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Salwan R, Sharma V, Das S. Phylogenetic and Structural Analysis of Bacterial Nitrilases for the Biodegradation of Nitrile Compounds. Curr Protein Pept Sci 2022; 23:874-882. [PMID: 36154580 DOI: 10.2174/1389203723666220921154409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/05/2022] [Accepted: 04/12/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND Microbial nitrilases play a vital role in the biodegradation of nitrilecontaining pollutants, effluent treatments in chemical and textile industries, and the biosynthesis of Indole-3-acetic acid (IAA) from tryptophan in plants. However, the lack of structural information limits the correlation between its activity and substrate specificity. METHODS The present study involves the genome mining of bacteria for the distribution and diversity of nitrilases, their phylogenetic analysis and structural characterization for motifs/ domains, followed by interaction with substrates. RESULTS Here, we mined the bacterial genomes for nitrilases and correlated their functions to hypothetical, uncharacterized, or putative ones. The comparative genomics revealed four AcNit, As7Nit, Cn5Nit and Cn9Nit predicted nitrilases encoding genes as uncharacterized subgroups of the nitrilase superfamily. The annotation of these nitrilases encoding genes revealed relatedness with nitrilase hydratases and cyanoalanine hydratases. At the proteomics level, the motif analysis of these protein sequences predicted a single motif of 20-28 aa, with glutamate (E), lysine (K) and cysteine (C) residues as a part of catalytic triad along with several other residues at the active site. The structural analysis of the nitrilases revealed geometrical and close conformation in the form of α-helices and β-sheets arranged in a sandwich structure. The catalytic residues constituted the substrate binding pocket and exhibited the broad nitrile substrate spectra for aromatic and aliphatic nitriles-containing compounds. The aromatic amino acid residues Y159 in the active site were predicted to be responsible for substrate specificity. The substitution of non-aromatic alanine residue in place of Y159 completely disrupted the catalytic activity for indole-3-acetonitrile (IAN). CONCLUSION The present study reports genome mining and simulation of structure-function relationship for uncharacterized bacterial nitrilases and their role in the biodegradation of pollutants and xenobiotics, which could be of applications in different industrial sectors.
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Affiliation(s)
- Richa Salwan
- College of Horticulture and Forestry (Dr. YS Parmar University of Horticulture and Forestry), Neri, Hamirpur (HP)- 177 001, India
| | - Vivek Sharma
- University Centre for Research and Development, Chandigarh University (PB)-140413, India
| | - Surajit Das
- Department of Life Science, Laboratory of Environmental Microbiology and Ecology (LEnME), National Institute of Technology Rourkela, Rourkela- 769 008, Odisha, India
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2
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Rational regulation of reaction specificity of nitrilase for efficient biosynthesis of 2-chloronicotinic acid through a single site mutation. Appl Environ Microbiol 2022; 88:e0239721. [PMID: 35020449 DOI: 10.1128/aem.02397-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrilase-catalyzed hydrolysis of 2-chloronicotinonitrile (2-CN) is a promising approach for efficient synthesis of 2-chloronicotinic acid (2-CA). Development of nitrilase with ideal catalytic properties is crucial for the biosynthetic route with industrial potentail. Herein, a nitrilase from Rhodococcus zopfii (RzNIT), which showed much higher hydration activity than hydrolysis activity, was designed for efficient hydrolysis of 2-CN. Two residues (N165 and W167) significantly affecting the reaction specificity were precisely identified. By tuning these two residues, a single mutation of W167G with abolished hydration activity and 20-fold improved hydrolysis activity was obtained. Molecular dynamics simulation and molecular docking revealed that the mutation generated a larger binding pocket, causing the substrate 2-CN bound more deeply in the pocket and the formation of delocalized π bond between the residues W190 and Y196, which reduced the negative influence of steric hindrance and electron effect caused by chlorine substituent. With mutant W167G as biocatalyst, 100 mM 2-CN was exclusively converted into 2-CA within 16 h. The study provides useful guidance in nitrilase engineering for simultaneous improvement of reaction specificity and catalytic activity, which are highly desirable in value-added carboxylic acids production from nitriles hydrolysis. Importance 2-CA is an important building block for agrochemicals and pharmaceuticals with rapid increase in demand in recent years. It is currently manufactured from 3-cyanopyridine by chemical methods. However, during the final step of 2-CN hydrolysis under high temperature and strong alkaline conditions, by-product 2-CM was generated except for the target product, leading to low yield and tedious separation steps. Nitrilase-mediated hydrolysis is regarded as a promising alternative for 2-CA production, which proceeds under mild conditions. Nevertheless, nitrilase capable of efficient hydrolysis of 2-CN was not reported till now, since the enzymes showed either extremely low activity or surprisingly high hydration activity towards 2-CN. Herein, the reaction specificity of RzNIT was precisely tuned through a single site mutation. The mutant exhibited remarkably enhanced hydrolysis activity without formation of by-products, providing a robust biocatalyst for 2-CA biosynthesis with industrial potential.
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Immobilization of Escherichia coli cells harboring a nitrilase with improved catalytic properties though polyethylenemine-induced silicification on zeolite. Int J Biol Macromol 2021; 193:1362-1370. [PMID: 34740683 DOI: 10.1016/j.ijbiomac.2021.10.196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/18/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022]
Abstract
In the chemical-biological synthesis route of gabapentin, immobilized Escherichia coli cells harboring nitrilase are used to catalyze the biotransformation of intermediate 1-cyanocyclohexaneacetonitile to 1-cyanocyclohexaneacetic acid. Herein, we present a novel cell immobilization method, which is based on cell adsorption using 75 g/L Escherichia coli cells and 6 g/L zeolite, cell crosslinking using 3 g/L polyethylenemine and biomimetic silicification using 18 g/L hydrolyzed tetramethylorthosilicate. The constructed "hybrid biomimetic silica particles (HBSPs)" with core-shell structure showed a specific activity of 147.2 ± 2.3 U/g, 82.6 ± 2.8% recovery of nitrilase activity and a half-life of 19.1 ± 1.9 h at 55 °C. 1-Cyanocyclohexaneacetonitrile (1.0 M) could be completely hydrolyzed by 50 g/L of HBSPs at pH 7.5, 35 °C in 4 h, providing 92.1 ± 3.2% yield of 1-cyanocyclohexaneacetic acid. In batch reactions, the HBSPs could be reused for 13 cycles and maintained 79.9 ± 4.1% residual activity after the 10th batch, providing an average product yield of 92.6% in the first 10 batches with a productivity of 619.3 g/L/day. In addition, multi-layer structures consisting of silica coating and polyethylenemine/glutaraldehyde crosslinking were constructed to enhance the mechanical strength of immobilized cells, and the effects of coating layers on the catalytic properties of immobilized cells was discussed.
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Zhang Q, Lu X, Zhang Y, Tang X, Zheng R, Zheng Y. Development of a robust nitrilase by fragment swapping and semi‐rational design for efficient biosynthesis of pregabalin precursor. Biotechnol Bioeng 2019; 117:318-329. [DOI: 10.1002/bit.27203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/06/2019] [Accepted: 10/13/2019] [Indexed: 01/20/2023]
Affiliation(s)
- Qin Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Xia‐Feng Lu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Yan Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Xiao‐Ling Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Ren‐Chao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Yu‐Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
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Krishnan A, Zhang YQ, Mou X. Isolation and Characterization of Microcystin-Degrading Bacteria from Lake Erie. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2018; 101:617-623. [PMID: 30368574 DOI: 10.1007/s00128-018-2468-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/17/2018] [Indexed: 06/08/2023]
Abstract
Heterotrophic bacteria are suggested as the major agents that degrade microcystins (MCs), a major cyanotoxins, in natural environments. However, little is known of the taxonomic and functional diversity of MC-degrading bacteria in Lake Erie of the Laurentian Great Lakes, the largest freshwater system on earth. This study obtained six bacterial pure isolates from Lake Erie with an ability to use MCs as the sole carbon and energy sources. MC degradation rates of the isolates were impacted by temperature and pH. The key gene for MC degradation (mlrA) were failed to be PCR amplified from for all 6 MC degraders, indicating they may possess a novel MC degradation pathway. In addition for potentials used in MC bioremediation, two isolates maybe can offer extra benefits as biofertilizers.
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Affiliation(s)
- Anjali Krishnan
- Biological Science Department, Kent State University, Kent, OH, 44242, USA
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Tiantan Xi Li, Beijing, 100050, China
| | - Xiaozhen Mou
- Biological Science Department, Kent State University, Kent, OH, 44242, USA.
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D'Angeli IM, Serrazanetti DI, Montanari C, Vannini L, Gardini F, De Waele J. Geochemistry and microbial diversity of cave waters in the gypsum karst aquifers of Emilia Romagna region, Italy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 598:538-552. [PMID: 28448941 DOI: 10.1016/j.scitotenv.2017.03.270] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/12/2017] [Accepted: 03/29/2017] [Indexed: 06/07/2023]
Abstract
Fifty-seven control points of waters (sinking streams, rivers in caves, and resurgences) hosted in gypsum karst areas in Emilia Romagna region (N-Italy) were sampled in the framework of a Project LIFE+08NAT/IT/000369 "Gypsum" in the period 2010-2014. The microbiology and chemistry of these waters have been analyzed to evaluate the impact of human activities or natural factors, in the gypsum karst systems. Waters have been analyzed for major chemistry (Ca, Mg, Na, K, SO4, HCO3, Cl, NO3) and some minor constituents (F, Br, NH4 and PO4), measuring pH, electric conductivity (EC), total dissolved solids (TDS) and temperature (T) in situ. The same samples have been analyzed with traditional microbiology techniques focused on total microbial count and on fecal microbiota, as index of human and/or animal contamination, and molecular biology techniques (sequencing of 16S rRNA segment and PCR-DGGE), focused on the characterization of microbial populations in the different sampling sites and determination of their variations and/or changes during the five years of the project. As expected, waters tend to be increasingly mineralized from sinking streams to resurgences, with only local and temporarily high contents in nitrates and ammonium, often related to the presence of bat colonies. PCR-DGGE revealed ecological changes, in terms of microbial populations present in the bulk water samples, in different sampling sites within the same cave. Although the impact of fecal microorganisms only rarely exceeded 2 log UFC/ml, the results evidenced fluctuations of these microorganisms mainly correlated to the season and to the biological activity of bats.
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Affiliation(s)
- Ilenia M D'Angeli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Zamboni 67, 40126 Bologna, Italy
| | - Diana I Serrazanetti
- Centro Interdipartimentale di Ricerca Industriale Agroalimentare, Università degli Studi di Bologna, Sede di Cesena, Piazza Goidanich 60, 47521 Cesena (FC), Italy
| | - Chiara Montanari
- Centro Interdipartimentale di Ricerca Industriale Agroalimentare, Università degli Studi di Bologna, Sede di Cesena, Piazza Goidanich 60, 47521 Cesena (FC), Italy
| | - Lucia Vannini
- Centro Interdipartimentale di Ricerca Industriale Agroalimentare, Università degli Studi di Bologna, Sede di Cesena, Piazza Goidanich 60, 47521 Cesena (FC), Italy; Dipartimento di Scienze e Tecnologie Agro-alimentari, Università degli Studi di Bologna, Sede di Cesena, Piazza Goidanich 60, 47521 Cesena (FC), Italy
| | - Fausto Gardini
- Centro Interdipartimentale di Ricerca Industriale Agroalimentare, Università degli Studi di Bologna, Sede di Cesena, Piazza Goidanich 60, 47521 Cesena (FC), Italy; Dipartimento di Scienze e Tecnologie Agro-alimentari, Università degli Studi di Bologna, Sede di Cesena, Piazza Goidanich 60, 47521 Cesena (FC), Italy
| | - Jo De Waele
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Zamboni 67, 40126 Bologna, Italy.
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Production of (R)-(−)-mandelic acid with nitrilase immobilized on D155 resin modified by l -lysine. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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8
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Semirational Engineering Accelerates the Laboratory Evolution of Nitrilase Catalytic Efficiency for Nicotinic Acid Biosynthesis. ChemCatChem 2017. [DOI: 10.1002/cctc.201700665] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Li H, Dong W, Zhang Y, Liu K, Zhang W, Zhang M, Ma J, Jiang M. Enhanced catalytic efficiency of nitrilase from Acidovorax facilis 72W and application in bioconversion of 3-cyanopyridine to nicotinic acid. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2017.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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High-throughput screening methods for nitrilases. Appl Microbiol Biotechnol 2016; 100:3421-32. [DOI: 10.1007/s00253-016-7381-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 10/22/2022]
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11
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Xue YP, Shi CC, Xu Z, Jiao B, Liu ZQ, Huang JF, Zheng YG, Shen YC. Design of Nitrilases with Superior Activity and Enantioselectivity towards Sterically Hindered Nitrile by Protein Engineering. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500039] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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12
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Zhang XH, Liu ZQ, Xue YP, Zheng YG. Activity improvement of a regioselective nitrilase from Acidovorax facilis and its application in the production of 1-(cyanocyclohexyl) acetic acid. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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13
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Jin LQ, Li ZT, Liu ZQ, Zheng YG, Shen YC. Efficient production of methionine from 2-amino-4-methylthiobutanenitrile by recombinant Escherichia coli harboring nitrilase. ACTA ACUST UNITED AC 2014; 41:1479-86. [DOI: 10.1007/s10295-014-1490-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 07/09/2014] [Indexed: 11/30/2022]
Abstract
Abstract
Methionine as an essential amino acid has been attracting more attention for its important applications in food and feed additives. In this study, for efficient production of methionine from 2-amino-4-methylthiobutanenitrile, a codon-optimized nitrilase gene was newly synthesized and expressed, and the catalytic conditions for methionine production were studied. The optimal temperature and pH for methionine synthesis were 40 °C and 7.5, respectively. The recombinant nitrilase was thermo-stable with half-life of 5.52 h at 40 °C. The substrate loading was optimized in given amount of catalyst and fixed substrate/catalyst ratio mode to achieve higher productivity. Methionine was produced in 100 % conversion within 120 min with a substrate loading of 300 mM. The production of methionine with the immobilized resting cells in packed-bed reactor was investigated. The immobilized nitrilase exhibited good operation stability and retained over 80 % of the initial activity after operating for 100 h. After separation, the purity and the total yield of methionine reached 99.1 and 97 %, respectively. This recombinant nitrilase could be a potential candidate for application in production of methionine.
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Affiliation(s)
- Li-Qun Jin
- Institute of Bioengineering, Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.413273.0 0000000105748737 Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| | - Zong-Tong Li
- Institute of Bioengineering, Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.413273.0 0000000105748737 Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| | - Zhi-Qiang Liu
- Institute of Bioengineering, Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.413273.0 0000000105748737 Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| | - Yu-Guo Zheng
- Institute of Bioengineering, Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.413273.0 0000000105748737 Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
| | - Yin-Chu Shen
- Institute of Bioengineering, Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
- grid.413273.0 0000000105748737 Engineering Research Center of Bioconversion and Biopurification of Ministry of Education Zhejiang University of Technology 310014 Hangzhou People’s Republic of China
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Li MY, Wang XD. The influence of hydroxypropyl-β-cyclodextrin on the enantioselective hydrolysis of 2-amino phenylpropionitrile catalyzed by recombinant nitrilase. BIORESOUR BIOPROCESS 2014. [DOI: 10.1186/s40643-014-0004-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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15
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Liu ZQ, Zhang XH, Xue YP, Xu M, Zheng YG. Improvement of Alcaligenes faecalis nitrilase by gene site saturation mutagenesis and its application in stereospecific biosynthesis of (R)-(-)-mandelic acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:4685-4694. [PMID: 24766313 DOI: 10.1021/jf405683f] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nitrilases have recently received considerable attention as the biocatalysts for stereospecific production of carboxylic acids. To improve the activity, the nitrilase from Alcaligenes faecalis was selected for further modification by the gene site saturation mutagenesis method (GSSM), based on homology modeling and previous reports about mutations. After mutagenesis, the positive mutants were selected using a convenient two-step high-throughput screening method based on product formation and pH indicator combined with the HPLC method. After three rounds of GSSM, Mut3 (Gln196Ser/Ala284Ile) with the highest activity and ability of tolerance to the substrate was selected. As compared to the wild-type A. faecalis nitrilase, Mut3 showed 154% higher specific activity. Mut3 could retain 91.6% of its residual activity after incubation at pH 6.5 for 6 h. In a fed-batch reaction with 800 mM mandelonitrile as the substrate, the cumulative production of (R)-(-)-mandelic acid after 7.5 h of conversion reached 693 mM with an enantiomeric excess of 99%, and the space-time productivity of Mut3 was 21.50-fold higher than that of wild-type nitrilase. The Km, Vmax, and k(cat) of wild-type and Mut3 for mandelonitrile were 20.64 mM, 33.74 μmol mg(-1) min(-1), 24.45 s(-1), and 9.24 mM, 47.68 μmol mg(-1) min(-1), and 34.55 s(-1), respectively. A homology modeling and molecular docking study showed that the diameter of the catalytic tunnel of Mut3 became longer and that the tunnel volume was smaller. These structural changes are proposed to improve the hydrolytic activity and pH stability of Mut3. Mut3 has the potential for industrial applications in the upscale production of (R)-(-)-mandelic acid.
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Affiliation(s)
- Zhi-Qiang Liu
- Institute of Bioengineering, Zhejiang University of Technology , Hangzhou, Zhejiang 310014, People's Republic of China
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16
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Ni K, Wang H, Zhao L, Zhang M, Zhang S, Ren Y, Wei D. Efficient production of (R)-(−)-mandelic acid in biphasic system by immobilized recombinant E. coli. J Biotechnol 2013; 167:433-40. [DOI: 10.1016/j.jbiotec.2013.07.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/17/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
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17
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Screening and Improving the Recombinant Nitrilases and Application in Biotransformation of Iminodiacetonitrile to Iminodiacetic Acid. PLoS One 2013; 8:e67197. [PMID: 23826231 PMCID: PMC3695085 DOI: 10.1371/journal.pone.0067197] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/15/2013] [Indexed: 11/26/2022] Open
Abstract
In this study, several nitrilase genes from phylogenetically distinct organisms were expressed and purified in E. coli in order to study their ability to mediate the biotransformation of nitriles. We identified three nitrilases: Acidovorax facilis nitrilase (AcN); Alcaligenes fecalis nitrilase (AkN); and Rhodococcus rhodochrous nitrilase (RkN), which catalyzed iminodiacetonitrile (IDAN) to iminodiacetic acid (IDA). AcN demonstrated 8.8-fold higher activity for IDAN degradation as compared to AkN and RkN. Based on homology modeling and previously described ‘hot spot’ mutations, several AcN mutants were screened for improved activity. One mutant M3 (F168V/L201N/S192F) was identified, which demonstrates a 41% enhancement in the conversion as well as a 2.4-fold higher catalytic efficiency towards IDAN as compared to wild-type AcN.
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Pawar SV, Meena VS, Kaushik S, Kamble A, Kumar S, Chisti Y, Banerjee UC. Stereo-selective conversion of mandelonitrile to (R)-(−)-mandelic acid using immobilized cells of recombinant Escherichia coli. 3 Biotech 2012. [PMCID: PMC3482447 DOI: 10.1007/s13205-012-0058-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Immobilized cells of a recombinant Escherichia coli expressing nitrilase from Pseudomonas putida were used to catalyze the hydrolysis of mandelonitrile (2-hydroxy-2-phenylacetonitrile) to (R)-(−)-mandelic acid. The cells had been immobilized by entrapment in an alginate matrix. Conditions for the hydrolysis reaction were optimized in shake flasks and in a packed bed reactor. In shake flasks the best conditions for the reaction were a temperature of 40 °C, pH 8, biocatalyst bead diameter of 4.3 mm, sodium alginate concentration in the gel matrix of 2 % (w/v, g/100 mL), a cell dry mass concentration in the bead matrix of 20 mg/mL, an initial substrate concentration of 50 mM and a reaction time of 60 min. Under these conditions, the conversion of mandelonitrile was nearly 95 %. In the packed bed reactor, a feed flow rate of 20 mL/h at a substrate concentration of 200 mM proved to be the best at 40 °C, pH 8, using 4.3 mm beads (2 % w/v sodium alginate in the gel matrix, 20 mg dry cell concentration per mL of gel matrix). This feed flow rate corresponded to a residence time of 0.975 h in the packed bed.
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Affiliation(s)
- Sandip V. Pawar
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Sector-67, SAS Nagar, 160 062 Punjab, India
| | - Vachan Singh Meena
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Sector-67, SAS Nagar, 160 062 Punjab, India
| | - Shubhangi Kaushik
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Sector-67, SAS Nagar, 160 062 Punjab, India
| | - Ashwini Kamble
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Sector-67, SAS Nagar, 160 062 Punjab, India
| | - Sandeep Kumar
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Sector-67, SAS Nagar, 160 062 Punjab, India
| | - Yusuf Chisti
- School of Engineering, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - U. C. Banerjee
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Sector-67, SAS Nagar, 160 062 Punjab, India
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Petříčková A, Veselá AB, Kaplan O, Kubáč D, Uhnáková B, Malandra A, Felsberg J, Rinágelová A, Weyrauch P, Křen V, Bezouška K, Martínková L. Purification and characterization of heterologously expressed nitrilases from filamentous fungi. Appl Microbiol Biotechnol 2011; 93:1553-61. [PMID: 21892598 DOI: 10.1007/s00253-011-3525-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Revised: 07/21/2011] [Accepted: 08/03/2011] [Indexed: 11/28/2022]
Abstract
Nitrilases from Aspergillus niger CBS 513.88, A. niger K10, Gibberella moniliformis, Neurospora crassa OR74A, and Penicillium marneffei ATCC 18224 were expressed in Escherichia coli BL21-Gold (DE3) after IPTG induction. N. crassa nitrilase exhibited the highest yield of 69,000 U L(-1) culture. Co-expression of chaperones (GroEL/ES in G. moniliformis and P. marneffei; GroEL/ES and trigger factor in N. crassa and A. niger CBS 513.88) enhanced the enzyme solubility. Specific activities of strains expressing the former two enzymes increased approximately fourfold upon co-expression of GroEL/ES. The enzyme from G. moniliformis (co-purified with GroEL) preferred benzonitrile as substrate (K(m) of 0.41 mM, V(max) of 9.7 μmol min(-1) mg(-1) protein). The P. marneffei enzyme (unstable in its purified state) exhibited the highest V(max) of 7.3 μmol min(-1) mg(-1) protein in cell-free extract, but also a high K(m) of 15.4 mM, for 4-cyanopyridine. The purified nitrilases from A. niger CBS 513.88 and N. crassa acted preferentially on phenylacetonitrile (K(m) of 3.4 and 2.0 mM, respectively; V(max) of 10.6 and 17.5 μmol min(-1) mg(-1) protein, respectively), and hydrolyzed also (R,S)-mandelonitrile with higher K(m) values. Significant amounts of amides were only formed by the G. moniliformis nitrilase from phenylacetonitrile and 4-cyanopyridine.
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Affiliation(s)
- Alena Petříčková
- Institute of Microbiology, Centre of Biocatalysis and Biotransformation, Prague, Czech Republic
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Strohmeier GA, Pichler H, May O, Gruber-Khadjawi M. Application of Designed Enzymes in Organic Synthesis. Chem Rev 2011; 111:4141-64. [DOI: 10.1021/cr100386u] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Gernot A. Strohmeier
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Oliver May
- DSM—Innovative Synthesis BV, Geleen, P.O. Box 18, 6160 MD Geleen, The Netherlands
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Kaplan O, Bezouška K, Plíhal O, Ettrich R, Kulik N, Vaněk O, Kavan D, Benada O, Malandra A, Sveda O, Veselá AB, Rinágelová A, Slámová K, Cantarella M, Felsberg J, Dušková J, Dohnálek J, Kotik M, Křen V, Martínková L. Heterologous expression, purification and characterization of nitrilase from Aspergillus niger K10. BMC Biotechnol 2011; 11:2. [PMID: 21210990 PMCID: PMC3023689 DOI: 10.1186/1472-6750-11-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 01/06/2011] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Nitrilases attract increasing attention due to their utility in the mild hydrolysis of nitriles. According to activity and gene screening, filamentous fungi are a rich source of nitrilases distinct in evolution from their widely examined bacterial counterparts. However, fungal nitrilases have been less explored than the bacterial ones. Nitrilases are typically heterogeneous in their quaternary structures, forming short spirals and extended filaments, these features making their structural studies difficult. RESULTS A nitrilase gene was amplified by PCR from the cDNA library of Aspergillus niger K10. The PCR product was ligated into expression vectors pET-30(+) and pRSET B to construct plasmids pOK101 and pOK102, respectively. The recombinant nitrilase (Nit-ANigRec) expressed in Escherichia coli BL21-Gold(DE3)(pOK101/pTf16) was purified with an about 2-fold increase in specific activity and 35% yield. The apparent subunit size was 42.7 kDa, which is approx. 4 kDa higher than that of the enzyme isolated from the native organism (Nit-ANigWT), indicating post-translational cleavage in the enzyme's native environment. Mass spectrometry analysis showed that a C-terminal peptide (Val327 - Asn₃₅₆) was present in Nit-ANigRec but missing in Nit-ANigWT and Asp₂₉₈-Val₃₁₃ peptide was shortened to Asp₂₉₈-Arg₃₁₀ in Nit-ANigWT. The latter enzyme was thus truncated by 46 amino acids. Enzymes Nit-ANigRec and Nit-ANigWT differed in substrate specificity, acid/amide ratio, reaction optima and stability. Refolded recombinant enzyme stored for one month at 4°C was fractionated by gel filtration, and fractions were examined by electron microscopy. The late fractions were further analyzed by analytical centrifugation and dynamic light scattering, and shown to consist of a rather homogeneous protein species composed of 12-16 subunits. This hypothesis was consistent with electron microscopy and our modelling of the multimeric nitrilase, which supports an arrangement of dimers into helical segments as a plausible structural solution. CONCLUSIONS The nitrilase from Aspergillus niger K10 is highly homologous (≥86%) with proteins deduced from gene sequencing in Aspergillus and Penicillium genera. As the first of these proteins, it was shown to exhibit nitrilase activity towards organic nitriles. The comparison of the Nit-ANigRec and Nit-ANigWT suggested that the catalytic properties of nitrilases may be changed due to missing posttranslational cleavage of the former enzyme. Nit-ANigRec exhibits a lower tendency to form filaments and, moreover, the sample homogeneity can be further improved by in vitro protein refolding. The homogeneous protein species consisting of short spirals is expected to be more suitable for structural studies.
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Affiliation(s)
- Ondřej Kaplan
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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An improved nitrilase-mediated bioprocess for synthesis of nicotinic acid from 3-cyanopyridine with hyperinduced Nocardia globerula NHB-2. J Ind Microbiol Biotechnol 2010; 38:1235-43. [DOI: 10.1007/s10295-010-0902-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Accepted: 11/04/2010] [Indexed: 10/18/2022]
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Construction and application of variants of the Pseudomonas fluorescens EBC191 arylacetonitrilase for increased production of acids or amides. Appl Environ Microbiol 2010; 76:3668-74. [PMID: 20382812 DOI: 10.1128/aem.00341-10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The arylacetonitrilase from Pseudomonas fluorescens EBC191 differs from previously studied arylacetonitrilases by its low enantiospecificity during the turnover of mandelonitrile and by the large amounts of amides that are formed in the course of this reaction. In the sequence of the nitrilase from P. fluorescens, a cysteine residue (Cys163) is present in direct neighborhood (toward the amino terminus) to the catalytic active cysteine residue, which is rather unique among bacterial nitrilases. Therefore, this cysteine residue was exchanged in the nitrilase from P. fluorescens EBC191 for various amino acid residues which are present in other nitrilases at the homologous position. The influence of these mutations on the reaction specificity and enantiospecificity was analyzed with (R,S)-mandelonitrile and (R,S)-2-phenylpropionitrile as substrates. The mutants obtained demonstrated significant differences in their amide-forming capacities. The exchange of Cys163 for asparagine or glutamine residues resulted in significantly increased amounts of amides formed. In contrast, a substitution for alanine or serine residues decreased the amounts of amides formed. The newly discovered mutation was combined with previously identified mutations which also resulted in increased amide formation. Thus, variants which possessed in addition to the mutation Cys163Asn also a deletion at the C terminus of the enzyme and/or the modification Ala165Arg were constructed. These constructs demonstrated increased amide formation capacity in comparison to the mutants carrying only single mutations. The recombinant plasmids that encoded enzyme variants which formed large amounts of mandeloamide or that formed almost stoichiometric amounts of mandelic acid from mandelonitrile were used to transform Escherichia coli strains that expressed a plant-derived (S)-hydroxynitrile lyase. The whole-cell biocatalysts obtained in this way converted benzaldehyde plus cyanide either to (S)-mandeloamide or (S)-mandelic acid with high yields and enantiopurities.
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Martínková L, Křen V. Biotransformations with nitrilases. Curr Opin Chem Biol 2010; 14:130-7. [DOI: 10.1016/j.cbpa.2009.11.018] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 11/17/2009] [Indexed: 10/20/2022]
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Schreiner U, Steinkellner G, Rozzell JD, Glieder A, Winkler M. Improved Fitness ofArabidopsis thalianaNitrilase 2. ChemCatChem 2010. [DOI: 10.1002/cctc.200900212] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rohwerder T, Müller RH. Biosynthesis of 2-hydroxyisobutyric acid (2-HIBA) from renewable carbon. Microb Cell Fact 2010; 9:13. [PMID: 20184738 PMCID: PMC2847961 DOI: 10.1186/1475-2859-9-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 02/25/2010] [Indexed: 11/10/2022] Open
Abstract
Nowadays a growing demand for green chemicals and cleantech solutions is motivating the industry to strive for biobased building blocks. We have identified the tertiary carbon atom-containing 2-hydroxyisobutyric acid (2-HIBA) as an interesting building block for polymer synthesis. Starting from this carboxylic acid, practically all compounds possessing the isobutane structure are accessible by simple chemical conversions, e. g. the commodity methacrylic acid as well as isobutylene glycol and oxide. During recent years, biotechnological routes to 2-HIBA acid have been proposed and significant progress in elucidating the underlying biochemistry has been made. Besides biohydrolysis and biooxidation, now a bioisomerization reaction can be employed, converting the common metabolite 3-hydroxybutyric acid to 2-HIBA by a novel cobalamin-dependent CoA-carbonyl mutase. The latter reaction has recently been discovered in the course of elucidating the degradation pathway of the groundwater pollutant methyl tert-butyl ether (MTBE) in the new bacterial species Aquincola tertiaricarbonis. This discovery opens the ground for developing a completely biotechnological process for producing 2-HIBA. The mutase enzyme has to be active in a suitable biological system producing 3-hydroxybutyryl-CoA, which is the precursor of the well-known bacterial bioplastic polyhydroxybutyrate (PHB). This connection to the PHB metabolism is a great advantage as its underlying biochemistry and physiology is well understood and can easily be adopted towards producing 2-HIBA. This review highlights the potential of these discoveries for a large-scale 2-HIBA biosynthesis from renewable carbon, replacing conventional chemistry as synthesis route and petrochemicals as carbon source.
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Affiliation(s)
- Thore Rohwerder
- Helmholtz Centre for Environmental Research, Department Environmental Microbiology, Leipzig, Germany.
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Thuku R, Brady D, Benedik M, Sewell B. Microbial nitrilases: versatile, spiral forming, industrial enzymes. J Appl Microbiol 2009; 106:703-27. [DOI: 10.1111/j.1365-2672.2008.03941.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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News & views. Biotechnol J 2008. [DOI: 10.1002/biot.200890038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Wu S, Fogiel AJ, Petrillo KL, Jackson RE, Parker KN, Dicosimo R, Ben-Bassat A, O'Keefe DP, Payne MS. Protein engineering of nitrilase for chemoenzymatic production of glycolic acid. Biotechnol Bioeng 2008; 99:717-20. [PMID: 17787011 DOI: 10.1002/bit.21643] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A key step in a chemoenzymatic process for the production of high-purity glycolic acid (GLA) is the enzymatic conversion of glycolonitrile (GLN) to ammonium glycolate using a nitrilase derived from Acidovorax facilis 72W. Protein engineering and over-expression of this nitrilase, combined with optimized fermentation of an E. coli transformant were used to increase the enzyme-specific activity up to 15-fold and the biocatalyst-specific activity up to 125-fold. These improvements enabled achievement of the desired volumetric productivity and biocatalyst productivity for the conversion of GLN to ammonium glycolate.
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Affiliation(s)
- Shijun Wu
- Central Research and Development Department, E.I. du Pont de Nemours and Co., Experimental Station, P.O. Box 80328, Wilmington, Delaware 19880-0328, USA
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