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Bun-Ichi Shimizu

Faculty
Department of Life Sciences
Institute of Life Innovation Studies
Course of Life Sciences
PositionProfessor
Mail
HomepageURLhttp://www2.toyo.ac.jp/~bsimz/ShimizuB_Labo/Welcome_to_Our_Site.html
Birthday
Last Updated :2019/10/04

Researcher Profile and Settings

Education

  •   2000 07  - 2000 07 , Kyoto University, PhD (Agricultural Science)
  •  - 2000 , Kyoto University
  •  - 2000 , Kyoto University, Graduate School, Division of Agriculture
  •  - 1995 , Kyoto University, Faculty of Agriculture

Degree

  • Doctor of Agriculture, Kyoto University
  • Master of Agriculture, Kyoto University

Academic & Professional Experience

  •   2016 04  - 2017 03 , Karolinska Institutet, Sweden, Department of Molecular Biophysics and Biochemistry, Visiting Professor
  •   2013 04  - 現在, Toyo University, Department of Life Sciences, Professor
  •   2009 04  - 2013 03 , Toyo University, Department of Life Sciences, Associate Professor
  •   2000 05  - 2007 03 , Kyoto University, Institute for Chemical Research, Assistant Professor
  •   2000 , Institute for Chemical Research, KYOTO UNIV. Instructor.

Research Activities

Research Areas

  • Agricultural chemistry, Bioproduction chemistry/Bioorganic chemistry

Research Interests

    Plants/Microbes/Secondary Metabolism/Coumarins/Biosynthesis/, Plants/Pathogenic Fungi/Resistance Reaction/Secondary Metabolism

Published Papers

  • Inflammatory response to dietary linoleic acid depends on FADS1 genotype., Maria A Lankinen • Alexander Fauland • Bun-ichi Shimizu • Jyrki Ågren • Craig E Wheelock • Markku Laakso • Ursula Schwab • Jussi Pihlajamäki, American journal of clinical nutrition, 109, (1) 165 - 175, 01 , Refereed
  • Synthesis and inhibitory activity of mechanism-based 4-coumaroyl-CoA ligase inhibitors, Bunta Watanabe, Hiroaki Kirikae, Takao Koeduka, Yoshinori Takeuchi, Tomoki Asai, Yoshiyuki Naito, Hideya Tokuoka, Shinri Horoiwa, Yoshiaki Nakagawa, Bun-ichi Shimizu, Masaharu Mizutani, Jun Hiratake, Bioorganic & Medicinal Chemistry, 26, 2466 - 2474, 04 , Refereed
  • Glucosyltransferase activity of Arabidopsis UGT71C1 towards pinoresinol and lariciresinol, Atsushi Okazawa, Tatsuya Kusunose, Eiichiro Ono, Hyun Jung Kim, Honoo Satake, Bun-ichi Shimizu, Masaharu Mizutani, Hikaru Seki, Toshiya Muranaka, Plant Biotechnology, 31, 561 - 566, 11 , Refereed
  • Glutathione-analogous peptidyl phosphorus esters as mechanism-based inhibitors of γ-glutamyl transpeptidase for probing cysteinyl-glycine binding site., Nakajima M, Watanabe B, Han L, Shimizu B, Wada K, Fukuyama K, Suzuki H, Hiratake J, Bioorganic & medicinal chemistry, 22, 1176 - 1194, 02 , Refereed
  • 2-Oxoglutarate-dependent dioxygenases in the biosynthesis of simple coumarins., Shimizu B, Frontiers in plant science, 5, Refereed
  • Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield., Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Kashiwagi T, Ujiie K, Shimizu B, Onishi A, Miyagawa H, Katoh E, Nature genetics, 45, 707 - 711, 06 , Refereed
  • A 2-oxoglutarate-dependent dioxygenase from Ruta graveolens L. exhibits p-coumaroyl CoA 2'-hydroxylase activity (C2'H): a missing step in the synthesis of umbelliferone in plants., Vialart G, Hehn A, Olry A, Ito K, Krieger C, Larbat R, Paris C, Shimizu B, Sugimoto Y, Mizutani M, Bourgaud F, The Plant journal : for cell and molecular biology, 70, 460 - 470, 05 , Refereed
  • Molecular cloning and functional analysis of the ortho-hydroxylases of p-coumaroyl coenzyme A/feruloyl coenzyme A involved in formation of umbelliferone and scopoletin in sweet potato, Ipomoea batatas (L.) Lam., Matsumoto S, Mizutani M, Sakata K, Shimizu B, Phytochemistry, 74, 49 - 57, 02 , Refereed
  • Rice CYP734As function as multisubstrate and multifunctional enzymes in brassinosteroid catabolism., Sakamoto T, Kawabe A, Tokida-Segawa A, Shimizu B, Takatsuto S, Shimada Y, Fujioka S, Mizutani M, The Plant journal : for cell and molecular biology, 67, 1 - 12, 07 , Refereed
  • Scopolin-hydrolyzing beta-glucosidases in roots of Arabidopsis., Ahn YO, Shimizu B, Sakata K, Gantulga D, Zhou C, Bevan DR, Esen A, Plant & cell physiology, 51, 132 - 143, 01 , Refereed
  • Scopoletin is biosynthesized via ortho-hydroxylation of feruloyl CoA by a 2-oxoglutarate-dependent dioxygenase in Arabidopsis thaliana., Kai K, Mizutani M, Kawamura N, Yamamoto R, Tamai M, Yamaguchi H, Sakata K, Shimizu B, The Plant journal : for cell and molecular biology, 55, 989 - 999, 09 , Refereed
  • Biosynthetic origin of the 1-oxygen of umbelliferone in the root tissue of sweet potato., Shimizu B, Kai K, Tamai M, Yamaguchi H, Mizutani M, Sakata K, Zeitschrift fur Naturforschung. C, Journal of biosciences, 63, 687 - 690, 09 , Refereed
  • Vicianin hydrolase is a novel cyanogenic beta-glycosidase specific to beta-vicianoside (6-O-alpha-L-arabinopyranosyl-beta-D-glucopyranoside) in seeds of Vicia angustifolia., Ahn YO, Saino H, Mizutani M, Shimizu B, Sakata K, Plant & cell physiology, 48, 938 - 947, 07 , Refereed
  • Chemical profiling and gene expression profiling during the manufacturing process of Taiwan oolong tea "Oriental Beauty"., Cho JY, Mizutani M, Shimizu B, Kinoshita T, Ogura M, Tokoro K, Lin ML, Sakata K, Bioscience, biotechnology, and biochemistry, 71, 1476 - 1486, 06 , Refereed
  • Accumulation of coumarins in Arabidopsis thaliana., Kai K, Shimizu B, Mizutani M, Watanabe K, Sakata K, Phytochemistry, 67, 379 - 386, 02 , Refereed
  • Phytotoxic components produced by pathogenic Fusarium against morning glory., Shimizu B, Saito F, Miyagawa H, Watanabe K, Ueno T, Sakata K, Ogawa K, Zeitschrift fur Naturforschung. C, Journal of biosciences, 60, 862 - 866, 11 , Refereed
  • Morning glory systemically accumulates scopoletin and scopolin after interaction with Fusarium oxysporum., Shimizu B, Miyagawa H, Ueno T, Sakata K, Watanabe K, Ogawa K, Zeitschrift fur Naturforschung. C, Journal of biosciences, 60, 83 - 90, 01 , Refereed
  • Molting hormonal and larvicidal activities of aliphatic acyl analogs of dibenzoylhydrazine insecticides., Shimizu B, Nakagawa Y, Hattori K, Nishimura K, Kurihara N, Ueno T, Steroids, 62, 638 - 642, 10 , Refereed

Misc

  • Laboratory for Biofunctional and Bioregulation Chemistry, (2009) 73 - 77,   2010 03 31
  • Biosynthetic pathway of coumarins in plants, (32) 16 - 17,   2010
  • 桂皮酸オルト位水酸化酵素の同定とクマリン生合成経路 2‐オキソグルタル酸依存性ジオキシゲナーゼが鍵段階を触媒する, 清水文一, 甲斐光輔, 水谷正治, 化学と生物, 46, (8) 518 - 520,   2008 08 01
  • Resisfance against Fusarium With Induced by Non-pathogenic Fusarium in Ipomoea tricolor, Jourual of Pesticide Sctence, 25, (4) 365 - 372,   2000
  • Molting hormoinal and larvicrdal activities of aliplatic acylanalogs of dybenzoylhydra.zine insecticilos, Steroids, 62,   1997

Books etc

  • Biochemistry in Plant Metabolism
    SHIMIZU Bun-ichi
    ContributorTaxonomy of metabolism in plantsYODOSHA  2019 01
  • Identification of aroma components during processing of the famous oolong tea “Oriental Beauty”
    Ogura M, Kinoshita T, Shimizu B, Shirai F, Tokoro K, Lin ML, Sakata K.
    Joint WorkACS Synposium Series 988American Chemical Society, Washington DC  2008

Conference Activities & Talks

  • Analysis of oxylipins in Arabidopsis leaves subjected to oxidative stress, Nishika Hiromasa, Shimizu Bun-ichi, Annual Meeting of the Japan Society for Bioscience, Biotechnology, and Agrochemistry (JSBBA),   2019 03 24
  • Ortho-hydroxylases from Populus trichocarpa have a catalytic activity for caffeoyl CoA. , SHIMIZU Bun-ichi,   2016 03 30
  • Exploration of substrate recognition mechanism of the ortho-hydroxylases from sweet potato by point mutational analysis, ○Hidetoshi Abe1, Sinpei Okawara1, Shingo Nagano2, Masaharu Mizutani3, Bun-ichi Shimizu1,   2015 03
  • Coumarin degradation metabolism via Melilotic acid by Pseudomonas spp., ○Shun TAMURA, Mami SHIMAZAKI, Masahiro IMAI, Kouki ONODA, Takahiro OKADA, Bun-ichi SHIMIZU,   2015 03
  • Cloning and functional analysis of genes encoding ortho-hydroxylases involved in scopoletin biosynthesis in Populus trichocarpa., SHIMIZU Bun-ichi○Akari Inaba, Bun-ichi Shimizu,   2015 03
  • Coumarin metabolism by isolated microorganisms from cherry tree.,   2014 08

Research Grants & Projects

  • Development of chemicals that control the glutathione metabolism and oxidative stress and their use for chemical biology, Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(B)), Jun HIRATAKE, Thisstudy concerns the development and applications of chemical tools that regulate the redox status of cells by designing and synthesizing specific inhibitors of γ-glutamylcysteine synthetase (GCS), therate-determiningenzymeinglutathione synthesis, and γ-glutamyl transpeptidase (GGT), the initial andprimarily important enzyme in the glutathione metabolism.The inhibitors are to serve as chemical probes to investigate the relationships between cell redox potential and various diseases and as leads to agrochemicals and pharmaceuticals, as well as to antiaging cosmetics.
  • Elucidation of the aroma formation of Darjeeling tea "Second flash" and development of new manufacturing process of black tea, Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(B)), 坂田 完三, Masaharu MIZUTANI, We made the joint羊esearch contract of two遥ears collaboration with Indian Tea Research Association (TRA) and Tocklai Tea Experimental Station (TIES). Accordingly, we performed the researches as follows:1) Investigation of the manufacturing of Darjeeling tea “Second flash"in India. At the end of May 2006, three researchers from Japan visited TTES at Tocklai, Assam and also Darjeeling in India. We, together with two researchers from TTES, visited several tea gardens in Darjeeling to see the tea manufacturing and the state of the insect擁nfestation. We also collected the tea samples at two gardens. We observed that two kinds of insects, jassid (green leaffly: Empoasca flavescens Fabr.) and thrips (Taeniothrips setiventris Bagnall), are mainly involved in the insect infestation in Darjeeling. In June 2007, Japanese researchers visited TTES. The in様aboratry breeding of the insects was performed at TTES, and the tea leaves artificially infested by the insects were prepared to analyze the effects of the infestation on the characteristic aroma formation of the tea.2) Elucidation of the characteristic aroma formation of Darjeeling tea “Second flash"produced with the insect擁nfested leaves. The samples collected at the Darjeeling tea gardens in 2006 were analyzed by GC-MS, and it was suggested that insect infestation is involved in the aroma formation such as monoterpene alcohols and hotrienol. It was also evident from the experiments in 2007that insect infestation is mainly concerned with the characteristic aroma formation. The other experiments conducted at a Japanese tea garden demonstrated that the infestation by tea green様eafhopper (a very similar insect to jassid) is involved in the formation of 2,6-dimethylocta-3,7-diene-2,6-diol.3) Attempts to develop a new manufacturing process of CTC black tea. We suggested to the TTES researchers that they should apply the concept in manufacturing Taiwan oolong tea to Indian black tea manufacturing to improve the quality of the flavor of CTC black tea. According to our suggestion, they tried the tea manufacturing with a pilot plant at TTES, and found that the additional processes of some mechanical damages on tea leaves during the withering may improve the quality of the tea flavor.
  • Molecular evolution of plant β-glucosidases deduced from clarification of substrate specificities and catalytic mechanisms of β-diglycosidases (glycosidases specific to disacchalide glycosides), Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(B)), Kanzo SAKATA, 1) Clarification of substrate specificities and catalytic mechanisms of diglycosidases1-a) X-Ray crystallographic analysis of β-primeverosidase from a tea plantWe have succeeded in synteshis of a potent glycosidase inhibitor, β-primeverosyl amidine, for a representative diglycosidase, β-primeverosidase. Single crystalls of β-primeverosidase binding the inhibitor was obtained and subjected to X-ray crystallographic analysis to obtain the structure of the protein with resolution of 1.8 A based on the structure of a family 1 β-glucosidase from maize. The structure allowed us to identify the amino acid residures that interact with disaccharide moiety of the substrates and to show the detailed structure of the opening part of catalytic site. Based on these observations and the substrate specificities of the enzyme we could have understood the substrate recognition mechanism of the enzyme in detail.1-b) Clarification of the substrate recognition mechanism of a diglycosidase by the use of 6'-substituted β-D-glucopyranosidesPseudo-disaccharide glycosides with various kinds of S-substituents (alcohols of C_<2_4> and D-xylopyranosyl) at C-6'of p-nitrophenyl (pNP) β-D-glucopyranosides were synthesized and subjected to hydrolysis by a diglycosidase, vicianin hydrolase. This diglycosidase shows high reactivity against pNP β-primeveroside, but little activity against 6'-S-substituted pNP β-primeveroside as well as pNPβ-D-glucopyranoside. This enzyme shows high activity against pseudo-diglycosides with a straight chain C3-alcohol substituent at C-6'. These observations suggest that the hydroxy group of the C_3-alcohol substituent interacts with the amino acid residues concerned with the recognition of the disaccharide moeiety of natural substrates.2) Distribution of diglycosidases in plant kingdom and analysis of molecular evolution of diglycosidasesBy the use of pNP P-primeveroside as a substrate diglycosidases were screened among plant crude enzymes randomly selected. Out of 18 kinds of plant species β-primeverosidase-like activity was found in the crude enzyme of 7 kinds of plants, indicating considerably wide distribution of diglycosidases among plant kingdom.Phylogenetic tree analysis of diglycosidases, β-primeverosidase, furcatin hydrolase and vicianin hydrolase in family 1 of glycosyl hydrolases were carried out based on their full amino acid sequences, indicating that these diglycosidases cluster with each other.
  • Bioorganic studies on plant glycosidases by using p-glycosylamidines as research tools, Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(B)), Jun HIRATAKE, The function and the physiological roles of plant β-glycosidases have been studied by using p-glycosylamidines as molecular probes. p-Glycosylamidines, newly developed p-glycosidase inhibitors that selectively inhibitβ-glycosidases according to their glycon substrate specificities, have been successfully used as ligand for affinity chromatography of glycosidases. High fidelities of β-glycosylamidines as specific binders toward theβ-glycosidases with the corresponding glycon substrate specificities enabled one-step affinity purification of specific β-glycosidases from natural samples according to their glycon substrate specificities as a sole marker. This method has been successfully used for the isolation of diglycoside-specific p-glycosidases from microbes and a p-N-acetylhexosaminidase from insect cells. The latter glycosidase is a key biosynthetic enzyme in processing insect-cell-specific N-glycans. With this research tool in hands, we have purified and characterized diglycoside-specific β-glycosidases (diglycosidases) from plants. The diglycosidases are thought to play a key role in self-defense system in plants by emitting defense chemicals such as linalool, 2-phenylethanol and mandelonitrile by cleaving their precursor diglycosides. β-Primeverosidase (PD), a typical diglycosidase found in tea leaves, has been purified to homogeneity by a newly developed pH-controlled affinity chromatography with p-primeverosylamidline as an affinity ligand. The enzymatic properties of PD and the binding mechanism of the β-primeverosylamidine inhibitor have been studied extensively. Furthermore, a gene encoding PD was cloned from tea leaves and was analyzed to find that the diglycosidases were a member of family 1 glycoside hydrolase with significant sequence similarities to the β-glucosidases in this family. This result suggests that plant diglycosidases have been evolved from family 1 β-glucosidases for cleavage of specific diglycosides and serve as a key enzyme in plant self-defense system. The recombinant PD was expressed and highly purified by the affinity chromatography for X-ray structural analysis. The high resolution X-ray crystal structure (1.8 Å) of PD in complex with the β-primeverosylamidine inhibitor revealed the amino acid residues recognizing the β-xylosyl moiety of β-primeveroside and the unique binding mode of β-primeverosylamidine ligand in the active site. These results cogently suggested the structural basis for their unique substrate specificities and the evolutional link between plant diglycosidases and family 1 p-glucosidases.
  • Clarification of Molecular Basis of the Characteristic Aroma Formation in the Formosa Oolong Ted Produced from Tea leaves Infested by the Tea Green Leafhopper, Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(B)), Kanzo SAKATA, Oriental Beauty is a flavor-rich oolong tea produced from tea leaves infested by the tea green leafhopper (Jacobiasca formosana) in Taiwan. We have studied to clarify the molecular basis of the characteristic aroma formation of the tea by various approaches such as natural product chemistry, biochemistry, and molecular biology. Oolong tea samples were prepared from tea leaves infeted/noninfested by the insects. Samples were obtained at each step of the manufacturing process and subjected to evaluation tests by professional tea tasters and to GC-MS analysis. The tea produced from tea leaves infested by the insects was found to be superior in the quality and quantity of aroma to that from tea leaves without or with much less the insect attack. Hotrienol and its related compound, 2,6-dimethyl-3.7-octadiene-2,6-diol, were confirmed to be responsible for the insect attack. Genes induced in response to the insect attack and the tea manufacturing processes were identified by the differential screening based on the Megasort analysis. Among them our interests were focused into the genes encoding the stress-responded ones and the amounts of the stress-responded compounds such as raffinose and abscisic acid in tea samples obtained at each step of the tea processing were quantitatively analyzed by HPLC. Both compounds were found to increase dramatically at the solar withering step in good correlation with the expression of the genes responsible for their biosynthesis at the step. These results have revealed that the tea leaves of Oriental Beauty are greatly affected by the stresses of the insect attack and the tea manufacturing processes such as solar withering and turning-over, and these stresses are important factors to increase the production of the aroma compounds characteristic to this characteristic oolong tea.
  • Establishment of A New Group of Glycosyl Hydrolase Family 1 Specific to Disaccharide Glycosides in Plant Kingdom, Ministry of Education, Culture, Sports, Science and Technology, Grants-in-Aid for Scientific Research(基盤研究(B)), Kanzo SAKATA, The following research results have been obtained by this research project.(A)Clarification of catalytic mechanisms of the diglycosidases and their stereostructures1)Substrate specificities of diglycosidases such as tea leaf β-primeverosidase (PRD), furcatin hydrolase (FH) in Viburnum furcatum, Vicianin hydrolase (VH) in Vicia angustifolia var. segetalis have been studied with various kinds of synthetic and natural substrates to show that these diglycosdiases are very specific to disaccharide glycosides with β-1,6 linkage.2)The full-length cDNA of PRD and VH were overexpressed in insect cells and that of. FH in E.coli. The recombinant PRD was obtained at ca. 30 mg/liter of the medium. This allowed us to try crystallization of the protein for X-ray crystallographic analysis.3)We have developed a new type of glycosidase inhibitors, glycosylamidines, with potent and selective activities. An affinity adsorbent with a ligand of β-primeverosyl has been prepared and was found to be quite effective for purification of PRD as well as the other diglycosidases.(B)Establishment of a new family of diglycosidases in plant kingdom and clarification of their physiological rolesThe anti-PRD antibody prepared with the recombinant PRD was found to be highly selective and sensitive. Application of this- antibody allowed us to know the expression of the PRD gene at higher level in the younger tea leaves and the localization of the PRD in cell membrane or intercellular space.Distribution of diglycosidases was surveyed by using. β-primeverosidase activity, detection of disaccharide formation with TLC and immunoblotting analysis with the anti-PRD antibody among several kinds of plants most of which are known to contain some disaccharide glycosides. The results strongly suggest wide range of distribution of diglycosidases in plant kingdom.
  • study on mechenism of pathogevests in plants.
  • Cloning of Enzymes Related to Plant Seconary Metabolisms