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Cancellieri MC, Nobbio C, Gatti FG, Brenna E, Parmeggiani F. Applications of biocatalytic CC bond reductions in the synthesis of flavours and fragrances. J Biotechnol 2024; 390:13-27. [PMID: 38761886 DOI: 10.1016/j.jbiotec.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Industrial biotechnology and biocatalysis can provide very effective synthetic tools to increase the sustainability of the production of fine chemicals, especially flavour and fragrance (F&F) ingredients, the market demand of which has been constantly increasing in the last years. One of the most important transformations in F&F chemistry is the reduction of CC bonds, typically carried out with metal-catalysed hydrogenations or hydride-based reagents. Its biocatalytic counterpart is a competitive alternative, showcasing a range of advantages such as excellent chemo-, regio- and stereoselectivity, ease of implementation, mild reaction conditions and modest environmental impact. In the present review, the application of biocatalysed alkene reductions (from microbial fermentations with wild-type strains to engineered isolated ene-reductase enzymes) to synthetic processes useful for the F&F industry will be described, highlighting not only the exquisite stereoselectivity achieved, but also the overall improvement when chirality is not involved. Multi-enzymatic cascades involving CC bioreductions are also examined, which allow much greater chemical complexity to be built in one-pot biocatalytic systems.
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Affiliation(s)
- Maria C Cancellieri
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy
| | - Celeste Nobbio
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy
| | - Francesco G Gatti
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy
| | - Elisabetta Brenna
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy.
| | - Fabio Parmeggiani
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano 20133, Italy.
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2
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Fan XY, Yu Y, Yao Y, Li WD, Tao FY, Wang N. Applications of Ene-Reductases in the Synthesis of Flavors and Fragrances. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38966982 DOI: 10.1021/acs.jafc.4c02897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Flavors and fragrances (F&F) are interesting organic compounds in chemistry. These compounds are widely used in the food, cosmetic, and medical industries. Enzymatic synthesis exhibits several advantages over natural extraction and chemical preparation, including a high yield, stable quality, mildness, and environmental friendliness. To date, many oxidoreductases and hydrolases have been used to biosynthesize F&F. Ene-reductases (ERs) are a class of biocatalysts that can catalyze the asymmetric reduction of α,β-unsaturated compounds and offer superior specificity and selectivity; therefore, ERs have been increasingly considered an ideal alternative to their chemical counterparts. This review summarizes the research progress on the use of ERs in F&F synthesis over the past 20 years, including the achievements of various scholars, the differences and similarities among the findings, and the discussions of future research trends related to ERs. We hope this review can inspire researchers to promote the development of biotechnology in the F&F industry.
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Affiliation(s)
- Xin-Yue Fan
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China
| | - Yuan Yu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China
| | - Yao Yao
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China
| | - Wen-Dian Li
- Harmful Components and Tar Reduction in Cigarette Key Laboratory of Sichuan Province, China Tobacco Sichuan Industrial Company, Limited, Chengdu, Sichuan 610066, People's Republic of China
- Sichuan Sanlian New Material Company, Limited, Chengdu, Sichuan 610041, People's Republic of China
| | - Fei-Yan Tao
- Harmful Components and Tar Reduction in Cigarette Key Laboratory of Sichuan Province, China Tobacco Sichuan Industrial Company, Limited, Chengdu, Sichuan 610066, People's Republic of China
- Sichuan Sanlian New Material Company, Limited, Chengdu, Sichuan 610041, People's Republic of China
| | - Na Wang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China
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3
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Fong JK, Mathieu Y, Vo MT, Bellemare A, Tsang A, Brumer H. Expansion of Auxiliary Activity Family 5 sequence space via biochemical characterization of six new copper radical oxidases. Appl Environ Microbiol 2024:e0101424. [PMID: 38953370 DOI: 10.1128/aem.01014-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024] Open
Abstract
Bacterial and fungal copper radical oxidases (CROs) from Auxiliary Activity Family 5 (AA5) are implicated in morphogenesis and pathogenesis. The unique catalytic properties of CROs also make these enzymes attractive biocatalysts for the transformation of small molecules and biopolymers. Despite a recent increase in the number of characterized AA5 members, especially from subfamily 2 (AA5_2), the catalytic diversity of the family as a whole remains underexplored. In the present study, phylogenetic analysis guided the selection of six AA5_2 members from diverse fungi for recombinant expression in Komagataella pfaffii (syn. Pichia pastoris) and biochemical characterization in vitro. Five of the targets displayed predominant galactose 6-oxidase activity (EC 1.1.3.9), and one was a broad-specificity aryl alcohol oxidase (EC 1.1.3.7) with maximum activity on the platform chemical 5-hydroxymethyl furfural (EC 1.1.3.47). Sequence alignment comparing previously characterized AA5_2 members to those from this study indicated various amino acid substitutions at active site positions implicated in the modulation of specificity.IMPORTANCEEnzyme discovery and characterization underpin advances in microbial biology and the application of biocatalysts in industrial processes. On one hand, oxidative processes are central to fungal saprotrophy and pathogenesis. On the other hand, controlled oxidation of small molecules and (bio)polymers valorizes these compounds and introduces versatile functional groups for further modification. The biochemical characterization of six new copper radical oxidases further illuminates the catalytic diversity of these enzymes, which will inform future biological studies and biotechnological applications.
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Affiliation(s)
- Jessica K Fong
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yann Mathieu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Minh Tri Vo
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Annie Bellemare
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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4
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Cherfaoui B, Chebrouk F, Hassaine R, Khalfaoui M, Boukennna L, Hamroun MSE, Abou-Mustapha M, Lazhar G. Hemi-synthesis of novel chiral benzodiazepine derivatives from Eucalyptus citriodora essential oil: 2D NMR experiments and differential scanning calorimetry study of diastereoisomers. Nat Prod Res 2024; 38:2486-2497. [PMID: 36890766 DOI: 10.1080/14786419.2023.2185888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/25/2023] [Indexed: 03/10/2023]
Abstract
An efficient in situ condensation of citronellal, the main constituent of Eucalyptus citriodora essential oil (51%), with different amine derivatives of 2,3-diaminomaleonitrile and 3-[(2-aminoaryl)amino]dimedone has led to novel chiral benzodiazepine structures. All reactions were precipitated in ethanol and pure products were obtained in good yields (58-75%) without any purification. The synthesized benezodiazepines were characterized by spectroscopic techniques, namely 1H-NMR, 13C-NMR, 2D NMR and FTIR. Differential Scanning Calorimetry (DSC) and HPLC were used to confirm the formation diastereomeric mixtures of benzodiazepine derivatives.
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Affiliation(s)
- Brahim Cherfaoui
- Scientific and Technical Center of Research in Physical and Chemical Analysis CRAPC, BP384, Tipaza, Algeria
- Laboratory of Polymeric Materials (LPM), Faculty of Chemistry, U.S.T.H.B., Algiers, Algeria
| | - Farid Chebrouk
- Scientific and Technical Center of Research in Physical and Chemical Analysis CRAPC, BP384, Tipaza, Algeria
- Laboratory of Biomathematics, Biochemistry, Biophysics and Scientometrics (L3BS), Faculty of Nature and Life Sciences (FSNV), University of Bejaia, Bejaia, Algeria
| | - Ridha Hassaine
- Scientific and Technical Center of Research in Physical and Chemical Analysis CRAPC, BP384, Tipaza, Algeria
- Laboratory of Catalysis and Synthesis in Organic Chemistry, Faculty of Sciences, University of Tlemcen, Tlemcen, Algeria
| | - Massaab Khalfaoui
- Laboratory of Polymeric Materials (LPM), Faculty of Chemistry, U.S.T.H.B., Algiers, Algeria
| | - Leϊla Boukennna
- Scientific and Technical Center of Research in Physical and Chemical Analysis CRAPC, BP384, Tipaza, Algeria
- Laboratory of Polymeric Materials (LPM), Faculty of Chemistry, U.S.T.H.B., Algiers, Algeria
| | | | - Mohamed Abou-Mustapha
- Scientific and Technical Center of Research in Physical and Chemical Analysis CRAPC, BP384, Tipaza, Algeria
| | - Gacem Lazhar
- Scientific and Technical Center of Research in Physical and Chemical Analysis CRAPC, BP384, Tipaza, Algeria
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5
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Zhang J, Li Y, Gao H, Zhang H, Zhang X, Rao Z, Xu M. N-terminal truncation (N-) and directional proton transfer in an old yellow enzyme enables tunable efficient producing (R)- or (S)-citronellal. Int J Biol Macromol 2024; 262:130129. [PMID: 38354939 DOI: 10.1016/j.ijbiomac.2024.130129] [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: 11/05/2023] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
(R)-Citronellal is a valuable molecule as the precursor for the industrial synthesis of (-)-menthol, one of the worldwide best-selling compounds in the flavors and fragrances field. However, its biocatalytic production, even from the optically pure substrate (E)-citral, is inherently limited by the activity of Old Yellow Enzyme (OYE). Herein, we rationally designed a different approach to increase the activity of OYE in biocatalytic production. The activity of OYE from Corynebacterium glutamicum (CgOYE) is increased, as well as superior thermal stability and pH tolerance via truncating the different lengths of regions at N-terminal of CgOYE. Next, we converted the truncation mutant N31-CgOYE, a protein involved in proton transfer for the asymmetric hydrogenation of CC bonds, into highly (R)- and (S)-stereoselective enzymes using only three mutations. The mixture of racemic (E/Z)-citral is reduced into the (R)-citronellal with ee and conversion up to 99 % by the mutant of CgOYE, overcoming the problem of the reduction for the mixtures of (E/Z)-citral in biocatalytic reaction. The present work provides a general and effective strategy for improving the activity of OYE, in which the partially conserved histidine residues provide "tunable gating" for the enantioselectivity for both the (R)- and (S)-isomerases.
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Affiliation(s)
- Jie Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yueshu Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Hui Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Hengwei Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China..
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6
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Luckie BA, Kashyap M, Pearson AN, Chen Y, Liu Y, Valencia LE, Carrillo Romero A, Hudson GA, Tao XB, Wu B, Petzold CJ, Keasling JD. Development of Corynebacterium glutamicum as a monoterpene production platform. Metab Eng 2024; 81:110-122. [PMID: 38056688 DOI: 10.1016/j.ymben.2023.11.009] [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: 09/02/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
Monoterpenes are commonly known for their role in the flavors and fragrances industry and are also gaining attention for other uses like insect repellant and as potential renewable fuels for aviation. Corynebacterium glutamicum, a Generally Recognized as Safe microbe, has been a choice organism in industry for the annual million ton-scale bioproduction of amino acids for more than 50 years; however, efforts to produce monoterpenes in C. glutamicum have remained relatively limited. In this study, we report a further expansion of the C. glutamicum biosynthetic repertoire through the development and optimization of a mevalonate-based monoterpene platform. In the course of our plasmid design iterations, we increased flux through the mevalonate-based bypass pathway, measuring isoprenol production as a proxy for monoterpene precursor abundance and demonstrating the highest reported titers in C. glutamicum to date at 1504.6 mg/L. Our designs also evaluated the effects of backbone, promoter, and GPP synthase homolog origin on monoterpene product titers. Monoterpene production was further improved by disrupting competing pathways for isoprenoid precursor supply and by implementing a biphasic production system to prevent volatilization. With this platform, we achieved 321.1 mg/L of geranoids, 723.6 mg/L of 1,8-cineole, and 227.8 mg/L of linalool. Furthermore, we determined that C. glutamicum first oxidizes geraniol through an aldehyde intermediate before it is asymmetrically reduced to citronellol. Additionally, we demonstrate that the aldehyde reductase, AdhC, possesses additional substrate promiscuity for acyclic monoterpene aldehydes.
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Affiliation(s)
- Bridget A Luckie
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Meera Kashyap
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Allison N Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Luis E Valencia
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint Program in Bioengineering, University of California, Berkeley, San Francisco, CA, 94720, USA
| | - Alexander Carrillo Romero
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Graham A Hudson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Xavier B Tao
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bryan Wu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA; Joint Program in Bioengineering, University of California, Berkeley, San Francisco, CA, 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark; Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
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7
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Michailidou F. The Scent of Change: Sustainable Fragrances Through Industrial Biotechnology. Chembiochem 2023; 24:e202300309. [PMID: 37668275 DOI: 10.1002/cbic.202300309] [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: 04/19/2023] [Revised: 05/29/2023] [Indexed: 09/06/2023]
Abstract
Current environmental and safety considerations urge innovation to address the need for sustainable high-value chemicals that are embraced by consumers. This review discusses the concept of sustainable fragrances, as high-value, everyday and everywhere chemicals. Current and emerging technologies represent an opportunity to produce fragrances in an environmentally and socially responsible way. Biotechnology, including fermentation, biocatalysis, and genetic engineering, has the potential to reduce the environmental footprint of fragrance production while maintaining quality and consistency. Computational and in silico methods, including machine learning (ML), are also likely to augment the capabilities of sustainable fragrance production. Continued innovation and collaboration will be crucial to the future of sustainable fragrances, with a focus on developing novel sustainable ingredients, as well as ethical sourcing practices.
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Affiliation(s)
- Freideriki Michailidou
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
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8
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Schober L, Dobiašová H, Jurkaš V, Parmeggiani F, Rudroff F, Winkler M. Enzymatic reactions towards aldehydes: An overview. FLAVOUR FRAG J 2023; 38:221-242. [PMID: 38505272 PMCID: PMC10947199 DOI: 10.1002/ffj.3739] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/21/2024]
Abstract
Many aldehydes are volatile compounds with distinct and characteristic olfactory properties. The aldehydic functional group is reactive and, as such, an invaluable chemical multi-tool to make all sorts of products. Owing to the reactivity, the selective synthesis of aldehydic is a challenging task. Nature has evolved a number of enzymatic reactions to produce aldehydes, and this review provides an overview of aldehyde-forming reactions in biological systems and beyond. Whereas some of these biotransformations are still in their infancy in terms of synthetic applicability, others are developed to an extent that allows their implementation as industrial biocatalysts.
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Affiliation(s)
- Lukas Schober
- Institute of Molecular BiotechnologyGraz University of TechnologyGrazAustria
| | - Hana Dobiašová
- Institute of Chemical and Environmental EngineeringSlovak University of TechnologyBratislavaSlovakia
| | - Valentina Jurkaš
- Institute of Molecular BiotechnologyGraz University of TechnologyGrazAustria
| | - Fabio Parmeggiani
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica “Giulio Natta”Politecnico di MilanoMilanItaly
| | - Florian Rudroff
- Institute of Applied Synthetic ChemistryTU WienViennaAustria
| | - Margit Winkler
- Institute of Molecular BiotechnologyGraz University of TechnologyGrazAustria
- Area BiotransformationsAustrian Center of Industrial BiotechnologyGrazAustria
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9
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Chiang CH, Wymore T, Rodríguez Benítez A, Hussain A, Smith JL, Brooks CL, Narayan ARH. Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction. Proc Natl Acad Sci U S A 2023; 120:e2218248120. [PMID: 37014851 PMCID: PMC10104550 DOI: 10.1073/pnas.2218248120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/06/2023] [Indexed: 04/05/2023] Open
Abstract
Controlling the selectivity of a reaction is critical for target-oriented synthesis. Accessing complementary selectivity profiles enables divergent synthetic strategies, but is challenging to achieve in biocatalytic reactions given enzymes' innate preferences of a single selectivity. Thus, it is critical to understand the structural features that control selectivity in biocatalytic reactions to achieve tunable selectivity. Here, we investigate the structural features that control the stereoselectivity in an oxidative dearomatization reaction that is key to making azaphilone natural products. Crystal structures of enantiocomplementary biocatalysts guided the development of multiple hypotheses centered on the structural features that control the stereochemical outcome of the reaction; however, in many cases, direct substitutions of active site residues in natural proteins led to inactive enzymes. Ancestral sequence reconstruction (ASR) and resurrection were employed as an alternative strategy to probe the impact of each residue on the stereochemical outcome of the dearomatization reaction. These studies suggest that two mechanisms are active in controlling the stereochemical outcome of the oxidative dearomatization reaction: one involving multiple active site residues in AzaH and the other dominated by a single Phe to Tyr switch in TropB and AfoD. Moreover, this study suggests that the flavin-dependent monooxygenases (FDMOs) adopt simple and flexible strategies to control stereoselectivity, which has led to stereocomplementary azaphilone natural products produced by fungi. This paradigm of combining ASR and resurrection with mutational and computational studies showcases sets of tools for understanding enzyme mechanisms and provides a solid foundation for future protein engineering efforts.
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Affiliation(s)
- Chang-Hwa Chiang
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
| | - Troy Wymore
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY11794
- Department of Chemistry, Stony Brook University, Stony Brook, NY11794
| | - Attabey Rodríguez Benítez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI48109
| | - Azam Hussain
- Macromolecular Science and Engineering Program, University of Michigan, Ann Arbor, MI48109
| | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Charles L. Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI48109
- Department of Biophysics, University of Michigan, Ann Arbor, MI48109
| | - Alison R. H. Narayan
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI48109
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10
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Chu GB, Li WY, Han XX, Sun HH, Han Y, Zhi GY, Zhang DH. Co-Immobilization of GOD & HRP on Y-Shaped DNA Scaffold and the Regulation of Inter-Enzyme Distance. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2301413. [PMID: 36929203 DOI: 10.1002/smll.202301413] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Indexed: 06/18/2023]
Abstract
In multienzymes cascade reaction, the inter-enzyme spacing is supposed to be a factor affecting the cascade activity. Here, a simple and efficient Y-shaped DNA scaffold is assembled using two partially complementary DNA single strands on magnetic microspheres, which is used to coimmobilize glucose oxidase (GOD) and horseradish peroxidase (HRP). As a result, on poly(vinyl acetate) magnetic microspheres (PVAC), GOD/HRP-DNA@PVAC multienzyme system is obtained, which can locate GOD and HRP accurately and control the inter-enzyme distance precisely. The distance between GOD and HRP is regulated by changing the length of DNA strand. It showed that the cascade activity is significantly distance-dependent. Moreover, the inter-enzyme spacing is not the closer the better, and too short distance would generate steric hindrance between enzymes. The cascade activity reached the maximum value of 967 U mg-1 at 13.6 nm, which is 3.5 times higher than that of free enzymes. This is ascribed to the formation of substrate channeling.
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Affiliation(s)
- Guan-Bo Chu
- College of Pharmaceutical Science, Hebei University, Baoding, 071002, P. R. China
| | - Wen-Yu Li
- College of Pharmaceutical Science, Hebei University, Baoding, 071002, P. R. China
| | - Xiao-Xia Han
- College of Pharmaceutical Science, Hebei University, Baoding, 071002, P. R. China
| | - Hui-Huang Sun
- College of Pharmaceutical Science, Hebei University, Baoding, 071002, P. R. China
| | - Yu Han
- College of Pharmaceutical Science, Hebei University, Baoding, 071002, P. R. China
| | - Gao-Ying Zhi
- Department of Computer Teaching, Hebei University, Baoding, 071002, P. R. China
| | - Dong-Hao Zhang
- College of Pharmaceutical Science, Hebei University, Baoding, 071002, P. R. China
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Science, Hebei University, Baoding, 071002, P. R. China
- Institute of Life Science and Green Development, Hebei University, Baoding, 071002, P. R. China
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11
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Copper radical oxidases: galactose oxidase, glyoxal oxidase, and beyond! Essays Biochem 2022; 67:597-613. [PMID: 36562172 DOI: 10.1042/ebc20220124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/14/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
The copper radical oxidases (CROs) are an evolutionary and functionally diverse group of enzymes established by the historically significant galactose 6-oxidase and glyoxal oxidase from fungi. Inducted in 2013, CROs now constitute Auxiliary Activity Family 5 (AA5) in the Carbohydrate-Active Enzymes (CAZy) classification. CROs catalyse the two-electron oxidation of their substrates using oxygen as the final electron acceptor and are particularly distinguished by a cross-linked tyrosine-cysteine co-factor that is integral to radical stabilization. Recently, there has been a significant increase in the biochemically and structurally characterized CROs, which has revealed an expanded natural diversity of catalytic activities in the family. This review provides a brief historical introduction to CRO biochemistry and structural biology as a foundation for an update on current advances in CRO enzymology, biotechnology, and biology across kingdoms of life.
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Yi J, Li Z. Artificial multi-enzyme cascades for natural product synthesis. Curr Opin Biotechnol 2022; 78:102831. [PMID: 36308987 DOI: 10.1016/j.copbio.2022.102831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/19/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022]
Abstract
Artificial multi-enzyme cascades bear great potential for offering sustainable synthesis of useful and valuable natural molecules. In the past two years, many new cascades were developed to produce natural alcohols, acids, esters, amino compounds, fatty acid derivatives, alkaloids, terpenoids, terpenes and monosaccharides from natural substrates and simple chemicals, respectively. These artificial cascades were constructed by combining individual enzymes designed using the retro-synthesis strategy and based on the available natural substrates and simple chemicals. While performing the cascades in vivo is often simple and straightforward, in vitro cascades usually require cofactor regeneration that was achieved by introducing one or more cofactor-regeneration modules in one pot. Protein engineering is frequently used to improve the performances of some enzymes in the cascades.
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Affiliation(s)
- Jieran Yi
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
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Collaborative catalysis for solar biosynthesis. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Feng J, Xue Y, Wang J, Xie X, Lu C, Chen H, Lu Y, Zhu L, Chu D, Chen X. Enhancing the asymmetric reduction activity of ene-reductases for the synthesis of a brivaracetam precursor. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.12.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Zhang C, Tang Y, Wang Q, He Y, Wang X, Beyer S, Guo J. Near infrared light-induced dynamic modulation of enzymatic activity through polyphenol-functionalized liquid metal nanodroplets. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Zhang L, King E, Black WB, Heckmann CM, Wolder A, Cui Y, Nicklen F, Siegel JB, Luo R, Paul CE, Li H. Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform. Nat Commun 2022; 13:5021. [PMID: 36028482 PMCID: PMC9418148 DOI: 10.1038/s41467-022-32727-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/13/2022] [Indexed: 11/09/2022] Open
Abstract
Noncanonical redox cofactors are attractive low-cost alternatives to nicotinamide adenine dinucleotide (phosphate) (NAD(P)+) in biotransformation. However, engineering enzymes to utilize them is challenging. Here, we present a high-throughput directed evolution platform which couples cell growth to the in vivo cycling of a noncanonical cofactor, nicotinamide mononucleotide (NMN+). We achieve this by engineering the life-essential glutathione reductase in Escherichia coli to exclusively rely on the reduced NMN+ (NMNH). Using this system, we develop a phosphite dehydrogenase (PTDH) to cycle NMN+ with ~147-fold improved catalytic efficiency, which translates to an industrially viable total turnover number of ~45,000 in cell-free biotransformation without requiring high cofactor concentrations. Moreover, the PTDH variants also exhibit improved activity with another structurally deviant noncanonical cofactor, 1-benzylnicotinamide (BNA+), showcasing their broad applications. Structural modeling prediction reveals a general design principle where the mutations and the smaller, noncanonical cofactors together mimic the steric interactions of the larger, natural cofactors NAD(P)+.
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Affiliation(s)
- Linyue Zhang
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - William B Black
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Christian M Heckmann
- Biocatalysis, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, Netherlands
| | - Allison Wolder
- Biocatalysis, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, Netherlands
| | - Youtian Cui
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Francis Nicklen
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, 2700 Stockton Boulevard, Suite 2102, Sacramento, CA, 95817, USA
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Ray Luo
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA
- Department Materials Science and Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Caroline E Paul
- Biocatalysis, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, Netherlands
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California Irvine, Irvine, CA, 92697, USA.
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA.
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Hagiwara H. Introduction of Chiral Centers to α- and/or β-Positions of Carbonyl Groups by Biocatalytic Asymmetric Reduction of α,β-Unsaturated Carbonyl Compounds. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221099054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biocatalytic asymmetric reductions of acyclic and cyclic α,β-unsaturated carbonyl compounds are favorable protocols for introduction of chiral centers to α- and/or β-positions of the carbonyl groups. Representative biocatalytic reductions of electron deficient olefins are compiled from a synthetic point of view according to compound types from the papers in 2012 to early 2022. Applications to syntheses of some enantiomericaly enriched perfumery ingredients are presented to show the feasibility of the biocatalytic reductions.
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Affiliation(s)
- Hisahiro Hagiwara
- Graduate School of Science and Technology, Niigata University, 8050, 2-Nocho, Ikarashi, Nishi-ku, Niigata, 950-2181, Japan
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