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Seligmann B, Liu S, Franke J. Chemical tools for unpicking plant specialised metabolic pathways. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102554. [PMID: 38820646 DOI: 10.1016/j.pbi.2024.102554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024]
Abstract
Elucidating the biochemical pathways of specialised metabolites in plants is key to enable or improve their sustainable biotechnological production. Chemical tools can greatly facilitate the discovery of biosynthetic genes and enzymes. Here, we summarise transdisciplinary approaches where methods from chemistry and chemical biology helped to overcome key challenges of pathway elucidation. Based on recent examples, we describe how state-of-the-art isotope labelling experiments can guide the selection of biosynthetic gene candidates, how affinity-based probes enable the identification of novel enzymes, how semisynthesis can improve the availability of elusive pathway intermediates, and how biomimetic reactions provide a better understanding of inherent chemical reactivity. We anticipate that a wider application of such chemical methods will accelerate the pace of pathway elucidation in plants.
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Affiliation(s)
- Benedikt Seligmann
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Shenyu Liu
- Leibniz University Hannover, Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany
| | - Jakob Franke
- Leibniz University Hannover, Institute of Botany, Herrenhäuser Str. 2, 30419 Hannover, Germany; Leibniz University Hannover, Centre of Biomolecular Drug Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany.
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2
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Zhao Y, Zhang Y, Yang H, Xu Z, Li Z, Zhang Z, Zhang W, Deng J. A comparative metabolomics analysis of phytochemcials and antioxidant activity between broccoli floret and by-products (leaves and stalks). Food Chem 2024; 443:138517. [PMID: 38295564 DOI: 10.1016/j.foodchem.2024.138517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Leaves and stalks, which account for about 45% and 25% of broccoli biomass, respectively, are usually discarded during broccoli production, leading to the waste of green resources. In this study, the phytochemical composition and antioxidant capacity of broccoli florets and their by-products (leaves and stalks) were comprehensively analyzed. The metabolomics identified several unique metabolites (e.g., scopoletin, Harpagoside, and sinalbin) in the leaves and stalks compared to florets. Notably, the leaves were found to be a rich source of flavonoids and coumarins, with superior antioxidant capacity. The random forest model and correlation analysis indicated that flavonoids, coumarin, and indole compounds were the important factors contributing to the antioxidant activity. Moreover, the stalks contained higher levels of carbohydrates and exhibited better antioxidant enzyme activity. Together, these results provided valuable data to support the comprehensive utilization of broccoli waste, the development of new products, and the expansion of the broccoli industry chain.
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Affiliation(s)
- Yaqi Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanli Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haixia Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhenzhen Xu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-food Safety and Quality, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhansheng Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhanquan Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenyuan Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianjun Deng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Chen Y, Wang T, Liang H, Ma D, Zhan R, Yang J, Yang P. Functional Characterization and Catalytic Activity Improvement of Borneol Acetyltransferase from Wurfbainia longiligularis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:13250-13261. [PMID: 38813660 DOI: 10.1021/acs.jafc.4c02915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
In plant secondary metabolite biosynthesis, acylation is a diverse physiological process, with BAHD acyltransferases playing an essential role. Borneol acetyltransferase (BAT) is an alcohol acetyltransferase, which catalyzes borneol and acetyl-CoA to synthesize bornyl acetate (BA). However, the enzymes involved in the biosynthesis of BA have so far only been characterized in Wurfbainia villosa, the studies on the WvBATs have only been conducted in vitro, and the catalytic activity was relatively low. In this research, three genes (WlBAT1, WlBAT2, and WlBAT3) have been identified to encode BATs that are capable of acetylating borneol to synthesize BA in vitro. We also determined that WlBAT1 has the highest catalytic efficiency for borneol-type substrates, including (+)-borneol, (-)-borneol, and isoborneol. Furthermore, we found that BATs could catalyze a wide range of substrate types in vitro, but in vivo, they exclusively catalyzed borneol-type substrates. Through molecular simulations and site-directed mutagenesis, it was revealed that residues D32, N36, H168, N297, N355, and H384 are crucial for the catalytic activity of WlBAT1, while the R382I-D385R double mutant of WlBAT1 exhibited an increasing acylation efficiency for borneol-type substrates in vitro and in vivo. These findings offer key genetic elements for the metabolic engineering of plants and synthetic biology to produce BA.
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Affiliation(s)
- Yuanxia Chen
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Tiantian Wang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Huilin Liang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Dongming Ma
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ruoting Zhan
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jinfen Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Peng Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
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Dai P, Ma Z, Yu X, Chen W, Teng P, Li Y, Xu Z, Xia Q, Liu Z, Zhang W. 3D-QSAR-Directed Synthesis of Halogenated Coumarin-3-Hydrazide Derivatives: Unveiling Their Potential as SDHI Antifungal Agents. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11938-11948. [PMID: 38752540 DOI: 10.1021/acs.jafc.4c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The pursuit of new succinate dehydrogenase (SDH) inhibitors is a leading edge in fungicide research and development. The use of 3D quantitative structure-activity relationship (3D-QSAR) models significantly enhances the development of compounds with potent antifungal properties. In this study, we leveraged the natural product coumarin as a molecular scaffold to synthesize 74 novel 3-coumarin hydrazide derivatives. Notably, compounds 4ap (0.28 μg/mL), 6ae (0.32 μg/mL), and 6ah (0.48 μg/mL) exhibited exceptional in vitro effectiveness against Rhizoctonia solani, outperforming the commonly used fungicide boscalid (0.52 μg/mL). Furthermore, compounds 4ak (0.88 μg/mL), 6ae (0.61 μg/mL), 6ah (0.65 μg/mL), and 6ak (1.11 μg/mL) showed significant activity against Colletotrichum orbiculare, surpassing both the SDHI fungicide boscalid (43.45 μg/mL) and the broad-spectrum fungicide carbendazim (2.15 μg/mL). Molecular docking studies and SDH enzyme assays indicate that compound 4ah may serve as a promising SDHI fungicide. Our ongoing research aims to refine this 3D-QSAR model further, enhance molecular design, and conduct additional bioactivity assays.
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Affiliation(s)
- Peng Dai
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zihua Ma
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiang Yu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Chen
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Teng
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufei Li
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Xu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing Xia
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zewen Liu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Weihua Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
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Zeng J, Liu X, Dong Z, Zhang F, Qiu F, Zhong M, Zhao T, Yang C, Zeng L, Lan X, Zhang H, Zhou J, Chen M, Tang K, Liao Z. Discovering a mitochondrion-localized BAHD acyltransferase involved in calystegine biosynthesis and engineering the production of 3β-tigloyloxytropane. Nat Commun 2024; 15:3623. [PMID: 38684703 PMCID: PMC11058270 DOI: 10.1038/s41467-024-47968-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Solanaceous plants produce tropane alkaloids (TAs) via esterification of 3α- and 3β-tropanol. Although littorine synthase is revealed to be responsible for 3α-tropanol esterification that leads to hyoscyamine biosynthesis, the genes associated with 3β-tropanol esterification are unknown. Here, we report that a BAHD acyltransferase from Atropa belladonna, 3β-tigloyloxytropane synthase (TS), catalyzes 3β-tropanol and tigloyl-CoA to form 3β-tigloyloxytropane, the key intermediate in calystegine biosynthesis and a potential drug for treating neurodegenerative disease. Unlike other cytosolic-localized BAHD acyltransferases, TS is localized to mitochondria. The catalytic mechanism of TS is revealed through molecular docking and site-directed mutagenesis. Subsequently, 3β-tigloyloxytropane is synthesized in tobacco. A bacterial CoA ligase (PcICS) is found to synthesize tigloyl-CoA, an acyl donor for 3β-tigloyloxytropane biosynthesis. By expressing TS mutant and PcICS, engineered Escherichia coli synthesizes 3β-tigloyloxytropane from tiglic acid and 3β-tropanol. This study helps to characterize the enzymology and chemodiversity of TAs and provides an approach for producing 3β-tigloyloxytropane.
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Affiliation(s)
- Junlan Zeng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaoqiang Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Zhaoyue Dong
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Fangyuan Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Fei Qiu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Mingyu Zhong
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Tengfei Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Chunxian Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Lingjiang Zeng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Centre, The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Xizang Characteristic Agricultural and Animal Husbandry Resources, Xizang Agricultural and Animal Husbandry College, Nyingchi, 860000, China
| | - Hongbo Zhang
- Key Laboratory of Synthetic Biology of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Junhui Zhou
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Min Chen
- College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, China
| | - Kexuan Tang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhihua Liao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, State Key Laboratory of Resource Insects, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, 400715, China.
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Yang Z, Zhou N, Jiang X, Wang L. Loop Evolutionary Patterns Shape Catalytic Efficiency of TRI101/201 for Trichothecenes: Insights into Protein-Substrate Interactions. J Chem Inf Model 2023; 63:6316-6331. [PMID: 37821422 DOI: 10.1021/acs.jcim.3c00787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Trichothecenes are highly toxic mycotoxins produced by Fusarium fungi, while TRI101/201 family enzymes play a crucial role in detoxification through acetylation. Studies on the substrate specificity and catalytic kinetics of TRI101/201 have revealed distinct kinetic characteristics, with significant differences observed in catalytic efficiency toward deoxynivalenol, while the catalytic efficiency for T-2 toxin remains relatively consistent. In this study, we used structural bioinformatics analysis and a molecular dynamics simulation workflow to investigate the mechanism underlying the differential catalytic activity of TRI101/201. The findings revealed that the binding stability between trichothecenes and TRI101/201 hinges primarily on a hydrophobic cage structure within the binding site. An intrinsic disordered loop, termed loop cover, defined the evolutionary patterns of the TRI101/201 protein family that are categorized into four subfamilies (V1/V2/V3/M). Furthermore, the unique loop displayed different conformations among these subfamilies' structures, which served to disrupt (V1/V2/V3) or reinforce (M) the hydrophobic cages. The disrupted cages enhanced the water exposure of the hydrophilic moieties of substrates like deoxynivalenol and thereby hindered their binding to the catalytic sites of V-type enzymes. In contrast, this water exposure does not affect substrates like T-2 toxin, which have more hydrophobic substituents, resulting in a comparable catalytic efficiency of both V- and M-type enzymes. Overall, our studies provide theoretical support for understanding the catalytic mechanism of TRI101/201, which shows how an intrinsic disordered loop could impact the protein-ligand binding and suggests a direction for rational protein design in the future.
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Affiliation(s)
- Zezheng Yang
- Taishan College, Shandong University, 266237 Qingdao, China
| | - Nana Zhou
- COFCO Nutrition and Health Research Institute, 102209 Beijing, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, 266237 Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
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Nakamichi Y, Saika A, Watanabe M, Fujii T, Morita T. Structural identification of catalytic His158 of PtMAC2p from Pseudozyma tsukubaensis, an acyltransferase involved in mannosylerythritol lipids formation. Front Bioeng Biotechnol 2023; 11:1243595. [PMID: 37920243 PMCID: PMC10619693 DOI: 10.3389/fbioe.2023.1243595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023] Open
Abstract
Mannosylerythritol lipids (MELs) are extracellular glycolipids produced by the basidiomycetous yeast strains. MELs consist of the disaccharide mannosylerythritol, which is acylated with fatty acids and acetylated at the mannose moiety. In the MEL biosynthesis pathway, an acyltransferase from Pseudozyma tsukubaensis, PtMAC2p, a known excellent MEL producer, has been identified to catalyze the acyl-transfer of fatty acid to the C3'-hydroxyl group of mono-acylated MEL; however, its structure remains unclear. Here, we performed X-ray crystallography of recombinant PtMAC2p produced in Escherichia coli and homogeneously purified it with catalytic activity in vitro. The crystal structure of PtMAC2p was determined by single-wavelength anomalous dispersion using iodide ions. The crystal structure shows that PtMAC2p possesses a large putative catalytic tunnel at the center of the molecule. The structural comparison demonstrated that PtMAC2p is homologous to BAHD acyltransferases, although its amino acid-sequence identity was low (<15%). Interestingly, the HXXXD motif, which is a conserved catalytic motif in the BAHD acyltransferase superfamily, is partially conserved as His158-Thr159-Leu160-Asn161-Gly162 in PtMAC2p, i.e., D in the HXXXD motif is replaced by G in PtMAC2p. Site-directed mutagenesis of His158 to Ala resulted in more than 1,000-fold decrease in the catalytic activity of PtMAC2p. These findings suggested that His158 in PtMAC2p is the catalytic residue. Moreover, in the putative catalytic tunnel, hydrophobic amino acid residues are concentrated near His158, suggesting that this region is a binding site for the fatty acid side chain of MEL (acyl acceptor) and/or acyl-coenzyme A (acyl donor). To our knowledge, this is the first study to provide structural insight into the catalytic activity of an enzyme involved in MEL biosynthesis.
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Affiliation(s)
- Yusuke Nakamichi
- Bioconversion Group, Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Japan
| | - Azusa Saika
- Biochemical Group, Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Masahiro Watanabe
- Bioconversion Group, Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Japan
| | - Tatsuya Fujii
- Bioconversion Group, Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Japan
| | - Tomotake Morita
- Bioconversion Group, Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Japan
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