1
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Chen Q, Wang J, Zhang S, Chen X, Hao J, Wu Q, Zhu D. Discovery and directed evolution of C-C bond formation enzymes for the biosynthesis of β-hydroxy-α-amino acids and derivatives. Crit Rev Biotechnol 2024:1-20. [PMID: 38566472 DOI: 10.1080/07388551.2024.2332295] [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: 11/24/2023] [Accepted: 02/16/2024] [Indexed: 04/04/2024]
Abstract
β-Hydroxy-α-amino acids (β-HAAs) have extensive applications in the pharmaceutical, chemical synthesis, and food industries. The development of synthetic methodologies aimed at producing optically pure β-HAAs has been driven by practical applications. Among the various synthetic methods, biocatalytic asymmetric synthesis is considered a sustainable approach due to its capacity to generate two stereogenic centers from simple prochiral precursors in a single step. Therefore, extensive efforts have been made in recent years to search for effective enzymes which enable such biotransformation. This review provides an overview on the discovery and engineering of C-C bond formation enzymes for the biocatalytic synthesis of β-HAAs. We highlight examples where the use of threonine aldolases, threonine transaldolases, serine hydroxymethyltransferases, α-methylserine aldolases, α-methylserine hydroxymethyltransferases, and engineered alanine racemases facilitated the synthesis of β-HAAs. Additionally, we discuss the potential future advancements and persistent obstacles in the enzymatic synthesis of β-HAAs.
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Affiliation(s)
- Qijia Chen
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Jingmin Wang
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Sisi Zhang
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Xi Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jianxiong Hao
- College of Food Science and Biology, University of Science and Technology, Shijiazhuang, China
| | - Qiaqing Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dunming Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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2
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Dwivedi SK, Arachchige DL, Waters M, Jaeger S, Mahmoud M, Olowolagba AM, Tucker DR, Geborkoff MR, Werner T, Luck RL, Godugu B, Liu H. Near-infrared Absorption and Emission Probes with Optimal Connection Bridges for Live Monitoring of NAD(P)H Dynamics in Living Systems. SENSORS AND ACTUATORS. B, CHEMICAL 2024; 402:135073. [PMID: 38559378 PMCID: PMC10976508 DOI: 10.1016/j.snb.2023.135073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Two NAD(P)H-biosensing probes consisting of 1,3,3-trimethyl-3H-indolium and 3-quinolinium acceptors, linked by thiophene, A, and 3,4-ethylenedioxythiophene, B, bridges are detailed. We synthesized probes C and D, replacing the thiophene connection in probe A with phenyl and 2,1,3-benzothiadiazole units, respectively. Probe E was prepared by substituting probe A's 3-quinolinium unit with a 1-methylquinoxalin-1-ium unit. Solutions are non-fluorescent but in the presence of NADH, exhibit near-infrared fluorescence at 742.1 nm and 727.2 nm for probes A and B, respectively, and generate absorbance signals at 690.6 nm and 685.9 nm. In contrast, probes C and D displayed pronounced interference from NADH fluorescence at 450 nm, whereas probe E exhibited minimal fluorescence alterations in response to NAD(P)H. Pre-treatment of A549 cells with glucose in the presence of probe A led to a significant increase in fluorescence intensity. Additionally, subjecting probe A to lactate and pyruvate molecules resulted in opposite changes in NAD(P)H levels, with lactate causing a substantial increase in fluorescence intensity, conversely, pyruvate resulted in a sharp decrease. Treatment of A549 cells with varying concentrations of the drugs cisplatin, gemcitabine, and camptothecin (5, 10, and 20 μM) led to a concentration-dependent increase in intracellular fluorescence intensity, signifying a rise in NAD(P)H levels. Finally, fruit fly larvae were treated with different concentrations of NADH and cisplatin illustrating applicability to live organisms. The results demonstrated a direct correlation between fluorescence intensity and the concentration of NADH and cisplatin, respectively, further confirming the efficacy of probe A in sensing changes in NAD(P)H levels within a whole organism.
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Affiliation(s)
- Sushil K Dwivedi
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931
- Health Research Institute, Michigan Technological University, Houghton, MI 49931
| | - Dilka Liyana Arachchige
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931
- Health Research Institute, Michigan Technological University, Houghton, MI 49931
| | - May Waters
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931
- Health Research Institute, Michigan Technological University, Houghton, MI 49931
| | - Sophia Jaeger
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931
- Health Research Institute, Michigan Technological University, Houghton, MI 49931
| | - Mohamed Mahmoud
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931
- Health Research Institute, Michigan Technological University, Houghton, MI 49931
| | - Adenike Mary Olowolagba
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931
- Health Research Institute, Michigan Technological University, Houghton, MI 49931
| | - Daniel R Tucker
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931
| | - Micaela R Geborkoff
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931
| | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931
| | - Rudy L Luck
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931
| | - Bhaskar Godugu
- Department of Chemistry, University of Pittsburgh, Chevron Science Center, 219 Parkman Avenue, Pittsburgh, PA 15260
| | - Haiying Liu
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931
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3
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Melman Y, Wells PK, Katz E, Smutok O. A universal nanostructured bioanalytical platform for NAD+-dependent enzymes based on the fluorescent output reading with a smartphone. Talanta 2022; 243:123325. [DOI: 10.1016/j.talanta.2022.123325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 10/19/2022]
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4
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Shen JD, Cai X, Liu ZQ, Zheng YG. Nitrilase: a promising biocatalyst in industrial applications for green chemistry. Crit Rev Biotechnol 2020; 41:72-93. [PMID: 33045860 DOI: 10.1080/07388551.2020.1827367] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nitrilases are widely distributed in nature and are able to hydrolyze nitriles into their corresponding carboxylic acids and ammonia. In industry, nitrilases have been used as green biocatalysts for the production of high value-added products. To date, biocatalysts are considered to be important alternatives to chemical catalysts due to increasing environmental problems and resource scarcity. This review provides an overview of recent advances of nitrilases in aspects of distribution, enzyme screening, molecular structure and catalytic mechanism, protein engineering, and their potential applications in industry.
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Affiliation(s)
- Ji-Dong Shen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
| | - Xue Cai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
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5
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Mei Z, Zhang K, Qu G, Li JK, Liu B, Ma JA, Tu R, Sun Z. High-Throughput Fluorescence Assay for Ketone Detection and Its Applications in Enzyme Mining and Protein Engineering. ACS OMEGA 2020; 5:13588-13594. [PMID: 32566823 PMCID: PMC7301380 DOI: 10.1021/acsomega.0c00245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Ketones are of great importance as building blocks in synthetic organic chemistry and biocatalysis. Most ketones cannot easily be quantitatively assayed due to the lack of visible photometric properties. Effective high-throughput assay (HTA) development is therefore necessary for ketone determination. Inspired by previous works of an aldehyde assay based on 2-amino benzamidoxime derivatives, we developed a colorimetric method for rapid a HTA of structurally diverse ketones by using para-methoxy-2-amino benzamidoxime (PMA). This PMA-based method is characterized by high sensitivity manner (μM) with low background, as checked by gas chromatography (GC). It can be used for quantitatively monitoring ketones by fluorescence screening in microtiter plates. Furthermore, this HTA method was employed in mining alcohol dehydrogenases (ADHs), and in directed evolution aimed at enhancing ADH activity in the catalytic transformation of alcohols to ketones. This work provides a general tool for ketone detection in biocatalyst development.
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Affiliation(s)
- Zelong Mei
- College
of Biotechnology, Tianjin University of
Science and Technology, Tianjin 300457, China
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Kun Zhang
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Ge Qu
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Jun-Kuan Li
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
- Department
of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences,
and Tianjin Collaborative Innovation Center of Chemical Science and
Engineering, Tianjin University, Tianjin 300072, China
| | - Baoyan Liu
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Jun-An Ma
- Department
of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences,
and Tianjin Collaborative Innovation Center of Chemical Science and
Engineering, Tianjin University, Tianjin 300072, China
| | - Ran Tu
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
| | - Zhoutong Sun
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport
Economic Area, Tianjin 300308, China
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6
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Liu Z, Chen X, Chen Q, Feng J, Wang M, Wu Q, Zhu D. Engineering of l-threonine aldolase for the preparation of 4-(methylsulfonyl)phenylserine, an important intermediate for the synthesis of florfenicol and thiamphenicol. Enzyme Microb Technol 2020; 137:109551. [DOI: 10.1016/j.enzmictec.2020.109551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/19/2020] [Accepted: 03/09/2020] [Indexed: 11/29/2022]
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7
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Egelkamp R, Friedrich I, Hertel R, Daniel R. From sequence to function: a new workflow for nitrilase identification. Appl Microbiol Biotechnol 2020; 104:4957-4970. [PMID: 32291488 PMCID: PMC7228900 DOI: 10.1007/s00253-020-10544-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/28/2020] [Accepted: 03/11/2020] [Indexed: 11/16/2022]
Abstract
Abstract Nitrilases are industrially important biocatalysts due to their ability to degrade nitriles to carboxylic acids and ammonia. In this study, a workflow for simple and fast recovery of nitrilase candidates from metagenomes is presented. For identification of active enzymes, a NADH-coupled high-throughput assay was established. Purification of enzymes could be omitted as the assay is based on crude extract containing the expressed putative nitrilases. In addition, long incubation times were avoided by combining nitrile and NADH conversion in a single reaction. This allowed the direct measurement of nitrile degradation and provided not only insights into substrate spectrum and specificity but also in degradation efficiency. The novel assay was used for investigation of candidate nitrilase-encoding genes. Seventy putative nitrilase-encoding gene and the corresponding deduced protein sequences identified during sequence-based screens of metagenomes derived from nitrile-treated microbial communities were analyzed. Subsequently, the assay was applied to 13 selected candidate genes and proteins. Six of the generated corresponding Escherichia coli clones produced nitrilases that showed activity and one unusual nitrilase was purified and analyzed. The activity of the novel arylacetonitrilase Nit09 exhibited a broad pH range and a high long-term stability. The enzyme showed high activity for arylacetonitriles with a KM of 1.29 mM and a Vmax of 13.85 U/mg protein for phenylacetonitrile. In conclusion, we provided a setup for simple and rapid analysis of putative nitrilase-encoding genes from sequence to function. The suitability was demonstrated by identification, isolation, and characterization of the arylacetonitrilase. Key points • A simple and fast high-throughput nitrilase screening was developed. • A set of putative nitrilases was successfully screened with the assay. • A novel arylacetonitrilase was identified, purified, and characterized in detail. Electronic supplementary material The online version of this article (10.1007/s00253-020-10544-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard Egelkamp
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Ines Friedrich
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Robert Hertel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany.
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8
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Časaitė V, Sadauskas M, Vaitekūnas J, Gasparavičiūtė R, Meškienė R, Skikaitė I, Sakalauskas M, Jakubovska J, Tauraitė D, Meškys R. Engineering of a chromogenic enzyme screening system based on an auxiliary indole-3-carboxylic acid monooxygenase. Microbiologyopen 2019; 8:e00795. [PMID: 30666828 PMCID: PMC6692525 DOI: 10.1002/mbo3.795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 11/24/2022] Open
Abstract
Here, we present a proof‐of‐principle for a new high‐throughput functional screening of metagenomic libraries for the selection of enzymes with different activities, predetermined by the substrate being used. By this approach, a total of 21 enzyme‐coding genes were selected, including members of xanthine dehydrogenase, aldehyde dehydrogenase (ALDH), and amidohydrolase families. The screening system is based on a pro‐chromogenic substrate, which is transformed by the target enzyme to indole‐3‐carboxylic acid. The later compound is converted to indoxyl by a newly identified indole‐3‐carboxylate monooxygenase (Icm). Due to the spontaneous oxidation of indoxyl to indigo, the target enzyme‐producing colonies turn blue. Two types of pro‐chromogenic substrates have been tested. Indole‐3‐carboxaldehydes and the amides of indole‐3‐carboxylic acid have been applied as substrates for screening of the ALDHs and amidohydrolases, respectively. Both plate assays described here are rapid, convenient, easy to perform, and adaptable for the screening of a large number of samples both in Escherichia coli and Rhodococcus sp. In addition, the fine‐tuning of the pro‐chromogenic substrate allows screening enzymes with the desired substrate specificity.
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Affiliation(s)
- Vida Časaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mikas Sadauskas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Justas Vaitekūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Renata Gasparavičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rita Meškienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Izabelė Skikaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mantas Sakalauskas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jevgenija Jakubovska
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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Tang XL, Lu XF, Wu ZM, Zheng RC, Zheng YG. Biocatalytic production of ( S )-2-aminobutanamide by a novel d -aminopeptidase from Brucella sp. with high activity and enantioselectivity. J Biotechnol 2018; 266:20-26. [DOI: 10.1016/j.jbiotec.2017.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/11/2017] [Accepted: 12/03/2017] [Indexed: 10/18/2022]
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10
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Fisk H, Xu Y, Westley C, Turner NJ, Micklefield J, Goodacre R. From Multistep Enzyme Monitoring to Whole-Cell Biotransformations: Development of Real-Time Ultraviolet Resonance Raman Spectroscopy. Anal Chem 2017; 89:12527-12532. [PMID: 29076721 DOI: 10.1021/acs.analchem.7b03742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Process analytical technologies (PAT) are used within industry to give real-time measurements of critical quality parameters, ultimately improving the quality by design (QbD) of the final product and reducing manufacturing costs. Spectroscopic and spectrophotometric methods are readily employed within PAT due to their ease of use, compatibility toward a range of sample types, robustness, and multiplexing capabilities. We have developed a UV resonance Raman (UVRR) spectroscopy approach to quantify industrially relevant biotransformations accurately, focusing on nitrile metabolizing enzymes: nitrile hydratase (NHase) and amidase versus nitrilase activity. Sensitive detection of the amide intermediate by UVRR spectroscopy enabled discrimination between the two nitrile-hydrolyzing pathways. Development of a flow-cell apparatus further exemplifies its suitability toward PAT measurements, incorporating in situ analysis within a closed system. Multivariate curve resolution-alternating least-squares (MCR-ALS) was applied to the UVRR spectra, as well as off-line HPLC measurements, to enable absolute quantification of substrate, intermediate, and product. Further application of hard modeling to MCR-ALS deconvolved concentration profiles enabled accurate kinetic determinations, thus removing the requirement for comparative off-line HPLC. Finally, successful quantitative measurements of in vivo activity using whole-cell biotransformations, where two Escherichia coli strains expressing either NHase (transforming benzonitrile to benzamide) or amidase (further conversion of benzamide to benzoic acid), illustrate the power, practicality, and sensitivity of this novel approach of multistep and, with further refinement, we believe, multiple micro-organism biotransformations.
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Affiliation(s)
- Heidi Fisk
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Chloe Westley
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicholas J Turner
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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11
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Westley C, Fisk H, Xu Y, Hollywood KA, Carnell AJ, Micklefield J, Turner NJ, Goodacre R. Real-Time Monitoring of Enzyme-Catalysed Reactions using Deep UV Resonance Raman Spectroscopy. Chemistry 2017; 23:6983-6987. [PMID: 28370547 PMCID: PMC5488198 DOI: 10.1002/chem.201701388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Indexed: 01/23/2023]
Abstract
For enzyme-catalysed biotransformations, continuous in situ detection methods minimise the need for sample manipulation, ultimately leading to more accurate real-time kinetic determinations of substrate(s) and product(s). We have established for the first time an on-line, real-time quantitative approach to monitor simultaneously multiple biotransformations based on UV resonance Raman (UVRR) spectroscopy. To exemplify the generality and versatility of this approach, multiple substrates and enzyme systems were used involving nitrile hydratase (NHase) and xanthine oxidase (XO), both of which are of industrial and biological significance, and incorporate multistep enzymatic conversions. Multivariate data analysis of the UVRR spectra, involving multivariate curve resolution-alternating least squares (MCR-ALS), was employed to effect absolute quantification of substrate(s) and product(s); repeated benchmarking of UVRR combined with MCR-ALS by HPLC confirmed excellent reproducibility.
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Affiliation(s)
- Chloe Westley
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | - Heidi Fisk
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | - Yun Xu
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | - Katherine A. Hollywood
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | | | - Jason Micklefield
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | - Nicholas J. Turner
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of BiotechnologyUniversity of Manchester131 Princess streetManchesterM1 7DNUK
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12
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Magomedova Z, Grecu A, Sensen CW, Schwab H, Heidinger P. Characterization of two novel alcohol short-chain dehydrogenases/reductases from Ralstonia eutropha H16 capable of stereoselective conversion of bulky substrates. J Biotechnol 2016; 221:78-90. [DOI: 10.1016/j.jbiotec.2016.01.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/19/2022]
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13
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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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14
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Threonine aldolases: perspectives in engineering and screening the enzymes with enhanced substrate and stereo specificities. Appl Microbiol Biotechnol 2016; 100:2579-90. [PMID: 26810201 PMCID: PMC4761611 DOI: 10.1007/s00253-015-7218-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/30/2015] [Accepted: 12/02/2015] [Indexed: 12/23/2022]
Abstract
Threonine aldolases have emerged as a powerful tool for asymmetric carbon-carbon bond formation. These enzymes catalyse the unnatural aldol condensation of different aldehydes and glycine to produce highly valuable β-hydroxy-α-amino acids with complete stereocontrol at the α-carbon and moderate specificity at the β-carbon. A range of microbial threonine aldolases has been recently recombinantly produced by several groups and their biochemical properties were characterized. Numerous studies have been conducted to improve the reaction protocols to enable higher conversions and investigate the substrate scope of enzymes. However, the application of threonine aldolases in organic synthesis is still limited due to often moderate yields and low diastereoselectivities obtained in the aldol reaction. This review briefly summarizes the screening techniques recently applied to discover novel threonine aldolases as well as enzyme engineering and mutagenesis studies which were accomplished to improve the catalytic activity and substrate specificity. Additionally, the results from new investigations on threonine aldolases including crystal structure determinations and structural-functional characterization are reviewed.
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15
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Yang C, Ying X, Yu M, Zhang Y, Xiong B, Song Q, Wang Z. Towards the discovery of alcohol dehydrogenases: NAD(P)H fluorescence-based screening and characterization of the newly isolated Rhodococcus erythropolis WZ010 in the preparation of chiral aryl secondary alcohols. J Ind Microbiol Biotechnol 2012; 39:1431-43. [PMID: 22743788 DOI: 10.1007/s10295-012-1160-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 06/11/2012] [Indexed: 10/28/2022]
Abstract
A simple and reliable procedure was developed to screen biocatalysts with high alcohol dehydrogenase activity, efficient internal coenzyme regeneration, and high stereoselectivity. The strategy of activity screening in a microtitre plate format was based on the detection of fluorescence of NAD(P)H originating from the oxidation of alcohols. The primary and secondary screenings from soil samples yielded a versatile bacterial biocatalyst Rhodococcus erythropolis WZ010 demonstrating potential for the preparation of chiral aryl secondary alcohols. In terms of activity and stereoselectivity, the optimized reaction conditions in the stereoselective oxidation were 30 °C, pH 10.5, and 250 rpm, whereas bioreduction using glucose as co-substrate was the most favorable at 35 °C and pH 7.5 in the static reaction mixture. Under the optimized conditions, fresh cells of the strain stereoselectively oxidized the (S)-enantiomer of racemic 1-phenylethanol (120 mM) to acetophenone and afforded the unoxidized (R)-1-phenylethanol in 49.4 % yield and >99.9 % enantiomeric excess (e.e.). In the reduction of 10 mM acetophenone, the addition of 100 mM glucose significantly increased the conversion rate from 3.1 to 97.4 %. In the presence of 800 mM glucose, acetophenone and other aromatic ketones (80 mM) were enantioselectively reduced to corresponding (S)-alcohols with excellent e.e. values. Both stereoselective oxidation and asymmetric reduction required no external cofactor regeneration system.
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Affiliation(s)
- Chi Yang
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou, 310014 Zhejiang, China
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16
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Brovetto M, Gamenara D, Méndez PS, Seoane GA. C-C bond-forming lyases in organic synthesis. Chem Rev 2011; 111:4346-403. [PMID: 21417217 DOI: 10.1021/cr100299p] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Margarita Brovetto
- Grupo de Fisicoquímica Orgánica y Bioprocesos, Departamento de Química Orgánica, DETEMA, Facultad de Química, Universidad de la República (UdelaR), Gral. Flores 2124, 11800 Montevideo, Uruguay
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17
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Lin ZJ, Zheng RC, Lei LH, Zheng YG, Shen YC. Ferrous and ferric ions-based high-throughput screening strategy for nitrile hydratase and amidase. J Microbiol Methods 2011; 85:214-20. [PMID: 21420446 DOI: 10.1016/j.mimet.2011.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 03/07/2011] [Accepted: 03/07/2011] [Indexed: 11/25/2022]
Abstract
Rapid and direct screening of nitrile-converting enzymes is of great importance in the development of industrial biocatalytic process for pharmaceuticals and fine chemicals. In this paper, a combination of ferrous and ferric ions was used to establish a novel colorimetric screening method for nitrile hydratase and amidase with α-amino nitriles and α-amino amides as substrates, respectively. Ferrous and ferric ions reacted sequentially with the cyanide dissociated spontaneously from α-amino nitrile solution, forming a characteristic deep blue precipitate. They were also sensitive to weak basicity due to the presence of amino amide, resulting in a yellow precipitate. When amino amide was further hydrolyzed to amino acid, it gave a light yellow solution. Mechanisms of color changes were further proposed. Using this method, two isolates with nitrile hydratase activity towards 2-amino-2,3-dimethyl butyronitrile, one strain capable of hydrating 2-amino-4-(hydroxymethyl phosphiny) butyronitrile and another microbe exhibiting amidase activity against 2-amino-4-methylsulfanyl butyrlamide were obtained from soil samples and culture collections of our laboratory. Versatility of this method enabled it the first direct and inexpensive high-throughput screening system for both nitrile hydratase and amidase.
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Affiliation(s)
- Zhi-Jian Lin
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
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18
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Schmidt M, Böttcher D, Bornscheuer UT. Directed Evolution of Industrial Biocatalysts. Ind Biotechnol (New Rochelle N Y) 2010. [DOI: 10.1002/9783527630233.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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19
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How to overcome limitations in biotechnological processes - examples from hydroxynitrile lyase applications. Trends Biotechnol 2009; 27:599-607. [DOI: 10.1016/j.tibtech.2009.07.005] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 07/01/2009] [Accepted: 07/13/2009] [Indexed: 11/17/2022]
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20
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Lavandera I, Kern A, Ferreira-Silva B, Glieder A, de Wildeman S, Kroutil W. Stereoselective Bioreduction of Bulky-Bulky Ketones by a Novel ADH from Ralstonia sp. J Org Chem 2008; 73:6003-5. [DOI: 10.1021/jo800849d] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Iván Lavandera
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Alexander Kern
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Bianca Ferreira-Silva
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Anton Glieder
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Stefaan de Wildeman
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Wolfgang Kroutil
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
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21
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Lavandera I, Kern A, Resch V, Ferreira-Silva B, Glieder A, Fabian WMF, de Wildeman S, Kroutil W. One-Way Biohydrogen Transfer for Oxidation of sec-Alcohols. Org Lett 2008; 10:2155-8. [DOI: 10.1021/ol800549f] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Iván Lavandera
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Alexander Kern
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Verena Resch
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Bianca Ferreira-Silva
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Anton Glieder
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Walter M. F. Fabian
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Stefaan de Wildeman
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
| | - Wolfgang Kroutil
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, Research Centre Applied Biocatalysis c/o Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14/2, 8010 Graz, Austria, Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria, and DSM Pharmaceutical Products, P.O. Box 18, 6160, MD Geleen, The Netherlands
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22
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Selection and screening for enzymes of nitrile metabolism. J Biotechnol 2008; 133:318-26. [DOI: 10.1016/j.jbiotec.2007.10.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 09/26/2007] [Accepted: 10/23/2007] [Indexed: 11/19/2022]
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23
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Lavandera I, Kern A, Schaffenberger M, Gross J, Glieder A, de Wildeman S, Kroutil W. An exceptionally DMSO-tolerant alcohol dehydrogenase for the stereoselective reduction of ketones. CHEMSUSCHEM 2008; 1:431-436. [PMID: 18702138 DOI: 10.1002/cssc.200800032] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A novel short-chain alcohol dehydrogenase from Paracoccus pantotrophus DSM 11072, which is applicable for hydrogen transfer, has been identified, cloned, and overexpressed in E. coli. The enzyme stereoselectively reduces several ketones in a sustainable substrate-coupled approach using 2-propanol (5% v/v) as hydrogen donor. The enzyme maintained its activity in organic co-solvents in biphasic as well as monophasic systems and was even active in micro-aqueous media (1% v/v aqueous buffer). In general, a higher conversion was observed at higher log P values of the solvent, however, DMSO, which exhibits the lowest log P value of all solvents investigated, was not only tolerated but led to a higher conversion and relative activity (110-210%). For example, the conversion after 24 h in 15% v/v DMSO was double that for the reaction performed in buffer. This tolerance to DMSO may be attributed to the ability of the wild-type strain to adapt and grow in media with high sulfur content.
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Affiliation(s)
- Iván Lavandera
- Research Centre Applied Biocatalysis c/o Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
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Steinreiber J, Fesko K, Mayer C, Reisinger C, Schürmann M, Griengl H. Synthesis of γ-halogenated and long-chain β-hydroxy-α-amino acids and 2-amino-1,3-diols using threonine aldolases. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.06.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Steinreiber J, Fesko K, Reisinger C, Schürmann M, van Assema F, Wolberg M, Mink D, Griengl H. Threonine aldolases—an emerging tool for organic synthesis. Tetrahedron 2007. [DOI: 10.1016/j.tet.2006.11.035] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Andexer J, Guterl JK, Pohl M, Eggert T. A high-throughput screening assay for hydroxynitrile lyase activity. Chem Commun (Camb) 2006:4201-3. [PMID: 17031431 DOI: 10.1039/b607863j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A high-throughput screening assay for hydroxynitrile lyase activity accepting a wide range of HNL-substrates is presented, which is useful either for enzyme fingerprinting or screening of huge variant libraries generated in metagenome or directed evolution approaches.
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Affiliation(s)
- Jennifer Andexer
- Institute of Molecular Enzyme Technology, Heinrich-Heine University Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
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