1
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Karvelis E, Swanson C, Tidor B. Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity. ACS Catal 2024; 14:10491-10509. [PMID: 39050899 PMCID: PMC11264209 DOI: 10.1021/acscatal.4c01446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/16/2024] [Accepted: 06/12/2024] [Indexed: 07/27/2024]
Abstract
The task of adapting enzymes for specific applications is often hampered by our incomplete ability to tune and tailor catalytic functions, particularly when seeking increased activity. Here, we develop and demonstrate a rational approach to address this challenge, applied to ketol-acid reductoisomerase (KARI), which has uses in industrial-scale isobutanol production. While traditional structure-based computational enzyme redesign strategies typically focus on the enzyme-bound ground state (GS) and transition state (TS), we postulated that additionally treating the underlying dynamics of complete turnover events that connect and pass through both states could further elucidate the structural properties affecting catalysis and help identify mutations that lead to increased catalytic activity. To examine the dynamics of substrate conversion with atomistic detail, we adapted and applied computational methods based on path sampling techniques to gather thousands of QM/MM simulations of attempted substrate turnover events by KARI: both productive (reactive) and unproductive (nonreactive) attempts. From these data, machine learning models were constructed and used to identify specific conformational features (interatomic distances, angles, and torsions) associated with successful, productive catalysis. Multistate protein redesign techniques were then used to select mutations that stabilized reactive-like structures over nonreactive-like ones while also meeting additional criteria consistent with enhanced specific activity. This procedure resulted in eight high-confidence enzyme mutants with a significant improvement in calculated specific activity relative to wild type (WT), with the fastest variant's increase in calculated k cat being (2 ± 1) × 104-fold. Collectively, these results suggest that introducing mutations designed to increase the population of reaction-promoting conformations of the enzyme-substrate complex before it reaches the barrier can provide an effective approach to engineering improved enzyme catalysts.
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Affiliation(s)
- Elijah Karvelis
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chloe Swanson
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bruce Tidor
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Computer
Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Hecko S, Schiefer A, Badenhorst CPS, Fink MJ, Mihovilovic MD, Bornscheuer UT, Rudroff F. Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity. Chem Rev 2023; 123:2832-2901. [PMID: 36853077 PMCID: PMC10037340 DOI: 10.1021/acs.chemrev.2c00304] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.
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Affiliation(s)
- Sebastian Hecko
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Astrid Schiefer
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Christoffel P S Badenhorst
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Michael J Fink
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Uwe T Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
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3
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Cui X, Du X, Zhao Q, Hu Y, Tian C, Song W. Efficient synthesis of Ala-Tyr by L-amino acid ligase coupled with ATP regeneration system. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04365-5. [PMID: 36689158 DOI: 10.1007/s12010-023-04365-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 01/24/2023]
Abstract
The multi-enzyme coupling reaction system has become a promising biomanufacturing platform for biochemical production. Tyr is an essential amino acid, but the limited solubility restricts its use. Tyrosyl dipeptide has been paid more attention due to its higher solubility. In this study, an efficient enzymatic cascade of Ala-Tyr synthesis was developed by a L-amino acid ligase together with polyphosphate kinase (PPK). Two L-amino acid ligases from Bacillus subtilis and Bacillus pumilus were selected and applied for Ala-Tyr synthesis. The L-amino acid ligase from B. subtilis (Bs) was selected and coupled with the PPK from Sulfurovum lithotrophicum (PPKSL) for regenerating ATP to produce Ala-Tyr in one pot. In the optimization system, 40.1 mM Ala-Tyr was produced within 3 h due to efficient ATP regeneration with hexametaphosphate (PolyP(6)) as the phosphate donor. The molar yield was 0.89 mol/mol based on the substrates added, while the productivity of Ala-Tyr achieved 13.4 mM/h, which were the highest yield and productivity ever reported about Ala-Tyr synthesis with L-amino acid ligase.
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Affiliation(s)
- Xiangwei Cui
- School of Life Science and Bioengineering, Jining University, Jining, 273155, China
| | - Xinxin Du
- School of Life Science and Bioengineering, Jining University, Jining, 273155, China
| | - Qiang Zhao
- School of Life Science and Bioengineering, Jining University, Jining, 273155, China
| | - Yanying Hu
- School of Life Science and Bioengineering, Jining University, Jining, 273155, China
| | - Caihong Tian
- School of Life Science and Bioengineering, Jining University, Jining, 273155, China
| | - Wenlu Song
- School of Engineering, Jining University, Jining, 273155, China.
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4
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Kaličanin N, Kovačević G, Spasojević M, Prodanović O, Jovanović-Šanta S, Škorić D, Opsenica D, Prodanović R. Immobilization of ArRMut11 omega-transaminase for increased operational stability and reusability in the synthesis of 3α-amino-5α-androstan-17β-ol. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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5
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Ma D, Cheng Z, Peplowski L, Han L, Xia Y, Hou X, Guo J, Yin D, Rao Y, Zhou Z. Insight into the broadened substrate scope of nitrile hydratase by static and dynamic structure analysis. Chem Sci 2022; 13:8417-8428. [PMID: 35919716 PMCID: PMC9297474 DOI: 10.1039/d2sc02319a] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/28/2022] [Indexed: 11/21/2022] Open
Abstract
The narrow substrate scope limits the wide industrial application of enzymes. Here, we successfully broadened the substrate scope of a nitrile hydratase (NHase) through mutation of two tunnel entrance residues based on rational tunnel calculation. Two variants, with increased specific activity, especially toward bulky substrates, were obtained. Crystal structure analysis revealed that the mutations led to the expansion of the tunnel entrance, which might be conducive to substrate entry. More importantly, molecular dynamics simulations illustrated that the mutations introduced anti-correlated movements to the regions around the substrate tunnel and the active site, which would promote substrate access during the dynamic process of catalysis. Additionally, mutations on the corresponding tunnel entrance residues on other NHases also enhanced their activity toward bulky substrates. These results not only revealed that residues located at the enzyme surface were a key factor in enzyme catalytic performance, but also provided dynamic evidence for insight into enzyme substrate scope broadening.
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Affiliation(s)
- Dong Ma
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University Wuxi Jiangsu 214122 China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University Wuxi Jiangsu 214122 China
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun Grudziadzka 5 87-100 Torun Poland
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University Wuxi Jiangsu 214122 China
| | - Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University Wuxi Jiangsu 214122 China
| | - Xiaodong Hou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University Wuxi Jiangsu 214122 China
| | - Junling Guo
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University Wuxi Jiangsu 214122 China
| | - Dejing Yin
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University Wuxi Jiangsu 214122 China
| | - Yijian Rao
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University Wuxi Jiangsu 214122 China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University Wuxi Jiangsu 214122 China
- Jiangnan University (Rugao) Food Biotechnology Research Institute Rugao Jiangsu China
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6
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Bordewick S, Berger RG, Ersoy F. Co-Immobilization of RizA Variants with Acetate Kinase for the Production of Bioactive Arginyl Dipeptides. Molecules 2022; 27:molecules27144352. [PMID: 35889224 PMCID: PMC9321006 DOI: 10.3390/molecules27144352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
The biocatalytic system comprised of RizA and acetate kinase (AckA) combines the specific synthesis of bioactive arginyl dipeptides with efficient ATP regeneration. Immobilization of this coupled enzyme system was performed and characterized in terms of activity, specificity and reusability of the immobilisates. Co-immobilization of RizA and AckA into a single immobilisate conferred no disadvantage in comparison to immobilization of only RizA, and a small addition of AckA (20:1) was sufficient for ATP regeneration. New variants of RizA were constructed by combining mutations to yield variants with increased biocatalytic activity and specificity. A selection of RizA variants were co-immobilized with AckA and used for the production of the salt-taste enhancers Arg-Ser and Arg-Ala and the antihypertensive Arg-Phe. The best variants yielded final dipeptide concentrations of 11.3 mM Arg-Ser (T81F_A158S) and 11.8 mM Arg-Phe (K83F_S156A), the latter of which represents a five-fold increase in comparison to the wild-type enzyme. T81F_A158S retained more than 50% activity for over 96 h and K83F_S156A for over 72 h. This study provides the first example of the successful co-immobilization of an l-amino acid ligase with an ATP-regenerating enzyme and paves the way towards a bioprocess for the production of bioactive dipeptides.
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7
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Mutagenesis of the l-Amino Acid Ligase RizA Increased the Production of Bioactive Dipeptides. Catalysts 2021. [DOI: 10.3390/catal11111385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The l-amino acid ligase RizA from B. subtilis selectively synthesizes dipeptides containing an N-terminal arginine. Many arginyl dipeptides have salt-taste enhancing properties while Arg-Phe has been found to have an antihypertensive effect. A total of 21 RizA variants were created by site-directed mutagenesis of eight amino acids in the substrate binding pocket. The variants were recombinantly produced in E. coli and purified by affinity chromatography. Biocatalytic reactions were set up with arginine and four amino acids differing in size and polarity (aspartic acid, serine, alanine, and phenylalanine) and were analyzed by RP-HPLC with fluorescence detection. Variant T81F significantly improved the yield in comparison to wild type RizA for aspartic acid (7 to 17%), serine (33 to 47%) and alanine (12 to 17%). S84F increased product yield similarly for aspartic acid (7 to 17%) and serine (33 to 42%). D376E increased the yield with alanine (12 to 19%) and phenylalanine (11 to 26%). The largest change was observed for S156A, which showed a yield for Arg-Phe of 40% corresponding to a 270% increase in product concentration. This study expands the knowledge about positions governing the substrate specificity of RizA and may help to inform future protein engineering endeavors.
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8
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Wang J, Gao C, Chen X, Liu L. Engineering the Cad pathway in Escherichia coli to produce glutarate from L-lysine. Appl Microbiol Biotechnol 2021; 105:3587-3599. [PMID: 33907891 DOI: 10.1007/s00253-021-11275-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/26/2021] [Accepted: 04/05/2021] [Indexed: 12/12/2022]
Abstract
For the efficient industrial production of glutarate, an important C5 platform chemical that is widely used in the chemical and pharmaceutical industries, a five-enzyme cascade pathway was designed and reconstructed in vitro to synthesize glutarate from L-lysine. Then, the imbalanced enzyme expression levels of L-lysine decarboxylase from Escherichia coli (EcCA), putrescine aminotransferase (KpcPA) and γ-aminovaleraldehyde dehydrogenase (KpcPD) from Klebsiella pneumoniae, and the poor catalytic efficiency of KpcPA were identified as the rate-limiting bottlenecks. To this end, ribosome binding site regulation was employed to coordinate the enzyme molar ratio of EcCA:KpcPA:KpcPD at approximately 4:8:7 (the optimum ratio obtained in vitro), and volume scanning and hydrophobicity scanning were applied to increase KpcPA activity toward cadaverine from 15.89 ± 0.52 to 75.87 ± 1.51 U·mg-1. Furthermore, the extracellular accumulation of 5-aminovalerate (5AVA) was considerably reduced by overexpressing gabP encoding the 5AVA importer. Combining these strategies into the engineered strain Glu-02, 77.62 g/L glutarate, the highest titer by E. coli to date, was produced from 100 g/L L-lysine in 42 h, with a yield and productivity of 0.78 g/g L-lysine and 1.85 g/L/h, respectively, at a 5-L scale. The results presented here provide a novel and potential enzymatic process at industrial-scale to produce glutarate from cheaper amino acids. KEY POINTS: • The bioconversion of l-lysine to glutarate using the Cad pathway was first achieved. • Enhancing the conversion efficiency of the Cad route maximizes glutarate in E. coli. • Achieving the highest titer of glutarate by E. coli to date.
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Affiliation(s)
- Jiaping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China. .,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.
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9
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Gupta S, Mazumder PB, Scott D, Ashokkumar M. Ultrasound-assisted production of biodiesel using engineered methanol tolerant Proteus vulgaris lipase immobilized on functionalized polysulfone beads. ULTRASONICS SONOCHEMISTRY 2020; 68:105211. [PMID: 32521485 DOI: 10.1016/j.ultsonch.2020.105211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/21/2020] [Accepted: 05/31/2020] [Indexed: 06/11/2023]
Abstract
In the present study, Proteus vulgaris lipase (PVL) was engineered using directed evolution to increase methanol tolerance so that it would be more tolerant and efficient for harsh conditions employed in biodiesel synthesis, which is limiting their industrial use. The influence of ultrasound under different experimental conditions on the biodiesel conversion yield using methanolysis of non-edible neem oil was also emphasized. A special attention was also paid to the immobilization of lipase on Polysulfone (PS) beads and comparative studies with industrially used Burkholderia cepacia lipase. The Engineered Proteus vulgaris lipase showed >80% activity after 3 h when incubated in 50% methanol with simultaneous sonication. The lipase retained improved longevity (~70% residual activity) over wild-type PVL over repeated use.
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Affiliation(s)
- Shweta Gupta
- Department of Biotechnology, Assam University Silchar, 788011 Assam, India
| | - P B Mazumder
- Department of Biotechnology, Assam University Silchar, 788011 Assam, India
| | - Daniel Scott
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, VIC 3010, Australia
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10
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Song W, Xu X, Gao C, Zhang Y, Wu J, Liu J, Chen X, Luo Q, Liu L. Open Gate of Corynebacterium glutamicum Threonine Deaminase for Efficient Synthesis of Bulky α-Keto Acids. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01672] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Xin Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Yuxuan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
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11
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Ureta MM, Martins GN, Figueira O, Pires PF, Castilho PC, Gomez-Zavaglia A. Recent advances in β-galactosidase and fructosyltransferase immobilization technology. Crit Rev Food Sci Nutr 2020; 61:2659-2690. [PMID: 32590905 DOI: 10.1080/10408398.2020.1783639] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The highly demanding conditions of industrial processes may lower the stability and affect the activity of enzymes used as biocatalysts. Enzyme immobilization emerged as an approach to promote stabilization and easy removal of enzymes for their reusability. The aim of this review is to go through the principal immobilization strategies addressed to achieve optimal industrial processes with special care on those reported for two types of enzymes: β-galactosidases and fructosyltransferases. The main methods used to immobilize these two enzymes are adsorption, entrapment, covalent coupling and cross-linking or aggregation (no support is used), all of them having pros and cons. Regarding the support, it should be cost-effective, assure the reusability and an easy recovery of the enzyme, increasing its stability and durability. The discussion provided showed that the type of enzyme, its origin, its purity, together with the type of immobilization method and the support will affect the performance during the enzymatic synthesis. Enzymes' immobilization involves interdisciplinary knowledge including enzymology, nanotechnology, molecular dynamics, cellular physiology and process design. The increasing availability of facilities has opened a variety of possibilities to define strategies to optimize the activity and re-usability of β-galactosidases and fructosyltransferases, but there is still great place for innovative developments.
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Affiliation(s)
- Maria Micaela Ureta
- Center for Research and Development in Food Cryotechnology (CIDCA, CCT-CONICET La Plata), La Plata, Argentina
| | | | - Onofre Figueira
- CQM - Centro de Química da Madeira, Universidade da Madeira, Funchal, Portugal
| | - Pedro Filipe Pires
- CQM - Centro de Química da Madeira, Universidade da Madeira, Funchal, Portugal
| | | | - Andrea Gomez-Zavaglia
- Center for Research and Development in Food Cryotechnology (CIDCA, CCT-CONICET La Plata), La Plata, Argentina
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12
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De Raffele D, Martí S, Moliner V. Understanding the Directed Evolution of De Novo Retro-Aldolases from QM/MM Studies. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Daria De Raffele
- Departament de Química Física i Analítica; Universitat Jaume I., 12071 Castellón, Spain
| | - Sergio Martí
- Departament de Química Física i Analítica; Universitat Jaume I., 12071 Castellón, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica; Universitat Jaume I., 12071 Castellón, Spain
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13
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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14
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Building Up Quaternary Stereocenters Through Biocatalyzed Direct Insertion of Carbon Nucleophiles on Ketones. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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15
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Rosini E, Pollegioni L. A comprehensive practical laboratory course on protein engineering: Evolution of a glycine oxidase variant active on the herbicide glyphosate. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:689-699. [PMID: 31444933 DOI: 10.1002/bmb.21291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/01/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Protein engineering represents a modern approach to generate novel proteins for the different fields of biotechnology. Here, we report about an 8-day laboratory activity in which students generate enzyme variants to degrade the herbicide glyphosate. The students conduct a true research experiment in an important field (bioremediation by novel, engineered enzymes) and are introduced to widely used techniques in molecular biology and protein biochemistry laboratories. Based on a docking analysis of glycine (the original substrate) and of glyphosate into the active site of glycine oxidase, residues putatively involved in substrate selectivity are identified that will become the target of site-saturation mutagenesis. Each group of students focuses on the library generated at one position and selects the most active variant based on colorimetric screening. Following protein overexpression in Escherichia coli, the selected glycine oxidase variants are purified and their kinetic properties on glycine and glyphosate assessed. The best variant identified by the whole class is then used for detecting the herbicide in water. With the help of the professor, students can improve technical skills, ability to evaluate results, team work activity, and critical thinking. © 2019 International Union of Biochemistry and Molecular Biology, 47(6):689-699, 2019.
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Affiliation(s)
- Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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16
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Ahmad AA, Kasim KF, Ma’Radzi AH, Gopinath SC. Peptic ulcer: Current prospects of diagnostic and nanobiotechnological trends on pathogenicity. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.06.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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17
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Enzymes from Marine Polar Regions and Their Biotechnological Applications. Mar Drugs 2019; 17:md17100544. [PMID: 31547548 PMCID: PMC6835263 DOI: 10.3390/md17100544] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
The microorganisms that evolved at low temperatures express cold-adapted enzymes endowed with unique catalytic properties in comparison to their mesophilic homologues, i.e., higher catalytic efficiency, improved flexibility, and lower thermal stability. Cold environments are therefore an attractive research area for the discovery of enzymes to be used for investigational and industrial applications in which such properties are desirable. In this work, we will review the literature on cold-adapted enzymes specifically focusing on those discovered in the bioprospecting of polar marine environments, so far largely neglected because of their limited accessibility. We will discuss their existing or proposed biotechnological applications within the framework of the more general applications of cold-adapted enzymes.
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18
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De Raffele D, Martí S, Moliner V. QM/MM Theoretical Studies of a de Novo Retro-Aldolase Design. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04457] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daria De Raffele
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
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19
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Gao S, Lu Y, Li Y, Huang R, Zheng G. Enhancement in the catalytic activity of Sulfolobus solfataricus P2 (+)-γ-lactamase by semi-rational design with the aid of a newly established high-throughput screening method. Appl Microbiol Biotechnol 2018; 103:251-263. [DOI: 10.1007/s00253-018-9428-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/26/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022]
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20
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Sehajpal P, Kirar S, Ghosh S, Banerjee UC. Generation of novel family of reductases from PCR based library for the synthesis of chiral alcohols and amines. Enzyme Microb Technol 2018; 118:83-91. [PMID: 30143204 DOI: 10.1016/j.enzmictec.2018.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 06/26/2018] [Accepted: 07/27/2018] [Indexed: 11/19/2022]
Abstract
Biocatalysis has shown tremendous potential in the synthesis of drugs and drug intermediates in the last decade. Screening of novel biocatalysts from the natural genome space is the growing trend to replenish the harsh chemical synthetic routes, commonly used in the pharmaceutical and chemical industry. Here, we report a novel ketoreductase (KERD) and a nitrile reductase isolated from the PCR based library generated from the genome of Rhodococcus ruber and Bacillus subtilis, respectively. Both the proteins are hypothetical in nature as there is no putative homology found in the database, although both the enzymes have significant activity towards the synthesis of chiral alcohols and amines. Enzyme activity over a wide range of substrates (aromatic and aliphatic) for both the novel catalysts was observed. From the unique gene sequence to activity over a broad range of substrate and >99% conversion at higher concentrations (100 mM and above) entitles both the hypothetical enzymes as novel. The novel KERD has shown >99% selectivity for the synthesis of (S)-phenylethanol which makes it a potential candidate for industrial catalysis. The novel nitrile reductase has also shown promising activity for the synthesis of (R)-2-phenylethanolamine, which is a difficult moiety to synthesize chemically. In this report, starting from a homology based library, two highly potent whole cell biocatalysts are obtained.
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Affiliation(s)
- Pallvi Sehajpal
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Sector 67, S. A. S. Nagar, 160062, Punjab, India
| | - Seema Kirar
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Sector 67, S. A. S. Nagar, 160062, Punjab, India
| | - Saptarshi Ghosh
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Sector 67, S. A. S. Nagar, 160062, Punjab, India
| | - Uttam Chand Banerjee
- Department of Pharmaceutical Technology (Biotechnology), National Institute of Pharmaceutical Education and Research, Sector 67, S. A. S. Nagar, 160062, Punjab, India.
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21
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Highly Efficient Deracemization of Racemic 2-Hydroxy Acids in a Three-Enzyme Co-Expression System Using a Novel Ketoacid Reductase. Appl Biochem Biotechnol 2018; 186:563-575. [PMID: 29675666 DOI: 10.1007/s12010-018-2760-0] [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: 02/02/2018] [Accepted: 04/10/2018] [Indexed: 12/26/2022]
Abstract
Enantiopure 2-hydroxy acids (2-HAs) are important intermediates for the synthesis of pharmaceuticals and fine chemicals. Deracemization of racemic 2-HAs into the corresponding single enantiomers represents an economical and highly efficient approach for synthesizing chiral 2-HAs in industry. In this work, a novel ketoacid reductase from Leuconostoc lactis (LlKAR) with higher activity and substrate tolerance towards aromatic α-ketoacids was discovered by genome mining, and then its enzymatic properties were characterized. Accordingly, an engineered Escherichia coli (HADH-LlKAR-GDH) co-expressing 2-hydroxyacid dehydrogenase, LlKAR, and glucose dehydrogenase was constructed for efficient deracemization of racemic 2-HAs. Most of the racemic 2-HAs were deracemized to their (R)-isomers at high yields and enantiomeric purity. In the case of racemic 2-chloromandelic acid, as much as 300 mM of substrate was completely transformed into the optically pure (R)-2-chloromandelic acid (> 99% enantiomeric excess) with a high productivity of 83.8 g L-1 day-1 without addition of exogenous cofactor, which make this novel whole-cell biocatalyst more promising and competitive in practical application.
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22
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Engineering the Enantioselectivity and Thermostability of a (+)-γ-Lactamase from Microbacterium hydrocarbonoxydans for Kinetic Resolution of Vince Lactam (2-Azabicyclo[2.2.1]hept-5-en-3-one). Appl Environ Microbiol 2017; 84:AEM.01780-17. [PMID: 29054871 DOI: 10.1128/aem.01780-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/29/2017] [Indexed: 11/20/2022] Open
Abstract
To produce promising biocatalysts, natural enzymes often need to be engineered to increase their catalytic performance. In this study, the enantioselectivity and thermostability of a (+)-γ-lactamase from Microbacterium hydrocarbonoxydans as the catalyst in the kinetic resolution of Vince lactam (2-azabicyclo[2.2.1]hept-5-en-3-one) were improved. Enantiomerically pure (-)-Vince lactam is the key synthon in the synthesis of antiviral drugs, such as carbovir and abacavir, which are used to fight against HIV and hepatitis B virus. The work was initialized by using the combinatorial active-site saturation test strategy to engineer the enantioselectivity of the enzyme. The approach resulted in two mutants, Val54Ser and Val54Leu, which catalyzed the hydrolysis of Vince lactam to give (-)-Vince lactam, with 99.2% (enantiomeric ratio [E] > 200) enantiomeric excess (ee) and 99.5% ee (E > 200), respectively. To improve the thermostability of the enzyme, 11 residues with high temperature factors (B-factors) calculated by B-FITTER or high root mean square fluctuation (RMSF) values from the molecular dynamics simulation were selected. Six mutants with increased thermostability were obtained. Finally, the mutants generated with improved enantioselectivity and mutants evolved for enhanced thermostability were combined. Several variants showing (+)-selectivity (E value > 200) and improved thermostability were observed. These engineered enzymes are good candidates to serve as enantioselective catalysts for the preparation of enantiomerically pure Vince lactam.IMPORTANCE Enzymatic kinetic resolution of the racemic Vince lactam using (+)-γ-lactamase is the most often utilized means of resolving the enantiomers for the preparation of carbocyclic nucleoside compounds. The efficiency of the native enzymes could be improved by using protein engineering methods, such as directed evolution and rational design. In our study, two properties (enantioselectivity and thermostability) of a γ-lactamase identified from Microbacterium hydrocarbonoxydans were tackled using a semirational design. The protein engineering was initialized by combinatorial active-site saturation test to improve the enantioselectivity. At the same time, two strategies were applied to identify mutation candidates to enhance the thermostability based on calculations from both a static (B-FITTER based on the crystal structure) and a dynamic (root mean square fluctuation [RMSF] values based on molecular dynamics simulations) way. After combining the mutants, we successfully obtained the final mutants showing better properties in both properties. The engineered (+)-lactamase could be a candidate for the preparation of (-)-Vince lactam.
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23
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Zhang Y, Supuran CT, Barboiu M. Exponential Activation of Carbonic Anhydrase by Encapsulation in Dynameric Host Matrices with Chiral Discrimination. Chemistry 2017; 24:715-720. [PMID: 29119623 DOI: 10.1002/chem.201704605] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Indexed: 12/12/2022]
Abstract
Herein an unexpected exponential activation of bovine carbonic anhydrase (bCA) in aqueous solutions in the presence of dynameric host matrices is reported. Successive experiments confirmed the important role of dynamic imine exchange within the dynameric host structures for direct enzyme activation. This allows for optimal encapsulation of the guest enzyme, whereas the presence of external proton-sponge amino groups is less important. Non-exchanging polymeric sec-amine congeners formed from imine reduction of dynameric structures show no obvious activation on bCA. Although the dynamers synthesized from diamino chiral-pair precursors displayed similar activation constants toward bCA, different activation delay times were observed from these two dynamers of opposite optical activity. The circular dichroism (CD) spectra demonstrate selective structural changes in the secondary structure of bCA upon dynameric encapsulation in aqueous solution. The different interaction molds observed in CD spectra for the dynamers with opposite chirality explain the longer activation time required for one of the dynamers.
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Affiliation(s)
- Yan Zhang
- Adaptive Supramolecular Nanosystems Group, Institut Européen des Membranes, University of Montpellier, ENSCM-CNRS, Place Eugène Bataillon, CC 047, 34095, Montpellier, France.,School of Pharmaceutical Sciences, Jiangnan University, Lihu Road 1800, 214122, Wuxi, P.R. China
| | - Claudiu T Supuran
- Laboratorio di Chimica Bio-inorganica, Università degli Studi di Firenze, Polo Scientifico, Rm. 188, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Mihail Barboiu
- Adaptive Supramolecular Nanosystems Group, Institut Européen des Membranes, University of Montpellier, ENSCM-CNRS, Place Eugène Bataillon, CC 047, 34095, Montpellier, France
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24
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Silva C, Martins M, Jing S, Fu J, Cavaco-Paulo A. Practical insights on enzyme stabilization. Crit Rev Biotechnol 2017; 38:335-350. [PMID: 28764566 DOI: 10.1080/07388551.2017.1355294] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Enzymes are efficient catalysts designed by nature to work in physiological environments of living systems. The best operational conditions to access and convert substrates at the industrial level are different from nature and normally extreme. Strategies to isolate enzymes from extremophiles can redefine new operational conditions, however not always solving all industrial requirements. The stability of enzymes is therefore a key issue on the implementation of the catalysts in industrial processes which require the use of extreme environments that can undergo enzyme instability. Strategies for enzyme stabilization have been exhaustively reviewed, however they lack a practical approach. This review intends to compile and describe the most used approaches for enzyme stabilization highlighting case studies in a practical point of view.
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Affiliation(s)
- Carla Silva
- a Centre of Biological Engineering (CEB) , University of Minho , Braga , Portugal
| | - Madalena Martins
- a Centre of Biological Engineering (CEB) , University of Minho , Braga , Portugal
| | - Su Jing
- b International Joint Research Laboratory for Textile and Fiber Bioprocesses , Jiangnan University , Wuxi , China
| | - Jiajia Fu
- c Key Laboratory of Science and Technology of Eco-Textiles , Ministry of Education, Jiangnan University , Wuxi , Jiangsu , China
| | - Artur Cavaco-Paulo
- a Centre of Biological Engineering (CEB) , University of Minho , Braga , Portugal.,b International Joint Research Laboratory for Textile and Fiber Bioprocesses , Jiangnan University , Wuxi , China
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25
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Organocatalysis and Biocatalysis Hand in Hand: Combining Catalysts in One-Pot Procedures. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700158] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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26
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Discovery and structural characterisation of new fold type IV-transaminases exemplify the diversity of this enzyme fold. Sci Rep 2016; 6:38183. [PMID: 27905516 PMCID: PMC5131300 DOI: 10.1038/srep38183] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/04/2016] [Indexed: 12/26/2022] Open
Abstract
Transaminases are useful biocatalysts for the production of amino acids and chiral amines as intermediates for a broad range of drugs and fine chemicals. Here, we describe the discovery and characterisation of new transaminases from microorganisms which were enriched in selective media containing (R)-amines as sole nitrogen source. While most of the candidate proteins were clearly assigned to known subgroups of the fold IV family of PLP-dependent enzymes by sequence analysis and characterisation of their substrate specificity, some of them did not fit to any of these groups. The structure of one of these enzymes from Curtobacterium pusillum, which can convert d-amino acids and various (R)-amines with high enantioselectivity, was solved at a resolution of 2.4 Å. It shows significant differences especially in the active site compared to other transaminases of the fold IV family and thus indicates the existence of a new subgroup within this family. Although the discovered transaminases were not able to convert ketones in a reasonable time frame, overall, the enrichment-based approach was successful, as we identified two amine transaminases, which convert (R)-amines with high enantioselectivity, and can be used for a kinetic resolution of 1-phenylethylamine and analogues to obtain the (S)-amines with e.e.s >99%.
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27
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Wallace PW, Haernvall K, Ribitsch D, Zitzenbacher S, Schittmayer M, Steinkellner G, Gruber K, Guebitz GM, Birner-Gruenberger R. PpEst is a novel PBAT degrading polyesterase identified by proteomic screening of Pseudomonas pseudoalcaligenes. Appl Microbiol Biotechnol 2016; 101:2291-2303. [PMID: 27872998 PMCID: PMC5320007 DOI: 10.1007/s00253-016-7992-8] [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: 07/20/2016] [Revised: 10/27/2016] [Accepted: 11/05/2016] [Indexed: 11/23/2022]
Abstract
A novel esterase, PpEst, that hydrolyses the co-aromatic-aliphatic polyester poly(1,4-butylene adipate-co-terephthalate) (PBAT) was identified by proteomic screening of the Pseudomonas pseudoalcaligenes secretome. PpEst was induced by the presence of PBAT in the growth media and had predicted arylesterase (EC 3.1.1.2) activity. PpEst showed polyesterase activity on both whole and milled PBAT film releasing terephthalic acid and 4-(4-hydroxybutoxycarbonyl)benzoic acid while end product inhibition by 4-(4-hydroxybutoxycarbonyl)benzoic acid was observed. Modelling of an aromatic polyester mimicking oligomer into the PpEst active site indicated that the binding pocket could be big enough to accommodate large polymers. This is the first report of a PBAT degrading enzyme being identified by proteomic screening and shows that this approach can contribute to the discovery of new polymer hydrolysing enzymes. Moreover, these results indicate that arylesterases could be an interesting enzyme class for identifications of polyesterases.
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Affiliation(s)
- Paal W Wallace
- Research Unit for Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 24, 8010, Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria.,Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Karolina Haernvall
- Austrian Centre of Industrial Biotechnology, Konrad Lorenz Strasse 20, 3430, Tulln, Austria
| | - Doris Ribitsch
- Austrian Centre of Industrial Biotechnology, Konrad Lorenz Strasse 20, 3430, Tulln, Austria.,Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Vienna, Austria
| | - Sabine Zitzenbacher
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Matthias Schittmayer
- Research Unit for Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 24, 8010, Graz, Austria.,Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Georg Steinkellner
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria
| | - Karl Gruber
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria.,Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/III, 8010, Graz, Austria
| | - Georg M Guebitz
- Austrian Centre of Industrial Biotechnology, Konrad Lorenz Strasse 20, 3430, Tulln, Austria.,Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Konrad Lorenz Strasse 20, 3430, Tulln, Vienna, Austria
| | - Ruth Birner-Gruenberger
- Research Unit for Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 24, 8010, Graz, Austria. .,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria. .,Omics Center Graz, BioTechMed-Graz, Graz, Austria.
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28
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Synergism of proteomics and mRNA sequencing for enzyme discovery. J Biotechnol 2016; 235:132-8. [DOI: 10.1016/j.jbiotec.2015.12.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/07/2015] [Accepted: 12/14/2015] [Indexed: 12/14/2022]
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29
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Zorn K, Oroz-Guinea I, Brundiek H, Bornscheuer UT. Engineering and application of enzymes for lipid modification, an update. Prog Lipid Res 2016; 63:153-64. [DOI: 10.1016/j.plipres.2016.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/30/2016] [Accepted: 06/10/2016] [Indexed: 12/21/2022]
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30
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Gaber Y, Ismail M, Bisagni S, Takwa M, Hatti-Kaul R. Rational mutagenesis of pig liver esterase (PLE-1) to resolve racemic clopidogrel. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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31
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Carnero A, Sanghvi YS, Gotor V, Fernández S, Ferrero M. Process Development of Biocatalytic Regioselective 5′-O-Levulinylation of 2′-Deoxynucleosides. Org Process Res Dev 2015. [DOI: 10.1021/acs.oprd.5b00152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alejandro Carnero
- Departamento
de Química Orgánica e Inorgánica and Instituto
Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006 Oviedo, Asturias, Spain
| | - Yogesh S. Sanghvi
- Rasayan Inc., 2802 Crystal
Ridge Road, Encinitas, California 92024-6615, United States
| | - Vicente Gotor
- Departamento
de Química Orgánica e Inorgánica and Instituto
Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006 Oviedo, Asturias, Spain
| | - Susana Fernández
- Departamento
de Química Orgánica e Inorgánica and Instituto
Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006 Oviedo, Asturias, Spain
| | - Miguel Ferrero
- Departamento
de Química Orgánica e Inorgánica and Instituto
Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006 Oviedo, Asturias, Spain
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32
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Guérard-Hélaine C, de Berardinis V, Besnard-Gonnet M, Darii E, Debacker M, Debard A, Fernandes C, Hélaine V, Mariage A, Pellouin V, Perret A, Petit JL, Sancelme M, Lemaire M, Salanoubat M. Genome Mining for Innovative Biocatalysts: New Dihydroxyacetone Aldolases for the Chemist’s Toolbox. ChemCatChem 2015. [DOI: 10.1002/cctc.201500014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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33
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Xu GC, Ni Y. Bioreductive preparation of ACE inhibitors precursor (R)-2-hydroxy-4-phenylbutanoate esters: Recent advances and future perspectives. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-015-0040-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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34
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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35
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Sprague D, Nugent BM, Yoder RA, Vara BA, Johnston JN. Adaptation of a small-molecule hydrogen-bond donor catalyst to an enantioselective hetero-Diels-Alder reaction hypothesized for brevianamide biosynthesis. Org Lett 2015; 17:880-3. [PMID: 25697748 PMCID: PMC4339957 DOI: 10.1021/ol503626w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Indexed: 12/22/2022]
Abstract
Chiral diamine-derived hydrogen-bond donors were evaluated for their ability to effect stereocontrol in an intramolecular hetero-Diels-Alder (HDA) reaction hypothesized in the biosynthesis of brevianamides A and B. Collectively, these results provide proof of principle that small-molecule hydrogen-bond catalysis, if even based on a hypothetical biosynthesis construct, holds significant potential within enantioselective natural product synthesis.
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Affiliation(s)
- Daniel
J. Sprague
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Benjamin M. Nugent
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ryan A. Yoder
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brandon A. Vara
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey N. Johnston
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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36
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Bormann S, Gomez Baraibar A, Ni Y, Holtmann D, Hollmann F. Specific oxyfunctionalisations catalysed by peroxygenases: opportunities, challenges and solutions. Catal Sci Technol 2015. [DOI: 10.1039/c4cy01477d] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Peroxygenases are promising oxyfunctionalisation catalysts for organic synthesis.
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Affiliation(s)
| | - Alvaro Gomez Baraibar
- Delft University of Technology
- Department of Biotechnology
- 2628 BL Delft
- The Netherlands
| | - Yan Ni
- Delft University of Technology
- Department of Biotechnology
- 2628 BL Delft
- The Netherlands
| | - Dirk Holtmann
- DECHEMA Research Institute
- 60486 Frankfurt am Main
- Germany
| | - Frank Hollmann
- Delft University of Technology
- Department of Biotechnology
- 2628 BL Delft
- The Netherlands
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37
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Characterizing Synthetic Biology Through Its Novel and Enhanced Functionalities. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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38
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Xu GC, Yu HL, Shang YP, Xu JH. Enantioselective bioreductive preparation of chiral halohydrins employing two newly identified stereocomplementary reductases. RSC Adv 2015. [DOI: 10.1039/c4ra16779a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Two robust stereocomplementary carbonyl reductases (DhCR andCgCR) for preparation of hylohydrins were identified through rescreening the carbonyl reductase toolbox.
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Affiliation(s)
- Guo-Chao Xu
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- and Shanghai Collaborative Innovation Center for Biomanufacturing Technology
- Shanghai 200237
- China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- and Shanghai Collaborative Innovation Center for Biomanufacturing Technology
- Shanghai 200237
- China
| | - Yue-Peng Shang
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- and Shanghai Collaborative Innovation Center for Biomanufacturing Technology
- Shanghai 200237
- China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering
- East China University of Science and Technology
- and Shanghai Collaborative Innovation Center for Biomanufacturing Technology
- Shanghai 200237
- China
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39
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40
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Yang G, Ding Y. Recent advances in biocatalyst discovery, development and applications. Bioorg Med Chem 2014; 22:5604-12. [DOI: 10.1016/j.bmc.2014.06.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 12/25/2022]
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41
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Schrewe M, Julsing MK, Bühler B, Schmid A. Whole-cell biocatalysis for selective and productive C-O functional group introduction and modification. Chem Soc Rev 2014; 42:6346-77. [PMID: 23475180 DOI: 10.1039/c3cs60011d] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
During the last decades, biocatalysis became of increasing importance for chemical and pharmaceutical industries. Regarding regio- and stereospecificity, enzymes have shown to be superior compared to traditional chemical synthesis approaches, especially in C-O functional group chemistry. Catalysts established on a process level are diverse and can be classified along a functional continuum starting with single-step biotransformations using isolated enzymes or microbial strains towards fermentative processes with recombinant microorganisms containing artificial synthetic pathways. The complex organization of respective enzymes combined with aspects such as cofactor dependency and low stability in isolated form often favors the use of whole cells over that of isolated enzymes. Based on an inventory of the large spectrum of biocatalytic C-O functional group chemistry, this review focuses on highlighting the potentials, limitations, and solutions offered by the application of self-regenerating microbial cells as biocatalysts. Different cellular functionalities are discussed in the light of their (possible) contribution to catalyst efficiency. The combined achievements in the areas of protein, genetic, metabolic, and reaction engineering enable the development of whole-cell biocatalysts as powerful tools in organic synthesis.
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Affiliation(s)
- Manfred Schrewe
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
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42
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Zhang ZJ, Pan J, Ma BD, Xu JH. Efficient Biocatalytic Synthesis of Chiral Chemicals. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 155:55-106. [DOI: 10.1007/10_2014_291] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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43
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Xu GC, Yu HL, Zhang ZJ, Xu JH. Stereocomplementary Bioreduction of β-Ketonitrile without Ethylated Byproduct. Org Lett 2013; 15:5408-11. [DOI: 10.1021/ol402733y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guo-Chao Xu
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
| | - Hui-Lei Yu
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
| | - Zhi-Jun Zhang
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
| | - Jian-He Xu
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People’s Republic of China
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44
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Schrittwieser JH, Resch V. The role of biocatalysis in the asymmetric synthesis of alkaloids. RSC Adv 2013; 3:17602-17632. [PMID: 25580241 PMCID: PMC4285126 DOI: 10.1039/c3ra42123f] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/28/2013] [Indexed: 12/11/2022] Open
Abstract
Alkaloids are not only one of the most intensively studied classes of natural products, their wide spectrum of pharmacological activities also makes them indispensable drug ingredients in both traditional and modern medicine. Among the methods for their production, biotechnological approaches are gaining importance, and biocatalysis has emerged as an essential tool in this context. A number of chemo-enzymatic strategies for alkaloid synthesis have been developed over the years, in which the biotransformations nowadays take an increasingly 'central' role. This review summarises different applications of biocatalysis in the asymmetric synthesis of alkaloids and discusses how recent developments and novel enzymes render innovative and efficient chemo-enzymatic production routes possible.
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Affiliation(s)
- Joerg H Schrittwieser
- Department of Biotechnology , Delft University of Technology , Julianalaan 136 , 2628 BL Delft , The Netherlands . ; ; ; Tel: +31 152 782683
| | - Verena Resch
- Department of Biotechnology , Delft University of Technology , Julianalaan 136 , 2628 BL Delft , The Netherlands . ; ; ; Tel: +31 152 782683
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45
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Giese B, Koenigstein S, Wigger H, Schmidt JC, von Gleich A. Rational Engineering Principles in Synthetic Biology: A Framework for Quantitative Analysis and an Initial Assessment. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s13752-013-0130-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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46
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Liu CH, Pan J, Ye Q, Xu JH. Enzymatic production of Cilastatin intermediate via highly enantioselective hydrolysis of methyl (±)-2,2-dimethylcyclopropane carboxylate using newly isolated Rhodococcus sp. ECU1013. Appl Microbiol Biotechnol 2013; 97:7659-67. [PMID: 23807665 DOI: 10.1007/s00253-013-5038-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/25/2013] [Accepted: 06/07/2013] [Indexed: 11/29/2022]
Abstract
(S)-(+)-2,2-Dimethylcyclopropane carboxylic acid [(S)-(+)-DMCPA] is a key chiral intermediate for production of Cilastatin, an excellent renal dehydropeptidase-I inhibitor. In this study, a new method for preparation of (S)-(+)-DMCPA with microbial esterases was investigated. A microbial screening program obtained six esterase-producing isolates that could display relatively high activities and enantioselectivities using racemic ethyl 2,2-dimethylcyclopropane carboxylate (DMCPE) as screening substrate, aiming at forming optically pure (S)-(+)-DMCPA. Further selection was carried out with substrates having different alcohol moieties, including methyl, ethyl, and 2-chloroethyl esters. Finally, one of these strains, numbered ECU1013, with high enantioselectivity toward the hydrolytic resolution of methyl 2,2-dimethylcyclopropane carboxylate (DMCPM), afforded the (S)-product in 92 % ee, and was later identified as Rhodococcus sp. According to our research, there were several active esterases to DMCPM in cells of Rhodococcus sp. ECU1013; however, (S)-preferential esterase was selectively enriched based on the time-dependent profile of esterases biosynthesis, thereby the enantiomeric excess of biotransformation product (ee p) was constantly increased, finally maintained at 95 % (S). To improve the yield, various organic solvents were employed for better dispersion of the hydrophobic substrate. As a result, (±)-DMCPM of up to 400 mM in the organic phase of isooctane was enantioselectively hydrolyzed into (S)-(+)-DMCPA, with an isolation yield of 38 % and a further increase of ee p to 99 %.
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Affiliation(s)
- Chao-Hong Liu
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
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47
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Sullivan B, Walton AZ, Stewart JD. Library construction and evaluation for site saturation mutagenesis. Enzyme Microb Technol 2013; 53:70-7. [PMID: 23683706 DOI: 10.1016/j.enzmictec.2013.02.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/15/2013] [Accepted: 02/20/2013] [Indexed: 01/24/2023]
Abstract
We developed a method for creating and evaluating site-saturation libraries that consistently yields an average of 27.4±3.0 codons of the 32 possible within a pool of 95 transformants. This was verified by sequencing 95 members from 11 independent libraries within the gene encoding alkene reductase OYE 2.6 from Pichia stipitis. Correct PCR primer design as well as a variety of factors that increase transformation efficiency were critical contributors to the method's overall success. We also developed a quantitative analysis of library quality (Q-values) that defines library degeneracy. Q-values can be calculated from standard fluorescence sequencing data (capillary electropherograms) and the degeneracy predicted from an early stage of library construction (pooled plasmids from the initial transformation) closely matched that observed after ca. 1000 library members were sequenced. Based on this experience, we suggest that this analysis can be a useful guide when applying our optimized protocol to new systems, allowing one to focus only on good-quality libraries and reject substandard libraries at an early stage. This advantage is particularly important when lower-throughput screening techniques such as chiral-phase GC must be employed to identify protein variants with desirable properties, e.g., altered stereoselectivities or when multiple codons are targeted for simultaneous randomization.
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Affiliation(s)
- Bradford Sullivan
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
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48
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computational enzyme design. Angew Chem Int Ed Engl 2013; 52:5700-25. [PMID: 23526810 DOI: 10.1002/anie.201204077] [Citation(s) in RCA: 355] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Indexed: 11/07/2022]
Abstract
Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.
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Affiliation(s)
- Gert Kiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA 90095, USA
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49
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computerbasiertes Enzymdesign. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204077] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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Davids T, Schmidt M, Böttcher D, Bornscheuer UT. Strategies for the discovery and engineering of enzymes for biocatalysis. Curr Opin Chem Biol 2013; 17:215-20. [PMID: 23523243 DOI: 10.1016/j.cbpa.2013.02.022] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 01/30/2013] [Accepted: 02/14/2013] [Indexed: 11/16/2022]
Abstract
Protein engineering is the most important method to overcome the limitations of natural enzymes as biocatalysts. The past few years have seen a tremendous increase in novel concepts to facilitate the design of mutant libraries for focused directed evolution mostly guided by advanced bioinformatic tools. In addition, advanced high-throughput methods were developed using, for example, FACS analysis or microfluidic systems. These achievements significantly facilitate the tailor-made design of enzymes to make them suitable for industrial applications.
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Affiliation(s)
- Timo Davids
- Institute of Biochemistry, Department of Biotechnology and Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
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