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Fujimaki S, Sakamoto S, Shimada S, Kino K, Furuya T. Engineering a coenzyme-independent dioxygenase for one-step production of vanillin from ferulic acid. Appl Environ Microbiol 2024; 90:e0023324. [PMID: 38727223 PMCID: PMC11218615 DOI: 10.1128/aem.00233-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/15/2024] [Indexed: 06/19/2024] Open
Abstract
Vanillin is one of the world's most important flavor and fragrance compounds used in foods and cosmetics. In plants, vanillin is reportedly biosynthesized from ferulic acid via the hydratase/lyase-type enzyme VpVAN. However, in biotechnological and biocatalytic applications, the use of VpVAN limits the production of vanillin. Although microbial enzymes are helpful as substitutes for plant enzymes, synthesizing vanillin from ferulic acid in one step using microbial enzymes remains a challenge. Here, we developed a single enzyme that catalyzes vanillin production from ferulic acid in a coenzyme-independent manner via the rational design of a microbial dioxygenase in the carotenoid cleavage oxygenase family using computational simulations. This enzyme acquired catalytic activity toward ferulic acid by introducing mutations into the active center to increase its affinity for ferulic acid. We found that the single enzyme can catalyze not only the production of vanillin from ferulic acid but also the synthesis of other aldehydes from p-coumaric acid, sinapinic acid, and coniferyl alcohol. These results indicate that the approach used in this study can greatly expand the range of substrates available for the dioxygenase family of enzymes. The engineered enzyme enables efficient production of vanillin and other value-added aldehydes from renewable lignin-derived compounds. IMPORTANCE The final step of vanillin biosynthesis in plants is reportedly catalyzed by the enzyme VpVAN. Prior to our study, VpVAN was the only reported enzyme that directly converts ferulic acid to vanillin. However, as many characteristics of VpVAN remain unknown, this enzyme is not yet suitable for biocatalytic applications. We show that an enzyme that converts ferulic acid to vanillin in one step could be constructed by modifying a microbial dioxygenase-type enzyme. The engineered enzyme is of biotechnological importance as a tool for the production of vanillin and related compounds via biocatalytic processes and metabolic engineering. The results of this study may also provide useful insights for understanding vanillin biosynthesis in plants.
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Affiliation(s)
- Shizuka Fujimaki
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Satsuki Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Shota Shimada
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Kuniki Kino
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Toshiki Furuya
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
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2
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Ali HS, de Visser SP. QM/MM Study Into the Mechanism of Oxidative C=C Double Bond Cleavage by Lignostilbene-α,β-Dioxygenase. Chemistry 2024; 30:e202304172. [PMID: 38373118 DOI: 10.1002/chem.202304172] [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: 12/14/2023] [Revised: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
The enzymatic biosynthesis of fragrance molecules from lignin fragments is an important reaction in biotechnology for the sustainable production of fine chemicals. In this work we investigated the biosynthesis of vanillin from lignostilbene by a nonheme iron dioxygenase using QM/MM and tested several suggested proposals via either an epoxide or dioxetane intermediate. Binding of dioxygen to the active site of the protein results in the formation of an iron(II)-superoxo species with lignostilbene cation radical. The dioxygenase mechanism starts with electrophilic attack of the terminal oxygen atom of the superoxo group on the central C=C bond of lignostilbene, and the second-coordination sphere effects in the substrate binding pocket guide the reaction towards dioxetane formation. The computed mechanism is rationalized with thermochemical cycles and valence bond schemes that explain the electron transfer processes during the reaction mechanism. Particularly, the polarity of the protein and the local electric field and dipole moments enable a facile electron transfer and an exergonic dioxetane formation pathway.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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3
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De Vitis V, Cannazza P, Mattio L, Romano D, Pinto A, Molinari F, Laurenzi T, Eberini I, Contente ML. Caulobacter segnis Dioxygenase CsO2: A Practical Biocatalyst for Stilbenoid Ozonolysis. Chembiochem 2023; 24:e202300477. [PMID: 37490046 DOI: 10.1002/cbic.202300477] [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: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 07/26/2023]
Abstract
Ozonolysis is a useful as well as dangerous reaction for performing alkene cleavage. On the other hand, enzymes are considered a more sustainable and safer alternative. Among them, Caulobacter segnis dioxygenase (CsO2) known so far for its ability to catalyze the coenzyme-free oxidation of vinylguaiacol into vanillin, was selected and its substrate scope evaluated towards diverse natural and synthetic stilbenoids. Under optimized conditions, CsO2 catalyzed the oxidative cleavage of the C=C double bonds of various trans-stilbenes, providing that a hydroxyl moiety was necessary in para-position of the phenyl group (e. g., resveratrol and its derivatives) for the reaction to take place, which was confirmed by modelling studies. The reactions occurred rapidly (0.5-3 h) with high conversions (95-99 %) and without formation of by-products. The resveratrol biotransformation was carried out on 50-mL scale thus confirming the feasibility of the biocatalytic system as a preparative method.
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Affiliation(s)
- Valerio De Vitis
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, via Celoria, 2, 20133, Milan, Italy
| | - Pietro Cannazza
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, via Celoria, 2, 20133, Milan, Italy
| | - Luce Mattio
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, via Celoria, 2, 20133, Milan, Italy
| | - Diego Romano
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, via Celoria, 2, 20133, Milan, Italy
| | - Andrea Pinto
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, via Celoria, 2, 20133, Milan, Italy
| | - Francesco Molinari
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, via Celoria, 2, 20133, Milan, Italy
| | - Tommaso Laurenzi
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", University of Milan, Via Balzaretti, 9, 20133, Milano, Italy
| | - Ivano Eberini
- Department of Pharmacological and Biomolecular Sciences "Rodolfo Paoletti", University of Milan, Via Balzaretti, 9, 20133, Milano, Italy
| | - Martina L Contente
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, via Celoria, 2, 20133, Milan, Italy
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4
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Bleem A, Kato R, Kellermyer ZA, Katahira R, Miyamoto M, Niinuma K, Kamimura N, Masai E, Beckham GT. Multiplexed fitness profiling by RB-TnSeq elucidates pathways for lignin-related aromatic catabolism in Sphingobium sp. SYK-6. Cell Rep 2023; 42:112847. [PMID: 37515767 DOI: 10.1016/j.celrep.2023.112847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/21/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023] Open
Abstract
Bioconversion of lignin-related aromatic compounds relies on robust catabolic pathways in microbes. Sphingobium sp. SYK-6 (SYK-6) is a well-characterized aromatic catabolic organism that has served as a model for microbial lignin conversion, and its utility as a biocatalyst could potentially be further improved by genome-wide metabolic analyses. To this end, we generate a randomly barcoded transposon insertion mutant (RB-TnSeq) library to study gene function in SYK-6. The library is enriched under dozens of enrichment conditions to quantify gene fitness. Several known aromatic catabolic pathways are confirmed, and RB-TnSeq affords additional detail on the genome-wide effects of each enrichment condition. Selected genes are further examined in SYK-6 or Pseudomonas putida KT2440, leading to the identification of new gene functions. The findings from this study further elucidate the metabolism of SYK-6, while also providing targets for future metabolic engineering in this organism or other hosts for the biological valorization of lignin.
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Affiliation(s)
- Alissa Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Ryo Kato
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Zoe A Kellermyer
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Rui Katahira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Masahiro Miyamoto
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Koh Niinuma
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Naofumi Kamimura
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Eiji Masai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
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Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation. Proc Natl Acad Sci U S A 2023; 120:e2212246120. [PMID: 36652470 PMCID: PMC9942872 DOI: 10.1073/pnas.2212246120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon-carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of erythro-1,2-diguaiacylpropane-1,3-diol (erythro-DGPD), a ring-opened lignin-derived β-1 dimer, was reported in Novosphingobium aromaticivorans. The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts erythro-DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the N. aromaticivorans LdpA and another homolog identified in Sphingobium sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C1 reaction product, and we further demonstrated that both enantiomers of erythro-DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.
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Xu Z, Peng B, Kitata RB, Nicora CD, Weitz KK, Pu Y, Shi T, Cort JR, Ragauskas AJ, Yang B. Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:117. [PMID: 36316752 PMCID: PMC9620641 DOI: 10.1186/s13068-022-02214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Bacterial lignin degradation is believed to be primarily achieved by a secreted enzyme system. Effects of such extracellular enzyme systems on lignin structural changes and degradation pathways are still not clearly understood, which remains as a bottleneck in the bacterial lignin bioconversion process. RESULTS This study investigated lignin degradation using an isolated secretome secreted by Pseudomonas putida KT2440 that grew on glucose as the only carbon source. Enzyme assays revealed that the secretome harbored oxidase and peroxidase/Mn2+-peroxidase capacity and reached the highest activity at 120 h of the fermentation time. The degradation rate of alkali lignin was found to be only 8.1% by oxidases, but increased to 14.5% with the activation of peroxidase/Mn2+-peroxidase. Gas chromatography-mass spectrometry (GC-MS) and two-dimensional 1H-13C heteronuclear single-quantum coherence (HSQC) NMR analysis revealed that the oxidases exhibited strong C-C bond (β-β, β-5, and β-1) cleavage. The activation of peroxidases enhanced lignin degradation by stimulating C-O bond (β-O-4) cleavage, resulting in increased yields of aromatic monomers and dimers. Further mass spectrometry-based quantitative proteomics measurements comprehensively identified different groups of enzymes particularly oxidoreductases in P. putida secretome, including reductases, peroxidases, monooxygenases, dioxygenases, oxidases, and dehydrogenases, potentially contributed to the lignin degradation process. CONCLUSIONS Overall, we discovered that bacterial extracellular degradation of alkali lignin to vanillin, vanillic acid, and other lignin-derived aromatics involved a series of oxidative cleavage, catalyzed by active DyP-type peroxidase, multicopper oxidase, and other accessory enzymes. These results will guide further metabolic engineering design to improve the efficiency of lignin bioconversion.
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Affiliation(s)
- Zhangyang Xu
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA
| | - Bo Peng
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA
| | - Reta Birhanu Kitata
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Carrie D. Nicora
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Karl K. Weitz
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Yunqiao Pu
- grid.135519.a0000 0004 0446 2659Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Tujin Shi
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - John R. Cort
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Arthur J. Ragauskas
- grid.135519.a0000 0004 0446 2659Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ,grid.411461.70000 0001 2315 1184Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA ,grid.411461.70000 0001 2315 1184Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN 37996 USA
| | - Bin Yang
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA ,grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
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7
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Miyamoto H, Asano F, Ishizawa K, Suda W, Miyamoto H, Tsuji N, Matsuura M, Tsuboi A, Ishii C, Nakaguma T, Shindo C, Kato T, Kurotani A, Shima H, Moriya S, Hattori M, Kodama H, Ohno H, Kikuchi J. A potential network structure of symbiotic bacteria involved in carbon and nitrogen metabolism of wood-utilizing insect larvae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155520. [PMID: 35508250 DOI: 10.1016/j.scitotenv.2022.155520] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 05/02/2023]
Abstract
Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive microbial structures are expected to reveal a novel rule underlying wood biomass processing. Here, structural inferences for inhabitant bacteria involved in carbon and nitrogen metabolism for beetle larvae, an insect model, were performed to explore the potential rules. Bacterial analysis of larval feces showed enrichment of the phyla Chroloflexi, Gemmatimonadetes, and Planctomycetes, and the genera Bradyrhizobium, Chonella, Corallococcus, Gemmata, Hyphomicrobium, Lutibacterium, Paenibacillus, and Rhodoplanes, as bacteria potential involved in plant growth promotion, nitrogen cycle modulation, and/or environmental protection. The fecal abundances of these bacteria were not necessarily positively correlated with their abundances in the habitat, indicating that they were selectively enriched in the feces of the larvae. Correlation and association analyses predicted that common fecal bacteria might affect carbon and nitrogen metabolism. Based on these hypotheses, structural equation modeling (SEM) statistically estimated that inhabitant bacterial groups involved in carbon and nitrogen metabolism were composed of the phylum Gemmatimonadetes and Planctomycetes, and the genera Bradyrhizobium, Corallococcus, Gemmata, and Paenibacillus, which were among the fecal-enriched bacteria. Nevertheless, the selected common bacteria, i.e., the phyla Acidobacteria, Armatimonadetes, and Bacteroidetes and the genera Candidatus Solibacter, Devosia, Fimbriimonas, Gemmatimonas Opitutus, Sphingobium, and Methanobacterium, were necessary to obtain good fit indices in the SEM. In addition, the composition of the bacterial groups differed depending upon metabolic targets, carbon and nitrogen, and their stable isotopes, δ13C and δ15N, respectively. Thus, the statistically derived causal structural models highlighted that the larval fecal-enriched bacteria and common symbiotic bacteria might selectively play a role in wood biomass carbon and nitrogen metabolism. This information could confer a new perspective that helps us use wood biomass more efficiently and might stimulate innovation in environmental industries in the future.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan; Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba 260-0034, Japan.
| | - Futo Asano
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan
| | | | - Wataru Suda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | | | - Naoko Tsuji
- Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
| | - Arisa Tsuboi
- Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan; Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba 260-0034, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Chitose Ishii
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan; Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba 260-0034, Japan
| | - Chie Shindo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hideaki Shima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Shigeharu Moriya
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Masahira Hattori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Hiroaki Kodama
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.
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8
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Daruwalla A, Sui X, Kiser PD. Preparation of carotenoid cleavage dioxygenases for X-ray crystallography. Methods Enzymol 2021; 671:243-271. [PMID: 35878980 PMCID: PMC10809780 DOI: 10.1016/bs.mie.2021.10.020] [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] [Indexed: 10/17/2022]
Abstract
Carotenoid cleavage dioxygenases (CCDs) constitute a superfamily of enzymes that are found in all domains of life where they play key roles in the metabolism of carotenoids and apocarotenoids as well as certain phenylpropanoids such as resveratrol. Interest in these enzymes stems not only from their biological importance but also from their remarkable catalytic properties including their regioselectivity, their ability to accommodate diverse substrates, and the additional activities (e.g., isomerase) that some of these enzyme possess. X-ray crystallography is a key experimental approach that has allowed detailed investigation into the structural basis behind the interesting biochemical features of these enzymes. Here, we describe approaches used by our lab that have proven successful in generating single crystals of these enzymes in resting or ligand-bound states for high-resolution X-ray diffraction analysis.
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Affiliation(s)
- Anahita Daruwalla
- Department of Physiology & Biophysics, University of California, Irvine School of Medicine, Irvine, CA, United States
| | - Xuewu Sui
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, United States; Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Philip D Kiser
- Department of Physiology & Biophysics, University of California, Irvine School of Medicine, Irvine, CA, United States; Department of Ophthalmology, Center for Translational Vision Research, University of California, Irvine School of Medicine, Irvine, CA, United States; Research Service, VA Long Beach Healthcare System, Long Beach, CA, United States.
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