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Ju S, Li D, Mai BK, Liu X, Vallota-Eastman A, Wu J, Valentine DL, Liu P, Yang Y. Stereodivergent photobiocatalytic radical cyclization through the repurposing and directed evolution of fatty acid photodecarboxylases. Nat Chem 2024:10.1038/s41557-024-01494-0. [PMID: 38632367 DOI: 10.1038/s41557-024-01494-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/28/2024] [Indexed: 04/19/2024]
Abstract
Despite their intriguing photophysical and photochemical activities, naturally occurring photoenzymes have not yet been repurposed for new-to-nature activities. Here we engineered fatty acid photodecarboxylases to catalyse unnatural photoredox radical C-C bond formation by leveraging the strongly oxidizing excited-state flavoquinone cofactor. Through genome mining, rational engineering and directed evolution, we developed a panel of radical photocyclases to facilitate decarboxylative radical cyclization with excellent chemo-, enantio- and diastereoselectivities. Our high-throughput experimental workflow allowed for the directed evolution of fatty acid photodecarboxylases. An orthogonal set of radical photocyclases was engineered to access all four possible stereoisomers of the stereochemical dyad, affording fully diastereo- and enantiodivergent biotransformations in asymmetric radical biocatalysis. Molecular dynamics simulations show that our evolved radical photocyclases allow near-attack conformations to be easily accessed, enabling chemoselective radical cyclization. The development of stereoselective radical photocyclases provides unnatural C-C-bond-forming activities in natural photoenzyme families, which can be used to tame the stereochemistry of free-radical-mediated reactions.
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Affiliation(s)
- Shuyun Ju
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Dian Li
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xin Liu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Alec Vallota-Eastman
- Interdepartmental Graduate Program for Marine Science, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Jianping Wu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - David L Valentine
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Earth Science, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA.
- Biomolecular Science and Engineering (BMSE) Program, University of California Santa Barbara, Santa Barbara, CA, USA.
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2
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Mou K, Guo Y, Xu W, Li D, Wang Z, Wu Q. Stereodivergent Protein Engineering of Fatty Acid Photodecarboxylase for Light-Driven Kinetic Resolution of Sec-Alcohol Oxalates. Angew Chem Int Ed Engl 2024; 63:e202318374. [PMID: 38195798 DOI: 10.1002/anie.202318374] [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: 12/07/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/11/2024]
Abstract
Stereodivergent engineering of one enzyme to create stereocomplementary variants for synthesizing optically pure molecules with tailor-made (R) or (S) configurations on an optional basis is highly desirable and challenging. This study aimed to engineer fatty acid photodecarboxylase from Chlorella variabilis (CvFAP) using the focused rational iterative site-specific mutagenesis (FRISM) strategy to obtain two highly stereocomplementary variants with excellent selectivity (both giving products with up to 99 % e.e.). These variants were used for the CvFAP-catalyzed light-driven kinetic resolution of oxalates or oxamic acids prepared from the corresponding sec-alcohols or amines, providing a new biotransformation process for preparing chiral sec-alcohols and amines. Molecular dynamics simulation, kinetic data and transient spectra revealed the source of selectivity. This study represents the first example of the kinetic resolution of sec-alcohols or amines catalyzed by a pair of stereocomplementary CvFAPs.
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Affiliation(s)
- Kaihao Mou
- Center of Chemistry for Frontier Technologies, Department of Chemistry, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China
| | - Yue Guo
- Center of Chemistry for Frontier Technologies, Department of Chemistry, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China
| | - Weihua Xu
- Center of Chemistry for Frontier Technologies, Department of Chemistry, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China
| | - Danyang Li
- Center of Chemistry for Frontier Technologies, Department of Chemistry, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China
| | - Zhiguo Wang
- Institute of Aging Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qi Wu
- Center of Chemistry for Frontier Technologies, Department of Chemistry, Zijingang Campus, Zhejiang University, Hangzhou, 310058, China
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3
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Sui Y, Guo X, Zhou R, Fu Z, Chai Y, Xia A, Zhao W. Photoenzymatic Decarboxylation to Produce Hydrocarbon Fuels: A Critical Review. Mol Biotechnol 2023:10.1007/s12033-023-00775-2. [PMID: 37349610 DOI: 10.1007/s12033-023-00775-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023]
Abstract
Photoenzymatic decarboxylation shows great promise as a pathway for the generation of hydrocarbon fuels. CvFAP, which is derived from Chlorella variabilis NC64A, is a photodecarboxylase capable of converting fatty acids into hydrocarbons. CvFAP is an example of coupling biocatalysis and photocatalysis to produce alkanes. The catalytic process is mild, and it does not yield toxic substances or excess by-products. However, the activity of CvFAP can be readily inhibited by several factors, and further enhancement is required to improve the enzyme yield and stability. In this article, we will examine the latest advancements in CvFAP research, with a particular focus on the enzyme's structural and catalytic mechanism, summarized some limitations in the application of CvFAP, and laboratory-level methods for enhancing enzyme activity and stability. This review can serve as a reference for future large-scale industrial production of hydrocarbon fuels.
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Affiliation(s)
- Yaqi Sui
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Xiaobo Guo
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Rui Zhou
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Zhisong Fu
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Yingxin Chai
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Ao Xia
- School of Energy and Power Engineering, Chongqing University, Chongqing, 400044, China
| | - Wenhui Zhao
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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4
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Emmanuel MA, Bender SG, Bilodeau C, Carceller JM, DeHovitz JS, Fu H, Liu Y, Nicholls BT, Ouyang Y, Page CG, Qiao T, Raps FC, Sorigué DR, Sun SZ, Turek-Herman J, Ye Y, Rivas-Souchet A, Cao J, Hyster TK. Photobiocatalytic Strategies for Organic Synthesis. Chem Rev 2023; 123:5459-5520. [PMID: 37115521 PMCID: PMC10905417 DOI: 10.1021/acs.chemrev.2c00767] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Biocatalysis has revolutionized chemical synthesis, providing sustainable methods for preparing various organic molecules. In enzyme-mediated organic synthesis, most reactions involve molecules operating from their ground states. Over the past 25 years, there has been an increased interest in enzymatic processes that utilize electronically excited states accessed through photoexcitation. These photobiocatalytic processes involve a diverse array of reaction mechanisms that are complementary to one another. This comprehensive review will describe the state-of-the-art strategies in photobiocatalysis for organic synthesis until December 2022. Apart from reviewing the relevant literature, a central goal of this review is to delineate the mechanistic differences between the general strategies employed in the field. We will organize this review based on the relationship between the photochemical step and the enzymatic transformations. The review will include mechanistic studies, substrate scopes, and protein optimization strategies. By clearly defining mechanistically-distinct strategies in photobiocatalytic chemistry, we hope to illuminate future synthetic opportunities in the area.
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Affiliation(s)
- Megan A Emmanuel
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sophie G Bender
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Catherine Bilodeau
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jose M Carceller
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Institute of Chemical Technology (ITQ), Universitat Politècnica de València, València 46022,Spain
| | - Jacob S DeHovitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Haigen Fu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Yi Liu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Bryce T Nicholls
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yao Ouyang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Claire G Page
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Tianzhang Qiao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Felix C Raps
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Damien R Sorigué
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Shang-Zheng Sun
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Joshua Turek-Herman
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yuxuan Ye
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ariadna Rivas-Souchet
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jingzhe Cao
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Todd K Hyster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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5
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Ge R, Zhang P, Dong X, Li Y, Sun Z, Zeng Y, Chen B, Zhang W. Photobiocatalytic Decarboxylation for the Synthesis of Fatty Epoxides from Renewable Fatty Acids. CHEMSUSCHEM 2022; 15:e202201275. [PMID: 36036214 DOI: 10.1002/cssc.202201275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Fatty epoxides are unique building blocks in organic transformations and materials production; however, their synthetic methodologies are currently not accessible from renewable fatty acids. Herein, a photoenzymatic decarboxylation of epoxy fatty acids into fatty epoxides was demonstrated using fatty acid photodecarboxylase (FAP) from Chlorella variabilis NC64A (CvFAP). Various fatty epoxides were synthesized in excellent selectivity by wild-type CvFAP. The decarboxylation reaction was also achieved with four new FAP homologues, potentially suggesting a broad availability of the biocatalysts for this challenging decarboxylation reaction. By combining CvFAP with lipase and peroxygenase, a multienzymatic cascade to transform oleic acid and its triglyceride into the corresponding fatty epoxides was established. The obtained fatty epoxides were further converted into rather unusual fatty compounds including diol, alcohol, ether, and chain-shortened carboxylic acids. The present photobiocatalytic synthesis of fatty epoxides from natural starting materials excels by its intrinsic selectivity, mild conditions, and independence of nicotinamide cofactors.
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Affiliation(s)
- Ran Ge
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, P. R. China
| | - Pengpeng Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, P. R. China
| | - Xuetian Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, P. R. China
| | - Yuanying Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, P. R. China
| | - Zhoutong Sun
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, P. R. China
| | - Yongyi Zeng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519080, P. R. China
| | - Bishuang Chen
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519080, P. R. China
| | - Wuyuan Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, P. R. China
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6
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Malihan‐Yap L, Grimm HC, Kourist R. Recent Advances in Cyanobacterial Biotransformations. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202200077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lenny Malihan‐Yap
- Graz University of Technology Institute of Molecular Biotechnology NAWI Graz 8010 Graz Austria
| | - Hanna C. Grimm
- Graz University of Technology Institute of Molecular Biotechnology NAWI Graz 8010 Graz Austria
| | - Robert Kourist
- Graz University of Technology Institute of Molecular Biotechnology NAWI Graz 8010 Graz Austria
- ACIB GmbH 8010 Graz Austria
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7
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Peoples J, Ruppe S, Mains K, Cipriano EC, Fox JM. A Kinetic Framework for Modeling Oleochemical Biosynthesis in E. coli. Biotechnol Bioeng 2022; 119:3149-3161. [PMID: 35959746 DOI: 10.1002/bit.28209] [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: 06/02/2022] [Revised: 08/01/2022] [Accepted: 08/07/2022] [Indexed: 11/06/2022]
Abstract
Microorganisms build fatty acids with biocatalytic assembly lines, or fatty acid synthases (FASs), that can be repurposed to produce a broad set of fuels and chemicals. Despite their versatility, the product profiles of FAS-based pathways are challenging to adjust without experimental iteration, and off-target products are common. This study uses a detailed kinetic model of the E. coli FAS as a foundation to model nine oleochemical pathways. These models provide good fits to experimental data and help explain unexpected results from in vivo studies. An analysis of pathways for alkanes and fatty acid ethyl esters, for example, suggests that reductions in titer caused by enzyme overexpression-an experimentally consistent phenomenon-can result from shifts in metabolite pools that are incompatible with the substrate specificities of downstream enzymes, and a focused examination of multiple alcohol pathways indicates that coordinated shifts in enzyme concentrations provide a general means of tuning the product profiles of pathways with promiscuous components. The study concludes by integrating all models into a graphical user interface. The models supplied by this work provide a versatile kinetic framework for studying oleochemical pathways in different biochemical contexts. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jackson Peoples
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303
| | - Sophia Ruppe
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303
| | - Kathryn Mains
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303
| | - Elia C Cipriano
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO, 80303
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