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Xia Y, Zhao J, Saeed M, Hussain N, Chen X, Guo Z, Yong Y, Chen H. Molecular Modification Strategies of Nitrilase for Its Potential Application in Agriculture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15106-15121. [PMID: 38949086 DOI: 10.1021/acs.jafc.4c03388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Some feed source plants will produce secondary metabolites such as cyanogenic glycosides during metabolism, which will produce some poisonous nitrile compounds after hydrolysis and remain in plant tissues. The consumption of feed-source plants without proper treatment affect the health of the animals' bodies. Nitrilases can convert nitriles and have been used in industry as green biocatalysts. However, due to their bottleneck problems, their application in agriculture is still facing challenges. Acid-resistant nitrilase preparations, high-temperature resistance, antiprotease activity, strong activity, and strict reaction specificity urgently need to be developed. In this paper, the application potential of nitrilase in agriculture, especially in feed processing industry was explored, the source properties and catalytic mechanism of nitrilase were reviewed, and modification strategies for nitrilase application in agriculture were proposed to provide references for future research and application of nitrilase in agricultural and especially in the biological feed scene.
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Affiliation(s)
- Yutong Xia
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Jia Zhao
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Muhammad Saeed
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
- Department of Poultry Science, Faculty of Animal Production and Technology, The Cholistan University of Veterinary and Animal Sciences, Bahawalpur 63100, Pakistan
| | - Nazar Hussain
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Xihua Chen
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Zhongjian Guo
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Yangchun Yong
- Biofuels Institute, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
| | - Huayou Chen
- School of the Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu Province 212013, China
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Bhalla TC, Thakur N, Kumar V. Arylacetonitrilases: Potential Biocatalysts for Green Chemistry. Appl Biochem Biotechnol 2024; 196:1769-1785. [PMID: 37453025 DOI: 10.1007/s12010-023-04643-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
Nitrilases are the enzymes that catalyze the hydrolysis of nitriles to corresponding carboxylic acid and ammonia. They are broadly categorized into aromatic, aliphatic, and arylacetonitrilases based on their substrate specificity. Most of the studies pertaining to these enzymes in the literature have focused on aromatic and aliphatic nitrilases. However, arylacetonitrilases have attracted the attention of academia and industry in the last several years due to their aryl specificity and enantioselectivity. They have emerged as interesting biocatalytic tools in green chemistry to synthesize useful aryl acids such as mandelic acid and derivatives of phenylacetic acid. The aim of the present review is to collate information on the arylacetonitrilases and their catalytic properties including enantioselectivity and potential applications in organic synthesis.
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Affiliation(s)
- Tek Chand Bhalla
- Department of Biotechnology, Himachal Pradesh University, Himachal Pradesh, Gyan-Path, Shimla, 171005, India.
| | - Neerja Thakur
- Department of Biotechnology, Himachal Pradesh University, Himachal Pradesh, Gyan-Path, Shimla, 171005, India
- Department of Biotechnology and Microbiology, Himachal Pradesh, Rajkiya Kanya Mahavidyalaya, Longwood, Shimla, 171001, India
| | - Vijay Kumar
- Department of Biotechnology, Himachal Pradesh University, Himachal Pradesh, Gyan-Path, Shimla, 171005, India
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Wang ZK, Gong JS, Feng DT, Su C, Li H, Rao ZM, Lu ZM, Shi JS, Xu ZH. Geometric Remodeling of Nitrilase Active Pocket Based on ALF-Scanning Strategy To Enhance Aromatic Nitrile Substrate Preference and Catalytic Efficiency. Appl Environ Microbiol 2023; 89:e0022023. [PMID: 37191513 PMCID: PMC10304902 DOI: 10.1128/aem.00220-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
Nitrilase can catalyze nitrile compounds to generate corresponding carboxylic acids. Nitrilases as promiscuous enzymes can catalyze a variety of nitrile substrates, such as aliphatic nitriles, aromatic nitriles, etc. However, researchers tend to prefer enzymes with high substrate specificity and high catalytic efficiency. In this study, we developed an active pocket remodeling (ALF-scanning) based on modulating the geometry of the nitrilase active pocket to alter substrate preference and improve catalytic efficiency. Using this strategy, combined with site-directed saturation mutagenesis, we successfully obtained 4 mutants with strong aromatic nitrile preference and high catalytic activity, W170G, V198L, M197F, and F202M, respectively. To explore the synergistic relationship of these 4 mutations, we constructed 6 double-combination mutants and 4 triple-combination mutants. By combining mutations, we obtained the synergistically enhanced mutant V198L/W170G, which has a significant preference for aromatic nitrile substrates. Compared with the wild type, its specific activities for 4 aromatic nitrile substrates are increased to 11.10-, 12.10-, 26.25-, and 2.55-fold, respectively. By mechanistic dissection, we found that V198L/W170G introduced a stronger substrate-residue π-alkyl interaction in the active pocket and obtained a larger substrate cavity (225.66 Å3 to 307.58 Å3), making aromatic nitrile substrates more accessible to be catalyzed by the active center. Finally, we conducted experiments to rationally design the substrate preference of 3 other nitrilases based on the substrate preference mechanism and also obtained the corresponding aromatic nitrile substrate preference mutants of these three nitrilases and these mutants with greatly improved catalytic efficiency. Notably, the substrate range of SmNit is widened. IMPORTANCE In this study, the active pocket was largely remodeled based on the ALF-scanning strategy we developed. It is believed that ALF-scanning not only could be employed for substrate preference modification but might also play a role in protein engineering of other enzymatic properties, such as substrate region selectivity and substrate spectrum. In addition, the mechanism of aromatic nitrile substrate adaptation we found is widely applicable to other nitrilases in nature. To a large extent, it could provide a theoretical basis for the rational design of other industrial enzymes.
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Affiliation(s)
- Zi-Kai Wang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, People’s Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, People’s Republic of China
| | - Jin-Song Gong
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, People’s Republic of China
- Yixing Institute of Food and Biotechnology Co., Ltd., Yixing, People’s Republic of China
| | - Dan-Ting Feng
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, People’s Republic of China
| | - Chang Su
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, People’s Republic of China
- Yixing Institute of Food and Biotechnology Co., Ltd., Yixing, People’s Republic of China
| | - Hui Li
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, People’s Republic of China
| | - Zhi-Ming Rao
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, People’s Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, People’s Republic of China
| | - Zhen-Ming Lu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, People’s Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, People’s Republic of China
| | - Jin-Song Shi
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, People’s Republic of China
- Yixing Institute of Food and Biotechnology Co., Ltd., Yixing, People’s Republic of China
| | - Zheng-Hong Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, People’s Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, People’s Republic of China
- Yixing Institute of Food and Biotechnology Co., Ltd., Yixing, People’s Republic of China
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Achudhan AB, Kannan P, Saleena LM. Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome. Front Mol Biosci 2023; 10:1123902. [PMID: 37006617 PMCID: PMC10063848 DOI: 10.3389/fmolb.2023.1123902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Introduction: Nitriles are the most toxic compounds that can lead to serious human illness through inhalation and consumption due to environmental pollution. Nitrilases can highly degrade nitriles isolated from the natural ecosystem. In the current study, we focused on the discovery of novel nitrilases from a coal metagenome using in silico mining.Methods: Coal metagenomic DNA was isolated and sequenced on the Illumina platform. Quality reads were assembled using MEGAHIT, and statistics were checked using QUAST. Annotation was performed using the automated tool SqueezeMeta. The annotated amino acid sequences were mined for nitrilase from the unclassified organism. Sequence alignment and phylogenetic analyses were carried out using ClustalW and MEGA11. Conserved regions of the amino acid sequences were identified using InterProScan and NCBI-CDD servers. The physicochemical properties of the amino acids were measured using ExPASy’s ProtParam. Furthermore, NetSurfP was used for 2D structure prediction, while AlphaFold2 in Chimera X 1.4 was used for 3D structure prediction. To check the solvation of the predicted protein, a dynamic simulation was conducted on the WebGRO server. Ligands were extracted from the Protein Data Bank (PDB) for molecular docking upon active site prediction using the CASTp server.Results and discussion:In silico mining of annotated metagenomic data revealed nitrilase from unclassified Alphaproteobacteria. By using the artificial intelligence program AlphaFold2, the 3D structure was predicted with a per-residue confidence statistic score of about 95.8%, and the stability of the predicted model was verified with molecular dynamics for a 100-ns simulation. Molecular docking analysis determined the binding affinity of a novel nitrilase with nitriles. The binding scores produced by the novel nitrilase were approximately similar to those of the other prokaryotic nitrilase crystal structures, with a deviation of ±0.5.
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Vaishnav A, Kumar R, Singh HB, Sarma BK. Extending the benefits of PGPR to bioremediation of nitrile pollution in crop lands for enhancing crop productivity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154170. [PMID: 35227717 DOI: 10.1016/j.scitotenv.2022.154170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/06/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Incessant release of nitrile group of compounds such as cyanides into agricultural land through industrial effluents and excessive use of nitrile pesticides has resulted in increased nitrile pollution. Release of nitrile compounds (NCs) as plant root exudates is also contributing to the problem. The released NCs interact with soil elements and persists for a long time. Persistent higher concentration of NCs in soil cause toxicity to beneficial microflora and affect crop productivity. The NCs can cause more problems to human health if they reach groundwater and enter the food chain. Nitrile degradation by soil bacteria can be a solution to the problem if thoroughly exploited. However, the impact of such bacteria in plant and soil environments is still not properly explored. Plant growth-promoting rhizobacteria (PGPR) with nitrilase activity has recently gained attention as potential solution to address the problem. This paper reviews the core issue of nitrile pollution in soil and the prospects of application of nitrile degrading bacteria for soil remediation, soil health improvement and plant growth promotion in nitrile-polluted soils. The possible mechanisms of PGPR that can be exploited to degrade NCs, converting them into plant useful compounds and synthesis of the phytohormone IAA from degraded NCs are also discussed at length.
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Affiliation(s)
- Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura 281406, India; Agroecology and Environment, Agroscope (Reckenholz), Zürich 8046, Switzerland
| | - Roshan Kumar
- National Centre for Biological Sciences (TIFR-NCBS), Bengaluru 560065, India
| | | | - Birinchi Kumar Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221110, India.
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Bessonnet T, Mariage A, Petit JL, Pellouin V, Debard A, Zaparucha A, Vergne-Vaxelaire C, de Berardinis V. Purification and Characterization of Nit phym , a Robust Thermostable Nitrilase From Paraburkholderia phymatum. Front Bioeng Biotechnol 2021; 9:686362. [PMID: 34277586 PMCID: PMC8280356 DOI: 10.3389/fbioe.2021.686362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Despite the success of some nitrilases in industrial applications, there is a constant demand to broaden the catalog of these hydrolases, especially robust ones with high operational stability. By using the criteria of thermoresistance to screen a collection of candidate enzymes heterologously expressed in Escherichia coli, the enzyme Nit phym from the mesophilic organism Paraburkholderia phymatum was selected and further characterized. Its quick and efficient purification by heat treatment is of major interest for large-scale applications. The purified nitrilase displayed a high thermostability with 90% of remaining activity after 2 days at 30°C and a half-life of 18 h at 60°C, together with a broad pH range of 5.5-8.5. Its high resistance to various miscible cosolvents and tolerance to high substrate loadings enabled the quantitative conversion of 65.5 g⋅L-1 of 3-phenylpropionitrile into 3-phenylpropionic acid at 50°C in 8 h at low enzyme loadings of 0.5 g⋅L-1, with an isolated yield of 90%. This study highlights that thermophilic organisms are not the only source of industrially relevant thermostable enzymes and extends the scope of efficient nitrilases for the hydrolysis of a wide range of nitriles, especially trans-cinnamonitrile, terephthalonitrile, cyanopyridines, and 3-phenylpropionitrile.
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Affiliation(s)
- Thomas Bessonnet
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Aline Mariage
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Virginie Pellouin
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Adrien Debard
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Anne Zaparucha
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Carine Vergne-Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Véronique de Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
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Müller E, Sosedov O, Gröning JAD, Stolz A. Synthesis of (R)-mandelic acid and (R)-mandelic acid amide by recombinant E. coli strains expressing a (R)-specific oxynitrilase and an arylacetonitrilase. Biotechnol Lett 2020; 43:287-296. [PMID: 32936375 PMCID: PMC7796878 DOI: 10.1007/s10529-020-02998-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/03/2020] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Chiral 2-hydroxycarboxylic acids and 2-hydroxycarboxamides are valuable synthons for the chemical industry. RESULTS The biocatalytic syntheses of (R)-mandelic acid and (R)-mandelic acid amide by recombinant Escherichia coli clones were studied. Strains were constructed which simultaneously expressed a (R)-specific oxynitrilase (hydroxynitrile lyase) from the plant Arabidopsis thaliana together with the arylacetonitrilase from the bacterium Pseudomonas fluorescens EBC191. In addition, recombinant strains were constructed which expressed a previously described acid tolerant variant of the oxynitrilase and an amide forming variant of the nitrilase. The whole cell catalysts which simultaneously expressed the (R)-specific oxynitrilase and the wild-type nitrilase transformed in slightly acidic buffer systems benzaldehyde plus cyanide preferentially to (R)-mandelic acid with ee-values > 95%. The combination of the (R)-specific oxynitrilase with the amide forming nitrilase variant gave whole cell catalysts which converted at pH-values ≤ pH 5 benzaldehyde plus cyanide with a high degree of enantioselectivity (ee > 90%) to (R)-mandelic acid amide. The acid and the amide forming catalysts also converted chlorinated benzaldehydes with cyanide to chlorinated mandelic acid or chlorinated mandelic acid amides. CONCLUSIONS Efficient systems for the biocatalytic production of (R)-2-hydroxycarboxylic acids and (R)-2-hydroxycarboxamides were generated.
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Affiliation(s)
- Erik Müller
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Olga Sosedov
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
- Present Address: Biochem Labor für chemische Analytik GmbH, Daimlerstr. 5B, 76185 Karlsruhe, Germany
| | | | - Andreas Stolz
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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Plant Nitrilase Homologues in Fungi: Phylogenetic and Functional Analysis with Focus on Nitrilases in Trametes versicolor and Agaricus bisporus. Molecules 2020; 25:molecules25173861. [PMID: 32854275 PMCID: PMC7503981 DOI: 10.3390/molecules25173861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/15/2020] [Accepted: 08/16/2020] [Indexed: 11/17/2022] Open
Abstract
Fungi contain many plant-nitrilase (NLase) homologues according to database searches. In this study, enzymes NitTv1 from Trametes versicolor and NitAb from Agaricus bisporus were purified and characterized as the representatives of this type of fungal NLase. Both enzymes were slightly more similar to NIT4 type than to NIT1/NIT2/NIT3 type of plant NLases in terms of their amino acid sequences. Expression of the synthetic genes in Escherichia coli Origami B (DE3) was induced with 0.02 mM isopropyl β-D-1-thiogalactopyranoside at 20 °C. Purification of NitTv1 and NitAb by cobalt affinity chromatography gave ca. 6.6 mg and 9.6 mg of protein per 100 mL of culture medium, respectively. Their activities were determined with 25 mM of nitriles in 50 mM Tris/HCl buffer, pH 8.0, at 30 °C. NitTv1 and NitAb transformed β-cyano-L-alanine (β-CA) with the highest specific activities (ca. 132 and 40 U mg−1, respectively) similar to plant NLase NIT4. β-CA was transformed into Asn and Asp as in NIT4 but at lower Asn:Asp ratios. The fungal NLases also exhibited significant activities for (aryl)aliphatic nitriles such as 3-phenylpropionitrile, cinnamonitrile and fumaronitrile (substrates of NLase NIT1). NitTv1 was more stable than NitAb (at pH 5–9 vs. pH 5–7). These NLases may participate in plant–fungus interactions by detoxifying plant nitriles and/or producing plant hormones. Their homology models elucidated the molecular interactions with various nitriles in their active sites.
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Hadi T, Nozzi N, Melby JO, Gao W, Fuerst DE, Kvam E. Rolling circle amplification of synthetic DNA accelerates biocatalytic determination of enzyme activity relative to conventional methods. Sci Rep 2020; 10:10279. [PMID: 32581345 PMCID: PMC7314814 DOI: 10.1038/s41598-020-67307-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/02/2020] [Indexed: 11/24/2022] Open
Abstract
The ability to quickly and easily assess the activity of large collections of enzymes for a desired substrate holds great promise in the field of biocatalysis. Cell-free synthesis, although not practically amenable for large-scale enzyme production, provides a way to accelerate the timeline for screening enzyme candidates using small-scale reactions. However, because cell-free enzyme synthesis requires a considerable amount of template DNA, the preparation of high-quality DNA "parts" in large quantities represents a costly and rate-limiting prerequisite for high throughput screening. Based on time-cost analysis and comparative activity data, a cell-free workflow using synthetic DNA minicircles and rolling circle amplification enables comparable biocatalytic activity to cell-based workflows in almost half the time. We demonstrate this capability using a panel of sequences from the carbon-nitrogen hydrolase superfamily that represent possible green catalysts for synthesizing small molecules with less waste compared to traditional industrial chemistry. This method provides a new alternative to more cumbersome plasmid- or PCR-based protein expression workflows and should be amenable to automation for accelerating enzyme screening in industrial applications.
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Affiliation(s)
- Timin Hadi
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania, 19426, USA
| | - Nicole Nozzi
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania, 19426, USA
| | - Joel O Melby
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania, 19426, USA
| | - Wei Gao
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA
| | - Douglas E Fuerst
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania, 19426, USA
| | - Erik Kvam
- GE Global Research, One Research Circle, Niskayuna, NY, 12309, USA.
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Genetic and Functional Diversity of Nitrilases in Agaricomycotina. Int J Mol Sci 2019; 20:ijms20235990. [PMID: 31795104 PMCID: PMC6928751 DOI: 10.3390/ijms20235990] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 12/27/2022] Open
Abstract
Nitrilases participate in the nitrile metabolism in microbes and plants. They are widely used to produce carboxylic acids from nitriles. Nitrilases were described in bacteria, Ascomycota and plants. However, they remain unexplored in Basidiomycota. Yet more than 200 putative nitrilases are found in this division via GenBank. The majority of them occur in the subdivision Agaricomycotina. In this work, we analyzed their sequences and classified them into phylogenetic clades. Members of clade 1 (61 proteins) and 2 (25 proteins) are similar to plant nitrilases and nitrilases from Ascomycota, respectively, with sequence identities of around 50%. The searches also identified five putative cyanide hydratases (CynHs). Representatives of clade 1 and 2 (NitTv1 from Trametes versicolor and NitAg from Armillaria gallica, respectively) and a putative CynH (NitSh from Stereum hirsutum) were overproduced in Escherichia coli. The substrates of NitTv1 were fumaronitrile, 3-phenylpropionitrile, β-cyano-l-alanine and 4-cyanopyridine, and those of NitSh were hydrogen cyanide (HCN), 2-cyanopyridine, fumaronitrile and benzonitrile. NitAg only exhibited activities for HCN and fumaronitrile. The substrate specificities of these nitrilases were largely in accordance with substrate docking in their homology models. The phylogenetic distribution of each type of nitrilase was determined for the first time.
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Comparative Analysis of the Conversion of Mandelonitrile and 2-Phenylpropionitrile by a Large Set of Variants Generated from a Nitrilase Originating from Pseudomonas fluorescens EBC191. Molecules 2019; 24:molecules24234232. [PMID: 31766372 PMCID: PMC6930498 DOI: 10.3390/molecules24234232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 11/17/2022] Open
Abstract
The arylacetonitrilase from the bacterium Pseudomonas fluorescens EBC191 has been intensively studied as a model to understand the molecular basis for the substrate-, reaction-, and enantioselectivity of nitrilases. The nitrilase converts various aromatic and aliphatic nitriles to the corresponding acids and varying amounts of the corresponding amides. The enzyme has been analysed by site-specific mutagenesis and more than 50 different variants have been generated and analysed for the conversion of (R,S)-mandelonitrile and (R,S)-2-phenylpropionitrile. These comparative analyses demonstrated that single point mutations are sufficient to generate enzyme variants which hydrolyse (R,S)-mandelonitrile to (R)-mandelic acid with an enantiomeric excess (ee) of 91% or to (S)-mandelic acid with an ee-value of 47%. The conversion of (R,S)-2-phenylpropionitrile by different nitrilase variants resulted in the formation of either (S)- or (R)-2-phenylpropionic acid with ee-values up to about 80%. Furthermore, the amounts of amides that are produced from (R,S)-mandelonitrile and (R,S)-2-phenylpropionitrile could be changed by single point mutations between 2%–94% and <0.2%–73%, respectively. The present study attempted to collect and compare the results obtained during our previous work, and to obtain additional general information about the relationship of the amide forming capacity of nitrilases and the enantiomeric composition of the products.
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GC-MS-based 13C metabolic flux analysis resolves the parallel and cyclic glucose metabolism of Pseudomonas putida KT2440 and Pseudomonas aeruginosa PAO1. Metab Eng 2019; 54:35-53. [DOI: 10.1016/j.ymben.2019.01.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 01/05/2023]
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Conversion of phenylglycinonitrile by recombinant Escherichia coli cells synthesizing variants of the arylacetonitrilase from Pseudomonas fluorescens EBC191. Appl Microbiol Biotechnol 2019; 103:6737-6746. [PMID: 31222384 DOI: 10.1007/s00253-019-09957-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/06/2019] [Accepted: 05/29/2019] [Indexed: 10/26/2022]
Abstract
The conversion of phenylglycinonitrile (2-aminophenylacetonitrile) by Escherichia coli strains was studied, which recombinantly expressed the arylacetonitrilase (NitA) from Pseudomonas fluorescens EBC191 and different nitrilase variants with altered reaction specificities. The whole-cell catalysts which formed the wild-type nitrilase converted (R,S)-phenylglycinonitrile preferentially to (S)-phenylglycine with a low degree of enantioselectivity. A recombinant strain which formed a variant of NitA produced mainly (S)-phenylglycine amide from (R,S)-phenylglycinonitrile and a second variant showed an almost complete enantioconversion and produced (R)-phenylglycine and left (S)-phenylglycinonitrile. The microbial-produced (S)-phenylglycinonitrile was used to study the chemical racemisation of (S)-phenylglycinonitrile at alkaline pH values in order to establish a dynamic kinetic resolution of the substrate. Subsequently, the conversion of (R,S)-phenylglycinonitrile by the whole-cell catalysts was studied at a pH of 10.8 which allowed a sufficient racemisation rate of phenylglycinonitrile. Surprisingly, under these conditions, strongly increased amounts of (S)-phenylglycine were formed by the recombinant E. coli cells expressing the amide-forming nitrilase variant. The aminopeptidase PepA from E. coli was identified by the construction of a deletion mutant and subsequent complementation as responsible amidase activity, which converted (S)-phenylglycine amide to (S)-phenylglycine.
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Chhiba-Govindjee VP, van der Westhuyzen CW, Bode ML, Brady D. Bacterial nitrilases and their regulation. Appl Microbiol Biotechnol 2019; 103:4679-4692. [DOI: 10.1007/s00253-019-09776-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/25/2022]
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Atalah J, Cáceres-Moreno P, Espina G, Blamey JM. Thermophiles and the applications of their enzymes as new biocatalysts. BIORESOURCE TECHNOLOGY 2019; 280:478-488. [PMID: 30826176 DOI: 10.1016/j.biortech.2019.02.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 05/20/2023]
Abstract
Ecological and efficient alternatives to industrial processes have sparked interest for using microorganisms and enzymes as biocatalysts. One of the difficulties is finding candidates capable of resisting the harsh conditions in which industrial processes usually take place. Extremophiles, microorganisms naturally found in "extreme" ecological niches, produce robust enzymes for bioprocesses and product development. Thermophiles like Geobacillus, Alyciclobacillus, Anoxybacillus, Pyrococcus and Thermoccocus are some of the extremophiles containing enzymes showing special promise for biocatalysis. Glutamate dehydrogenase used in food processes, laccases and xylanases in pulp and paper processes, nitrilases and transaminases for pharmaceutical drug synthesis and lipases present in detergents, are examples of the increasing use of enzymes for biocatalytic synthesis from thermophilic microorganisms. Some of these enzymes from thermophiles have been expressed as recombinant enzymes and are already in the market. Here we will review recent discoveries of thermophilic enzymes and their current and potential applications in industry.
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Affiliation(s)
- Joaquín Atalah
- Fundación Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago, Chile
| | | | - Giannina Espina
- Fundación Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago, Chile
| | - Jenny M Blamey
- Fundación Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago, Chile; Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda 3363, Estación Central, Santiago, Chile.
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