1
|
Aspacio D, Zhang Y, Cui Y, Luu E, King E, Black WB, Perea S, Zhu Q, Wu Y, Luo R, Siegel JB, Li H. Shifting redox reaction equilibria on demand using an orthogonal redox cofactor. Nat Chem Biol 2024:10.1038/s41589-024-01702-5. [PMID: 39138383 DOI: 10.1038/s41589-024-01702-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 07/16/2024] [Indexed: 08/15/2024]
Abstract
Nature's two redox cofactors, nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), are held at different reduction potentials, driving catabolism and anabolism in opposite directions. In biomanufacturing, there is a need to flexibly control redox reaction direction decoupled from catabolism and anabolism. We established nicotinamide mononucleotide (NMN+) as a noncanonical cofactor orthogonal to NAD(P)+. Here we present the development of Nox Ortho, a reduced NMN+ (NMNH)-specific oxidase, that completes the toolkit to modulate NMNH:NMN+ ratio together with an NMN+-specific glucose dehydrogenase (GDH Ortho). The design principle discovered from Nox Ortho engineering and modeling is facilely translated onto six different enzymes to create NMN(H)-orthogonal biocatalysts with a consistent ~103-106-fold cofactor specificity switch from NAD(P)+ to NMN+. We assemble these enzymes to produce stereo-pure 2,3-butanediol in cell-free systems and in Escherichia coli, enabled by NMN(H)'s distinct redox ratio firmly set by its designated driving forces, decoupled from both NAD(H) and NADP(H).
Collapse
Affiliation(s)
- Derek Aspacio
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Yulai Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Youtian Cui
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Emma Luu
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - William B Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Sean Perea
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Qiang Zhu
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
- Department of Material Science and Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Yongxian Wu
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
- Department of Material Science and Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Ray Luo
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
- Department of Material Science and Engineering, University of California, Irvine, Irvine, CA, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Justin B Siegel
- Genome Center, University of California, Davis, Davis, CA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA.
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA.
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA.
| |
Collapse
|
2
|
Yang G, Pećanac O, Wijma HJ, Rozeboom HJ, de Gonzalo G, Fraaije MW, Mascotti ML. Evolution of the catalytic mechanism at the dawn of the Baeyer-Villiger monooxygenases. Cell Rep 2024; 43:114130. [PMID: 38640062 DOI: 10.1016/j.celrep.2024.114130] [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: 10/03/2023] [Revised: 02/15/2024] [Accepted: 04/04/2024] [Indexed: 04/21/2024] Open
Abstract
Enzymes are crucial for the emergence and sustenance of life on earth. How they became catalytically active during their evolution is still an open question. Two opposite explanations are plausible: acquiring a mechanism in a series of discrete steps or all at once in a single evolutionary event. Here, we use molecular phylogeny, ancestral sequence reconstruction, and biochemical characterization to follow the evolution of a specialized group of flavoprotein monooxygenases, the bacterial Baeyer-Villiger monooxygenases (BVMOs). These enzymes catalyze an intricate chemical reaction relying on three different elements: a reduced nicotinamide cofactor, dioxygen, and a substrate. Characterization of ancestral BVMOs shows that the catalytic mechanism evolved in a series of steps starting from a FAD-binding protein and further acquiring reactivity and specificity toward each of the elements participating in the reaction. Together, the results of our work portray how an intrinsically complex catalytic mechanism emerged during evolution.
Collapse
Affiliation(s)
- Guang Yang
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Ognjen Pećanac
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Hein J Wijma
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Henriëtte J Rozeboom
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Gonzalo de Gonzalo
- Departamento de Química Orgánica, Universidad de Sevilla, and Centro de Innovación en Química Avanzada (ORFEO-CINQA), 41012 Sevilla, Spain
| | - Marco W Fraaije
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Maria Laura Mascotti
- Molecular Enzymology Group, University of Groningen, 9747 AG Groningen, the Netherlands; IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina.
| |
Collapse
|
3
|
Zhang L, Zhou R, Fu X, Zhang G, Zhang L, Zhou SF, Jiang W. Specific coenzyme preference switching for an aldo-keto reductase that synthesizes the chiral intermediate of duloxetine. Enzyme Microb Technol 2023; 171:110326. [PMID: 37717530 DOI: 10.1016/j.enzmictec.2023.110326] [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: 07/02/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
The synthesis of chiral intermediates for the traditional antidepressant duloxetine has gained significant attention as the number of depressed patients continues to grow. S-N, N-Dimethyl-3-hydroxy-3-(2-thienyl)-1-propanamide (S-DHTP) is a critical intermediate in the synthesis of duloxetine, and the chemical synthesis process is complex and environmentally unfriendly. Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a major cost driver in the biocatalytic production of S-DHTP from N, N-Dimethyl-3-keto-3-(2-thienyl)-1-propanamide (DKTP). Here, we successfully modified the coenzyme preference of an aldo-keto reductase (AKR7-2-1) to use the cheaper reduced nicotinamide adenine dinucleotide (NADH) through a coenzyme preference modification approach. We utilized protein engineering to create a superior mutant, Y53F, which increased the coenzyme specificity of AKR7-2-1 by 875-fold and improved its thermal stability, enhancing its potential for industrial applications. Molecular dynamics simulations were performed to demonstrate the effect of mutations at key sites on the protein, revealing the altered coenzyme preference and increased thermal stability from structural and energetic changes. This study validates the viability of the coenzyme preference modification strategy for aldo-keto reductase, offering valuable insights for fellow researchers and guiding future investigations.
Collapse
Affiliation(s)
- Lingzhi Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Rui Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Xiaoli Fu
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Guangya Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China
| | - Lijuan Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Shu-Feng Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China.
| | - Wei Jiang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, Fujian Province, PR China.
| |
Collapse
|
4
|
Willetts A. Bicyclo[3.2.0]carbocyclic Molecules and Redox Biotransformations: The Evolution of Closed-Loop Artificial Linear Biocatalytic Cascades and Related Redox-Neutral Systems. Molecules 2023; 28:7249. [PMID: 37959669 PMCID: PMC10649493 DOI: 10.3390/molecules28217249] [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: 08/22/2023] [Revised: 10/11/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
The role of cofactor recycling in determining the efficiency of artificial biocatalytic cascades has become paramount in recent years. Closed-loop cofactor recycling, which initially emerged in the 1990s, has made a valuable contribution to the development of this aspect of biotechnology. However, the evolution of redox-neutral closed-loop cofactor recycling has a longer history that has been integrally linked to the enzymology of oxy-functionalised bicyclo[3.2.0]carbocyclic molecule metabolism throughout. This review traces that relevant history from the mid-1960s to current times.
Collapse
Affiliation(s)
- Andrew Willetts
- Curnow Consultancies Ltd., Trewithen House, Helston TR13 9PQ, Cornwall, UK
| |
Collapse
|
5
|
Ma W, Geng Q, Chen C, Zheng YC, Yu HL, Xu JH. Engineering a Formate Dehydrogenase for NADPH Regeneration. Chembiochem 2023; 24:e202300390. [PMID: 37455264 DOI: 10.1002/cbic.202300390] [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: 05/24/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Nicotinamide adenine dinucleotide (NADH) and nicotinamide adenine dinucleotide phosphate (NADPH) constitute major hydrogen donors for oxidative/reductive bio-transformations. NAD(P)H regeneration systems coupled with formate dehydrogenases (FDHs) represent a dreamful method. However, most of the native FDHs are NAD+ -dependent and suffer from insufficient reactivity compared to other enzymatic tools, such as glucose dehydrogenase. An efficient and competitive NADP+ -utilizing FDH necessitates the availability and robustness of NADPH regeneration systems. Herein, we report the engineering of a new FDH from Candida dubliniensis (CdFDH), which showed no strict NAD+ preference by a structure-guided rational/semi-rational design. A combinatorial mutant CdFDH-M4 (D197Q/Y198R/Q199N/A372S/K371T/▵Q375/K167R/H16L/K159R) exhibited 75-fold intensification of catalytic efficiency (kcat /Km ). Moreover, CdFDH-M4 has been successfully employed in diverse asymmetric oxidative/reductive processes with cofactor total turnover numbers (TTNs) ranging from 135 to 986, making it potentially useful for NADPH-required biocatalytic transformations.
Collapse
Affiliation(s)
- Wei Ma
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Qiang Geng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Cheng Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Yu-Cong Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| |
Collapse
|
6
|
Aspacio D, Zhang Y, Cui Y, King E, Black WB, Perea S, Luu E, Siegel JB, Li H. Shifting Redox Reaction Equilibria on Demand Using an Orthogonal Redox Cofactor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555398. [PMID: 37693387 PMCID: PMC10491207 DOI: 10.1101/2023.08.29.555398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Natural metabolism relies on chemical compartmentalization of two redox cofactors, NAD+ and NADP+, to orchestrate life-essential redox reaction directions. However, in whole cells the reliance on these canonical cofactors limits flexible control of redox reaction direction as these reactions are permanently tied to catabolism or anabolism. In cell-free systems, NADP+ is too expensive in large scale. We have previously reported the use of nicotinamide mononucleotide, (NMN+) as a low-cost, noncanonical redox cofactor capable of specific electron delivery to diverse chemistries. Here, we present Nox Ortho, an NMNH-specific water-forming oxidase, that completes the toolkit to modulate NMNH/NMN+ ratio. This work uncovers an enzyme design principle that succeeds in parallel engineering of six butanediol dehydrogenases as NMN(H)-orthogonal biocatalysts consistently with a 103 - 106 -fold cofactor specificity switch from NAD(P)+ to NMN+. We combine these to produce chiral-pure 2,3-butanediol (Bdo) isomers without interference from NAD(H) or NADP(H) in vitro and in E. coli cells. We establish that NMN(H) can be held at a distinct redox ratio on demand, decoupled from both NAD(H) and NADP(H) redox ratios in vitro and in vivo.
Collapse
Affiliation(s)
- Derek Aspacio
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Yulai Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Youtian Cui
- Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - William B. Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Sean Perea
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Emma Luu
- Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Justin B. Siegel
- Genome Center, University of California, Davis, Davis, California 95616, United States
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
- Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| |
Collapse
|
7
|
Chánique AM, Polidori N, Sovic L, Kracher D, Assil-Companioni L, Galuska P, Parra LP, Gruber K, Kourist R. A Cold-Active Flavin-Dependent Monooxygenase from Janthinobacterium svalbardensis Unlocks Applications of Baeyer–Villiger Monooxygenases at Low Temperature. ACS Catal 2023; 13:3549-3562. [PMID: 36970468 PMCID: PMC10028610 DOI: 10.1021/acscatal.2c05160] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/31/2023] [Indexed: 03/02/2023]
Abstract
Cold-active enzymes maintain a large part of their optimal activity at low temperatures. Therefore, they can be used to avoid side reactions and preserve heat-sensitive compounds. Baeyer-Villiger monooxygenases (BVMO) utilize molecular oxygen as a co-substrate to catalyze reactions widely employed for steroid, agrochemical, antibiotic, and pheromone production. Oxygen has been described as the rate-limiting factor for some BVMO applications, thereby hindering their efficient utilization. Considering that oxygen solubility in water increases by 40% when the temperature is decreased from 30 to 10 °C, we set out to identify and characterize a cold-active BVMO. Using genome mining in the Antarctic organism Janthinobacterium svalbardensis, a cold-active type II flavin-dependent monooxygenase (FMO) was discovered. The enzyme shows promiscuity toward NADH and NADPH and high activity between 5 and 25 °C. The enzyme catalyzes the monooxygenation and sulfoxidation of a wide range of ketones and thioesters. The high enantioselectivity in the oxidation of norcamphor (eeS = 56%, eeP > 99%, E > 200) demonstrates that the generally higher flexibility observed in the active sites of cold-active enzymes, which compensates for the lower motion at cold temperatures, does not necessarily reduce the selectivity of these enzymes. To gain a better understanding of the unique mechanistic features of type II FMOs, we determined the structure of the dimeric enzyme at 2.5 Å resolution. While the unusual N-terminal domain has been related to the catalytic properties of type II FMOs, the structure shows a SnoaL-like N-terminal domain that is not interacting directly with the active site. The active site of the enzyme is accessible only through a tunnel, with Tyr-458, Asp-217, and His-216 as catalytic residues, a combination not observed before in FMOs and BVMOs.
Collapse
Affiliation(s)
- Andrea M. Chánique
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7810000, Chile
| | - Nakia Polidori
- NAWI Graz, BioTechMed Graz, Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, Graz 8010, Austria
| | - Lucija Sovic
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Daniel Kracher
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Leen Assil-Companioni
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- ACIB GmbH, Petersgasse 14/1, Graz 8010, Austria
| | - Philipp Galuska
- NAWI Graz, BioTechMed Graz, Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, Graz 8010, Austria
| | - Loreto P. Parra
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7810000, Chile
| | - Karl Gruber
- NAWI Graz, BioTechMed Graz, Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, Graz 8010, Austria
| | - Robert Kourist
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- ACIB GmbH, Petersgasse 14/1, Graz 8010, Austria
| |
Collapse
|
8
|
Biocatalytic Cascade of Sebacic Acid Production with In Situ Co-Factor Regeneration Enabled by Engineering of an Alcohol Dehydrogenase. Catalysts 2022. [DOI: 10.3390/catal12111318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Sebacic acid (1,10-decanedioic acid) is an important chemical intermediate. Traditional chemical oxidation methods for sebacic acid production do not conform with “green” manufacturing. With the rapid development of enzymatic technologies, a biocatalytic cascade method based on the Baeyer–Villiger monooxygenase was developed. The most attractive point of the method is the oleic acid that can be utilized as raw material, which is abundant in nature. However, this bio-catalysis process needs co-factor electron carriers, and the high cost of the co-factor limits its progress. In this piece of work, a co-factor in situ regeneration system between ADH from Micrococcus luteus WIUJH20 (MlADH) and BVMO is proposed. Since the co-factors of both enzymes are different, switching the co-factor preference of native MlADH from NAD+ to NADP+ is necessary. Switching research was carried out based on in silico simulation, and the sites of Tyr36, Asp 37, Ala38, and Val39 were selected for mutation investigation. The experimental results demonstrated that mutants of MlADH_D37G and MlADH_D37G/A38T/V39K would utilize NADP+ efficiently, and the mutant of MlADH_D37G/A38T/V39K demonstrated the highest sebacic acid yield with the combination of BVMO. The results indicated that the in situ co-factor generation system is successfully developed, which would improve the efficiency of the biocatalytic cascade for sebacic acid production and is helpful for simplifying product isolation, thus, reducing the cost of the enzymatic transformations process.
Collapse
|
9
|
Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
Collapse
Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| |
Collapse
|
10
|
Mansouri HR, Gracia Carmona O, Jodlbauer J, Schweiger L, Fink MJ, Breslmayr E, Laurent C, Feroz S, P. Goncalves LC, Rial DV, Mihovilovic MD, Bommarius AS, Ludwig R, Oostenbrink C, Rudroff F. Mutations Increasing Cofactor Affinity, Improve Stability and Activity of a Baeyer–Villiger Monooxygenase. ACS Catal 2022; 12:11761-11766. [PMID: 36249873 PMCID: PMC9552169 DOI: 10.1021/acscatal.2c03225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/31/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Hamid R. Mansouri
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Oriol Gracia Carmona
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Julia Jodlbauer
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Lorenz Schweiger
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Michael J. Fink
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Erik Breslmayr
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Christophe Laurent
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Saima Feroz
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
- Department of Biosciences, College of Science, University of Hafr Al Batin, PO Box 1803, Hafr Al Batin, 39524, Saudi Arabia
| | - Leticia C. P. Goncalves
- Institut de Chimie de Nice CRNS UMR7272, Université Côte d’Azur, 28 Avenue Valrose, 06108 Nice, France
| | - Daniela V. Rial
- Área Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Suipacha 531, S2002LRK Rosario, Argentina
| | - Marko D. Mihovilovic
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Engineered Biosystems Building (EBB), Georgia Institute of Technology, 950 Atlantic Drive, N.W., Atlanta, Georgia 30332, United States
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| |
Collapse
|
11
|
Seo E, Kim M, Park S, Park S, Oh D, Bornscheuer U, Park J. Enzyme Access Tunnel Engineering in Baeyer‐Villiger Monooxygenases to Improve Oxidative Stability and Biocatalyst Performance. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202101044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Eun‐Ji Seo
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - Myeong‐Ju Kim
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - So‐Yeon Park
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| | - Seongsoon Park
- Department of Chemistry, Center for NanoBio Applied Technology Sungshin Women's University Seoul 01133 Republic of Korea
| | - Deok‐Kun Oh
- Department of Bioscience and Biotechnology Konkuk University Seoul 05029 Republic of Korea
| | - Uwe Bornscheuer
- Institute of Biochemistry, Department of Biotechnology & Enzyme Catalysis Greifswald University Greifswald 17487 Germany
| | - Jin‐Byung Park
- Department of Food Science and Engineering Ewha Womans University Seoul 03760 Republic of Korea
| |
Collapse
|
12
|
Xiong W, Liu B, Shen Y, Jing K, Savage TR. Protein engineering design from directed evolution to de novo synthesis. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
13
|
Maxel S, Saleh S, King E, Aspacio D, Zhang L, Luo R, Li H. Growth-Based, High-Throughput Selection for NADH Preference in an Oxygen-Dependent Biocatalyst. ACS Synth Biol 2021; 10:2359-2370. [PMID: 34469126 PMCID: PMC10362907 DOI: 10.1021/acssynbio.1c00258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclohexanone monooxygenases (CHMO) consume molecular oxygen and NADPH to catalyze the valuable oxidation of cyclic ketones. However, CHMO usage is restricted by poor stability and stringent specificity for NADPH. Efforts to engineer CHMO have been limited by the sensitivity of the enzyme to perturbations in conformational dynamics and long-range interactions that cannot be predicted. We demonstrate an aerobic, high-throughput growth selection platform in Escherichia coli for oxygenase evolution based on NADH redox balance. We applied this NADH-dependent selection to alter the cofactor specificity of CHMO to accept NADH, a less expensive cofactor than NADPH. We first identified the variant CHMO DTNP (S208D-K326T-K349N-L143P) with a ∼1200-fold relative cofactor specificity switch from NADPH to NADH compared to the wild type through semirational design. Molecular modeling suggests CHMO DTNP activity is driven by cooperative fine-tuning of cofactor contacts. Additional evolution of CHMO DTNP through random mutagenesis yielded the variant CHMO DTNPY with a ∼2900-fold relative specificity switch compared to the wild type afforded by an additional distal mutation, H163Y. These results highlight the difficulty in engineering functionally innovative variants from static models and rational designs, and the need for high throughput selection methods. Our introduced tools for oxygenase engineering accelerate the advancements of characteristics essential for industrial feasibility.
Collapse
Affiliation(s)
- Sarah Maxel
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Samer Saleh
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Edward King
- Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Derek Aspacio
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Linyue Zhang
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Ray Luo
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
- Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
- Biomedical Engineering, University of California, Irvine, California 92697, United States
| | - Han Li
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
- Biomedical Engineering, University of California, Irvine, California 92697, United States
| |
Collapse
|
14
|
Lindenburg L, Hollfelder F. “NAD‐display”: Ultrahigh‐Throughput in Vitro Screening of NAD(H) Dehydrogenases Using Bead Display and Flow Cytometry. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
- Current address: Genmab Uppsalalaan 15 3584 CT Utrecht The Netherlands
| | - Florian Hollfelder
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| |
Collapse
|
15
|
Lindenburg L, Hollfelder F. "NAD-display": Ultrahigh-Throughput in Vitro Screening of NAD(H) Dehydrogenases Using Bead Display and Flow Cytometry. Angew Chem Int Ed Engl 2021; 60:9015-9021. [PMID: 33470025 PMCID: PMC8048591 DOI: 10.1002/anie.202013486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/21/2020] [Indexed: 12/25/2022]
Abstract
NAD(H)‐utiliing enzymes have been the subject of directed evolution campaigns to improve their function. To enable access to a larger swath of sequence space, we demonstrate the utility of a cell‐free, ultrahigh‐throughput directed evolution platform for dehydrogenases. Microbeads (1.5 million per sample) carrying both variant DNA and an immobilised analogue of NAD+ were compartmentalised in water‐in‐oil emulsion droplets, together with cell‐free expression mixture and enzyme substrate, resulting in the recording of the phenotype on each bead. The beads’ phenotype could be read out and sorted for on a flow cytometer by using a highly sensitive fluorescent protein‐based sensor of the NAD+:NADH ratio. Integration of this “NAD‐display” approach with our previously described Split & Mix (SpliMLiB) method for generating large site‐saturation libraries allowed straightforward screening of fully balanced site saturation libraries of formate dehydrogenase, with diversities of 2×104. Based on modular design principles of synthetic biology NAD‐display offers access to sophisticated in vitro selections, avoiding complex technology platforms.
Collapse
Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.,Current address: Genmab, Uppsalalaan 15, 3584 CT, Utrecht, The Netherlands
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| |
Collapse
|
16
|
King E, Maxel S, Li H. Engineering natural and noncanonical nicotinamide cofactor-dependent enzymes: design principles and technology development. Curr Opin Biotechnol 2020; 66:217-226. [PMID: 32956903 PMCID: PMC7744333 DOI: 10.1016/j.copbio.2020.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/14/2020] [Accepted: 08/16/2020] [Indexed: 12/20/2022]
Abstract
Nicotinamide cofactors enable oxidoreductases to catalyze a myriad of important reactions in biomanufacturing. Decades of research has focused on optimizing enzymes which utilize natural nicotinamide cofactors, namely nicotinamide adenine dinucleotide (phosphate) (NAD(P)+). Recent findings reignite the interest in engineering enzymes to utilize noncanonical cofactors, the mimetics of NAD+ (mNADs), which exhibit superior industrial properties in vitro and enable specific electron delivery in vivo. We compare recent advances in engineering natural versus noncanonical cofactor-utilizing enzymes, discuss design principles discovered, and survey emerging high-throughput platforms beyond the traditional 96-well plate-based methods. Obtaining mNAD-dependent enzymes remains challenging with a limited toolkit. To this end, we highlight design principles and technologies which can potentially be translated from engineering natural to noncanonical cofactor-dependent enzymes.
Collapse
Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Sarah Maxel
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, USA
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, USA.
| |
Collapse
|
17
|
Gmelch TJ, Sperl JM, Sieber V. Molecular Dynamics Analysis of a Rationally Designed Aldehyde Dehydrogenase Gives Insights into Improved Activity for the Non-Native Cofactor NAD .. ACS Synth Biol 2020; 9:920-929. [PMID: 32208678 DOI: 10.1021/acssynbio.9b00527] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aldehyde dehydrogenase from Thermoplasma acidophilum was previously implemented as a key enzyme in a synthetic cell-free reaction cascade for the production of alcohols. In order to engineer the enzyme's cofactor specificity from NADP+ to NAD+, we identified selectivity-determining residues with the CSR-SALAD tool and investigated further positions based on the crystal structure. Stepwise combination of the initially discovered six point mutations allowed us to monitor the cross effects of each mutation, resulting in a final variant with reduced KM for the non-native cofactor NAD+ (from 18 to 0.6 mM) and an increased activity for the desired substrate d-glyceraldehyde (from 0.4 to 1.5 U/mg). Saturation mutagenesis of the residues at the entrance of the substrate pocket could eliminate substrate inhibition. Molecular dynamics simulations showed a significant gain of flexibility at the cofactor binding site for the final variant. The concomitant increase in stability against isobutanol and only a minor reduction in its temperature stability render the final variant a promising candidate for future optimization of our synthetic cell-free enzymatic cascade.
Collapse
Affiliation(s)
- Tobias J. Gmelch
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, D-94315 Straubing, Germany
| | - Josef M. Sperl
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, D-94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, D-94315 Straubing, Germany
- Catalysis Research Center, Technical University of Munich, Garching 85748, Germany
- Bio-, Electro- and Chemocatalysis (BioCat) Branch, Fraunhofer Institute of Interfacial Biotechnology (IGB), Straubing 94315, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| |
Collapse
|
18
|
Narunsky A, Kessel A, Solan R, Alva V, Kolodny R, Ben-Tal N. On the evolution of protein-adenine binding. Proc Natl Acad Sci U S A 2020; 117:4701-4709. [PMID: 32079721 PMCID: PMC7060716 DOI: 10.1073/pnas.1911349117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Proteins' interactions with ancient ligands may reveal how molecular recognition emerged and evolved. We explore how proteins recognize adenine: a planar rigid fragment found in the most common and ancient ligands. We have developed a computational pipeline that extracts protein-adenine complexes from the Protein Data Bank, structurally superimposes their adenine fragments, and detects the hydrogen bonds mediating the interaction. Our analysis extends the known motifs of protein-adenine interactions in the Watson-Crick edge of adenine and shows that all of adenine's edges may contribute to molecular recognition. We further show that, on the proteins' side, binding is often mediated by specific amino acid segments ("themes") that recur across different proteins, such that different proteins use the same themes when binding the same adenine-containing ligands. We identify numerous proteins that feature these themes and are thus likely to bind adenine-containing ligands. Our analysis suggests that adenine binding has emerged multiple times in evolution.
Collapse
Affiliation(s)
- Aya Narunsky
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat Aviv, Israel
| | - Amit Kessel
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat Aviv, Israel
| | - Ron Solan
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat Aviv, Israel
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Rachel Kolodny
- Department of Computer Science, University of Haifa, Mount Carmel, 3498838 Haifa, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Ramat Aviv, Israel;
| |
Collapse
|
19
|
Abstract
Type I Baeyer–Villiger monooxygenases (BVMOs) are flavin-dependent monooxygenases that catalyze the oxidation of ketones to esters or lactones, a reaction otherwise performed in chemical processes by employing hazardous and toxic peracids. Even though various BVMOs are extensively studied for their promising role in industrial biotechnology, there is still a demand for enzymes that are able to retain activity at high saline concentrations. To this aim, and based on comparative in silico analyses, we cloned HtBVMO from the extremely halophilic archaeon Haloterrigena turkmenica DSM 5511. When expressed in standard mesophilic cell factories, proteins adapted to hypersaline environments often behave similarly to intrinsically disordered polypeptides. Nevertheless, we managed to express HtBVMO in Escherichia coli and could purify it as active enzyme. The enzyme was characterized in terms of its salt-dependent activity and resistance to some water–organic-solvent mixtures. Although HtBVMO does not seem suitable for industrial applications, it provides a peculiar example of an alkalophilic and halophilic BVMO characterized by an extremely negative charge. Insights into the behavior and structural properties of such salt-requiring may contribute to more efficient strategies for engineering the tuned stability and solubility of existing BVMOs.
Collapse
|
20
|
Schmidt S, Bornscheuer UT. Baeyer-Villiger monooxygenases: From protein engineering to biocatalytic applications. FLAVIN-DEPENDENT ENZYMES: MECHANISMS, STRUCTURES AND APPLICATIONS 2020; 47:231-281. [DOI: 10.1016/bs.enz.2020.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
21
|
Song JW, Seo JH, Oh DK, Bornscheuer UT, Park JB. Design and engineering of whole-cell biocatalytic cascades for the valorization of fatty acids. Catal Sci Technol 2020. [DOI: 10.1039/c9cy01802f] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review presents the key factors to construct a productive whole-cell biocatalytic cascade exemplified for the biotransformation of renewable fatty acids.
Collapse
Affiliation(s)
- Ji-Won Song
- Department of Food Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Joo-Hyun Seo
- Department of Bio and Fermentation Convergence Technology
- Kookmin University
- Seoul 02707
- Republic of Korea
| | - Doek-Kun Oh
- Department of Bioscience and Biotechnology
- Konkuk University
- Seoul 143-701
- Republic of Korea
| | - Uwe T. Bornscheuer
- Institute of Biochemistry
- Department of Biotechnology & Enzyme Catalysis
- Greifswald University
- 17487 Greifswald
- Germany
| | - Jin-Byung Park
- Department of Food Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
- Institute of Molecular Microbiology and Biosystems Engineering
| |
Collapse
|
22
|
Seo EJ, Kim HJ, Kim MJ, Kim JS, Park JB. Cofactor specificity engineering of a long-chain secondary alcohol dehydrogenase from Micrococcus luteus for redox-neutral biotransformation of fatty acids. Chem Commun (Camb) 2019; 55:14462-14465. [PMID: 31728457 DOI: 10.1039/c9cc06447h] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Structure-based engineering of a NAD+-dependent secondary alcohol dehydrogenase from Micrococcus luteus led to a 1800-fold increase in catalytic efficiency for NADP+. Furthermore, the engineered enzymes (e.g., D37S/A38R/V39S/T15I) were successfully coupled to a NADPH-dependent Baeyer-Villiger monooxygenase from Pseudomonas putida KT2440 for redox-neutral biotransformations of C18 fatty acids into C9 chemicals.
Collapse
Affiliation(s)
- Eun-Ji Seo
- Department of Food Science & Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
| | | | | | | | | |
Collapse
|
23
|
Li Y, Pan H, Chang Y, Dong N, Zou L, Liang P, Tian W, Chang Z. Identification of key sites determining the cofactor specificity and improvement of catalytic activity of a steroid 5β-reductase from Capsella rubella. Enzyme Microb Technol 2019; 134:109483. [PMID: 32044030 DOI: 10.1016/j.enzmictec.2019.109483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 10/25/2022]
Abstract
Progesterone 5β-reductases (P5βRs) are involved in 5β-cardenolide formation by stereo-specific reduction of the △4,5 double bond of steroid precursors. In this study a steroid 5β-reductase was identified in Capsella rubella (CrSt5βR1) and its function in steroid 5β-reduction was validated experimentally. CrSt5βR1 is capable of enantioselectively reducing the activated CC bond of broad substrates such as steroids and enones by using NADPH as a cofactor and therefore has the potential as a biocatalyst in organic synthesis. However, for industrial purposes the cheaper NADH is the preferred cofactor. By applying rational design based on literature and complementary mutagenesis strategies, we successfully identified two key amino acid residues determining the cofactor specificity of the enzyme. The R63 K mutation enables the enzyme to convert progesterone to 5β-pregnane-3,20-dione with NADH as cofactor, whereas the wild-type CrSt5βR1 is strictly NADPH-dependent. By further introducing the R64H mutation, the double mutant R63K_R64H of CrSt5βR1 was shown to increase enzymatic activity by13.8-fold with NADH as a cofactor and to increase the NADH/NADPH conversion ratio by 10.9-fold over the R63 K single mutant. This finding was successfully applied to change the cofactor specificity and to improve activity of other members of the same enzyme family, AtP5βR and DlP5βR. CrSt5βR1 mutants are expected to have the potential for biotechnological applications in combination with the well-established NADH regeneration systems.
Collapse
Affiliation(s)
- Yuanyuan Li
- School of Life Science and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Hongyan Pan
- School of Life Science and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Yaowen Chang
- School of Life Science and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Na Dong
- School of Life Science and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Lei Zou
- School of Life Science and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Wei Tian
- School of Life Science and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
| | - Zunxue Chang
- School of Life Science and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
| |
Collapse
|
24
|
Fürst MJLJ, Gran-Scheuch A, Aalbers FS, Fraaije MW. Baeyer–Villiger Monooxygenases: Tunable Oxidative Biocatalysts. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03396] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maximilian J. L. J. Fürst
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
| | - Alejandro Gran-Scheuch
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Friso S. Aalbers
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen 9747AG, The Netherlands
| |
Collapse
|
25
|
Multi-level engineering of Baeyer-Villiger monooxygenase-based Escherichia coli biocatalysts for the production of C9 chemicals from oleic acid. Metab Eng 2019; 54:137-144. [DOI: 10.1016/j.ymben.2019.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/29/2019] [Accepted: 03/31/2019] [Indexed: 12/12/2022]
|
26
|
Efficient Synthesis of Methyl 3-Acetoxypropionate by a Newly Identified Baeyer-Villiger Monooxygenase. Appl Environ Microbiol 2019; 85:AEM.00239-19. [PMID: 30926727 DOI: 10.1128/aem.00239-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/24/2019] [Indexed: 11/20/2022] Open
Abstract
Baeyer-Villiger monooxygenases (BVMOs) are an emerging class of promising biocatalysts for the oxidation of ketones to prepare corresponding esters or lactones. Although many BVMOs have been reported, the development of highly efficient enzymes for use in industrial applications is desirable. In this work, we identified a BVMO from Rhodococcus pyridinivorans (BVMORp) with a high affinity toward aliphatic methyl ketones (Km < 3.0 μM). The enzyme was highly soluble and relatively stable, with a half-life of 23 h at 30°C and pH 7.5. The most effective substrate discovered so far is 2-hexanone (k cat = 2.1 s-1; Km = 1.5 μM). Furthermore, BVMORp exhibited excellent regioselectivity toward most aliphatic ketones, preferentially forming typical (i.e., normal) products. Using the newly identified BVMORp as the catalyst, a high concentration (26.0 g/liter; 200 mM) of methyl levulinate was completely converted to methyl 3-acetoxypropionate after 4 h, with a space-time yield of 5.4 g liter-1 h-1 Thus, BVMORp is a promising biocatalyst for the synthesis of 3-hydroxypropionate from readily available biobased levulinate to replace the conventional fermentation.IMPORTANCE BVMOs are emerging as a green alternative to traditional oxidants in the BV oxidation of ketones. Although many BVMOs are discovered and used in organic synthesis, few are really applied in industry, especially in the case of aliphatic ketones. Herein, a highly soluble and relatively stable monooxygenase from Rhodococcus pyridinivorans (BVMORp) was identified with high activity and excellent regioselectivity toward most aliphatic ketones. BVMORp possesses unusually high substrate loading during the catalysis of the oxidation of biobased methyl levulinate to 3-hydroxypropionic acid derivatives. This study indicates that the synthesis of 3-hydroxypropionate from readily available biobased levulinate by BVMORp-catalyzed oxidation holds great promise to replace traditional fermentation.
Collapse
|
27
|
Löwe J, Blifernez-Klassen O, Baier T, Wobbe L, Kruse O, Gröger H. Type II flavoprotein monooxygenase PsFMO_A from the bacterium Pimelobacter sp. Bb-B catalyzes enantioselective Baeyer-Villiger oxidations with a relaxed cofactor specificity. J Biotechnol 2019; 294:81-87. [DOI: 10.1016/j.jbiotec.2019.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 01/30/2023]
|
28
|
Hu Y, Wang J, Cen Y, Zheng H, Huang M, Lin X, Wu Q. “Top” or “bottom” switches of a cyclohexanone monooxygenase controlling the enantioselectivity of the sandwiched substrate. Chem Commun (Camb) 2019; 55:2198-2201. [DOI: 10.1039/c8cc09951k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single mutation F432I/L or L435A/G remarkably reversed the (−)-selectivity of WT CHMOAcineto.
Collapse
Affiliation(s)
- Yujing Hu
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
- School of Chemistry and Chemical Engineering
| | - Jie Wang
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
| | - Yixin Cen
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
| | - He Zheng
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
| | - Meilan Huang
- School of Chemistry and Chemical Engineering
- Queen's University
- UK
| | - Xianfu Lin
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
| | - Qi Wu
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- China
| |
Collapse
|
29
|
You ZN, Chen Q, Shi SC, Zheng MM, Pan J, Qian XL, Li CX, Xu JH. Switching Cofactor Dependence of 7β-Hydroxysteroid Dehydrogenase for Cost-Effective Production of Ursodeoxycholic Acid. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03561] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhi-Neng You
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qi Chen
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Shou-Cheng Shi
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Ming-Min Zheng
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiang Pan
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiao-Long Qian
- Suzhou Bioforany EnzyTech Co. Ltd., No. 8 Yanjiuyuan Road, Economic Development Zone, Changshu, Jiangsu 215512, China
| | - Chun-Xiu Li
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jian-He Xu
- Laboratory of Biocatalysis and Synthetic Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| |
Collapse
|
30
|
Moore JC, Rodriguez-Granillo A, Crespo A, Govindarajan S, Welch M, Hiraga K, Lexa K, Marshall N, Truppo MD. "Site and Mutation"-Specific Predictions Enable Minimal Directed Evolution Libraries. ACS Synth Biol 2018; 7:1730-1741. [PMID: 29782150 DOI: 10.1021/acssynbio.7b00359] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Directed evolution experiments designed to improve the activity of a biocatalyst have increased in sophistication from the early days of completely random mutagenesis. Sequence-based and structure-based methods have been developed to identify "hotspot" positions that when randomized provide a higher frequency of beneficial mutations that improve activity. These focused mutagenesis methods reduce library sizes and therefore reduce screening burden, accelerating the rate of finding improved enzymes. Looking for further acceleration in finding improved enzymes, we investigated whether two existing methods, one sequence-based (Protein GPS) and one structure-based (using Bioluminate and MOE), were sufficiently predictive to provide not just the hotspot position, but also the amino acid substitution that improved activity at that position. By limiting the libraries to variants that contained only specific amino acid substitutions, library sizes were kept to less than 100 variants. For an initial round of ATA-117 R-selective transaminase evolution, we found that the methods used produced libraries where 9% and 18% of the amino acid substitutions chosen were amino acids that improved reaction performance in lysates. The ability to create combinations of mutations as part of the initial design was confounded by the relatively large number of predicted mutations that were inactivating (30% and 45% for the sequence-based and structure-based methods, respectively). Despite this, combining several mutations identified within a given method produced variant lysates 7- and 9-fold more active than the wild-type lysate, highlighting the capability of mutations chosen this way to generate large advances in activity in addition to the reductions in screening.
Collapse
Affiliation(s)
| | | | | | | | - Mark Welch
- ATUM, 37950 Central Court, Newark, California 94560, United States
| | | | | | | | | |
Collapse
|
31
|
Improving catalytic activity of the Baeyer-Villiger monooxygenase-based Escherichia coli biocatalysts for the overproduction of (Z)-11-(heptanoyloxy)undec-9-enoic acid from ricinoleic acid. Sci Rep 2018; 8:10280. [PMID: 29980730 PMCID: PMC6035261 DOI: 10.1038/s41598-018-28575-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/21/2018] [Indexed: 12/21/2022] Open
Abstract
Baeyer–Villiger monooxygenases (BVMOs) can be used for the biosynthesis of lactones and esters from ketones. However, the BVMO-based biocatalysts are not so stable under process conditions. Thereby, this study focused on enhancing stability of the BVMO-based biocatalysts. The biotransformation of ricinoleic acid into (Z)-11-(heptanoyloxy)undec-9-enoic acid by the recombinant Escherichia coli expressing the BVMO from Pseudomonas putida and an alcohol dehydrogenase from Micrococcus luteus was used as a model system. After thorough investigation of the key factors to influence stability of the BVMO, Cys302 was identified as an engineering target. The substitution of Cys302 to Leu enabled the engineered enzyme (i.e., E6BVMOC302L) to become more stable toward oxidative and thermal stresses. The catalytic activity of E6BVMOC302L-based E. coli biocatalysts was also greater than the E6BVMO-based biocatalysts. Another factor to influence biocatalytic performance of the BVMO-based whole-cell biocatalysts was availability of carbon and energy source during biotransformations. Glucose feeding into the reaction medium led to a marked increase of final product concentrations. Overall, the bioprocess engineering to improve metabolic stability of host cells in addition to the BVMO engineering allowed us to produce (Z)-11-(heptanoyloxy)undec-9-enoic acid to a concentration of 132 mM (41 g/L) from 150 mM ricinoleic acid within 8 h.
Collapse
|
32
|
Chánique AM, Parra LP. Protein Engineering for Nicotinamide Coenzyme Specificity in Oxidoreductases: Attempts and Challenges. Front Microbiol 2018; 9:194. [PMID: 29491854 PMCID: PMC5817062 DOI: 10.3389/fmicb.2018.00194] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/29/2018] [Indexed: 01/10/2023] Open
Abstract
Oxidoreductases are ubiquitous enzymes that catalyze an extensive range of chemical reactions with great specificity, efficiency, and selectivity. Most oxidoreductases are nicotinamide cofactor-dependent enzymes with a strong preference for NADP or NAD. Because these coenzymes differ in stability, bioavailability and costs, the enzyme preference for a specific coenzyme is an important issue for practical applications. Different approaches for the manipulation of coenzyme specificity have been reported, with different degrees of success. Here we present various attempts for the switching of nicotinamide coenzyme preference in oxidoreductases by protein engineering. This review covers 103 enzyme engineering studies from 82 articles and evaluates the accomplishments in terms of coenzyme specificity and catalytic efficiency compared to wild type enzymes of different classes. We analyzed different protein engineering strategies and related them with the degree of success in inverting the cofactor specificity. In general, catalytic activity is compromised when coenzyme specificity is reversed, however when switching from NAD to NADP, better results are obtained. In most of the cases, rational strategies were used, predominantly with loop exchange generating the best results. In general, the tendency of removing acidic residues and incorporating basic residues is the strategy of choice when trying to change specificity from NAD to NADP, and vice versa. Computational strategies and algorithms are also covered as helpful tools to guide protein engineering strategies. This mini review aims to give a general introduction to the topic, giving an overview of tools and information to work in protein engineering for the reversal of coenzyme specificity.
Collapse
Affiliation(s)
- Andrea M Chánique
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Loreto P Parra
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile.,Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
33
|
Balke K, Beier A, Bornscheuer UT. Hot spots for the protein engineering of Baeyer-Villiger monooxygenases. Biotechnol Adv 2018; 36:247-263. [DOI: 10.1016/j.biotechadv.2017.11.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/15/2017] [Accepted: 11/17/2017] [Indexed: 10/18/2022]
|
34
|
Enzymatic Oxyfunctionalization Driven by Photosynthetic Water-Splitting in the Cyanobacterium Synechocystis sp. PCC 6803. Catalysts 2017. [DOI: 10.3390/catal7080240] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
|
35
|
Mthethwa KS, Kassier K, Engel J, Kara S, Smit MS, Opperman DJ. Fungal BVMOs as alternatives to cyclohexanone monooxygenase. Enzyme Microb Technol 2017; 106:11-17. [PMID: 28859804 DOI: 10.1016/j.enzmictec.2017.06.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/19/2017] [Accepted: 06/30/2017] [Indexed: 12/12/2022]
Abstract
FAD-dependent Baeyer-Villiger monooxygenases (BVMOs) have proven to be useful biocatalysts in the selective and specific oxygenation of various ketones. Despite the cloning, heterologous expression and characterization of close to 80 members of this enzyme family, some sub-groups of BVMOs still remain underrepresented and their evolutionary relationship uncertain. Until recently, very few fungal BVMOs have been described. Our previous investigations into BVMOs from the fungus Aspergillus flavus, yielded very little activity on simple cyclic ketones. Here we report on another four BVMOs from A. flavus that are more closely related to cyclohexanone monooxygenase (CHMO) from Acinetobacter sp. NCIMB 9871. Evolutionary analysis with other characterized BVMOs show their closest relationship to be with either cycloalkanone monooxygenase (CAMO) or 2-oxo-Δ3-4,5,5-trimethylcyclopentenylacetyl-coenzyme A monooxygenase (OTEMO). The OTEMO-related BVMOAFL706 and BVMOAFL334 were heterologously expressed in E. coli, purified and shown to be able to convert a range of cyclic and substituted cyclic ketones. Of the unsubstituted cyclic ketones, cyclohexanone showed the highest conversion with maximum turnover frequencies reaching 4.3s-1 for BVMOAFL706. Unlike CHMOacinet, and many of the closely related BVMOs, no substrate inhibition was observed with cyclohexanone to a concentration of up to 30mM, creating the possibility for applications requiring high substrate loading. Aliphatic ketones were also readily converted with excellent regioselectivity. Similar to CHMOacinet, acetophenones were not converted and the oxidation of rac-cis-bicyclo[3.2.0]hept-2-en-6-one occurs enantiodivergently, with the (1R,5S) isomer converted to the "normal" lactone and the (1S,5R) isomer to the "abnormal" lactone.
Collapse
Affiliation(s)
- Katlego Siphamandla Mthethwa
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
| | - Karin Kassier
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
| | - Jennifer Engel
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg, 21073, Germany
| | - Selin Kara
- Institute of Technical Biocatalysis, Hamburg University of Technology, Denickestr. 15, Hamburg, 21073, Germany
| | - Martha Sophia Smit
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
| | - Diederik Johannes Opperman
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa.
| |
Collapse
|
36
|
Balke K, Bäumgen M, Bornscheuer UT. Controlling the Regioselectivity of Baeyer-Villiger Monooxygenases by Mutation of Active-Site Residues. Chembiochem 2017; 18:1627-1638. [PMID: 28504873 DOI: 10.1002/cbic.201700223] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Indexed: 11/12/2022]
Abstract
Baeyer-Villiger monooxygenase (BVMO)-mediated regiodivergent conversions of asymmetric ketones can lead to the formation of "normal" or "abnormal" lactones. In a previous study, we were able to change the regioselectivity of a BVMO by mutation of the active-site residues to smaller amino acids, which thus created more space. In this study, we demonstrate that this method can also be used for other BVMO/substrate combinations. We investigated the regioselectivity of 2-oxo-Δ3 -4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase from Pseudomonas putida (OTEMO) for cis-bicyclo[3.2.0]hept-2-en-6-one (1) and trans-dihydrocarvone (2), and we were able to switch the regioselectivity of this enzyme for one of the substrate enantiomers. The OTEMO wild-type enzyme converted (-)-1 into an equal (50:50) mixture of the normal and abnormal products. The F255A/F443V variant produced 90 % of the normal product, whereas the W501V variant formed up to 98 % of the abnormal product. OTEMO F255A exclusively produced the normal lactone from (+)-2, whereas the wild-type enzyme was selective for the production of the abnormal product. The positions of these amino acids were equivalent to those mutated in the cyclohexanone monooxygenases from Arthrobacter sp. and Acinetobacter sp. (CHMOArthro and CHMOAcineto ) to switch their regioselectivity towards (+)-2, which suggests that there are hot spots in the active site of BVMOs that can be targeted with the aim to change the regioselectivity.
Collapse
Affiliation(s)
- Kathleen Balke
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Marcus Bäumgen
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| |
Collapse
|
37
|
Huang L, Romero E, Ressmann AK, Rudroff F, Hollmann F, Fraaije MW, Kara S. Nicotinamide Adenine Dinucleotide-Dependent Redox-Neutral Convergent Cascade for Lactonizations with Type II Flavin-Containing Monooxygenase. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700401] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lei Huang
- Institute of Technical Biocatalysis; Hamburg University of Technology; Denickestr. 15 21073 Hamburg Germany
| | - Elvira Romero
- Molecular Enzymology Group; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Anna K. Ressmann
- Institute of Applied Synthetic Chemistry; TU Wien; Getreidemarkt 9/163-OC 1060 Vienna Austria
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry; TU Wien; Getreidemarkt 9/163-OC 1060 Vienna Austria
| | - Frank Hollmann
- Biocatalysis; Department of Biotechnology; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Selin Kara
- Institute of Technical Biocatalysis; Hamburg University of Technology; Denickestr. 15 21073 Hamburg Germany
| |
Collapse
|
38
|
Goncalves LCP, Kracher D, Milker S, Fink MJ, Rudroff F, Ludwig R, Bommarius AS, Mihovilovic MD. Mutagenesis-Independent Stabilization of Class B Flavin Monooxygenases in Operation. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700585] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Leticia C. P. Goncalves
- Institute of Applied Synthetic Chemistry; Vienna University of Technology; Getreidemarkt 9/163 1060 Vienna Austria
| | - Daniel Kracher
- Biocatalysis and Biosensing Research Group; Department of Food Science and Technology; BOKU-University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
| | - Sofia Milker
- Institute of Applied Synthetic Chemistry; Vienna University of Technology; Getreidemarkt 9/163 1060 Vienna Austria
| | - Michael J. Fink
- Institute of Applied Synthetic Chemistry; Vienna University of Technology; Getreidemarkt 9/163 1060 Vienna Austria
- Department of Chemistry and Chemical Biology; Harvard University; 12 Oxford St Cambridge, MA 02138 USA
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry; Vienna University of Technology; Getreidemarkt 9/163 1060 Vienna Austria
| | - Roland Ludwig
- Biocatalysis and Biosensing Research Group; Department of Food Science and Technology; BOKU-University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
| | - Andreas S. Bommarius
- School of Chemical and Biomolecular Engineering; School of Chemistry and Biochemistry; Georgia Institute of Technology; Atlanta, GA 30332 USA
| | - Marko D. Mihovilovic
- Institute of Applied Synthetic Chemistry; Vienna University of Technology; Getreidemarkt 9/163 1060 Vienna Austria
| |
Collapse
|