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Hwang J, Lee MJ, Lee SG, Do H, Lee JH. Structural insights into the distinct substrate preferences of two bacterial epoxide hydrolases. Int J Biol Macromol 2024; 264:130419. [PMID: 38423431 DOI: 10.1016/j.ijbiomac.2024.130419] [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: 11/20/2023] [Revised: 01/22/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
Epoxide hydrolases (EHs), which catalyze the transformation of epoxides to diols, are present in many eukaryotic and prokaryotic organisms. They have recently drawn considerable attention from organic chemists owing to their application in the semisynthesis of enantiospecific diol compounds. Here, we report the crystal structures of BoEH from Bosea sp. PAMC 26642 and CaEH from Caballeronia sordidicola PAMC 26510 at 1.95 and 2.43 Å resolution, respectively. Structural analysis showed that the overall structures of BoEH and CaEH commonly possess typical α/β hydrolase fold with the same ring-opening residues (Tyr-Tyr) and conserved catalytic triad residues (Asp-Asp-His). However, the two enzymes were found to have significantly different sequence compositions in the cap domain region, which is involved in the formation of the substrate-binding site in both enzymes. Enzyme activity assay results showed that BoEH had the strongest activity toward the linear aliphatic substrates, whereas CaEH had a higher preference for aromatic- and cycloaliphatic substrates. Computational docking simulations and tunnel identification revealed important residues with different substrate-binding preferences. Collectively, structure comparison studies, together with ligand docking simulation results, suggested that the differences in substrate-binding site residues were highly correlated with substrate specificity.
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Affiliation(s)
- Jisub Hwang
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Min Ju Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Sung Gu Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Hackwon Do
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.
| | - Jun Hyuck Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.
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Chatterjee A, Puri S, Sharma PK, Deepa PR, Chowdhury S. Nature-inspired Enzyme engineering and sustainable catalysis: biochemical clues from the world of plants and extremophiles. Front Bioeng Biotechnol 2023; 11:1229300. [PMID: 37409164 PMCID: PMC10318364 DOI: 10.3389/fbioe.2023.1229300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
The use of enzymes to accelerate chemical reactions for the synthesis of industrially important products is rapidly gaining popularity. Biocatalysis is an environment-friendly approach as it not only uses non-toxic, biodegradable, and renewable raw materials but also helps to reduce waste generation. In this context, enzymes from organisms living in extreme conditions (extremozymes) have been studied extensively and used in industries (food and pharmaceutical), agriculture, and molecular biology, as they are adapted to catalyze reactions withstanding harsh environmental conditions. Enzyme engineering plays a key role in integrating the structure-function insights from reference enzymes and their utilization for developing improvised catalysts. It helps to transform the enzymes to enhance their activity, stability, substrates-specificity, and substrate-versatility by suitably modifying enzyme structure, thereby creating new variants of the enzyme with improved physical and chemical properties. Here, we have illustrated the relatively less-tapped potentials of plant enzymes in general and their sub-class of extremozymes for industrial applications. Plants are exposed to a wide range of abiotic and biotic stresses due to their sessile nature, for which they have developed various mechanisms, including the production of stress-response enzymes. While extremozymes from microorganisms have been extensively studied, there are clear indications that plants and algae also produce extremophilic enzymes as their survival strategy, which may find industrial applications. Typical plant enzymes, such as ascorbate peroxidase, papain, carbonic anhydrase, glycoside hydrolases and others have been examined in this review with respect to their stress-tolerant features and further improvement via enzyme engineering. Some rare instances of plant-derived enzymes that point to greater exploration for industrial use have also been presented here. The overall implication is to utilize biochemical clues from the plant-based enzymes for robust, efficient, and substrate/reaction conditions-versatile scaffolds or reference leads for enzyme engineering.
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Affiliation(s)
| | | | | | - P. R. Deepa
- *Correspondence: P. R. Deepa, ; Shibasish Chowdhury,
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Bučko M, Kaniaková K, Hronská H, Gemeiner P, Rosenberg M. Epoxide Hydrolases: Multipotential Biocatalysts. Int J Mol Sci 2023; 24:7334. [PMID: 37108499 PMCID: PMC10138715 DOI: 10.3390/ijms24087334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Epoxide hydrolases are attractive and industrially important biocatalysts. They can catalyze the enantioselective hydrolysis of epoxides to the corresponding diols as chiral building blocks for bioactive compounds and drugs. In this review article, we discuss the state of the art and development potential of epoxide hydrolases as biocatalysts based on the most recent approaches and techniques. The review covers new approaches to discover epoxide hydrolases using genome mining and enzyme metagenomics, as well as improving enzyme activity, enantioselectivity, enantioconvergence, and thermostability by directed evolution and a rational design. Further improvements in operational and storage stabilization, reusability, pH stabilization, and thermal stabilization by immobilization techniques are discussed in this study. New possibilities for expanding the synthetic capabilities of epoxide hydrolases by their involvement in non-natural enzyme cascade reactions are described.
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Affiliation(s)
- Marek Bučko
- Department of Glycobiotechnology, Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia;
| | - Katarína Kaniaková
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (K.K.); (H.H.); (M.R.)
| | - Helena Hronská
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (K.K.); (H.H.); (M.R.)
| | - Peter Gemeiner
- Department of Glycobiotechnology, Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia;
| | - Michal Rosenberg
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia; (K.K.); (H.H.); (M.R.)
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Ali M, Ishqi HM, Husain Q. Enzyme engineering: Reshaping the biocatalytic functions. Biotechnol Bioeng 2020; 117:1877-1894. [DOI: 10.1002/bit.27329] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/13/2020] [Accepted: 03/09/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Misha Ali
- Department of Biochemistry, Faculty of Life SciencesAligarh Muslim University Aligarh Uttar Pradesh India
| | | | - Qayyum Husain
- Department of Biochemistry, Faculty of Life SciencesAligarh Muslim University Aligarh Uttar Pradesh India
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Sharma A, Gupta G, Ahmad T, Mansoor S, Kaur B. Enzyme Engineering: Current Trends and Future Perspectives. FOOD REVIEWS INTERNATIONAL 2019. [DOI: 10.1080/87559129.2019.1695835] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Anshula Sharma
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Gaganjot Gupta
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Tawseef Ahmad
- Department of Biotechnology, Punjabi University, Patiala, India
| | | | - Baljinder Kaur
- Department of Biotechnology, Punjabi University, Patiala, India
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Enhanced catalytic efficiency and enantioselectivity of epoxide hydrolase from Agrobacterium radiobacter AD1 by iterative saturation mutagenesis for (R)-epichlorohydrin synthesis. Appl Microbiol Biotechnol 2017; 102:733-742. [DOI: 10.1007/s00253-017-8634-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/31/2017] [Accepted: 11/07/2017] [Indexed: 01/06/2023]
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Fraraccio S, Strejcek M, Dolinova I, Macek T, Uhlik O. Secondary compound hypothesis revisited: Selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE). Sci Rep 2017; 7:8406. [PMID: 28814712 PMCID: PMC5559444 DOI: 10.1038/s41598-017-07760-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/29/2017] [Indexed: 12/20/2022] Open
Abstract
Cis-1,2-dichloroethylene (cDCE), which is a common hazardous compound, often accumulates during incomplete reductive dechlorination of higher chlorinated ethenes (CEs) at contaminated sites. Simple monoaromatics, such as toluene and phenol, have been proven to induce biotransformation of cDCE in microbial communities incapable of cDCE degradation in the absence of other carbon sources. The goal of this microcosm-based laboratory study was to discover non-toxic natural monoaromatic secondary plant metabolites (SPMEs) that could enhance cDCE degradation in a similar manner to toluene and phenol. Eight SPMEs were selected on the basis of their monoaromatic molecular structure and widespread occurrence in nature. The suitability of the SPMEs chosen to support bacterial growth and to promote cDCE degradation was evaluated in aerobic microbial cultures enriched from cDCE-contaminated soil in the presence of each SPME tested and cDCE. Significant cDCE depletions were achieved in cultures enriched on acetophenone, phenethyl alcohol, p-hydroxybenzoic acid and trans-cinnamic acid. 16S rRNA gene sequence analysis of each microbial community revealed ubiquitous enrichment of bacteria affiliated with the genera Cupriavidus, Rhodococcus, Burkholderia, Acinetobacter and Pseudomonas. Our results provide further confirmation of the previously stated secondary compound hypothesis that plant metabolites released into the rhizosphere can trigger biodegradation of environmental pollutants, including cDCE.
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Affiliation(s)
- Serena Fraraccio
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic.
| | - Michal Strejcek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Iva Dolinova
- Technical University of Liberec, Liberec, Czech Republic
| | - Tomas Macek
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic.
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Wood TL, Guha R, Tang L, Geitner M, Kumar M, Wood TK. Living biofouling-resistant membranes as a model for the beneficial use of engineered biofilms. Proc Natl Acad Sci U S A 2016; 113:E2802-11. [PMID: 27140616 PMCID: PMC4878488 DOI: 10.1073/pnas.1521731113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Membrane systems are used increasingly for water treatment, recycling water from wastewater, during food processing, and energy production. They thus are a key technology to ensure water, energy, and food sustainability. However, biofouling, the build-up of microbes and their polymeric matrix, clogs these systems and reduces their efficiency. Realizing that a microbial film is inevitable, we engineered a beneficial biofilm that prevents membrane biofouling, limiting its own thickness by sensing the number of its cells that are present via a quorum-sensing circuit. The beneficial biofilm also prevents biofilm formation by deleterious bacteria by secreting nitric oxide, a general biofilm dispersal agent, as demonstrated by both short-term dead-end filtration and long-term cross-flow filtration tests. In addition, the beneficial biofilm was engineered to produce an epoxide hydrolase so that it efficiently removes the environmental pollutant epichlorohydrin. Thus, we have created a living biofouling-resistant membrane system that simultaneously reduces biofouling and provides a platform for biodegradation of persistent organic pollutants.
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Affiliation(s)
- Thammajun L Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
| | - Rajarshi Guha
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802
| | - Li Tang
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802
| | - Michael Geitner
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802
| | - Manish Kumar
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802;
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802; The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
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Jemli S, Ayadi-Zouari D, Hlima HB, Bejar S. Biocatalysts: application and engineering for industrial purposes. Crit Rev Biotechnol 2014; 36:246-58. [DOI: 10.3109/07388551.2014.950550] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Cytochrome P450 initiates degradation of cis-dichloroethene by Polaromonas sp. strain JS666. Appl Environ Microbiol 2013; 79:2263-72. [PMID: 23354711 DOI: 10.1128/aem.03445-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polaromonas sp. strain JS666 grows on cis-1,2-dichoroethene (cDCE) as the sole carbon and energy source under aerobic conditions, but the degradation mechanism and the enzymes involved are unknown. In this study, we established the complete pathway for cDCE degradation through heterologous gene expression, inhibition studies, enzyme assays, and analysis of intermediates. Several lines of evidence indicate that a cytochrome P450 monooxygenase catalyzes the initial step of cDCE degradation. Both the transient accumulation of dichloroacetaldehyde in cDCE-degrading cultures and dichloroacetaldehyde dehydrogenase activities in cell extracts of JS666 support a pathway for degradation of cDCE through dichloroacetaldehyde. The mechanism minimizes the formation of cDCE epoxide. The molecular phylogeny of the cytochrome P450 gene and the organization of neighboring genes suggest that the cDCE degradation pathway recently evolved in a progenitor capable of degrading 1,2-dichloroethane either by the recruitment of the cytochrome P450 monooxygenase gene from an alkane catabolic pathway or by selection for variants of the P450 in a preexisting 1,2-dichloroethane catabolic pathway. The results presented here add yet another role to the broad array of productive reactions catalyzed by cytochrome P450 enzymes.
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Wang Z, Wang Y, Su Z. Purification and characterization of a cis-epoxysuccinic acid hydrolase from Nocardia tartaricans CAS-52, and expression in Escherichia coli. Appl Microbiol Biotechnol 2012; 97:2433-41. [DOI: 10.1007/s00253-012-4102-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 04/09/2012] [Accepted: 04/11/2012] [Indexed: 10/28/2022]
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12
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Liu ZQ, Zhang LP, Cheng F, Ruan LT, Hu ZC, Zheng YG, Shen YC. Characterization of a newly synthesized epoxide hydrolase and its application in racemic resolution of (R,S)-epichlorohydrin. CATAL COMMUN 2011. [DOI: 10.1016/j.catcom.2011.09.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Prasad S, Bocola M, Reetz MT. Revisiting the Lipase from Pseudomonas aeruginosa: Directed Evolution of Substrate Acceptance and Enantioselectivity Using Iterative Saturation Mutagenesis. Chemphyschem 2011; 12:1550-7. [DOI: 10.1002/cphc.201100031] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Indexed: 11/10/2022]
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Zhang LF, Wu JM, Feng H. Homology modelling and site-directed mutagenesis studies of the epoxide hydrolase from Phanerochaete chrysosporium. ACTA ACUST UNITED AC 2011; 149:673-84. [DOI: 10.1093/jb/mvr015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Reetz MT, Prasad S, Carballeira JD, Gumulya Y, Bocola M. Iterative saturation mutagenesis accelerates laboratory evolution of enzyme stereoselectivity: rigorous comparison with traditional methods. J Am Chem Soc 2010; 132:9144-52. [PMID: 20536132 DOI: 10.1021/ja1030479] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Efficacy in laboratory evolution of enzymes is currently a pressing issue, making comparative studies of different methods and strategies mandatory. Recent reports indicate that iterative saturation mutagenesis (ISM) provides a means to accelerate directed evolution of stereoselectivity and thermostability, but statistically meaningful comparisons with other methods have not been documented to date. In the present study, the efficacy of ISM has been rigorously tested by applying it to the previously most systematically studied enzyme in directed evolution, the lipase from Pseudomonas aeruginosa as a catalyst in the stereoselective hydrolytic kinetic resolution of a chiral ester. Upon screening only 10,000 transformants, unprecedented enantioselectivity was achieved (E = 594). ISM proves to be considerably more efficient than all previous systematic efforts utilizing error-prone polymerase chain reaction at different mutation rates, saturation mutagenesis at hot spots, and/or DNA shuffling, pronounced positive epistatic effects being the underlying reason.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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Reetz MT. Gerichtete Evolution stereoselektiver Enzyme: Eine ergiebige Katalysator‐Quelle für asymmetrische Reaktionen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000826] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Manfred T. Reetz
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Deutschland), Fax: (+49) 208‐306‐2985 http://www.mpi‐muelheim.mpg.de/mpikofo_home.html
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Reetz MT. Laboratory Evolution of Stereoselective Enzymes: A Prolific Source of Catalysts for Asymmetric Reactions. Angew Chem Int Ed Engl 2010; 50:138-74. [DOI: 10.1002/anie.201000826] [Citation(s) in RCA: 441] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Manfred T. Reetz
- Max‐Planck‐Institut für Kohlenforschung, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) 208‐306‐2985 http://www.mpi‐muelheim.mpg.de/mpikofo_home.html
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Mattes TE, Alexander AK, Coleman NV. Aerobic biodegradation of the chloroethenes: pathways, enzymes, ecology, and evolution. FEMS Microbiol Rev 2010; 34:445-75. [DOI: 10.1111/j.1574-6976.2010.00210.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Lee J, Hiibel SR, Reardon KF, Wood TK. Identification of stress-related proteins in Escherichia coli using the pollutant cis-dichloroethylene. J Appl Microbiol 2009; 108:2088-102. [PMID: 19919618 DOI: 10.1111/j.1365-2672.2009.04611.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AIMS To complement our proteome study, whole-transcriptome analyses were utilized here to identify proteins related to degrading cis-1,2-dichloroethylene (cis-DCE). METHODS AND RESULTS Metabolically engineered Escherichia coli strains were utilized expressing an evolved toluene ortho-monooxygenase along with either (i) glutathione S-transferase and altered gamma-glutamylcysteine synthetase or (ii) a rationally engineered epoxide hydrolase. cis-DCE degradation induced 30 known stress genes and 32 uncharacterized genes. Because of the reactive cis-DCE epoxides formed, we hypothesized that some of these uncharacterized genes may be related to a variety of stresses. Using isogenic mutants, IbpB, YchH, YdeI, YeaR, YgiW, YoaG and YodD were related to hydrogen peroxide, cadmium and acid stress. Additional whole-transcriptome studies with hydrogen peroxide stress using the most hydrogen peroxide-sensitive mutants, ygiW and ychH, identified that FliS, GalS, HcaR, MglA, SufE, SufS, Tap, TnaB, YhcN and YjaA are also involved in the stress response of E. coli to hydrogen peroxide, cadmium and acid, as well as are involved in biofilm formation. CONCLUSION Seventeen proteins are involved in the stress network for this organism, and YhcN and YchH were shown to be important for the degradation of cis-DCE. SIGNIFICANCE AND IMPACT OF THE STUDY Six previously uncharacterized proteins (YchH, YdeI, YgiW, YhcN, YjaA and YodD) were shown to be stress proteins.
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Affiliation(s)
- J Lee
- Artie McFerrin Department of Chemical Engineering, Texas A & M University, College Station, TX 77843-3122, USA
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Abstract
Anthropogenic compounds used as pesticides, solvents and explosives often persist in the environment and can cause toxicity to humans and wildlife. The persistence of anthropogenic compounds is due to their recent introduction into the environment; microbes in soil and water have had relatively little time to evolve efficient mechanisms for degradation of these new compounds. Some anthropogenic compounds are easily degraded, whereas others are degraded very slowly or only partially, leading to accumulation of toxic products. This review examines the factors that affect the ability of microbes to degrade anthropogenic compounds and the mechanisms by which new pathways emerge in nature. New approaches for engineering microbes with enhanced degradative abilities include assembly of pathways using enzymes from multiple organisms, directed evolution of inefficient enzymes, and genome shuffling to improve microbial fitness under the challenging conditions posed by contaminated environments.
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Reetz MT, Bocola M, Wang LW, Sanchis J, Cronin A, Arand M, Zou J, Archelas A, Bottalla AL, Naworyta A, Mowbray SL. Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage. J Am Chem Soc 2009; 131:7334-43. [PMID: 19469578 DOI: 10.1021/ja809673d] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Directed evolution of enzymes as enantioselective catalysts in organic chemistry is an alternative to traditional asymmetric catalysis using chiral transition-metal complexes or organocatalysts, the different approaches often being complementary. Moreover, directed evolution studies allow us to learn more about how enzymes perform mechanistically. The present study concerns a previously evolved highly enantioselective mutant of the epoxide hydrolase from Aspergillus niger in the hydrolytic kinetic resolution of racemic glycidyl phenyl ether. Kinetic data, molecular dynamics calculations, molecular modeling, inhibition experiments, and X-ray structural work for the wild-type (WT) enzyme and the best mutant reveal the basis of the large increase in enantioselectivity (E = 4.6 versus E = 115). The overall structures of the WT and the mutant are essentially identical, but dramatic differences are observed in the active site as revealed by the X-ray structures. All of the experimental and computational results support a model in which productive positioning of the preferred (S)-glycidyl phenyl ether, but not the (R)-enantiomer, forms the basis of enhanced enantioselectivity. Predictions regarding substrate scope and enantioselectivity of the best mutant are shown to be possible.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mulheim/Ruhr, Germany.
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Choi SH, Kim HS, Lee EY. Comparative homology modeling-inspired protein engineering for improvement of catalytic activity of Mugil cephalus epoxide hydrolase. Biotechnol Lett 2009; 31:1617-24. [DOI: 10.1007/s10529-009-0055-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 06/02/2009] [Accepted: 06/02/2009] [Indexed: 11/28/2022]
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Improved enantioselective conversion of styrene epoxides and meso-epoxides through epoxide hydrolases with a mutated nucleophile-flanking residue. Enzyme Microb Technol 2009. [DOI: 10.1016/j.enzmictec.2008.09.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Reetz MT, Kahakeaw D, Sanchis J. Shedding light on the efficacy of laboratory evolution based on iterative saturation mutagenesis. ACTA ACUST UNITED AC 2009; 5:115-22. [DOI: 10.1039/b814862g] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Molecular approaches in bioremediation. Curr Opin Biotechnol 2008; 19:572-8. [DOI: 10.1016/j.copbio.2008.10.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 10/14/2008] [Accepted: 10/16/2008] [Indexed: 01/08/2023]
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Reetz MT, Sanchis J. Constructing and Analyzing the Fitness Landscape of an Experimental Evolutionary Process. Chembiochem 2008; 9:2260-7. [DOI: 10.1002/cbic.200800371] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Reetz MT, Kahakeaw D, Lohmer R. Addressing the Numbers Problem in Directed Evolution. Chembiochem 2008; 9:1797-804. [DOI: 10.1002/cbic.200800298] [Citation(s) in RCA: 334] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Wang P. Multi-scale features in recent development of enzymic biocatalyst systems. Appl Biochem Biotechnol 2008; 152:343-52. [PMID: 18574568 DOI: 10.1007/s12010-008-8243-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Accepted: 03/31/2008] [Indexed: 12/01/2022]
Abstract
Functional relation among elements of different size scales in a system is probably a main challenge across the areas of the science of engineering ever since their emergence. Multi-scale time and size correlation for description and prediction of complex systems, however, has been systematically examined only recently with the aid of new computational tools. In the pursuit of efficient and sustainable chemical processing technologies, people have seen a growing emphasis on synthetic biotechnology in recent R&D efforts. In particular, industrial enzyme technologies are attracting enormous attention. Having been traditionally developed for food and detergent applications, industrial enzyme technologies are being re-examined and tested to their limits to keep abreast of the challenges in drug, biochemical, and the emerging biorenewable energy industries. Toward that, enzymes are required to function in non-conventional conditions, such as organic solvents, extreme pH, and temperatures; they also have to compete against alternative chemical technologies in terms of costs and efficiency. Accordingly, enzymic biocatalyst systems are being tackled dynamically at all size levels through efforts ranging from molecular level protein engineering and modification, nanoscale structure fabrication, and microenvironment manipulation to the construction of microchip devices and macroscopic industrial bioreactors and devices. These efforts are probably still on a case-to-case trial basis without much consideration of cross-scale correlations. Discovering, understanding, and controlling of the common features that relate functions of biocatalysts at different size scales may eventually be realized in future.
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Affiliation(s)
- Ping Wang
- Department of Bioproducts and Biosystems Engineering, Biotechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
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29
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Kadonosono T, Kato-Murai M, Ueda M. Alteration of substrate specificity of rat neurolysin from matrix metalloproteinase-2/9-type to -3-type specificity by comprehensive mutation. Protein Eng Des Sel 2008; 21:507-13. [DOI: 10.1093/protein/gzn026] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Qian Z, Fields CJ, Lutz S. Investigating the Structural and Functional Consequences of Circular Permutation on Lipase B fromCandida Antarctica. Chembiochem 2007; 8:1989-96. [PMID: 17876754 DOI: 10.1002/cbic.200700373] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The engineering of lipase B from Candida antarctica (CALB) by circular permutation has yielded over sixty hydrolase variants, and several show significantly improved catalytic performance. Here we report a detailed characterization of ten selected enzyme variants by kinetic and spectroscopic methods to further elucidate the impact of circular permutation on the structure and function of CALB. Our experiments identify lipase variants with up to 175-fold enhanced k(cat)/K(M) values over wild-type. In addition, circular permutation does not change the enzymes' enantiopreference and preserves or even improves their enantioselectivity compared to that of the wild-type enzyme. Finally, our spectroscopic analyses suggest that the structural effects of circular permutation on CALB are mostly local, concentrating on regions near the native and new protein termini. The observed changes in secondary structure and protein thermostability vary among enzyme variants but directly correlate with the locations of the new termini, a first step towards a predictive framework.
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Affiliation(s)
- Zhen Qian
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
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31
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Chaparro-Riggers JF, Polizzi KM, Bommarius AS. Better library design: data-driven protein engineering. Biotechnol J 2007; 2:180-91. [PMID: 17183506 DOI: 10.1002/biot.200600170] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Data-driven protein engineering is increasingly used as an alternative to rational design and combinatorial engineering because it uses available knowledge to limit library size, while still allowing for the identification of unpredictable substitutions that lead to large effects. Recent advances in computational modeling and bioinformatics, as well as an increasing databank of experiments on functional variants, have led to new strategies to choose particular amino acid residues to vary in order to increase the chances of obtaining a variant protein with the desired property. Strategies for limiting diversity at each position, design of small sub-libraries, and the performance of scouting experiments, have also been developed or even automated, further reducing the library size.
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Affiliation(s)
- Javier F Chaparro-Riggers
- School of Chemical and Biomolecular Engineering, Parker H. Petit Institute of Bioengineering and Bioscience, Atlanta, GA, USA
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32
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Kotik M, Stepánek V, Kyslík P, Maresová H. Cloning of an epoxide hydrolase-encoding gene from Aspergillus niger M200, overexpression in E. coli, and modification of activity and enantioselectivity of the enzyme by protein engineering. J Biotechnol 2007; 132:8-15. [PMID: 17875334 DOI: 10.1016/j.jbiotec.2007.08.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 07/18/2007] [Accepted: 08/01/2007] [Indexed: 11/19/2022]
Abstract
The gene encoding an epoxide hydrolase from Aspergillus niger M200 has been cloned and its sequence determined. The gene is interrupted by seven introns, one exon being only nine nucleotides long. The non-coding 5'- and 3'-regions of the mRNA are composed of 47 and 76 nucleotides, respectively. Overexpression of the fungal epoxide hydrolase in E. coli TOP10 has led to a 15-fold increase in specific activity (compared to the wild-type strain). Saturation mutagenesis at codon 217 resulted in the discovery of nine enzyme variants showing in several cases profound differences in activity and enantioselectivity towards various epoxides when compared to the data of the wild-type enzyme. The site 217 is located at the entrance of the tunnel that provides the substrate with access to the active site. The exchange of Ala at this position for Cys has led to a doubled enantioselectivity (E-value of 5.0) towards benzyl glycidyl ether. The same substitution resulted in a threefold-enhanced activity of the enzyme towards allyl glycidyl ether and styrene oxide without affecting enantioselectivity. The variant A217L showed an enhanced enantioselectivity towards tert-butyl glycidyl ether reaching an E-value of 100 (from 60 for the wild-type enzyme). Replacement of A217 by Val has led to higher activity towards allyl glycidyl ether by a factor of six. The substitutions Ala-->Glu and Ala-->Gln increased the enantioselectivity towards allyl glycidyl ether and styrene oxide by over 50% to E-values of 10 and 16, respectively. The study underlines that single amino acid exchanges in the substrate tunnel region can lead to significant improvements in enantioselectivity and activity of the epoxide hydrolase from A. niger M200.
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Affiliation(s)
- Michael Kotik
- Laboratory of Enzyme Technology, Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídenská 1083, 142 20 Prague 4, Czech Republic.
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33
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Herman A, Tawfik DS. Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): a versatile tool for generating targeted libraries. Protein Eng Des Sel 2007; 20:219-26. [PMID: 17483523 DOI: 10.1093/protein/gzm014] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The directed evolution of proteins has benefited greatly from site-specific methods of diversification such as saturation mutagenesis. These techniques target diversity to a number of chosen positions that are usually non-contiguous in the protein's primary structure. However, the number of targeted positions can be large, thus leading to impractically large library size, wherein almost all library variants are inactive and the likelihood of selecting desirable properties is extremely small. We describe a versatile combinatorial method for the partial diversification of large sets of residues. Our library oligonucleotides comprise randomized codons that are flanked by wild-type sequences. Adding these oligonucleotides to an assembly PCR of wild-type gene fragments incorporates the randomized cassettes, at their target sites, into the reassembled gene. Varying the oligonucleotides concentration resulted in library variants that carry a different average number of mutated positions that comprise a random subset of the entire set of diversified codons. This method, dubbed Incorporating Synthetic Oligos via Gene Reassembly (ISOR), was used to create libraries of a cytosine-C5 methyltransferase wherein 45 individual positions were randomized. One library, containing an average of 5.6 mutated residues per gene, was selected, and mutants with wild-type-like activities isolated. We also created libraries of serum paraoxonase PON1 harboring insertions and deletions (indels) in various areas surrounding the active site. Screening these libraries yielded a range of mutants with altered substrate specificities and indicated that certain regions of this enzyme have a surprisingly high tolerance to indels.
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Affiliation(s)
- Asael Herman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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34
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Leonard E, Lim KH, Saw PN, Koffas MAG. Engineering central metabolic pathways for high-level flavonoid production in Escherichia coli. Appl Environ Microbiol 2007; 73:3877-86. [PMID: 17468269 PMCID: PMC1932724 DOI: 10.1128/aem.00200-07] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The identification of optimal genotypes that result in improved production of recombinant metabolites remains an engineering conundrum. In the present work, various strategies to reengineer central metabolism in Escherichia coli were explored for robust synthesis of flavanones, the common precursors of plant flavonoid secondary metabolites. Augmentation of the intracellular malonyl coenzyme A (malonyl-CoA) pool through the coordinated overexpression of four acetyl-CoA carboxylase (ACC) subunits from Photorhabdus luminescens (PlACC) under a constitutive promoter resulted in an increase in flavanone production up to 576%. Exploration of macromolecule complexes to optimize metabolic efficiency demonstrated that auxiliary expression of PlACC with biotin ligase from the same species (BirAPl) further elevated flavanone synthesis up to 1,166%. However, the coexpression of PlACC with Escherichia coli BirA (BirAEc) caused a marked decrease in flavanone production. Activity improvement was reconstituted with the coexpression of PlACC with a chimeric BirA consisting of the N terminus of BirAEc and the C terminus of BirAPl. In another approach, high levels of flavanone synthesis were achieved through the amplification of acetate assimilation pathways combined with the overexpression of ACC. Overall, the metabolic engineering of central metabolic pathways described in the present work increased the production of pinocembrin, naringenin, and eriodictyol in 36 h up to 1,379%, 183%, and 373%, respectively, over production with the strains expressing only the flavonoid pathway, which corresponded to 429 mg/liter, 119 mg/liter, and 52 mg/liter, respectively.
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Affiliation(s)
- Effendi Leonard
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, 904 Furnas Hall, Buffalo, NY 14260, USA
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35
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Chica RA, Doucet N, Pelletier JN. Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. Curr Opin Biotechnol 2007; 16:378-84. [PMID: 15994074 DOI: 10.1016/j.copbio.2005.06.004] [Citation(s) in RCA: 262] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Revised: 06/10/2005] [Accepted: 06/22/2005] [Indexed: 10/25/2022]
Abstract
Many research groups successfully rely on whole-gene random mutagenesis and recombination approaches for the directed evolution of enzymes. Recent advances in enzyme engineering have used a combination of these random methods of directed evolution with elements of rational enzyme modification to successfully by-pass certain limitations of both directed evolution and rational design. Semi-rational approaches that target multiple, specific residues to mutate on the basis of prior structural or functional knowledge create 'smart' libraries that are more likely to yield positive results. Efficient sampling of mutations likely to affect enzyme function has been conducted both experimentally and, on a much greater scale, computationally, with remarkable improvements in substrate selectivity and specificity and in the de novo design of enzyme activities within scaffolds of known structure.
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Affiliation(s)
- Roberto A Chica
- Département de chimie, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, Québec, H3C 3J7, Canada
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36
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Reetz MT, Carballeira JD. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2007; 2:891-903. [PMID: 17446890 DOI: 10.1038/nprot.2007.72] [Citation(s) in RCA: 588] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Iterative saturation mutagenesis (ISM) is a new and efficient method for the directed evolution of functional enzymes. It reduces the necessary molecular biological work and the screening effort drastically. It is based on a Cartesian view of the protein structure, performing iterative cycles of saturation mutagenesis at rationally chosen sites in an enzyme, a given site being composed of one, two or three amino acid positions. The basis for choosing these sites depends on the nature of the catalytic property to be improved, e.g., enantioselectivity, substrate acceptance or thermostability. In the case of thermostability, sites showing highest B-factors (available from X-ray data) are chosen. The pronounced increase in thermostability of the lipase from Bacillus subtilis (Lip A) as a result of applying ISM is illustrated here.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim/Ruhr, Germany.
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37
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Lee EY, Shuler ML. Molecular engineering of epoxide hydrolase and its application to asymmetric and enantioconvergent hydrolysis. Biotechnol Bioeng 2007; 98:318-27. [PMID: 17405175 DOI: 10.1002/bit.21444] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Safety and regulatory issues favor increasing use of enantiopure compounds in pharmaceuticals. Enantiopure epoxides and diols are valuable intermediates in organic synthesis for the production of optically active pharmaceuticals. Enantiopure epoxide can be prepared using epoxide hydrolase (EH)-catalyzed asymmetric hydrolysis of its racemate. Enantioconvergent hydrolysis of racemic epoxides by EHs possessing complementary enantioselectivity and regioselectivity can lead to the formation of enantiopure vicinal diols with high yield. EHs are cofactor-independent and easy-to-use catalysts. EHs will attract much attention as commercial biocatalysts for the preparation of enantiopure epoxides and diols. In this paper, recent progress in molecular engineering of EHs is reviewed. Some examples and prospects of asymmetric and enantioconvergent hydrolysis reactions are discussed as supplements to molecular engineering to improve EH performance.
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Affiliation(s)
- Eun Yeol Lee
- Department of Food Science and Biotechnology, Kyungsung University, Daeyeon-dong, Nam-gu, Busan 608-736, Republic of Korea.
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38
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Abstract
Directed evolution is being used increasingly in industrial and academic laboratories to modify and improve commercially important enzymes. Laboratory evolution is thought to make its biggest contribution in explorations of non-natural functions, by allowing us to distinguish the properties nurtured by evolution. In this review we report the significant advances achieved with respect to the methods of biocatalyst improvement and some critical properties and applications of the modified enzymes. The application of directed evolution has been elaborately demonstrated for protein solubility, stability and catalytic efficiency. Modification of certain enzymes for their application in enantioselective catalysis has also been elucidated. By providing a simple and reliable route to enzyme improvement, directed evolution has emerged as a key technology for enzyme engineering and biocatalysis.
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Affiliation(s)
- Jasjeet Kaur
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
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39
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Cao L, Lee J, Chen W, Wood TK. Enantioconvergent production of (R)-1-phenyl-1,2-ethanediol from styrene oxide by combining the Solanum tuberosum and an evolved Agrobacterium radiobacter AD1 epoxide hydrolases. Biotechnol Bioeng 2006; 94:522-9. [PMID: 16498626 DOI: 10.1002/bit.20860] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Soluble epoxide hydrolase (EH) from the potato Solanum tuberosum and an evolved EH of the bacterium Agrobacterium radiobacter AD1, EchA-I219F, were purified for the enantioconvergent hydrolysis of racemic styrene oxide into the single product (R)-1-phenyl-1,2-ethanediol, which is an important intermediate for pharmaceuticals. EchA-I219F has enhanced enantioselectivity (enantiomeric ratio of 91 based on products) for converting (R)-styrene oxide to (R)-1-phenyl-1,2-ethanediol (2.0 +/- 0.2 micromol/min/mg), and the potato EH converts (S)-styrene oxide primarily to the same enantiomer, (R)-1-phenyl-1,2-ethanediol (22 +/- 1 micromol/min/mg), with an enantiomeric ratio of 40 +/- 17 (based on substrates). By mixing these two purified enzymes, inexpensive racemic styrene oxide (5 mM) was converted at 100% yield to 98% enantiomeric excess (R)-1-phenyl-1,2-ethanediol at 4.7 +/- 0.7 micromol/min/mg. Hence, at least 99% of substrate is converted into a single stereospecific product at a rapid rate.
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Affiliation(s)
- Li Cao
- Department of Chemical Engineering, University of Connecticut, Storrs, Connecticut 06269-3222, USA
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40
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Rui L, Cao L, Chen W, Reardon KF, Wood TK. Protein engineering of epoxide hydrolase from Agrobacterium radiobacter AD1 for enhanced activity and enantioselective production of (R)-1-phenylethane-1,2-diol. Appl Environ Microbiol 2005; 71:3995-4003. [PMID: 16000814 PMCID: PMC1169048 DOI: 10.1128/aem.71.7.3995-4003.2005] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA shuffling and saturation mutagenesis of positions F108, L190, I219, D235, and C248 were used to generate variants of the epoxide hydrolase of Agrobacterium radiobacter AD1 (EchA) with enhanced enantioselectivity and activity for styrene oxide and enhanced activity for 1,2-epoxyhexane and epoxypropane. EchA variant I219F has more than fivefold-enhanced enantioselectivity toward racemic styrene oxide, with the enantiomeric ratio value (E value) for the production of (R)-1-phenylethane-1,2-diol increased from 17 for the wild-type enzyme to 91, as well as twofold-improved activity for the production of (R)-1-phenylethane-1,2-diol (1.96 +/- 0.09 versus 1.04 +/- 0.07 micromol/min/mg for wild-type EchA). Computer modeling indicated that this mutation significantly alters (R)-styrene oxide binding in the active site. Another three variants from EchA active-site engineering, F108L/C248I, I219L/C248I, and F108L/I219L/C248I, also exhibited improved enantioselectivity toward racemic styrene oxide in favor of production of the corresponding diol in the (R) configuration (twofold enhancement in their E values). Variant F108L/I219L/C248I also demonstrated 10-fold- and 2-fold-increased activity on 5 mM epoxypropane (24 +/- 2 versus 2.4 +/- 0.3 micromol/min/mg for the wild-type enzyme) and 5 mM 1,2-epoxyhexane (5.2 +/- 0.5 versus 2.6 +/- 0.0 micromol/min/mg for the wild-type enzyme). Both variants L190F (isolated from a DNA shuffling library) and L190Y (created from subsequent saturation mutagenesis) showed significantly enhanced activity for racemic styrene oxide hydrolysis, with 4.8-fold (8.6 +/- 0.3 versus 1.8 +/- 0.2 micromol/min/mg for the wild-type enzyme) and 2.7-fold (4.8 +/- 0.8 versus 1.8 +/- 0.2 micromol/min/mg for the wild-type enzyme) improvements, respectively. L190Y also hydrolyzed 1,2-epoxyhexane 2.5 times faster than the wild-type enzyme.
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Affiliation(s)
- Lingyun Rui
- Department of Chemical Engineering and Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3222, USA
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41
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Parales RE, Ditty JL. Laboratory evolution of catabolic enzymes and pathways. Curr Opin Biotechnol 2005; 16:315-25. [PMID: 15961033 DOI: 10.1016/j.copbio.2005.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 02/15/2005] [Accepted: 03/23/2005] [Indexed: 11/25/2022]
Abstract
The laboratory evolution of environmentally relevant enzymes and proteins has resulted in the generation of optimized and stabilized enzymes, as well as enzymes with activity against new substrates. Numerous methods, including random mutagenesis, site-directed mutagenesis and DNA shuffling, have been widely used to generate variants of existing enzymes. These evolved catabolic enzymes have application for improving biodegradation pathways, generating engineered pathways for the degradation of particularly recalcitrant compounds, and for the development of biocatalytic processes to produce useful compounds. Regulatory proteins associated with catabolic pathways have been utilized to generate biosensors for the detection of bioavailable concentrations of environmentally relevant chemicals.
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Affiliation(s)
- Rebecca E Parales
- Section of Microbiology, 226 Briggs Hall, University of California, Davis, California 95616, USA.
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