1
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Hélaine V, Gastaldi C, Lemaire M, Clapés P, Guérard-Hélaine C. Recent Advances in the Substrate Selectivity of Aldolases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Virgil Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Cédric Gastaldi
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Marielle Lemaire
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Pere Clapés
- Biological Chemistry Department, Institute for Advanced Chemistry of Catalonia, IQAC−CSIC, 08034 Barcelona, Spain
| | - Christine Guérard-Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
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2
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Abstract
Biocatalysis has an enormous impact on chemical synthesis. The waves in which biocatalysis has developed, and in doing so changed our perception of what organic chemistry is, were reviewed 20 and 10 years ago. Here we review the consequences of these waves of development. Nowadays, hydrolases are widely used on an industrial scale for the benign synthesis of commodity and bulk chemicals and are fully developed. In addition, further enzyme classes are gaining ever increasing interest. Particularly, enzymes catalysing selective C-C-bond formation reactions and enzymes catalysing selective oxidation and reduction reactions are solving long-standing synthetic challenges in organic chemistry. Combined efforts from molecular biology, systems biology, organic chemistry and chemical engineering will establish a whole new toolbox for chemistry. Recent developments are critically reviewed.
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Affiliation(s)
- Ulf Hanefeld
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
| | - Frank Hollmann
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, The Netherlands.
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3
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Dai Y, Zhang J, Jiang B, Zhang T, Chen J. New strategy for rare sugars biosynthesis: Aldol reactions using dihydroxyacetone phosphate (DHAP)-dependent aldolases. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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4
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Rigual AJ, Cantero J, Risso M, Rodríguez P, Rodríguez S, Paulino M, Gamenara D, Veiga N. New mechanistic insights into the reversible aldol reaction catalysed by Rhamnulose-1-phosphate aldolase from Escherichia coli. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2020.111131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Zeng R, Liu J, Ding S, Sun L, Wu L, Cao L, Qiu J. Construction of Class I Aldolases-like Carboxyl-Controlled-Graphene Oxide Supported 3-Aminopropyl-triethoxysilane Heterogeneous Catalysts for Aldol Reaction. Catal Letters 2019. [DOI: 10.1007/s10562-019-03048-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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6
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Desmons S, Fauré R, Bontemps S. Formaldehyde as a Promising C1 Source: The Instrumental Role of Biocatalysis for Stereocontrolled Reactions. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03128] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Sarah Desmons
- LCC-CNRS, Université de Toulouse, CNRS, Toulouse, France
- TBI, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
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7
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Chambre D, Guérard-Hélaine C, Darii E, Mariage A, Petit JL, Salanoubat M, de Berardinis V, Lemaire M, Hélaine V. 2-Deoxyribose-5-phosphate aldolase, a remarkably tolerant aldolase towards nucleophile substrates. Chem Commun (Camb) 2019; 55:7498-7501. [PMID: 31187106 DOI: 10.1039/c9cc03361k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We explored a collection of 2-deoxyribose-5-phosphate aldolases (DERAs) from biodiversity for their nucleophile substrate promiscuity. The DERAs were screened using as nucleophiles propanone, propanal, cyclobutanone, cyclopentanone, dihydroxyacetone, and glycolaldehyde with l-glyceraldehyde-3-phosphate as an electrophile in aldol addition. A DERA from Arthrobacter chlorophenolicus (DERAArthro) efficiently allowed the synthesis of the corresponding aldol adducts in good yields, displaying complementarity in terms of configuration and substrate specificity with fructose-6-phosphate aldolase, the only previously known aldolase with a large nucleophile tolerance.
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Affiliation(s)
- Domitille Chambre
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France.
| | - Christine Guérard-Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France.
| | - Ekaterina Darii
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Aline Mariage
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Marcel Salanoubat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Véronique de Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Marielle Lemaire
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France.
| | - Virgil Hélaine
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France.
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8
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Yang J, Zhu Y, Qu G, Zeng Y, Tian C, Dong C, Men Y, Dai L, Sun Z, Sun Y, Ma Y. Biosynthesis of dendroketose from different carbon sources using in vitro and in vivo metabolic engineering strategies. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:290. [PMID: 30386427 PMCID: PMC6202814 DOI: 10.1186/s13068-018-1293-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/15/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Asymmetric aldol-type C-C bond formation with ketones used as electrophilic receptor remains a challenging reaction for aldolases as biocatalysts. To date, only one kind of dihydroxyacetone phosphate (DHAP)-dependent aldolases has been discovered and applied to synthesize branched-chain sugars directly using DHAP and dihydroxyacetone (DHA) as substrate. However, the unstable and high-cost properties of DHAP limit large-scale application. Therefore, biosynthesis of branched-chain sugar from low-cost and abundant carbon sources is essential. RESULTS The detailed catalytic property of l-rhamnulose-1-phosphate aldolase (RhaD) and l-fuculose-1-phosphate aldolase (FucA) from Escherichia coli in catalyzing the aldol reactions with DHA as electrophilic receptors was characterized. Furthermore, we calculated the Bürgi-Dunitz trajectory using molecular dynamics simulations, thereby revealing the original sources of the catalytic efficiency of RhaD and FucA. A multi-enzyme reaction system composed of formolase, DHA kinase, RhaD, fructose-1-phosphatase, and polyphosphate kinase was constructed to in vitro produce dendroketose, a branched-chain sugar, from one-carbon formaldehyde. The conversion rate reached 86% through employing a one-pot, two-stage reaction process. Moreover, we constructed two artificial pathways in Corynebacterium glutamicum to obtain this product in vivo starting from glucose or glycerol. Fermentation with glycerol as feedstock produced 6.4 g/L dendroketose with a yield of 0.45 mol/mol glycerol, representing 90% of the maximum theoretical value. Additionally, the dendroketose production reached 36.3 g/L with a yield of 0.46 mol/mol glucose when glucose served as the sole carbon resource. CONCLUSIONS The detailed enzyme kinetics data of the two DHAP-dependent aldolases with DHA as electrophilic receptors were presented in this study. In addition, insights into this catalytic property were given via in silico simulations. Moreover, the cost-effective synthesis of dendroketose starting from one-, three-, and six-carbon resources was achieved through in vivo and in vitro metabolic engineering strategies. This rare branched-chain ketohexose may serve as precursor to prepare 4-hydroxymethylfurfural and branched-chain alkanes using chemical method.
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Affiliation(s)
- Jiangang Yang
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yueming Zhu
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Ge Qu
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yan Zeng
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Chaoyu Tian
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Caixia Dong
- School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Yan Men
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Longhai Dai
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Zhoutong Sun
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yuanxia Sun
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yanhe Ma
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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9
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Roldán R, Hernandez K, Joglar J, Bujons J, Parella T, Sánchez-Moreno I, Hélaine V, Lemaire M, Guérard-Hélaine C, Fessner WD, Clapés P. Biocatalytic Aldol Addition of Simple Aliphatic Nucleophiles to Hydroxyaldehydes. ACS Catal 2018; 8:8804-8809. [PMID: 30221031 PMCID: PMC6135579 DOI: 10.1021/acscatal.8b02486] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/07/2018] [Indexed: 01/06/2023]
Abstract
Asymmetric aldol addition of simple aldehydes and ketones to electrophiles is a cornerstone reaction for the synthesis of unusual sugars and chiral building blocks. We investigated d-fructose-6-phosphate aldolase from E. coli (FSA) D6X variants as catalysts for the aldol additions of ethanal and nonfunctionalized linear and cyclic aliphatic ketones as nucleophiles to nonphosphorylated hydroxyaldehydes. Thus, addition of propanone, cyclobutanone, cyclopentanone, or ethanal to 3-hydroxypropanal or (S)- or (R)-3-hydroxybutanal catalyzed by FSA D6H and D6Q variants furnished rare deoxysugars in 8-77% isolated yields with high stereoselectivity (97:3 dr and >95% ee).
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Affiliation(s)
- Raquel Roldán
- Biological Chemistry Department, Instituto de Química Avanzada de Cataluña IQAC−CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Karel Hernandez
- Biological Chemistry Department, Instituto de Química Avanzada de Cataluña IQAC−CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Jesús Joglar
- Biological Chemistry Department, Instituto de Química Avanzada de Cataluña IQAC−CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Jordi Bujons
- Biological Chemistry Department, Instituto de Química Avanzada de Cataluña IQAC−CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Israel Sánchez-Moreno
- University Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Virgil Hélaine
- University Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Marielle Lemaire
- University Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Christine Guérard-Hélaine
- University Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, D-64287 Darmstadt, Germany
| | - Pere Clapés
- Biological Chemistry Department, Instituto de Química Avanzada de Cataluña IQAC−CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
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10
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Hernández K, Szekrenyi A, Clapés P. Nucleophile Promiscuity of Natural and Engineered Aldolases. Chembiochem 2018; 19:1353-1358. [DOI: 10.1002/cbic.201800135] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Karel Hernández
- Department of Chemical Biology and Molecular Modelling; Catalonia Institute for Advanced Chemistry IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Anna Szekrenyi
- Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss-Strasse 4 64287 Darmstadt Germany
| | - Pere Clapés
- Department of Chemical Biology and Molecular Modelling; Catalonia Institute for Advanced Chemistry IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
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11
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Baś S, Kusy R, Pasternak-Suder M, Nicolas C, Mlynarski J, Martin OR. Total synthesis of pipecolic acid and 1-C-alkyl 1,5-iminopentitol derivatives by way of stereoselective aldol reactions from (S)-isoserinal. Org Biomol Chem 2018; 16:1118-1125. [PMID: 29362764 DOI: 10.1039/c7ob02797d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A short synthesis of iminosugars and pipecolic acid derivatives has been realized through aldol addition of a pyruvate, a range of ketones and (S)-isoserinal, followed by catalytic reductive intramolecular amination. The stereoselective aldol reaction was achieved successfully by using tertiary amines or di-zinc aldol catalysts, thus constituting two parallel routes to optically pure products with good yields and high diastereoselectivities. These carbohydrate analogues may be the inhibitors of potent glycosidases and glycosyltransferases.
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Affiliation(s)
- Sebastian Baś
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.
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12
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Li A, Cai L, Chen Z, Wang M, Wang N, Nakanishi H, Gao XD, Li Z. Recent advances in the synthesis of rare sugars using DHAP-dependent aldolases. Carbohydr Res 2017; 452:108-115. [PMID: 29096183 DOI: 10.1016/j.carres.2017.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/04/2017] [Accepted: 10/17/2017] [Indexed: 01/02/2023]
Abstract
The occurrence rates of non-communicable diseases like obesity, diabetes and hyperlipidemia have increased remarkably due to excessive consumption of a high-energy diet. Rare sugars therefore have become increasingly attractive owing to their unique nutritional properties. In the past two decades, various rare sugars have been successfully prepared guided by the "Izumoring strategy". As a valuable complement to the Izumoring approach, the controllable dihydroxyacetone phosphate (DHAP)-dependent aldolases have generally predictable regio- and stereoselectivity, which makes them powerful tools in C-C bond construction and rare sugar production. However, the main disadvantage for this group of aldolases is their strict substrate specificity toward the donor molecule DHAP, a very expensive and relatively unstable compound. Among the current methods involving DHAP, the one that couples DHAP production from inexpensive starting materials (for instance, glycerol, DL-glycerol 3-phosphate, dihydroxyacetone, and glucose) with aldol condensation appears to be the most promising. This review thus focuses on recent advances in the application of L-rhamnulose-1-phosphate aldolase (RhaD), L-fuculose-1-phosphate aldolase (FucA), and D-fructose-1,6-bisphosphate aldolase (FruA) for rare sugar synthesis in vitro and in vivo, while illustrating strategies for supplying DHAP in efficient and economical ways.
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Affiliation(s)
- Aimin Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Li Cai
- Department of Chemistry, University of South Carolina Lancaster, 476 Hubbard Drive, Lancaster, SC, 29720, USA
| | - Zhou Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Mayan Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Ning Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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13
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Yang J, Sun S, Men Y, Zeng Y, Zhu Y, Sun Y, Ma Y. Transformation of formaldehyde into functional sugars via multi-enzyme stepwise cascade catalysis. Catal Sci Technol 2017. [DOI: 10.1039/c7cy01062a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Artificial multi-enzyme systems for the transformation of the prebiotic compound formaldehyde into stereodefined functional sugars by stepwise cascade biocatalysis.
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Affiliation(s)
- Jiangang Yang
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
- China
| | - Shangshang Sun
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
- China
| | - Yan Men
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
- China
| | - Yan Zeng
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
- China
| | - Yueming Zhu
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
- China
| | - Yuanxia Sun
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
- China
| | - Yanhe Ma
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
- China
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14
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Busto E. Recent Developments in the Preparation of Carbohydrate Derivatives from Achiral Building Blocks by using Aldolases. ChemCatChem 2016. [DOI: 10.1002/cctc.201600366] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Eduardo Busto
- Organic Chemistry I Department; Complutense University of Madrid; 28040 Madrid Spain
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15
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Schmidt NG, Eger E, Kroutil W. Building Bridges: Biocatalytic C-C-Bond Formation toward Multifunctional Products. ACS Catal 2016; 6:4286-4311. [PMID: 27398261 PMCID: PMC4936090 DOI: 10.1021/acscatal.6b00758] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/13/2016] [Indexed: 12/12/2022]
Abstract
Carbon-carbon bond formation is the key reaction for organic synthesis to construct the carbon framework of organic molecules. The review gives a selection of biocatalytic C-C-bond-forming reactions which have been investigated during the last 5 years and which have already been proven to be applicable for organic synthesis. In most cases, the reactions lead to products functionalized at the site of C-C-bond formation (e.g., α-hydroxy ketones, aminoalcohols, diols, 1,4-diketones, etc.) or allow to decorate aromatic and heteroaromatic molecules. Furthermore, examples for cyclization of (non)natural precursors leading to saturated carbocycles are given as well as the stereoselective cyclopropanation of olefins affording cyclopropanes. Although many tools are already available, recent research also makes it clear that nature provides an even broader set of enzymes to perform specific C-C coupling reactions. The possibilities are without limit; however, a big library of variants for different types of reactions is required to have the specific enzyme for a desired specific (stereoselective) reaction at hand.
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Affiliation(s)
- Nina G. Schmidt
- ACIB
GmbH c/o, Department of Chemistry, University
of Graz, Heinrichstrasse
28, 8010 Graz, Austria
| | - Elisabeth Eger
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- ACIB
GmbH c/o, Department of Chemistry, University
of Graz, Heinrichstrasse
28, 8010 Graz, Austria
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010 Graz, Austria
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16
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Güclü D, Szekrenyi A, Garrabou X, Kickstein M, Junker S, Clapés P, Fessner WD. Minimalist Protein Engineering of an Aldolase Provokes Unprecedented Substrate Promiscuity. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02805] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Deniz Güclü
- Institut
für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Anna Szekrenyi
- Instituto de Quı́mica Avanzada de Cataluña-IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Xavier Garrabou
- Instituto de Quı́mica Avanzada de Cataluña-IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Michael Kickstein
- Institut
für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Sebastian Junker
- Institut
für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
| | - Pere Clapés
- Instituto de Quı́mica Avanzada de Cataluña-IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Wolf-Dieter Fessner
- Institut
für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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17
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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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18
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Wei M, Li Z, Li T, Wu B, Liu Y, Qu J, Li X, Li L, Cai L, Wang PG. Transforming Flask Reaction into Cell-Based Synthesis: Production of Polyhydroxylated Molecules via Engineered Escherichia coli. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00953] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mohui Wei
- Center
for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Zijie Li
- The
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry
of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Tiehai Li
- Center
for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Baolin Wu
- Center
for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yunpeng Liu
- Center
for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Jingyao Qu
- Center
for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Xu Li
- Center
for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Lei Li
- Center
for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Li Cai
- Department
of Chemistry, University of South Carolina Salkehatchie, Walterboro, South Carolina 29488, United States
| | - Peng George Wang
- Center
for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300457, China
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Camps Bres F, Guérard-Hélaine C, Hélaine V, Fernandes C, Sánchez-Moreno I, Traïkia M, García-Junceda E, Lemaire M. l-Rhamnulose-1-phosphate and l-fuculose-1-phosphate aldolase mediated multi-enzyme cascade systems for nitrocyclitol synthesis. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Windle CL, Müller M, Nelson A, Berry A. Engineering aldolases as biocatalysts. Curr Opin Chem Biol 2014; 19:25-33. [PMID: 24780276 PMCID: PMC4012138 DOI: 10.1016/j.cbpa.2013.12.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 11/30/2022]
Abstract
Aldolases are seen as an attractive route to the production of biologically important compounds due to their ability to form carbon-carbon bonds. However, for many industrial reactions there are no naturally occurring enzymes, and so many different engineering approaches have been used to address this problem. Engineering methods have been used to alter the stability, substrate specificity and stereospecificity of aldolases to produce excellent enzymes for biocatalytic processes. Recently greater understanding of the aldolase mechanism has allowed many successes with both rational engineering approaches and computational design of aldolases. Rational engineering approaches have produced desired enzymes quickly and efficiently while combination of computational design with laboratory methods has created enzymes with activity approaching that of natural enzymes.
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Affiliation(s)
- Claire L Windle
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Marion Müller
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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21
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DHAP-dependent aldolases from (hyper)thermophiles: biochemistry and applications. Extremophiles 2013; 18:1-13. [DOI: 10.1007/s00792-013-0593-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 10/10/2013] [Indexed: 12/20/2022]
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Widmann M, Pleiss J, Samland AK. Computational tools for rational protein engineering of aldolases. Comput Struct Biotechnol J 2012; 2:e201209016. [PMID: 24688657 PMCID: PMC3962226 DOI: 10.5936/csbj.201209016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/31/2012] [Accepted: 11/07/2012] [Indexed: 11/22/2022] Open
Abstract
In this mini-review we describe the different strategies for rational protein engineering and summarize the computational tools available. Computational tools can either be used to design focused libraries, to predict sequence-function relationships or for structure-based molecular modelling. This also includes de novo design of enzymes. Examples for protein engineering of aldolases and transaldolases are given in the second part of the mini-review.
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Affiliation(s)
- Michael Widmann
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Anne K Samland
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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24
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Baker P, Seah SYK. Rational approaches for engineering novel functionalities in carbon-carbon bond forming enzymes. Comput Struct Biotechnol J 2012; 2:e201209003. [PMID: 24688644 PMCID: PMC3962088 DOI: 10.5936/csbj.201209003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 09/13/2012] [Accepted: 09/15/2012] [Indexed: 01/17/2023] Open
Abstract
Enzymes that catalyze carbon-carbon bond formation can be exploited as biocatalyst for synthetic organic chemistry. However, natural enzymes frequently do not possess the required properties or specificities to catalyze industrially useful transformations. This mini-review describes recent work using knowledge-guided site-specific mutagenesis of key active site residues to alter substrate specificity, stereospecificity and reaction specificity of these enzymes. In addition, examples of de novo designed enzymes that catalyze C-C bond reactions not found in nature will be discussed.
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Affiliation(s)
- Perrin Baker
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario Canada, N1G 2W1
| | - Stephen Y K Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario Canada, N1G 2W1
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25
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Cheriyan M, Toone EJ, Fierke CA. Improving upon nature: active site remodeling produces highly efficient aldolase activity toward hydrophobic electrophilic substrates. Biochemistry 2012; 51:1658-68. [PMID: 22316217 DOI: 10.1021/bi201899b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The substrate specificity of enzymes is frequently narrow and constrained by multiple interactions, limiting the use of natural enzymes in biocatalytic applications. Aldolases have important synthetic applications, but the usefulness of these enzymes is hampered by their narrow reactivity profile with unnatural substrates. To explore the determinants of substrate selectivity and alter the specificity of Escherichia coli 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, we employed structure-based mutagenesis coupled with library screening of mutant enzymes localized to the bacterial periplasm. We identified two active site mutations (T161S and S184L) that work additively to enhance the substrate specificity of this aldolase to include catalysis of retro-aldol cleavage of (4S)-2-keto-4-hydroxy-4-(2'-pyridyl)butyrate (S-KHPB). These mutations improve the value of k(cat)/K(M)(S-KHPB) by >450-fold, resulting in a catalytic efficiency that is comparable to that of the wild-type enzyme with the natural substrate while retaining high stereoselectivity. Moreover, the value of k(cat)(S-KHPB) for this mutant enzyme, a parameter critical for biocatalytic applications, is 3-fold higher than the maximal value achieved by the natural aldolase with any substrate. This mutant also possesses high catalytic efficiency for the retro-aldol cleavage of the natural substrate, KDPG, and a >50-fold improved activity for cleavage of 2-keto-4-hydroxy-octonoate, a nonfunctionalized hydrophobic analogue. These data suggest a substrate binding mode that illuminates the origin of facial selectivity in aldol addition reactions catalyzed by KDPG and 2-keto-3-deoxy-6-phosphogalactonate aldolases. Furthermore, targeting mutations to the active site provides a marked improvement in substrate selectivity, demonstrating that structure-guided active site mutagenesis combined with selection techniques can efficiently identify proteins with characteristics that compare favorably to those of naturally occurring enzymes.
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Affiliation(s)
- Manoj Cheriyan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Gómez L, Garrabou X, Joglar J, Bujons J, Parella T, Vilaplana C, Cardona PJ, Clapés P. Chemoenzymatic synthesis, structural study and biological activity of novel indolizidine and quinolizidine iminocyclitols. Org Biomol Chem 2012; 10:6309-21. [DOI: 10.1039/c2ob25943e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Monrad RN, Madsen R. Modern methods for shortening and extending the carbon chain in carbohydrates at the anomeric center. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.08.047] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Behrens GA, Hummel A, Padhi SK, Schätzle S, Bornscheuer UT. Discovery and Protein Engineering of Biocatalysts for Organic Synthesis. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100446] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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New opportunities for biocatalysis: driving the synthesis of chiral chemicals. Curr Opin Biotechnol 2011; 22:784-92. [PMID: 21783357 DOI: 10.1016/j.copbio.2011.07.002] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 06/29/2011] [Accepted: 07/01/2011] [Indexed: 02/08/2023]
Abstract
Various biocatalytic methods have been developed for the synthesis of chiral chemicals, which have made their synthesis more environmentally friendly and product-specific. New opportunities for biocatalysis, including new scientific developments in genomics and protein engineering technologies, novel process developments and the increased availability of useful enzymes, offer many possibilities for the manufacture of new chiral compounds and deliver greener and economically competitive processes. In this review, new opportunities for biocatalysis in the preparation of chiral molecules are outlined and highlighted.
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Garrabou X, Calveras J, Joglar J, Parella T, Bujons J, Clapés P. Highly efficient aldol additions of DHA and DHAP to N-Cbz-amino aldehydes catalyzed by l-rhamnulose-1-phosphate and l-fuculose-1-phosphate aldolases in aqueous borate buffer. Org Biomol Chem 2011; 9:8430-6. [DOI: 10.1039/c1ob06263h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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