chaperones, respectively. This increase is possibly due to the soluble expression of the recombinant NHase assisted by molecular chaperones. Furthermore, GroEL/ES and DnaK/J-GrpE were determined to promote the maturation of the Co-type NHase in E. coli under the absence of the parental activator gene. These knowledge regarding the chaperones effect on the NHase expression are useful for understanding the biosynthesis of Co-type NHase.
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Affiliation(s)
- Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 310012, PR China
| | - Qiuyan Wang
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 310012, PR China
| | - Lijun Meng
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310028, PR China
| | - Jing Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310028, PR China
| | - Zhengfen Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310028, PR China
| | - Xiaopu Yin
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 310012, PR China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310028, PR China
| | - Shaoyun Chen
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053, PR China.
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310028, PR China.
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21
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Simultaneous purification of nitrile hydratase and amidase of Alcaligenes sp. MTCC 10674. 3 Biotech 2014; 4:375-381. [PMID: 28324474 PMCID: PMC4145624 DOI: 10.1007/s13205-013-0163-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 08/12/2013] [Indexed: 10/31/2022] Open
Abstract
Alcaligenes sp. MTCC 10674 has a bienzymatic system for the hydrolysis of nitriles. The nitrile hydratase and amidase have been purified simultaneously to homogeneity using a combination of (NH)4SO4 precipitation, ion exchange chromatography and gel permeation chromatography. Nitrile hydratase and amidase have molecular weight of 47 and 114 kDa, respectively and exist as heterodimer. Optimum temperatures for maximum activity of nitrile hydratase and amidase were 15 °C (2.4 U/mg protein) and 45 °C (2.3 U/mg protein), respectively. Nitrile hydratase showed maximum 7.8 U/mg protein at 50 mM acrylonitrile and amidase has 9.2 U/mg protein at 25 mM propionamide. Nitrile hydratase has Vmax 10 μmol/min/mg and Km 40 mM, while amidase has Vmax 12.5 μmol/min/mg and Km 45.5 mM, respectively. Heavy metal ions Hg2+, Ag+, Pb2+ and Cu2+ were strong inhibitors of nitrile hydratase and amidase activity.
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22
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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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23
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Discovery of a new Fe-type nitrile hydratase efficiently hydrating aliphatic and aromatic nitriles by genome mining. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.10.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Pei X, Zhang H, Meng L, Xu G, Yang L, Wu J. Efficient cloning and expression of a thermostable nitrile hydratase in Escherichia coli using an auto-induction fed-batch strategy. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Characterization of ‘pinky’ strain grown in culture of Rhodobacter sphaeroides R26.1. Chem Res Chin Univ 2013. [DOI: 10.1007/s40242-013-2318-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Gumataotao N, Kuhn ML, Hajnas N, Holz RC. Identification of an active site-bound nitrile hydratase intermediate through single turnover stopped-flow spectroscopy. J Biol Chem 2013; 288:15532-6. [PMID: 23589282 DOI: 10.1074/jbc.m112.398909] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Stopped-flow kinetic data were obtained for the iron-type nitrile hydratase from Rhodococcus equi TG328-2 (ReNHase) using methacrylonitrile as the substrate. Multiple turnover experiments suggest a three-step kinetic model that allows for the reversible binding of substrate, the presence of an intermediate, and the formation of product. Microscopic rate constants determined from these data are in good agreement with steady state data confirming that the stopped-flow method used was appropriate for the reaction. Single turnover stopped-flow experiments were used to identify catalytic intermediates. These data were globally fit confirming a three-step kinetic model. Independent absorption spectra acquired between 0.005 and 0.5 s of the reaction reveal a significant increase in absorbance at 375, 460, and 550 nm along with the hypsochromic shift of an Fe(3+)←S ligand-to-metal charge transfer band from 700 to 650 nm. The observed UV-visible absorption bands for the Fe(3+)-nitrile intermediate species are similar to low spin Fe(3+)-enzyme and model complexes bound by NO or N3((-)). These data provide spectroscopic evidence for the direct coordination of the nitrile substrate to the nitrile hydratase active site low spin Fe(3+) center.
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Affiliation(s)
- Natalie Gumataotao
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, USA
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27
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The Fe-type nitrile hydratase from Comamonas testosteroni Ni1 does not require an activator accessory protein for expression in Escherichia coli. Biochem Biophys Res Commun 2012; 424:365-70. [DOI: 10.1016/j.bbrc.2012.06.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 06/11/2012] [Indexed: 11/23/2022]
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28
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Zhang HJ, Zhou QW, Zhou GC, Cao YM, Dai YJ, Ji WW, Shang GD, Yuan S. Biotransformation of the neonicotinoid insecticide thiacloprid by the bacterium Variovorax boronicumulans strain J1 and mediation of the major metabolic pathway by nitrile hydratase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:153-159. [PMID: 22148554 DOI: 10.1021/jf203232u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A neonicotinoid insecticide thiacloprid-degrading bacterium strain J1 was isolated from soil and identified as Variovorax boronicumulans by 16S rRNA gene sequence analysis. Liquid chromatography-mass spectrometry and nuclear magnetic resonance analysis indicated the major pathway of thiacloprid (THI) metabolism by V. boronicumulans J1 involved hydrolysis of the N-cyanoimino group to form an N-carbamoylinino group containing metabolite, THI amide. Resting cells of V. boronicumulans J1 degraded 62.5% of the thiacloprid at a concentration of 200 mg/L in 60 h, and 98% of the reduced thiacloprid was converted to the final metabolite thiacloprid amide. A 2.6 kb gene cluster from V. boronicumulans J1 that includes the full length of the nitrile hydratase gene was cloned and investigated by degenerate primer polymerase chain reaction (PCR) and inverse PCR. The nitrile hydratase gene has a length of 1304 bp and codes a cobalt-type nitrile hydratase with an α-subunit of 213 amino acids and a β-subunit of 221 amino acids. The nitrile hydratase gene was recombined into plasmid pET28a and overexpressed in Escherichia coli BL21 (DE3). The resting cells of recombinant E. coli BL21 (DE3)-pET28a-NHase with overexpression of nitrile hydratase transformed thiacloprid to its amide metabolite, whereas resting cells of the control E. coli BL21 (DE3)-pET28a did not. Therefore, the major hydration pathway of thiacloprid is mediated by nitrile hydratase.
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Affiliation(s)
- Hui-Juan Zhang
- 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 210046, People's Republic of China
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29
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García-Álvarez R, Díez J, Crochet P, Cadierno V. Arene–Ruthenium(II) Complexes Containing Inexpensive Tris(dimethylamino)phosphine: Highly Efficient Catalysts for the Selective Hydration of Nitriles into Amides. Organometallics 2011. [DOI: 10.1021/om2006563] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rocío García-Álvarez
- Departamento de Química Orgánica e Inorgánica, Instituto Universitario de Química Organometálica “Enrique Moles” (Unidad Asociada al CSIC), Facultad de Química, Universidad de Oviedo, Julián Clavería 8, E-33006 Oviedo, Spain
| | - Josefina Díez
- Departamento de Química Orgánica e Inorgánica, Instituto Universitario de Química Organometálica “Enrique Moles” (Unidad Asociada al CSIC), Facultad de Química, Universidad de Oviedo, Julián Clavería 8, E-33006 Oviedo, Spain
| | - Pascale Crochet
- Departamento de Química Orgánica e Inorgánica, Instituto Universitario de Química Organometálica “Enrique Moles” (Unidad Asociada al CSIC), Facultad de Química, Universidad de Oviedo, Julián Clavería 8, E-33006 Oviedo, Spain
| | - Victorio Cadierno
- Departamento de Química Orgánica e Inorgánica, Instituto Universitario de Química Organometálica “Enrique Moles” (Unidad Asociada al CSIC), Facultad de Química, Universidad de Oviedo, Julián Clavería 8, E-33006 Oviedo, Spain
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30
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Ibuprofenamide: a convenient method of synthesis by catalytic hydration of 2-(4-isobutylphenyl)propionitrile in pure aqueous medium. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.06.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Hiseni A, Arends IWCE, Otten LG. Biochemical characterization of the carotenoid 1,2-hydratases (CrtC) from Rubrivivax gelatinosus and Thiocapsa roseopersicina. Appl Microbiol Biotechnol 2011; 91:1029-36. [PMID: 21590288 PMCID: PMC3145076 DOI: 10.1007/s00253-011-3324-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/03/2011] [Accepted: 04/09/2011] [Indexed: 11/28/2022]
Abstract
Two carotenoid 1,2-hydratase (CrtC) genes from the photosynthetic bacteria Rubrivivax gelatinosus and Thiocapsa roseopersicina were cloned and expressed in Escherichia coli in an active form and purified by affinity chromatography. The biochemical properties of the recombinant enzymes and their substrate specificities were studied. The purified CrtCs catalyze cofactor independently the conversion of lycopene to 1-HO- and 1,1′-(HO)2-lycopene. The optimal pH and temperature for hydratase activity was 8.0 and 30°C, respectively. The apparent Km and Vmax values obtained for the hydration of lycopene were 24 μM and 0.31 nmol h−1 mg−1 for RgCrtC and 9.5 μM and 0.15 nmol h−1 mg−1 for TrCrtC, respectively. Sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis revealed two protein bands of 44 and 38 kDa for TrCrtC, which indicate protein processing. Both hydratases are also able to convert the unnatural substrate geranylgeraniol (C20 substrate), which functionally resembles the natural substrate lycopene.
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Affiliation(s)
- Aida Hiseni
- Biocatalysis and Organic Chemistry, Department of Biotechnology, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands
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32
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Nitrile hydratases (NHases): At the interface of academia and industry. Biotechnol Adv 2010; 28:725-41. [DOI: 10.1016/j.biotechadv.2010.05.020] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 05/16/2010] [Accepted: 05/17/2010] [Indexed: 11/19/2022]
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33
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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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