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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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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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Sun S, Zhou J, Jiang J, Dai Y, Sheng M. Nitrile Hydratases: From Industrial Application to Acetamiprid and Thiacloprid Degradation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10440-10449. [PMID: 34469128 DOI: 10.1021/acs.jafc.1c03496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The widespread application of neonicotinoid insecticides (NEOs) in agriculture causes a series of environmental and ecological problems. Microbial remediation is a popular approach to relieve these negative impacts, but the associated molecular mechanisms are rarely explored. Nitrile hydratase (NHase), an enzyme commonly used in industry for amide production, was discovered to be responsible for the degradation of acetamiprid (ACE) and thiacloprid (THI) by microbes. Since then, research into NHases in NEO degradation has attracted increasing attention. In this review, microbial degradation of ACE and THI is briefly described. We then focus on NHase evolution, gene composition, maturation mechanisms, expression, and biochemical properties with regard to application of NHases in NEO degradation for bioremediation.
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Affiliation(s)
- Shilei Sun
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jiangsheng Zhou
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Yijun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Miaomiao Sheng
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 310053, People's Republic of China
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Shen JD, Cai X, Ni YW, Jin LQ, Liu ZQ, Zheng YG. Structural insights into the thermostability mechanism of a nitrile hydratase from Caldalkalibacillus thermarum by comparative molecular dynamics simulation. Proteins 2021; 89:978-987. [PMID: 33749895 DOI: 10.1002/prot.26076] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/19/2021] [Accepted: 03/13/2021] [Indexed: 11/07/2022]
Abstract
Nitrile hydratase (NHase), an excellent bio-catalyst for the synthesis of amide compounds, was composed of two heterologous subunits. A thermoalkaliphilic NHase NHCTA1 (Tm = 71.3°C) obtained by in silico screening in our study exhibited high flexibility of α-subunit but excellent thermostability, as opposed to previous examples. To gain a deeper structural insight into the thermostability of NHCTA1, comparative molecular dynamics simulation of NHCTA1 and reported NHases was carried out. By comparison, we speculated that β-subunit played a key role in adjusting the flexibility of α-subunit and the different conformations of linker in "α5-helix-coil ring" supersecondary structure of β-subunit can affect the interaction between β-subunit and α-subunit. Mutant NHCTA1-α6 C with a random coil linker and mutant NHCTA1-αβγ with a truncated linker were therefore constructed to understand the impact on NHCTA1 thermostability by varying the supersecondary structure. The varied thermostability of NHCTA1-α6 C and NHCTA1-αβγ (Tmα6C = 74.4°C, Tmαβγ = 65.6°C) verified that the flexibility of α-subunit adjusted by β-subunit was relevant to the stability of NHCTA1. This study gained an insight into the NNHCTA1 thermostability by virtual dynamics comparison and experimental studies without crystallization, and this approach could be applied to other industrial-important enzymes.
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Affiliation(s)
- Ji-Dong Shen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xue Cai
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Ye-Wen Ni
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Li-Qun Jin
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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Busch H, Hagedoorn PL, Hanefeld U. Rhodococcus as A Versatile Biocatalyst in Organic Synthesis. Int J Mol Sci 2019; 20:E4787. [PMID: 31561555 PMCID: PMC6801914 DOI: 10.3390/ijms20194787] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022] Open
Abstract
The application of purified enzymes as well as whole-cell biocatalysts in synthetic organic chemistry is becoming more and more popular, and both academia and industry are keen on finding and developing novel enzymes capable of performing otherwise impossible or challenging reactions. The diverse genus Rhodococcus offers a multitude of promising enzymes, which therefore makes it one of the key bacterial hosts in many areas of research. This review focused on the broad utilization potential of the genus Rhodococcus in organic chemistry, thereby particularly highlighting the specific enzyme classes exploited and the reactions they catalyze. Additionally, close attention was paid to the substrate scope that each enzyme class covers. Overall, a comprehensive overview of the applicability of the genus Rhodococcus is provided, which puts this versatile microorganism in the spotlight of further research.
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Affiliation(s)
- Hanna Busch
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Ulf Hanefeld
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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Yamamura ET, Tsuzaki K, Kita S. A novel method of producing the key intermediate ASI-2 of ranirestat using a porcine liver esterase (PLE) substitute enzyme. Biosci Biotechnol Biochem 2019; 83:1124-1135. [PMID: 30782084 DOI: 10.1080/09168451.2019.1580139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
(R)-2-amino-2-ethoxycarbonylsuccinimide (ASI-2) is a key intermediate used in the pharmaceutical industry and is valuable for the industrial synthesis of ranirestat, which is a potent aldose reductase inhibitor. ASI-2 was synthesized in a process combining chemical synthesis and bioconversion. Bioconversion in this study is a key reaction, since optically active carboxylic acid derivative ((R)-1-ethyl hydrogen 3-benzyloxycarbonylamino-3-ethoxycarbonylsuccinate, Z-MME-AE) is synthesized from a prochiral ester, diethyl 2-benzyloxycarbonylamino-2-ethoxycarbonylsuccinate, Z-MDE-AE, at a theoretical yield of 100%. Upon screening for microorganisms that asymmetrically hydrolyze Z-MDE-AE, Bacillus thuringiensis NBRC13866 was found. A novel esterase EstBT that produces Z-MME-AE was purified from Bacillus thuringiensis NBRC13866 and was stably produced in Escherichia coli JM109 cells. Using EstBT rather than porcine liver esterase (PLE), ASI-2 was synthesized with a 17% higher total yield by a novel method, suggesting that the esterase EstBT is a PLE substitute enzyme and therefore, may be of interest for future industrial applications.
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Affiliation(s)
- Ei-Tora Yamamura
- a Technical Department , Kyowa Pharma Chemical Co., Ltd ., Takaoka , Japan
| | - Kazuya Tsuzaki
- a Technical Department , Kyowa Pharma Chemical Co., Ltd ., Takaoka , Japan
| | - Shinji Kita
- a Technical Department , Kyowa Pharma Chemical Co., Ltd ., Takaoka , Japan
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Isolation of two plasmids, pRET1100 and pRET1200, from Rhodococcus erythropolis IAM1400 and construction of a Rhodococcus–Escherichia coli shuttle vector. J Biosci Bioeng 2018; 125:625-631. [DOI: 10.1016/j.jbiosc.2018.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/14/2017] [Accepted: 01/01/2018] [Indexed: 11/17/2022]
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8
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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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9
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Draft Genome Sequence of an Aldoxime Degrader, Rhodococcus sp. Strain YH3-3. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00406-16. [PMID: 27198031 PMCID: PMC4888990 DOI: 10.1128/genomea.00406-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rhodococcus sp. strain YH3-3 has been isolated as an (E)-pyridine-3-aldoxime degrader. Here, we report the draft genome sequence of this strain, with a size of 7,316,908 bp, average G+C content of 62.15%, and 7,281 predicted protein-coding sequences.
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10
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Microbial transformation of nitriles to high-value acids or amides. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014. [PMID: 19475377 DOI: 10.1007/10_2008_25] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Biotransformation of nitriles mediated by nitrile-amide converting enzymes has attracted considerable attention and developed tremendously in the recent years in China since it offers a valuable alternative to traditional chemical reaction which requires harsh conditions. As a result, an upsurge of these promising enzymes (including nitrile hydratase, nitrilase and amidase) has been taking place. This review aims at describing these enzymes in detail. A variety of microorganisms harboring nitrile-amide converting activities have been isolated and identified in China, some of which have already applied with moderate success. Currently, a wide range of high-value compounds such as aliphatic, alicyclic, aromatic and heterocyclic amides and their corresponding acids were provided by these nitrile-amide degrading organisms. Simultaneously, with the increasing demand of chiral substances, the enantioselectivity of the nitrilase superfamily is widely investigated and exploited in China, especially the bioconversion of optically active alpha-substituted phenylacetamides, acids and 2,2-dimethylcyclopropanecarboxamide and 2,2-dimethylcyclopropanecarboxylic acid by means of the catalysts exhibiting excellent stereoselectivity. Besides their synthetic value, the nitrile-amide converting enzymes also play an important role in environmental protection. In this context, cloning of the genes and expression of these enzymes are presented. In the near future in China, an increasing number of novel nitrile-amide converting organisms will be screened and their potential in the synthesis of useful acids and amides will be further exploited.
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11
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Woi PM, Bakar MAA, Rosli AN, Lee VS, Ahmad MR, Zain S, Alias Y. Does cation break the cyano bond? A critical evaluation of nitrile-cation interaction. J Mol Model 2014; 20:2219. [PMID: 24770548 DOI: 10.1007/s00894-014-2219-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 03/23/2014] [Indexed: 11/26/2022]
Abstract
DFT and G4 results reveal that cations display the following trends in imparting its positive charge to acrylonitrile; H⁺ > Li⁺ > Na⁺ > K⁺ for group I and Be²⁺ > Mg²⁺ > Ca²⁺ for group II. Solvation by water molecules and interaction with cation make the cyano bond more polarized and exhibits ketene-imine character. Bond order in nitrile-cation complexes has been predicted based on the s character of the covalent bond orbitals. Mulliken, CHELPG, and NPA charges are in good agreement in predicting positive charge buildup and GIAO nuclear deshileding on C1. G4 enthalpies show that Mg²⁺ is more strongly bound to acrylonitrile than to acetonitrile by 3 kcal mol⁻¹, and the proton affinity of the former is higher by 0.8 kcal mol⁻¹. G4 enthalpies of reductions support prior experimental observation that metalated conjugated nitriles show enhanced reactivity toward weak nucleophiles to afford Michael addition products.
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Affiliation(s)
- Pei Meng Woi
- Department of Chemistry, Faculty of Science Building, University of Malaya, 50603, Kuala Lumpur, Malaysia,
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12
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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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Pratush A, Seth A, Bhalla TC. Purification and characterization of nitrile hydratase of mutant 4D of Rhodococcus rhodochrous PA-34. 3 Biotech 2013; 3:165-171. [PMID: 28324571 PMCID: PMC3597139 DOI: 10.1007/s13205-012-0081-5] [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: 04/25/2012] [Accepted: 07/18/2012] [Indexed: 10/28/2022] Open
Abstract
Nitrile hydratase (NHase; E.C. 4.2.1.84) has been purified and characterized using ammonium sulfate precipitation, ion exchange chromatography and gel filtration chromatography from the mutant 4D of Rhodococcus rhodochrous PA-34. The SDS-PAGE and MALDI-TOF analysis of the purified enzyme revealed that it is dimmer consisting of α- and β-subunits with a molecular mass of 25 and 30 kDa, respectively. The Km and Vmax values were 102 mM and 350.8 μmol/min/mg using 3-cyanopyridine as substrate. The purified NHase was stable in higher concentration of potassium ions and in acidic pH 5.5 as compared to NHase of the wild R. rhodochrous PA-34. The analysis of the N-terminal amino acid sequence of this enzyme revealed that this enzyme has 90 % homology with the high molecular weight nitrile hydratase of R. rhodochrous J1.
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Wang S, Dai Y, Wang J, Shen Y, Zhai Y, Zheng H, Wang M. Molecular insights into substrate specificity of Rhodococcus ruber CGMCC3090 by gene cloning and homology modeling. Enzyme Microb Technol 2013; 52:111-7. [DOI: 10.1016/j.enzmictec.2012.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 11/10/2012] [Accepted: 11/12/2012] [Indexed: 11/29/2022]
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Kumar D, Masitas CA, Nguyen TN, Grapperhaus CA. Bioinspired catalytic nitrile hydration by dithiolato, sulfinato/thiolato, and sulfenato/sulfinato ruthenium complexes. Chem Commun (Camb) 2013. [DOI: 10.1039/c2cc35256g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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Yasukawa K, Hasemi R, Asano Y. Dynamic Kinetic Resolution of α-Aminonitriles to Form Chiral α-Amino Acids. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100360] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Yousefi M, Mohammadi M, Habibi Z, Cheraghi Z. Nitrile biotransformation by whole cells ofAspergillussp. PTCC 5266. BIOCATAL BIOTRANSFOR 2011. [DOI: 10.3109/10242422.2010.550002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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18
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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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19
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Martínková L, Uhnáková B, Pátek M, Nesvera J, Kren V. Biodegradation potential of the genus Rhodococcus. ENVIRONMENT INTERNATIONAL 2009; 35:162-77. [PMID: 18789530 DOI: 10.1016/j.envint.2008.07.018] [Citation(s) in RCA: 284] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 07/02/2008] [Accepted: 07/22/2008] [Indexed: 05/24/2023]
Abstract
A large number of aromatic compounds and organic nitriles, the two groups of compounds covered in this review, are intermediates, products, by-products or waste products of the chemical and pharmaceutical industries, agriculture and the processing of fossil fuels. The majority of these synthetic substances (xenobiotics) are toxic and their release and accumulation in the environment pose a serious threat to living organisms. Bioremediation using various bacterial strains of the genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites. The large genomes of rhodococci, their redundant and versatile catabolic pathways, their ability to uptake and metabolize hydrophobic compounds, to form biofilms, to persist in adverse conditions and the availability of recently developed tools for genetic engineering in rhodococci make them suitable industrial microorganisms for biotransformations and the biodegradation of many organic compounds. The peripheral and central catabolic pathways in rhodococci are characterized for each type of aromatics (hydrocarbons, phenols, halogenated, nitroaromatic, and heterocyclic compounds) in this review. Pathways involved in the hydrolysis of nitrile pollutants (aliphatic nitriles, benzonitrile analogues) and the corresponding enzymes (nitrilase, nitrile hydratase) are described in detail. Examples of regulatory mechanisms for the expression of the catabolic genes are given. The strains that efficiently degrade the compounds in question are highlighted and examples of their use in biodegradation processes are presented.
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Affiliation(s)
- Ludmila Martínková
- Centre of Biocatalysis and Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, CZ-142 20 Prague 4, Czech Republic.
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Feng YS, Chen PC, Wen FS, Hsiao WY, Lee CM. Nitrile hydratase from Mesorhizobium sp. F28 and its potential for nitrile biotransformation. Process Biochem 2008. [DOI: 10.1016/j.procbio.2008.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Choi YH, Uhm KN, Kim HK. Biochemical characterization of Rhodococcus erythropolis N′4 nitrile hydratase acting on 4-chloro-3-hydroxybutyronitrile. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.molcatb.2008.03.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Song L, Wang M, Yang X, Qian S. Purification and characterization of the enantioselective nitrile hydratase from Rhodococcus sp. AJ270. Biotechnol J 2007; 2:717-24. [PMID: 17330219 DOI: 10.1002/biot.200600215] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Nitrile hydratase (NHase, EC 4.2.1.84) from Rhodococcus sp. AJ270 was purified with 23.96% yield after sonication, ammonium sulfate fractionation, ion exchange, hydrophobic and gel-filtration column chromatography. The enzyme showed intriguing characteristics: it hydrated not only aliphatic and heterocyclic nitriles but also aromatic ones. Some substrates were also hydrated enantioselectively to the corresponding amides. The enantiomeric excess (ee) value of the enzyme hydrating trans-2,2-dimethyl-3-phenylcyclopropanecarbonitrile was 84.7. The enzyme is composed of two subunits: an alpha subunit and beta subunit of 22 975 Da and 23 493 Da, respectively. The optimal temperature and pH for the catalytic reaction of the enzyme was 25 degrees C and pH 7.6. The enzyme activity of the purified NHase was strongly inhibited by some oxidizing agents and heavy metals.
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Affiliation(s)
- Liya Song
- State Key Laboratories of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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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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24
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Sari MA, Jaouen M, Saroja NR, Artaud I. Influence of cobalt substitution on the activity of iron-type nitrile hydratase: are cobalt type nitrile hydratases regulated by carbon monoxide? J Inorg Biochem 2006; 101:614-22. [PMID: 17267045 DOI: 10.1016/j.jinorgbio.2006.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 12/07/2006] [Accepted: 12/08/2006] [Indexed: 11/15/2022]
Abstract
Comamonas testosteroni Ni1 nitrile hydratase is a Fe-type nitrile hydratase whose native and recombinant forms are identical. Here, the iron of Ni1 nitrile hydratase was replaced by cobalt using a chaperone based Escherichia coli expression system. Cobalt (CoNi1) and iron (FeNi1) enzymes share identical Vmax (30 nmol min(-1) mg(-1)) and Km (200 microM) toward their substrate and identical Ki values for the known competitive inhibitors of FeNi1. However, nitrophenols used as inhibitors do display a different inhibition pattern on both enzymes. Furthermore, CoNi1 and FeNi1 are also different in their sensitivity to nitric oxide and carbon monoxide, CO being selective of the cobalt enzyme. These differences are rationalized in relation to the nature of the catalytic metal center in the enzyme.
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Affiliation(s)
- Marie-Agnès Sari
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université René Descartes, UMR 8601 CNRS, 45 Rue des Saint-Pères, 75270 Paris Cedex 06, France.
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25
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Gelo-Pujic M, Marion C, Mauger C, Michalon M, Schlama T, Turconi J. Biohydrolysis of (S)-3-(thiophen-2-ylthio)butanenitrile. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.09.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Kato Y, Asano Y. Molecular and enzymatic analysis of the “aldoxime–nitrile pathway” in the glutaronitrile degrader Pseudomonas sp. K-9. Appl Microbiol Biotechnol 2006; 70:92-101. [PMID: 16003557 DOI: 10.1007/s00253-005-0044-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2005] [Revised: 04/29/2005] [Accepted: 05/30/2005] [Indexed: 12/01/2022]
Abstract
A gene cluster responsible for aldoxime metabolism in the glutaronitrile degrader Pseudomonas sp. K-9 was analyzed genetically and enzymatically. The cluster was composed of genes coding for aldoxime dehydratase (Oxd), nitrile hydratase (NHase), NHase activator, amidase, acyl-CoA ligase, and some regulatory and functionally unknown proteins, which were similar to proteins appearing in the "aldoxime-nitrile pathway" gene cluster from strains having Fe-containing NHase. A key enzyme in the cluster, OxdK, which has 32.7-90.3 % identity with known Oxds, was overexpressed in Escherichia coli cells under the control of a T7 promoter in its His(6)-tagged form, purified, and characterized. The enzyme showed similar characteristics with the known Oxds coexisting with an Fe-containing NHase in its subunit structure, substrate specificity, and effects on various compounds. The enzyme can be classified into a group of "aliphatic aldoxime dehydratase (EC 4.99.1.5)." The existence of a gene cluster of enzymes responsible for aldoxime metabolism via the aldoxime-nitrile pathway (aldoxime-->nitrile-->amide-->acid-->acyl-CoA) in Pseudomonas sp. K-9, and the fact that the proteins comprising the cluster are similar to those acting on aliphatic type substrates, evidently clarified the alkylaldoxime-degrading pathway in that strain.
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Affiliation(s)
- Yasuo Kato
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Kosugi, Toyama 939-0398, Japan
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27
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Kato Y, Yoshida S, Xie SX, Asano Y. Aldoxime dehydratase co-existing with nitrile hydratase and amidase in the iron-type nitrile hydratase-producer Rhodococcus sp. N-771. J Biosci Bioeng 2005; 97:250-9. [PMID: 16233624 DOI: 10.1016/s1389-1723(04)70200-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Accepted: 01/26/2004] [Indexed: 10/26/2022]
Abstract
We identified an aldoxime dehydratase (Oxd) gene in the 5'-flanking region of the nitrile hydratase-amidase gene cluster in the photoreactive iron-type nitrile hydratase-producer, Rhodococcus sp. N-771. The enzyme showed 96.3%, 77.6%, and 30.4% identities with the Oxds of Rhodococcus globerulus A-4, Pseudomonas chlororaphis B23, and Bacillus sp. OxB-1, respectively. The enzyme was expressed in Escherichia coli under the control of the lac- or T7 promoters in its intact and His6-tagged forms, purified, and characterized. The enzyme had heme b as a prosthetic group, catalyzed a stoichiometric dehydration of aldoxime into nitrile, and exhibited the highest activity at neutral pH and at around 30 degrees C similar to the known Oxd from Bacillus sp. OxB-1. The activity was enhanced by reducing agents, such as Na2S, Na2S2(O4), 2-mercaptoethanol, and L-cysteine and supplementary additions of electron acceptors such as flavins, sulfite ion, and vitamin K3. The effect of various chemicals on the enzyme activity was different in the presence and absence of the reducing reagent, Na2S. The enzyme preferentially acts on aliphatic-type substrates and the substrate specificity of the enzyme coincides with that reported for nitrile hydratase produced by the strain.
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Affiliation(s)
- Yasuo Kato
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Kosugi, Toyama 939-0398, Japan
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28
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Cameron RA, Sayed M, Cowan DA. Molecular analysis of the nitrile catabolism operon of the thermophile Bacillus pallidus RAPc8. Biochim Biophys Acta Gen Subj 2005; 1725:35-46. [PMID: 15955632 DOI: 10.1016/j.bbagen.2005.03.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Revised: 03/24/2005] [Accepted: 03/28/2005] [Indexed: 11/19/2022]
Abstract
The gene cluster containing the nitrile hydratase (NHase) and amidase genes of a moderate thermophile, B. pallidus RAPc8 has been cloned and sequenced. The (5.9 kb) section of cloned DNA contained eight complete open reading frames, encoding (in order), amidase (belonging to the nitrilase related aliphatic amidase family), nitrile hydratase beta and alpha subunits (of the cobalt containing class), a 122-amino acid accessory protein, designated P14K, a homologue of the 2Fe-2S class of ferredoxins and three putative proteins with distinct homology to the cobalt uptake proteins cbiM, cbiN and cbiQ of the S. typhimurium LT2 cobalamin biosynthesis pathway. The amidase and nitrile hydratase genes were subcloned and inducibly expressed in Escherichia coli, to levels of approximately 37 U/mg and 49 U/mg, respectively, without the co-expression of additional flanking genes. However, co-expression of P14K with the NHase structural genes significantly enhanced the specific activity of the recombinant NHase. This is the first description of an accessory protein involved in thermostable NHase expression. Modelling of the P14K protein structure has suggested that this protein functions as a subunit-specific chaperone, aiding in the folding of the NHase alpha subunit prior to alpha-beta subunit association and the formation of alpha(2)beta(2) NHase holoenzyme.
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Affiliation(s)
- Rory A Cameron
- Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
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29
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O'Mahony R, Doran J, Coffey L, Cahill OJ, Black GW, O'Reilly C. Characterisation of the nitrile hydratase gene clusters of Rhodococcus erythropolis strains AJ270 and AJ300 and Microbacterium sp. AJ115 indicates horizontal gene transfer and reveals an insertion of IS1166. Antonie van Leeuwenhoek 2005; 87:221-32. [PMID: 15803388 DOI: 10.1007/s10482-004-3721-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Accepted: 09/23/2004] [Indexed: 10/25/2022]
Abstract
The nitrile metabolising strains AJ270, AJ300 and AJ115 were isolated from the same location. The strains have very similar nitrile metabolising profiles. Sequencing of the 16S rRNA gene indicates that strains AJ270 and AJ300 are novel strains of Rhodococcus erythropolis while strain AJ115 is a novel Microbacterium strain very closely related to Microbacterium oxydans and Microbacterium liquefaciens. Analysis of the structure of the nitrile hydratase/amidase gene clusters in the three strains indicates that this region is identical in these strains and that this structure is different to other nitrile hydratase/amidase gene clusters. The major difference seen is the insertion of a complete copy of the insertion sequence IS1166 in the nhr2 gene. This copy of IS1166 generates a 10 bp direct duplication at the point of insertion and has one ORF encoding a protein of 434 amino acids, with 98% homology to the transposase of IS666 from Mycobacterium avium. A gene oxd, encoding aldoxime dehydratase is found upstream of the nitrile hydratase gene cluster and an open reading frame encoding a protein with homology to GlnQ type ABC transporters is found downstream of the nitrile hydratase/amidase genes. The identity of the nitrile hydratase/amidase gene clusters in the three strains suggests horizontal gene transfer of this region. Analysis of the strains for both linear and circular plasmids indicates that both are present in the strains but hybridisation studies indicate that the nitrile hydratase/amidase gene cluster is chromosomally located. The nitrile hydratase/amidase enzymes of strain AJ270 are inducible with acetonitrile or acetamide. Interestingly although a number of Fe-type nitrile hydratases have been shown to be photosensitive, the enzyme from strain AJ270 is not.
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Affiliation(s)
- Rebecca O'Mahony
- Department of Chemical and Life Sciences, Waterford Institute of Technology, Cork Road, Waterford, Ireland
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30
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Doran JP, Duggan P, Masterson M, Turner PD, O'Reilly C. Expression and purification of a recombinant enantioselective amidase. Protein Expr Purif 2005; 40:190-6. [PMID: 15721788 DOI: 10.1016/j.pep.2004.12.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Revised: 12/19/2004] [Indexed: 10/25/2022]
Abstract
Microbacterium sp. AJ115 metabolises a wide range of nitriles using the two-step nitrile hydratase/amidase pathway. In this study, the amidase gene of Microbacterium sp. AJ115 has been inserted into the pCal-n-EK expression vector and expressed in Escherichia coli BL21(DE3)pLysS. The expressed protein is active in E. coli and expression of the amidase gene allows E. coli to grow on acetamide as sole carbon and/or nitrogen source. Expression of active amidase in E. coli was temperature dependent with high activity found when cultures were grown between 20 and 30 degrees C but no activity at 37 degrees C. On induction, the amidase represents 28% of the total soluble protein in E. coli. The expressed amidase has been purified in a single step from the crude lysate using the calmodulin-binding peptide (CBP) affinity tag. The V(max) and K(m) of the purified enzyme with acetamide (50 mM) were 4.4 micromol/min/mg protein and 4.5mM, respectively. The temperature optimum was found to be 50 degrees C. Purified enzyme demonstrated enantioselectivity with the ability to preferentially act on the S enantiomer of racemic (R,S)-2-phenylpropionamide. S-2-phenylpropionic acid is produced with an enantiomeric excess of >82% at 50% conversion of the parent amide.
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Affiliation(s)
- John P Doran
- Department of Chemical and Life Sciences, Waterford Institute of Technology, Cork Road, Waterford, Ireland
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31
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Šnajdrová R, Kristová-Mylerová V, Crestia D, Nikolaou K, Kuzma M, Lemaire M, Gallienne E, Bolte J, Bezouška K, Křen V, Martı́nková L. Nitrile biotransformation by Aspergillus niger. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.molcatb.2003.12.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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Kovacs JA. Synthetic analogues of cysteinate-ligated non-heme iron and non-corrinoid cobalt enzymes. Chem Rev 2004; 104:825-48. [PMID: 14871143 PMCID: PMC4487544 DOI: 10.1021/cr020619e] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julie A Kovacs
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
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33
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Lu J, Zheng Y, Yamagishi H, Odaka M, Tsujimura M, Maeda M, Endo I. Motif CXCC in nitrile hydratase activator is critical for NHase biogenesis in vivo. FEBS Lett 2003; 553:391-6. [PMID: 14572657 DOI: 10.1016/s0014-5793(03)01070-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Nitrile hydratase (NHase) activator from Rhodococcus sp. N-771 is required for NHase functional expression. The motif 73CXCC76 in the NHase activator sequence was here revealed to be vital for its function by site-directed mutagenesis. All three substitutions of the cysteines by serines resulted in a much lower level of expression of active NHase. Furthermore, interaction between NHase activator and NHase was detected and the critical role of NHase activator was not exhibited in the cysteine oxidization process of NHase. These findings suggest NHase activator mainly participates in iron trafficking in NHase biogenesis as an iron type metallochaperone.
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Affiliation(s)
- Jun Lu
- The Institute of Physical and Chemical Research, Wako Shi, 351-0198 Saitama, Japan.
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34
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Cowan DA, Cameron RA, Tsekoa TL. Comparative biology of mesophilic and thermophilic nitrile hydratases. ADVANCES IN APPLIED MICROBIOLOGY 2003; 52:123-58. [PMID: 12964242 DOI: 10.1016/s0065-2164(03)01005-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Don A Cowan
- Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa
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35
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Oinuma KI, Hashimoto Y, Konishi K, Goda M, Noguchi T, Higashibata H, Kobayashi M. Novel aldoxime dehydratase involved in carbon-nitrogen triple bond synthesis of Pseudomonas chlororaphis B23. Sequencing, gene expression, purification, and characterization. J Biol Chem 2003; 278:29600-8. [PMID: 12773527 DOI: 10.1074/jbc.m211832200] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Analysis of the nitrile hydratase gene cluster involved in nitrile metabolism of Pseudomonas chlororaphis B23 revealed that it contains one open reading frame encoding aldoxime dehydratase upstream of the amidase gene. The amino acid sequence deduced from this open reading frame shows similarity (32% identity) with that of Bacillus phenylacetaldoxime dehydratase (Kato, Y., Nakamura, K., Sakiyama, H., Mayhew, S. G., and Asano, Y. (2000) Biochemistry 39, 800-809). The gene product expressed in Escherichia coli catalyzed the dehydration of aldoxime into nitrile. The Pseudomonas aldoxime dehydratase (OxdA) was purified from the E. coli transformant and characterized. OxdA shows an absorption spectrum with a Soret peak that is characteristic of heme, demonstrating that it is a hemoprotein. For its activity, this enzyme required a reducing reagent, Na2S2O4, but did not require FMN, which is crucial for the Bacillus enzyme. The enzymatic reaction was found to be catalyzed when the heme iron of the enzyme was in the ferrous state. Calcium as well as iron was included in the enzyme. OxdA reduced by Na2S2O4 had a molecular mass of 76.2 kDa and consisted of two identical subunits. The kinetic parameters of OxdA indicated that aliphatic aldoximes are more effective substrates than aromatic aldoximes. A variety of spectral shifts in the absorption spectra of OxdA were observed upon the addition of each of various compounds (i.e. redox reagents and heme ligands). Moreover, the addition of the substrate to OxdA gave a peak that would be derived from the intermediate in the nitrile synthetic reaction. P. chlororaphis B23 grew and showed the OxdA activity when cultured in a medium containing aldoxime as the sole carbon and nitrogen source. Together with these findings, Western blotting analysis of the extracts using anti-OxdA antiserum revealed that OxdA is responsible for the metabolism of aldoxime in vivo in this strain.
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Affiliation(s)
- Ken-Ichi Oinuma
- Institute of Applied Biochemistry, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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36
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Kato Y, Asano Y. High-level expression of a novel FMN-dependent heme-containing lyase, phenylacetaldoxime dehydratase of Bacillus sp. strain OxB-1, in heterologous hosts. Protein Expr Purif 2003; 28:131-9. [PMID: 12651117 DOI: 10.1016/s1046-5928(02)00638-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We examined the overexpression of a novel FMN-dependent heme-containing lyase, phenylacetaldoxime dehydratase (Oxd) of Bacillus sp. strain OxB-1, in Escherichia coli and Bacillus subtilis. Several plasmids were constructed to express the enzyme under the control of the lac promoter or its own promoter, together with or without nitrilase and a possible regulatory protein that is present in the wild-type genome. The enzyme was expressed using E. coli transfected with the plasmid pOxD-9OF. Expression was under the control of the lac promoter in the pUC18 vector and was much more effective when the start codon was changed from TTG to ATG. When the transfected cells were grown at 37 degrees C, the enzyme was produced mainly in inactive inclusion bodies, whereas the enzyme was largely soluble and active when the cells were grown at 30 degrees C. The production of active enzyme was markedly enhanced by increasing the volume of culture medium. This had the effect of slowing the rate of apoenzyme synthesis. A slow rate of synthesis allows for a more efficient incorporation of heme cofactor into the apoenzyme than a fast rate of synthesis. Under optimized conditions, the enzyme was produced in an active and soluble form at 15,000U/L of culture, which is about 1500-fold higher than the amount produced by the wild-type strain. Moreover, the enzyme comprised over 40% of total extractable cellular protein.
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Affiliation(s)
- Yasuo Kato
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, Kosugi, Toyama 939-0398, Japan
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37
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Brandão PFB, Clapp JP, Bull AT. Discrimination and taxonomy of geographically diverse strains of nitrile-metabolizing actinomycetes using chemometric and molecular sequencing techniques. Environ Microbiol 2002; 4:262-76. [PMID: 12030852 DOI: 10.1046/j.1462-2920.2002.00292.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mycolic acid-containing actinomycetes capable of metabolizing nitriles were recovered from deep-sea sediments and terrestrial soils by enrichment culture on acetonitrile, benzonitrile, succinonitrile or bromoxynil. A total of 43 nitrile-degrading strains were isolated and, together with previously recovered nitrile-degrading rhodococci, were identified by a polyphasic taxonomic approach, which included mycolic acid profiles, pyrolysis mass spectrometry (PyMS), genomic fingerprinting based on sequence variability of the 16S ribosomal RNA gene using polymerase chain reaction-restriction fragment length polymorphism-single-strand conformational polymorphism, and 16S rRNA gene sequence comparison. Isolates phylogenetically related to Rhodococcus erythropolis dominated the culturable microorganisms from most marine and terrestrial samples. These isolates clustered together in a major pyrogroup that showed high congruence with PRS profiles of the 16S rRNA gene. Such high congruence also was obtained for other recovered isolates that were assigned to species of Rhodococcus and Gordonia. Sequencing data validated the results obtained by PRS analysis and enabled phylogenetic relationships to be established. Some of the recovered bacteria probably represent novel microbial species. The fact that nitrile-metabolizing microorganisms were recovered from a wide range of habitat types suggests that nitrile transforming enzymatic activity is geographically widely distributed in nature.
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Affiliation(s)
- Pedro F B Brandão
- Research School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
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38
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Asano Y. Overview of screening for new microbial catalysts and their uses in organic synthesis--selection and optimization of biocatalysts. J Biotechnol 2002; 94:65-72. [PMID: 11792452 DOI: 10.1016/s0168-1656(01)00419-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a typical example of screening for a microbial biocatalyst from nature, isolation of aldoxime-degrading microorganisms, characterization of a new enzyme phenylacetaldoxime dehydratase, and application of this enzyme to nitrile synthesis are described. The pathway in which aldoximes are successively degraded via nitrile in microorganisms could be named as 'aldoxime-nitrile pathway'. As an example of a post-screening procedure, a directed molecular evolution technique was successfully used to change the properties of nucleoside pyrophosphate phosphotransferase to make it suitable for synthesis of inosine-5'-monophosphate (5'-IMP). With the mutant enzyme, the efficiency of the production of 5'-IMP, a food additive, was much improved.
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Affiliation(s)
- Yasuhisa Asano
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Kosugi, Toyama 939-0398, Japan.
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39
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Abstract
The distribution of phenylacetaldoxime-degrading and pyridine-3-aldoxime-degrading ability was examined with intact cells of 975 microorganisms, including 45 genera of bacteria, 11 genera of actinomyces, 22 genera of yeasts, and 37 genera of fungi, by monitoring the decrease of the aldoximes by high-pressure liquid chromatography. The abilities were found to be widely distributed in bacteria, actinomyces, fungi, and some yeasts: 98 and 107 strains degraded phenylacetaldoxime and pyridine-3-aldoxime, respectively. All of the active strains exhibited not only the aldoxime-dehydration activity to form nitrile but also nitrile-hydrolyzing activity. On the other hand, all of 19 nitrile-degrading microorganisms (13 species, 7 genera) were found to exhibit aldoxime dehydration activity. It is shown that aldoxime dehydratase and nitrile-hydrolyzing activities are widely distributed among 188 aldoxime and 19 nitrile degraders and that the enzymes were induced by aldoximes or nitriles.
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Affiliation(s)
- Y Kato
- Biotechnology Research Center, Faculty of Engineering, Toyama Prefectural University, Kosugi, Toyama 939-0398, Japan
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40
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Abstract
A number of nitrile-related enzymes have been screened over the past year for use in synthetic applications. There have also been significant advances in our understanding of the structures and modes of regulation of metal-containing nitrile hydratases. Enzyme structural characterization has provided new insights into how the molecular structure determines the enzyme function and how an enzyme can be endowed with new properties. This information has important implications for potential future applications other than the present industrial production of acrylamide and nicotinamide.
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Affiliation(s)
- M Kobayashi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Institute of Applied Biochemistry, The University of Tsukuba, Kyoto, Tsukuba, 305-8572, Japan
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41
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Kato Y, Nakamura K, Sakiyama H, Mayhew SG, Asano Y. Novel heme-containing lyase, phenylacetaldoxime dehydratase from Bacillus sp. strain OxB-1: purification, characterization, and molecular cloning of the gene. Biochemistry 2000; 39:800-9. [PMID: 10651646 DOI: 10.1021/bi991598u] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel dehydratase that catalyzes the stoichiometric dehydration of Z-phenylacetaldoxime to phenylacetonitrile has been purified 483-fold to homogeneity from a cell-free extract of Bacillus sp. strain OxB-1 isolated from soil. It has a M(r) of about 40 000 and is composed of a single polypeptide chain with a loosely bound protoheme IX. The enzyme is inactive unless FMN is added to the assay, but low activity is also observed when sulfite replaces FMN. The activity in the presence of FMN is enhanced 5-fold under anaerobic conditions compared to the activity measured in air. The enzyme has maximum activity at pH 7.0 and 30 degrees C, and it is stable at up to 45 degrees C at around neutral pH. The aerobically measured activity in the presence of FMN is also enhanced by Fe(2+), Sn(2+), SO(3)(2)(-), and NaN(3). Metal-chelating reagents, carbonyl reagents, electron donors, and ferri- and ferrocyanides strongly inhibit the enzyme with K(i) values in the micromolar range. The enzyme is active with arylalkylaldoximes and to a lesser extent with alkylaldoximes. The enzyme prefers the Z-form of phenylacetaldoxime over its E-isomer. On the basis of its substrate specificity, the enzyme has been tentatively named phenylacetaldoxime dehydratase. The gene coding for the enzyme was cloned into plasmid pUC18, and a 1053 base-pair open reading frame that codes for 351 amino acid residues was identified as the oxd gene. A nitrilase, which participates in aldoxime metabolism in the organism, was found to be coded by the region just upstream from the oxd gene. In addition an open reading frame (orf2), whose gene product is similar to bacterial regulatory (DNA-binding) proteins, was found just upstream from the coding region of the nitrilase. These findings provide genetic evidence for a novel gene cluster that is responsible for aldoxime metabolism in this microorganism.
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Affiliation(s)
- Y Kato
- Biotechnology Research Center, Toyama Prefectural University, Kosugi, Toyama 939-0398, Japan
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