研究者データベース

高須賀 太一(タカスカ タイチ)
農学研究院 連携研究部門 連携推進分野
准教授

基本情報

所属

  • 農学研究院 連携研究部門 連携推進分野

職名

  • 准教授

学位

  • PhD(2009年 Purdue University)

ホームページURL

J-Global ID

研究分野

  • ライフサイエンス / ゲノム生物学

職歴

  • 2019年04月 - 現在 北海道大学 農学研究院 准教授
  • 2014年11月 - 2019年03月 北海道大学 農学研究院 テニュア・トラック助教
  • 2010年01月 - 2014年11月 Department of Biochemistry, University of WIsconsin-Madison Research Associate

学歴

  •         - 2009年11月   Ph.D, Purdue University, West Lafayette,   Department of Biological Sciences,   Biochemistry and Molecular Biology

所属学協会

  • 日本生化学会   The American Chemical Society   日本分子生物学会   

研究活動情報

論文

  • Biochemical characterization of plant aromatic aminotransferases
    Kooper, K, Hataya, S, Hall, A.G, Takasuka, T.E, Maeda, H.A
    Methods Enzymol. 2022年12月 [査読有り][招待有り]
  • Tomoaki Anabuki, Keisuke Ohashi, Taichi E. Takasuka, Hideyuki Matsuura, Kosaku Takahashi
    Molecules 27 1 161 - 161 2021年12月28日 [査読有り]
     
    Abscisic acid (ABA, 1) is a plant hormone that regulates various plant physiological processes such as seed developing and stress responses. The ABA signaling system has been elucidated; binding of ABA with PYL proteins triggers ABA signaling. We have previously reported a new method to isolate a protein targeted with a bioactive small molecule using a biotin linker with alkyne and amino groups, a protein cross-linker, and a bioactive small molecule with an azido group (azido probe). This method was used to identify the unknown ABA binding protein of Arabidopsis thaliana. As a result, AtTrxh3, a thioredoxin, was isolated as an ABA binding protein. Our developed method can be applied to the identification of binding proteins of bioactive compounds.
  • Kei‐ichi Okimune, Shogo Hataya, Kazuki Matsumoto, Kanako Ushirogata, Petra Banko, Seiji Takeda, Taichi E. Takasuka
    FEBS Open Bio 2021年10月06日 [査読有り]
  • Keisuke Ohashi, Shogo Hataya, Akane Nakata, Kazuki Matsumoto, Natsumi Kato, Wakana Sato, Camila Carlos-Shanley, Emily T. Beebe, Cameron R. Currie, Brian G. Fox, Taichi E. Takasuka
    Applied and Environmental Microbiology 87 14 2021年06月25日 [査読有り]
     
    Streptomyces sp. SirexAA-E, a microbial symbiont of biomass-harvesting insects, secretes a suite of polysaccharide-degrading enzymes dependent on the available carbon sources.
  • Yaeta Endo, Nobuaki Takemori, Szilvia K. Nagy, Kei‐ichi Okimune, Rohinton Kamakaka, Hitoshi Onouchi, Taichi E. Takasuka
    FEBS Open Bio 11 6 1552 - 1564 2021年06月 [査読有り]
     
    DNA is packaged with histones to form chromatin that impinges on all nuclear processes, including transcription, replication and repair, in the eukaryotic nucleus. A complete understanding of these molecular processes requires analysis of chromatin context in vitro. Here, Drosophila four core histones were produced in a native and unmodified form using wheat germ cell-free protein synthesis. In the assembly reaction, four unpurified core histones and three chromatin assembly factors (dNAP-1, dAcf1 and dISWI) were incubated with template DNA. We then assessed stoichiometry with the histones, nucleosome arrays, supercoiling and the ability of the chromatin to serve as a substrate for histone-modifying enzymes. Overall, our method provides a new avenue to produce chromatin that can be useful in a wide range of chromatin research.
  • Akira Yoshinari, Takuya Hosokawa, Marcel Pascal Beier, Keishi Oshima, Yuka Ogino, Chiaki Hori, Taichi E Takasuka, Yoichiro Fukao, Toru Fujiwara, Junpei Takano
    The Plant Cell 33 2 420 - 438 2020年12月03日 [査読有り]
     
    Abstract Plants take up and translocate nutrients through transporters. In Arabidopsis thaliana, the borate exporter BOR1 acts as a key transporter under boron (B) limitation in the soil. Upon sufficient-B supply, BOR1 undergoes ubiquitination and is transported to the vacuole for degradation, to avoid overaccumulation of B. However, the mechanisms underlying B-sensing and ubiquitination of BOR1 are unknown. In this study, we confirmed the lysine-590 residue in the C-terminal cytosolic region of BOR1 as the direct ubiquitination site and showed that BOR1 undergoes K63-linked polyubiquitination. A forward genetic screen identified that amino acid residues located in vicinity of the substrate-binding pocket of BOR1 are essential for the vacuolar sorting. BOR1 variants that lack B-transport activity showed a significant reduction of polyubiquitination and subsequent vacuolar sorting. Coexpression of wild-type (WT) and a transport-defective variant of BOR1 in the same cells showed degradation of the WT but not the variant upon sufficient-B supply. These findings suggest that polyubiquitination of BOR1 relies on its conformational transition during the transport cycle. We propose a model in which BOR1, as a B transceptor, directly senses the B concentration and promotes its own polyubiquitination and vacuolar sorting for quick and precise maintenance of B homeostasis.
  • Kei-Ichi Okimune, Szilvia K Nagy, Shogo Hataya, Yaeta Endo, Taichi E Takasuka
    BMC biotechnology 20 1 62 - 62 2020年12月01日 [査読有り]
     
    BACKGROUND: Elaboration of the epigenetic regulation of chromatin is a long-standing aim in molecular and cellular biology. Hence, there is a great demand for the development of in vitro methods to reconstitute chromatin that can be used directly for biochemical assays. The widely used wheat germ cell-free protein expression method provides broad applications to investigate the function and structure of eukaryotic proteins. Such advantages, including high translation efficiency, flexibility, and possible automatization, are beneficial for achieving native-like chromatin substrates for in vitro studies. RESULTS: We describe a novel, single-step in vitro chromatin assembly method by using the wheat germ cell-free protein synthesis. We demonstrated that both Drosophila and human chromatins can be reconstituted in the course of the in vitro translation of core histones by the addition of chromatin assembly factors, circular plasmid, and topoisomerase I in an ATP-dependent manner. Drosophila chromatin assembly was performed in 4 h at 26 °C, in the presence of premixed mRNAs encoding the core histones, dAcf1/dISWI chromatin remodeling complex, and nucleosome assembly protein, dNAP1. Similarly, the human chromatin was assembled by co-expressing the human core histones with Drosophila chromatin remodeling factor, dISWI, and chromatin chaperone, dNLP, for 6 h at 26 °C. The presence of reconstituted chromatin was monitored by DNA supercoiling assay, also the regular spacing of nucleosomes was assessed by Micrococcal nuclease assay. Furthermore, Drosophila linker histone H1-containing chromatin was reconstituted, affirming that the in vitro assembled chromatin is suitable for downstream applications. CONCLUSIONS: The method described in this study allows the assembly of Drosophila and human chromatins, possibly in native-like form, by using a wheat germ cell-free protein expression. Although both chromatins were reconstituted successfully, there were unexpected differences with respect to the required ratio of histone-coding mRNAs and the reaction time. Overall, our new in vitro chromatin reconstitution method will aid to characterize the unrevealed structure, function, and regulation of chromatin dynamics.
  • Evan M Glasgow, Elias I Kemna, Craig A Bingman, Nicole L Ing, Kai Deng, Christopher M Bianchetti, Taichi E Takasuka, Trent R Northen, Brian G Fox
    The Journal of biological chemistry 2020年10月16日 [査読有り]
     
    Broad-specificity glycoside hydrolases (GHs) contribute to plant biomass hydrolysis by degrading a diverse range of polysaccharides, making them useful catalysts for renewable energy and biocommodity production. Discovery of new GHs with improved kinetic parameters or more tolerant substrate binding sites could increase the efficiency of renewable bioenergy production even further. GH5 has over 50 subfamilies exhibiting selectivities for reaction with β-(1,4)-linked oligo- and polysaccharides. Among these, subfamily 4 (GH5_4) contains numerous broad-selectivity endoglucanases that hydrolyze cellulose, xyloglucan, and mixed-linkage glucans. We previously surveyed the whole subfamily and found over 100 new broad-specificity endoglucanases, although the structural origins of broad specificity remained unclear. A mechanistic understanding of GH5_4 substrate specificity would help inform the best protein design strategies and the most appropriate industrial application of broad-specificity endoglucanases. Here we report structures of ten new GH5_4 enzymes from cellulolytic microbes and characterize their substrate selectivity using normalized reducing sugar assays and mass spectrometry. We found that GH5_4 enzymes have the highest catalytic efficiency for hydrolysis of xyloglucan, glucomannan and soluble β-glucans, with opportunistic secondary reactions on cellulose, mannan, and xylan. The positions of key aromatic residues determine the overall reaction rate and breadth of substrate tolerance, and they contribute to differences in oligosaccharide cleavage patterns. Our new composite model identifies several critical structural features that confer broad specificity and may be readily engineered into existing industrial enzymes. We demonstrate that GH5_4 endoglucanases can have broad specificity without sacrificing high activity, making them a valuable addition to the biomass deconstruction toolset.
  • Chiaki Hori, Ruopu Song, Kazuki Matsumoto, Ruy Matsumoto, Benjamin B Minkoff, Shuzo Oita, Hideho Hara, Taichi E Takasuka
    Applied and environmental microbiology 2020年02月14日 [査読有り][通常論文]
     
    Wood-devastating insects utilize their symbiotic microbes with lignocellulose-degrading abilities to extract energy from recalcitrant woods. It is well known that free-living lignocellulose-degrading fungi secrete various carbohydrate-active enzymes (CAZymes) to degrade plant cell wall components, mainly cellulose, hemicellulose and lignin. However, CAZymes from insect-symbiotic fungi have not been well documented except for a few examples. In this study, an insect-associated fungus, Daldinia decipiens oita was isolated as a potential symbiotic fungus of female Xiphydriaalbopicta captured from Hokkaido forest. This fungus was grown in seven different media containing a single carbon source, glucose, cellulose, xylan, mannan, pectin, poplar, or larch, and the secreted proteins were identified by LC-MS/MS. 128 CAZymes including domains of 92 glycoside hydrolases (GHs), 15 carbohydrate esterases (CEs), 5 polysaccharide lyases (PLs), 17 auxiliary activities (AAs), and 11 carbohydrate-binding modules (CBMs) were identified, and these are involved in degradation of cellulose and hemicellulose but not lignin. Together with the result of polysaccharide-degrading activity measurements, we concluded that D. decipiens oita tightly regulates the expression of these CAZymes in response to the tested plant cell wall materials. Overall, this study described the detailed proteomic approach of a woodwasp-associated fungus and revealed that the new isolate, D. decipiens oita, secretes diverse CAZymes to efficiently degrade lignocellulose in the symbiotic environment.ImportanceRecent studies show the potential impacts of insect symbiont microbes on biofuels application with regards to their degradation capability of a recalcitrant plant cell wall. In this study, we describe a novel fungal isolate, D. decipiens oita, as a single symbiotic fungus from the Xiphydria woodwasp found in northern forests of Japan. Our detailed secretome analyses of D. decipiens oita together with activity measurements reveal that this insect-associated fungus exhibits high and broad activities for plant cell wall material degradation, suggesting potential applications within the biomass conversion industry for plant mass degradation.
  • Tomoaki Anabuki, Yusuke Ito, Keisuke Ohashi, Taichi E Takasuka, Hideyuki Matsuura, Kosaku Takahashi
    Bioorganic & medicinal chemistry letters 29 21 126634 - 126634 2019年11月01日 [査読有り][通常論文]
     
    Target protein identification of bioactive small molecules is one of the most important research in forward chemical genetics. The affinity chromatography technique to use a resin bound with a small molecule is often used for identification of a target protein of a bioactive small molecule. Here we report a new method to isolate a protein targeted with a bioactive small molecule using a biotin linker with alkyne and amino groups, protein cross-linker containing disulfide bond, and a bioactive small molecule with an azido group (azido probe). After an azido probe is associated with a target protein, the complex of a target protein and azido probe is covalently bound through the biotin linker by azide-alkyne Huisgen cycloaddition and protein cross-linker containing disulfide bond. This ternary complex is immobilized on an affinity matrix with streptavidin, and then the target protein is selectively eluted with a buffer containing a reducing agent for cleavage of disulfide bonds. This method uses a probe having an azido group, which a small functional group, and has the possibility to be a solution strategy to overcome the hindrance of a functional group introduced into the probe that reduces association a target protein. The effectiveness of the method in this study was shown using linker 1, 3'-azidoabscisic acid 3, and protein cross-linker containing a disulfide bond (DTSSP 5).
  • Mia Terashima, Keisuke Ohashi, Taichi E. Takasuka, Hisaya Kojima, Manabu Fukui
    ENVIRONMENTAL MICROBIOLOGY REPORTS 11 2 227 - 235 2019年04月 [査読有り][通常論文]
     
    Hymenobacter nivis P3(T) is a heterotrophic bacterium isolated from Antarctic red snow generated by algal blooms. Despite being non-photosynthetic, H. nivis was dominantly found in the red snow environment that is exposed to high light and UV irradiation, suggesting that this species can flourish under such harsh conditions. In order to further understand the adaptive strategies on the snow surface environment of Antarctica, the genome of H. nivis P3(T) was sequenced and analyzed, which identified genes putatively encoding for light-reactive proteins such as proteorhodopsin, phytochrome, photolyase and several copies of cryptochromes. Culture-based experiments revealed that H. nivis P3(T) growth was significantly enhanced under light conditions, while dark conditions had increased extracellular polymeric substances. Furthermore, the expression of several putative light-reactive proteins was determined by proteomic analysis. These results indicate that H. nivis P3(T) is able to potentially utilize light, which may explain its dominance on the red snow surface environment of Antarctica. Originality-significance statement The role of proteorhodopsin in heterotrophic bacteria is not well-characterized, as only a handful of proteorhodopsin-harbouring isolates were shown to have a light-enhanced phenotype through culture-based experiments to date. This is the first study that demonstrates light-stimulated growth and protein expression evidence of photoactive proteins for a non-marine psychrophile and for a member of the genus Hymenobacter. It is also the first study that provides comprehensive proteome information for this genus. This study presents significant results in understanding the adaptive mechanism of a heterotrophic non-photosynthetic bacterium thriving on the snow surface environment of Antarctica as well as demonstrating the role of light-utilization in promoting growth, possibly through proteorhodopsin.
  • Tomohiro Watanabe, Hisaya Kojima, Kazuhiro Umezawa, Chiaki Hori, Taichi E. Takasuka, Yukako Kato, Manabu Fukui
    FRONTIERS IN MICROBIOLOGY 10 316  2019年02月 [査読有り][通常論文]
     
    Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria. Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family 'Sulfuricellaceae'. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterohbacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences.
  • Glasgow EM, Vander Meulen KA, Takasuka TE, Bianchetti CM, Bergeman LF, Deutsch S, Fox BG
    Journal of molecular biology 2019年01月 [査読有り][通常論文]
  • Ankit Ravankar, Shotaro Imai, Abhijeet Ravankar, Tomohiro Agatsuma, Tomomichi Kato, Taichi Takasuka, Teruyuki Tsuji, Kaori K. Shigetomi, Ken Saito
    Proceedings - 2018 7th International Congress on Advanced Applied Informatics, IIAI-AAI 2018 414 - 418 2018年07月02日 [査読有り][通常論文]
     
    © 2018 IEEE. The current graduate school education system has largely been focusing on producing better learners and problem solvers. The rise of problem based learning approaches are testimonial to the importance of such skills at all levels of education from early childhood to graduate school level. However, most of the programs so far have focused primarily on producing better problem solvers neglecting problem finding at large. Problem finding, an important skill is a subset and first step in creative problem solving. Most studies on problem finding skills have only focused on industries and corporations for training employees to think out of the box for innovative product design and development. At school or university level, students are generally given a well-defined problem in most Problem Based Learning (PBL) scenarios and problem discovery or how to deal with ill-structured problems is mostly ignored. In this study, we present the Nitobe School Program and discuss our unique curriculum to teach problem finding in graduate school education. We show how introducing problem finding at graduate level increases student's ability to comprehend difficult and wicked problems in a team based learning environment. Moreover, we present how it influences creativity in graduate students resulting in better problem solvers.
  • Ningning Cheng, Keiichi Koda, Yutaka Tamai, Yoko Yamamoto, Taichi E. Takasuka, Yasumitsu Uraki
    BIORESOURCE TECHNOLOGY 232 126 - 132 2017年05月 [査読有り][通常論文]
     
    Amphipathic lignin derivatives (A-LDs) prepared from the black liquor of soda pulping of Japanese cedar are strong accelerators for bioethanol production under a fed-batch simultaneous enzymatic saccharification and fermentation (SSF) process. To improve the bioethanol production concentration, conditions such as reaction temperature, stirring program, and A-LDs loadings were optimized in both small scale and large scale fed-batch SSF. The fed-batch SSF in the presence of 3.0 g/L A-LDs at 38 degrees C gave the maximum ethanol production and a high enzyme recovery rate. Furthermore, a jar-fermenter equipped with a powerful mechanical stirrer was designed for 1.5 L-scale fed-batch SSF to achieve rigorous mixing during high substrate loading. Finally, the 1.5 L fed-batch SSF with a substrate loading of 30% (w/v) produced a high ethanol concentration of 87.9 g/L in the presence of A-LDs under optimized conditions. (C) 2017 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
  • Imai S, Ravankar RA, Shimamura M, Takasuka TE, Chiba G, Yamanaka Y
    International Journal of Institutional Research and Management. 1 17 - 35 2017年04月 [査読有り][通常論文]
  • Ravankar RA, Imai S, Shiamura M, Chiba G, Takasuka TE
    J Higher Education and Lifelong Learning 24 24 9 - 20 北海道大学高等教育推進機構 2017年04月 [査読有り][通常論文]
     
    In recent years, problem-based learning (PBL) techniques have been gaining momentum inschools and university curricula around the world. The main advantage of the PBL method is that it promotescreative problem solving, improves cognition and enhances overall thought processes in learners. For mostPBL-style programmes, problem solving is at the core, although the notion of problem discovery or problemfinding is not seriously considered. In most cases, students are always presented with a structured and welldefinedproblem, but have no experience of solving an ill-structured problem or ʻwicked' problem. Thepresent study focuses on problem finding as a critical step towards developing problem solving skills inuniversity graduate students. The study aims at understanding the importance of problem formulation andcreativity, and focuses as well on our attempt to teach problem finding as an important tool in thedevelopment of creative thinking and problem solving among graduate students. The study is part of a specialgraduate programme called the Nitobe School at Hokkaido University in Japan, which started in 2015. In anactive learning classroom setting, this course is intended to support graduate students in their discovery of illstructuredproblems, help them to understand their formulation and thereby improve their problem solvingskills. We present the results of our teaching method for the first year at the Nitobe School and share ourfindings through this work.
  • Adam J. Book, Gina R. Lewin, Bradon R. McDonald, Taichi E. Takasuka, Evelyn Wendt-Pienkowski, Drew T. Doering, Steven Suh, Kenneth F. Raffa, Brian G. Fox, Cameron R. Currie
    PLOS BIOLOGY 14 6 2016年06月 [査読有り][通常論文]
     
    The evolution of cellulose degradation was a defining event in the history of life. Without efficient decomposition and recycling, dead plant biomass would quickly accumulate and become inaccessible to terrestrial food webs and the global carbon cycle. On land, the primary drivers of plant biomass deconstruction are fungi and bacteria in the soil or associated with herbivorous eukaryotes. While the ecological importance of plant-decomposing microbes is well established, little is known about the distribution or evolution of cellulolytic activity in any bacterial genus. Here we show that in Streptomyces, a genus of Actinobacteria abundant in soil and symbiotic niches, the ability to rapidly degrade cellulose is largely restricted to two clades of host-associated strains and is not a conserved characteristic of the Streptomyces genus or host-associated strains. Our comparative genomics identify that while plant biomass degrading genes (CAZy) are widespread in Streptomyces, key enzyme families are enriched in highly cellulolytic strains. Transcriptomic analyses demonstrate that cellulolytic strains express a suite of multi-domain CAZy enzymes that are coregulated by the CebR transcriptional regulator. Using targeted gene deletions, we verify the importance of a highly expressed cellulase (GH6 family cellobiohydrolase) and the CebR transcriptional repressor to the cellulolytic phenotype. Evolutionary analyses identify complex genomic modifications that drive plant biomass deconstruction in Streptomyces, including acquisition and selective retention of CAZy genes and transcriptional regulators. Our results suggest that host-associated niches have selected some symbiotic Streptomyces for increased cellulose degrading activity and that symbiotic bacteria are a rich biochemical and enzymatic resource for biotechnology.
  • 高須賀太一, 堀千明, James Ellinger, 飛松裕基
    化学と生物 54 3 156‐158  2016年02月 [査読有り][通常論文]
  • Shotaro Imai, Ankit A. Ravankar, Michiyo Shimamura, Taichi E. Takasuka, Go Chiba, Yasuhiro Yamanaka
    PROCEEDINGS 2016 5TH IIAI INTERNATIONAL CONGRESS ON ADVANCED APPLIED INFORMATICS IIAI-AAI 2016 537 - 541 2016年 [査読有り][通常論文]
     
    The new graduate school education program Nitobe School was launched in 2015 as one of main education projects of "Top Global University Project" in Hokkaido University. This new graduate program is aimed to supply currently undermined skill-set to students from different home graduate or professional school. The scope of the Nitobe School program is to foster students to be a global leader who might contribute not only for local societies but also internationally by Team-Based-Learning (TBL) and Project-Based-Learning (PBL) methods. Since students have different expertise including the area of STEM and humanity, teachers cannot guide classes with their field, rather teachers need to educate students using a general topics. This general education program apparently requires different approaches from the conventional one. After completion of the first year of Nitobe School, we took place the survey that asked students how they felt about our new teaching methods. Overall, students appreciated with the new methods that we carried out, but there are some spaces for further improvement. In this report, we suggest potential ways to improve the Nitobe School program, which will be able to enhance further educating students, and at the same time educate teachers toward the TBL and PBL.
  • Ankit A. Ravankar, Shotaro Imai, Michiyo Shimamura, Go Chiba, Taichi Takasuka, Yasuhiro Yamanaka
    PROCEEDINGS 2016 5TH IIAI INTERNATIONAL CONGRESS ON ADVANCED APPLIED INFORMATICS IIAI-AAI 2016 542 - 546 2016年 [査読有り][通常論文]
     
    The present university education system has been designed to make graduate students good problem solvers such that they can contribute to society through the skills acquired in the graduate schools. With focus on developing critical thinking and reasoning to solve local and global problems such programs have gained immense popularity among teachers and professors in schools and universities and termed as "Problem-Based-Learning" (PBL). However, there has been very few programs that encourage students to become better Problem finders. This study is based on our own experience of teaching problem-finding as an important skill for a special graduate program in university education and our findings on its implication on students ability to comprehend real world problems.
  • Johnnie A. Walker, Taichi E. Takasuka, Kai Deng, Christopher M. Bianchetti, Hannah S. Udell, Ben M. Prom, Hyunkee Kim, Paul D. Adams, Trent R. Northen, Brian G. Fox
    BIOTECHNOLOGY FOR BIOFUELS 8 220  2015年12月 [査読有り][通常論文]
     
    Background: Carbohydrate binding modules (CBMs) bind polysaccharides and help target glycoside hydrolases catalytic domains to their appropriate carbohydrate substrates. To better understand how CBMs can improve cellulolytic enzyme reactivity, representatives from each of the 18 families of CBM found in Ruminoclostridium thermocellum were fused to the multifunctional GH5 catalytic domain of CelE (Cthe_0797, CelEcc), which can hydrolyze numerous types of polysaccharides including cellulose, mannan, and xylan. Since CelE is a cellulosomal enzyme, none of these fusions to a CBM previously existed. Results: CelEcc_CBM fusions were assayed for their ability to hydrolyze cellulose, lichenan, xylan, and mannan. Several CelEcc_CBM fusions showed enhanced hydrolytic activity with different substrates relative to the fusion to CBM3a from the cellulosome scaffoldin, which has high affinity for binding to crystalline cellulose. Additional binding studies and quantitative catalysis studies using nanostructure-initiator mass spectrometry (NIMS) were carried out with the CBM3a, CBM6, CBM30, and CBM44 fusion enzymes. In general, and consistent with observations of others, enhanced enzyme reactivity was correlated with moderate binding affinity of the CBM. Numerical analysis of reaction time courses showed that CelEcc_CBM44, a combination of a multifunctional enzyme domain with a CBM having broad binding specificity, gave the fastest rates for hydrolysis of both the hexose and pentose fractions of ionic-liquid pretreated switchgrass. Conclusion: We have shown that fusions of different CBMs to a single multifunctional GH5 catalytic domain can increase its rate of reaction with different pure polysaccharides and with pretreated biomass. This fusion approach, incorporating domains with broad specificity for binding and catalysis, provides a new avenue to improve reactivity of simple combinations of enzymes within the complexity of plant biomass.
  • Christopher M. Bianchetti, Taichi E. Takasuka, Sam Deutsch, Hannah S. Udell, Eric J. Yik, Lai F. Bergeman, Brian G. Fox
    JOURNAL OF BIOLOGICAL CHEMISTRY 290 19 11819 - 11832 2015年05月 [査読有り][通常論文]
     
    Background: SacteLam55A is a GH55 enzyme from highly cellulolytic Streptomyces sp. SirexAA-E. Results: Substrate-bound structures identify residues involved in binding, catalysis, enforcement of reaction specificity, and possibly processivity. Conclusion: Natural GH55 are exo--1,3-glucanases with a broad range of temperature and pH optima. Significance: Experimental annotation of GH phylogenetic space by use of bioinformatics, high throughput cell-free translation, biochemical assay, and structure determination is feasible. The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo--1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 -1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on approximate to 30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties.
  • Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG
    Frontiers in bioengineering and biotechnology 3 165  2015年 [査読有り][通常論文]
  • Deng K, Guenther JM, Gao J, Bowen BP, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR
    Frontiers in bioengineering and biotechnology 3 153  2015年 [査読有り][通常論文]
  • Adam J. Book, Gina R. Lewin, Bradon R. McDonald, Taichi E. Takasuka, Drew T. Doering, Aaron S. Adams, Joshua A. V. Blodgett, Jon Clardy, Kenneth F. Raffa, Brian G. Fox, Cameron R. Currie
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY 80 15 4692 - 4701 2014年08月 [査読有り][通常論文]
     
    Actinobacteria in the genus Streptomyces are critical players in microbial communities that decompose complex carbohydrates in the soil, and these bacteria have recently been implicated in the deconstruction of plant polysaccharides for some herbivorous insects. Despite the importance of Streptomyces to carbon cycling, the extent of their plant biomass-degrading ability remains largely unknown. In this study, we compared four strains of Streptomyces isolated from insect herbivores that attack pine trees: DpondAA-B6 (SDPB6) from the mountain pine beetle, SPB74 from the southern pine beetle, and SirexAA-E (SACTE) and SirexAA-G from the woodwasp, Sirex noctilio. Biochemical analysis of secreted enzymes demonstrated that only two of these strains, SACTE and SDPB6, were efficient at degrading plant biomass. Genomic analyses indicated that SACTE and SDPB6 are closely related and that they share similar compositions of carbohydrate-active enzymes. Genome-wide proteomic and transcriptomic analyses revealed that the major exocellulases (GH6 and GH48), lytic polysaccharide monooxygenases (AA10), and mannanases (GH5) were conserved and secreted by both organisms, while the secreted endocellulases (GH5 and GH9 versus GH9 and GH12) were from diverged enzyme families. Together, these data identify two phylogenetically related insect-associated Streptomyces strains with high biomass-degrading activity and characterize key enzymatic similarities and differences used by these organisms to deconstruct plant biomass.
  • Adam J. Book, Ragothaman M. Yennamalli, Taichi E. Takasuka, Cameron R. Currie, George N. Phillips, Brian G. Fox
    BIOTECHNOLOGY FOR BIOFUELS 7 109  2014年08月 [査読有り][通常論文]
     
    Background: Understanding the diversity of lignocellulose-degrading enzymes in nature will provide insights for the improvement of cellulolytic enzyme cocktails used in the biofuels industry. Two families of enzymes, fungal AA9 and bacterial AA10, have recently been characterized as crystalline cellulose or chitin-cleaving lytic polysaccharide monooxygenases (LPMOs). Here we analyze the sequences, structures, and evolution of LPMOs to understand the factors that may influence substrate specificity both within and between these enzyme families. Results: Comparative analysis of sequences, solved structures, and homology models from AA9 and AA10 LPMO families demonstrated that, although these two LPMO families are highly conserved, structurally they have minimal sequence similarity outside the active site residues. Phylogenetic analysis of the AA10 family identified clades with putative chitinolytic and cellulolytic activities. Estimation of the rate of synonymous versus non-synonymous substitutions (dN/dS) within two major AA10 subclades showed distinct selective pressures between putative cellulolytic genes (subclade A) and CBP21-like chitinolytic genes (subclade D). Estimation of site-specific selection demonstrated that changes in the active sites were strongly negatively selected in all subclades. Furthermore, all codons in the subclade D had dN/dS values of less than 0.7, whereas codons in the cellulolytic subclade had dN/dS values of greater than 1.5. Positively selected codons were enriched at sites localized on the surface of the protein adjacent to the active site. Conclusions: The structural similarity but absence of significant sequence similarity between AA9 and AA10 families suggests that these enzyme families share an ancient ancestral protein. Combined analysis of amino acid sites under Darwinian selection and structural homology modeling identified a subclade of AA10 with diversifying selection at different surfaces, potentially used for cellulose-binding and protein-protein interactions. Together, these data indicate that AA10 LPMOs are under selection to change their function, which may optimize cellulolytic activity. This work provides a phylogenetic basis for identifying and classifying additional cellulolytic or chitinolytic LPMOs.
  • Taichi E. Takasuka, Christopher M. Bianchetti, Yuki Tobimatsu, Lai F. Bergeman, John Ralph, Brian G. Fox
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 82 7 1245 - 1257 2014年07月 [査読有り][通常論文]
     
    SACTE_5457 is secreted by Streptomyces sp. SirexAA-E, a highly cellulolytic actinobacterium isolated from a symbiotic community composed of insects, fungi, and bacteria. Here we report the 1.84 angstrom resolution crystal structure and functional characterization of SACTE_5457. This enzyme is a member of the glycosyl hydrolase family 46 and is composed of two -helical domains that are connected by an -helical linker. The catalytic residues (Glu74 and Asp92) are separated by 10.3 angstrom, matching the distance predicted for an inverting hydrolysis reaction. Normal mode analysis suggests that the connecting -helix is flexible and allows the domain motion needed to place active site residues into an appropriate configuration for catalysis. SACTE_5457 does not react with chitin, but hydrolyzes chitosan substrates with an approximate to 4-fold improvement in k(cat)/K-M as the percentage of acetylation and the molecular weights decrease. Analysis of the time dependence of product formation shows that oligosaccharides with degree of polymerization <4 are not hydrolyzed. By combining the results of substrate docking to the X-ray structure and end-product analysis, we deduce that SACTE_5457 preferentially binds substrates spanning the -2 to +2 sugar binding subsites, and that steric hindrance prevents binding of N-acetyl-d-glucosamine in the +2 subsite and may weakly interfere with binding of N-acetyl-d-glucosamine in the +1 subsites. A proposal for how these constraints account for the observed product distributions is provided. Proteins 2014; 82:1245-1257. (c) 2013 Wiley Periodicals, Inc.
  • Kai Deng, Taichi E. Takasuka, Richard Heins, Xiaoliang Cheng, Lai F. Bergeman, Jian Shi, Ryan Aschenbrener, Sam Deutsch, Seema Singh, Kenneth L. Sale, Blake A. Simmons, Paul D. Adams, Anup K. Singh, Brian G. Fox, Trent R. Northen
    ACS CHEMICAL BIOLOGY 9 7 1470 - 1479 2014年07月 [査読有り][通常論文]
     
    Glycoside hydrolases (GHs) are critical to cycling of plant biomass in the environment, digestion of complex polysaccharides by the human gut microbiome, and industrial activities such as deployment of cellulosic biofuels. High-throughput sequencing methods show tremendous sequence diversity among GHs, yet relatively few examples from the over 150,000 unique domain arrangements containing GHs have been functionally characterized. Here, we show how cell-free expression, bioconjugate chemistry, and surface-based mass spectrometry can be used to study glycoside hydrolase reactions with plant biomass. Detection of soluble products is achieved by coupling a unique chemical probe to the reducing end of oligosaccharides in a stable oxime linkage, while the use of C-13-labeled monosaccharide standards (xylose and glucose) allows quantitation of the derivatized glycans. We apply this oxime-based nanostructure-initiator mass spectrometry (NIMS) method to characterize the functional diversity of GHs secreted by Clostridium thermocellum, a model cellulolytic organism. New reaction specificities are identified, and differences in rates and yields of individual enzymes are demonstrated in reactions with biomass substrates. Numerical analyses of time series data suggests that synergistic combinations of mono- and multifunctional GHs can decrease the complexity of enzymes needed for the hydrolysis of plant biomass during the production of biofuels.
  • Takasuka TE, Acheson JF, Bianchetti CM, Prom BM, Bergeman LF, Book AJ, Currie CR, Fox BG
    PloS one 9 4 e94166  4 2014年04月 [査読有り][通常論文]
     
    beta-mannanase SACTE_2347 from cellulolytic Streptomyces sp. SirexAA-E is abundantly secreted into the culture medium during growth on cellulosic materials. The enzyme is composed of domains from the glycoside hydrolase family 5 (GH5), fibronectin type-III (Fn3), and carbohydrate binding module family 2 (CBM2). After secretion, the enzyme is proteolyzed into three different, catalytically active variants with masses of 53, 42 and 34 kDa corresponding to the intact protein, loss of the CBM2 domain, or loss of both the Fn3 and CBM2 domains. The three variants had identical N-termini starting with Ala51, and the positions of specific proteolytic reactions in the linker sequences separating the three domains were identified. To conduct biochemical and structural characterizations, the natural proteolytic variants were reproduced by cloning and heterologously expressed in Escherichia coli. Each SACTE_2347 variant hydrolyzed only beta-1,4 mannosidic linkages, and also reacted with pure mannans containing partial galactosyl-and/ or glucosyl substitutions. Examination of the X-ray crystal structure of the GH5 domain of SACTE_2347 suggests that two loops adjacent to the active site channel, which have differences in position and length relative to other closely related mannanases, play a role in producing the observed substrate selectivity.
  • Taichi E. Takasuka, Yi-Ju Hsieh, Arnold Stein
    APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY 172 1 1 - 8 2014年01月 [査読有り][通常論文]
     
    We described a simple and quick miniaturized sequencing gel system for DNA analysis. Two major modifications were made to the previously reported miniaturized DNA sequencing gel system to achieve high-resolution hydroxyl radical cleavage analysis: including formamide in the miniaturized gel and providing uniform heating during electrophoresis. Our method enables one to reduce the cost for chemicals and to significantly reduce electrophoresis time. Furthermore, minimal gel handling simplifies the entire process. We show that the resolution of DNA fragments obtained by hydroxyl radical cleavage for the miniaturized gel is similar to that of a large conventional sequencing gel.
  • Takasuka TE, Walker JA, Bergeman LF, Vander Meulen KA, Makino S, Elsen NL, Fox BG
    Methods in molecular biology (Clifton, N.J.) 1118 71 - 95 2014年 [査読有り][通常論文]
  • Christopher M. Bianchetti, Connor H. Harmann, Taichi E. Takasuka, Gregory L. Hura, Kevin Dyer, Brian G. Fox
    JOURNAL OF BIOLOGICAL CHEMISTRY 288 25 18574 - 18587 2013年06月 [査読有り][通常論文]
     
    Streptomyces sp. SirexAA-E is a highly cellulolytic bacterium isolated from an insect/microbe symbiotic community. When grown on lignin-containing biomass, it secretes SACTE_2871, an aromatic ring dioxygenase domain fused to a family 5/12 carbohydrate-binding module (CBM 5/12). Here we present structural and catalytic studies of this novel fusion enzyme, thus providing insight into its function. The dioxygenase domain has the core beta-sandwich fold typical of this enzyme family but lacks a dimerization domain observed in other intradiol dioxygenases. Consequently, the x-ray structure shows that the enzyme is monomeric and the Fe(III)-containing active site is exposed to solvent in a shallow depression on a planar surface. Purified SACTE_2871 catalyzes the O-2-dependent intradiol cleavage of catechyl compounds from lignin biosynthetic pathways, but not their methylated derivatives. Binding studies show that SACTE_2871 binds synthetic lignin polymers and chitin through the interactions of the CBM 5/12 domain, representing a new binding specificity for this fold-family. Based on its unique structural features and functional properties, we propose that SACTE_2871 contributes to the invasive nature of the insect/microbial community by destroying precursors needed by the plant for de novo lignin biosynthesis as part of its natural wounding response.
  • Takasuka TE, Book AJ, Lewin GR, Currie CR, Fox BG
    Scientific reports 3 1030  2013年 [査読有り][通常論文]
  • Aarthi Chandrasekaran, Kai Deng, Chung-Yan Koh, Taichi Takasuka, Lai F. Bergeman, Brian G. Fox, Paul D. Adams, Anup K. Singh
    CHEMICAL COMMUNICATIONS 49 48 5441 - 5443 2013年 [査読有り][通常論文]
     
    We describe a simple, multiplexed assay that integrates glycan synthesis, bioconjugation to microspheres, fluorescent chemical/biochemical detection and multiparameter flow cytometric analysis to screen activities of different families of carbohydrate-active enzymes.
  • Allison Riederer, Taichi E. Takasuka, Shin-ichi Makino, David M. Stevenson, Yury V. Bukhman, Nathaniel L. Elsen, Brian G. Fox
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY 77 4 1243 - 1253 2011年02月 [査読有り][通常論文]
     
    A microarray study of chemostat growth on insoluble cellulose or soluble cellobiose has provided substantial new information on Clostridium thermocellum gene expression. This is the first comprehensive examination of gene expression in C. thermocellum under defined growth conditions. Expression was detected from 2,846 of 3,189 genes, and regression analysis revealed 348 genes whose changes in expression patterns were growth rate and/or substrate dependent. Successfully modeled genes included those for scaffoldin and cellulosomal enzymes, intracellular metabolic enzymes, transcriptional regulators, sigma factors, signal transducers, transporters, and hypothetical proteins. Unique genes encoding glycolytic pathway and ethanol fermentation enzymes expressed at high levels simultaneously with previously established maximal ethanol production were also identified. Ranking of normalized expression intensities revealed significant changes in transcriptional levels of these genes. The pattern of expression of transcriptional regulators, sigma factors, and signal transducers indicates that response to growth rate is the dominant global mechanism used for control of gene expression in C. thermocellum.
  • Andrew Miller, Jiji Chen, Taichi E. Takasuka, Jennifer L. Jacobi, Paul D. Kaufman, Joseph M. K. Irudayaraj, Ann L. Kirchmaier
    JOURNAL OF BIOLOGICAL CHEMISTRY 285 45 35142 - 35154 2010年11月 [査読有り][通常論文]
     
    In Saccharomyces cerevisiae, silent chromatin is formed at HMR upon the passage through S phase, yet neither the initiation of DNA replication at silencers nor the passage of a replication fork through HMR is required for silencing. Paradoxically, mutations in the DNA replication processivity factor, POL30, disrupt silencing despite this lack of requirement for DNA replication in the establishment of silencing. We tested whether pol30 mutants could establish silencing at either replicated or non-replicated HMR loci during S phase and found that pol30 mutants were defective in establishing silencing at HMR regardless of its replication status. Although previous studies tie the silencing defect of pol30 mutants to the chromatin assembly factors Asf1p and CAF-1, we found pol30 mutants did not exhibit a gross defect in packaging HMR into chromatin. Rather, the pol30 mutants exhibited defects in histone modifications linked to ASF1 and CAF-1-dependent pathways, including SAS-I-and Rtt109p-dependent acetylation events at H4-K16 and H3-K9 (plus H3-K56; Miller, A., Yang, B., Foster, T., and Kirchmaier, A. L. (2008) Genetics 179, 793-809). Additional experiments using FLIM-FRET revealed that Pol30p interacted with SAS-I and Rtt109p in the nuclei of living cells. However, these interactions were disrupted in pol30 mutants with defects linked to ASF1- and CAF-1-dependent pathways. Together, these results imply that Pol30p affects epigenetic processes by influencing the composition of chromosomal histone modifications.
  • Taichi E. Takasuka, Arnold Stein
    NUCLEIC ACIDS RESEARCH 38 17 5672 - 5680 2010年09月 [査読有り][通常論文]
     
    Several periodic motifs have been implicated in facilitating the bending of DNA around the histone core of the nucleosome. For example, di-nucleotides AA/TT/TA and GC at similar to 10-bp periods, but offset by 5 bp, are found with higher-than-expected occurrences in aligned nucleosomal DNAs in vitro and in vivo. Additionally, regularly oscillating period-10 trinucleotide motifs non-T, A/T, G and their complements have been implicated in the formation of regular nucleosome arrays. The effects of these periodic motifs on nucleosome formation have not been systematically tested directly by competitive reconstitution assays. We show that, in general, none of these period-10 motifs, except TA, in certain sequence contexts, facilitates nucleosome formation. The influence of periodic TAs on nucleosome formation is appreciable; with some of the 200-bp DNAs out-competing bulk nucleosomal DNA by more than 400-fold. Only the nucleotides immediately flanking TA influence its nucleosome-forming ability. Period-10 TA, when flanked by a pair of permissive nucleotides, facilitates DNA bending through compression of the minor groove. The free energy change for nucleosome formation decreases linearly with the number of consecutive TAs, up to eight. We suggest how these data can be reconciled with previous findings.
  • Arnold Stein, Taichi E. Takasuka, Clayton K. Collings
    NUCLEIC ACIDS RESEARCH 38 3 709 - 719 2010年01月 [査読有り][通常論文]
     
    Large-scale and genome-wide studies have concluded that similar to 80% of the yeast (Saccharomyces cerevisiae) genome is occupied by positioned nucleosomes. In vivo this nucleosome organization can result from a variety of mechanisms, including the intrinsic DNA sequence preferences for wrapping the DNA around the histone core. Recently, a genome-wide study was reported using massively parallel sequencing to directly compare in vivo and in vitro nucleosome positions. It was concluded that intrinsic DNA sequence preferences indeed have a dominant role in determining the in vivo nucleosome organization of the genome, consistent with a genomic code for nucleosome positioning. Some other studies disagree with this view. Using the large amount of data now available from several sources, we have attempted to clarify a fundamental question concerning the packaging of genomic DNA: to what extent are nucleosome positions in vivo determined by histone-DNA sequence preferences? We have analyzed data obtained from different laboratories in the same way, and have directly compared these data. We also identify possible problems with some of the experimental designs used and with the data analysis. Our findings suggest that DNA sequence preferences have only small effects on the positioning of individual nucleosomes throughout the genome in vivo.
  • Taichi E. Takasuka, Alfred Cioffi, Arnold Stein
    PLOS ONE 3 7 e2643  2008年07月 [査読有り][通常論文]
     
    Little is known about the possible function of the bulk of the human genome. We have recently shown that long-range regular oscillation in the motif non-T, A/T, G (VWG) existing at ten-nucleotide multiples influences large-scale nucleosome array formation. In this work, we have determined the locations of all 100 kb regions that are predicted to form distinctive chromatin structures throughout each human chromosome (except Y). Using these data, we found that a significantly greater fraction of 300 kb sequences lacked annotated transcripts in genomic DNA regions >= 300 kb that contained nearly continuous chromatin organizing signals than in control regions. We also found a relationship between the meiotic recombination frequency and the presence of strong VWG chromatin organizing signals. Large (>= 300 kb) genomic DNA regions having low average recombination frequency are enriched in chromatin organizing signals. As additional controls, we show using chromosome 1 that the VWG motif signals are not enriched in randomly selected DNA regions having the mean size of the recombination coldspots, and that non-VWG motif sets do not generate signals that are enriched in recombination coldspots. We also show that tandemly repeated alpha satellite DNA contains strong VWG signals for the formation of distinctive nucleosome arrays, consistent with the low recombination activity of centromeres. Our correlations cannot be explained simply by variations in the GC content. Our findings suggest that a specific set of periodic DNA motifs encoded in genomic DNA, which provide signals for chromatin organization, influence human chromosome function.

書籍

  • 北から南から
    高須賀太一 (担当:その他)
    日本生化学会生化学誌 2019年12月
  • 多糖類利用に向けたセルロース分解性昆虫共生細菌の発見およびそれらが産出する糖質分解酵素の機能・構造解析
    大橋慧介, 堀千明, 高須賀 太一 (担当:共著範囲:責任著者)
    日本生化学会生化学誌 2017年05月
  • 森林生態系におけるキバチ共生細菌による木質分解ノクチリオキバチの木材分解にかかわる酵素の探索
    高須賀 太一, 堀千明, James Ellinger, 飛松 裕基 (担当:共著範囲:責任著者)
    日本農芸化学会 化学と生物 2016年02月

講演・口頭発表等

  • Development of a high throughput aminotransferase assay platform using cell-free protein synthesis and nanostructure-initiator mass spectrometry (NIMS)
    Hataya Shogo, Takasuka Taichi
    日本分子生物学会年会 2021年12月 ポスター発表
  • 小麦胚芽無細胞タンパク質合成を用いた酵母ヘテロクロマチンの再構築
    嶋津 匠, 沖宗 慶一, 幡谷 省悟, 高須賀 太一
    日本分子生物学会年会 2021年12月
  • 植物バイオマス分解性放線菌における、 キシラン資化関連遺伝子の転写 調節因子の探索および機能解析
    大橋 慧介, 中田 朱音, 長野 竜也, 高須賀 太一
    日本分子生物学会年会 2021年12月
  • 定量プロテオミクスによるセルロース分解性放線菌(Streptomyces. sp. SirexAA-E)のキシラン応答性の解明
    長野 竜也, 大橋 慧介, 中田 朱音, 高須賀 太一
    日本分子生物学会年会 2021年12月
  • In vitro chromatin assembly platform for Arabidopsis thaliana  [通常講演]
    Petra Banko, Okimune Keiichi, Nagy Szilvia, Hamasaki Akinori, Morishita Ryo, Takasuka Taichi
    日本分子生物学会 2021年12月 ポスター発表
  • コムギ胚芽無細胞タンパク質合成法を利用したテトラソーム及びヌクレオ ソームの再構築  [通常講演]
    沖宗 慶一, 幡谷 省悟, 松本 一樹, 後潟 夏菜子, Banko Petra, 武田 晴治, 高須賀 太一
    日本分子生物学会年会 2021年12月 ポスター発表
  • セルロース分解性ストレプトマイセス属における、恒常的な酵素産生を目指したCRISPR/Casによるゲノム編集技術の確立
    中田 朱音, 大橋 慧介, 高須賀 太一
    日本農芸化学会2021年度大会 2021年03月 口頭発表(一般)
  • セルロース分解性昆虫共生ストレプトミセス属放線菌における、マンノース/マンノビオース応答性の解明
    大橋 慧介, 幡谷 省悟, 中田 朱音, 松本 一樹, 加藤 夏海, キャメロン カリー, ブライアン フォックス, 高須賀 太一
    日本農芸化学会2021年度大会 2021年03月 口頭発表(一般)
  • 無細胞タンパク質共翻訳によるショウジョウバエのヌクレオソーム再構築  [通常講演]
    沖宗慶一, 幡谷省悟, 松本一樹, 後潟夏菜子, 高須賀太一
    日本農芸化学会2021年度大会 2021年03月 口頭発表(一般)
  • コムギ胚芽無細胞タンパク質共翻訳によるハエとヒトのクロマチン再構築  [通常講演]
    沖宗 慶一, シルビア ナジ, 幡谷 省悟, 遠藤 弥重太, 高須賀 太一
    第43回日本分子生物学会年会 2020年12月 ポスター発表
  • Development of epigenetic enzyme screening method using in vitro reconsituted Drosophila chromatin
    沖宗慶一, 松本一樹, 高須賀太一
    第20回日本蛋白質化学会年会 2020年06月
  • Development of epigenetic enzyme screening using in vitro reconstituted human chromatin  [通常講演]
    沖宗 慶一, ナジ シルビア, 高須賀 太一
    第42回日本分子生物学会年会 2019年12月 ポスター発表
  • Molecular mechanisms of a novel xylan-responsive transcriptional regulator in the cellulolytic Streptomyces sp. SirexAA-E  [通常講演]
    中田 朱音, 大橋 慧介, 高須賀 太一
    第42回日本分子生物学会年会 2019年12月 ポスター発表
  • Development of epigenetic enzyme screening method using in vitro reconsituted Drosophila nucleosome.
    松本 一樹, ナジ シルビア, 高須賀 太一
    第42回日本分子生物学会年会 2019年12月 ポスター発表
  • Monosaccharide specific enzyme secretion in two insect symbiont Streptomyces  [通常講演]
    大橋慧介, 松本一樹, 高須賀太一
    日本農芸化学会2018年度大会 2018年03月
  • In vitro reconstitution of PCNA-p15 centered DNA replication and repair complexes
    松本一樹, 高須賀太一
    2017年度生命科学系学会合同年次大会 2017年12月
  • プロテオームおよび生化学的解析を通した昆虫共生ストレプトミセス放線菌の有する植物バイオマス分解能力の解明
    大橋慧介, 高須賀太一
    2017年度生命科学系学会合同年次大会 2017年12月
  • Phylogenetic-guided PDI functional annotation to establish in vitro oxidative protein folding
    Nagy Szilvia, 高須賀太一
    2017年度生命科学系学会合同年次大会 2017年12月
  • セルロース分解性ストレプトミセスにおける植物バイオマス分解酵素発現機構の解明  [通常講演]
    高須賀太一
    2017年度生命科学系学会合同年次大会 2017年12月
  • ワークショップ「研究者人生における様々な選択肢」
    高須賀太一, 他男女共同参画推進委員
    2017年度生命科学系学会合同年次大会 シンポジウム・ワークショップパネル(指名)
  • Omics and genome-enabled technology to understand phylogenetic-based enzyme functions  [招待講演]
    高須賀太一
    環境微生物系学会合同大会2017 2017年08月 口頭発表(招待・特別)
  • Phylogenetic-guided biochemical annotation for glycoside hydrolase families  [招待講演]
    高須賀太一
    第15回日本蛋白質化学会年会 2015年06月 口頭発表(招待・特別)

その他活動・業績

特許

  • 特願2022-071114:植物クロマチンの試験管内再構築法  2022年04月22日
    高須賀太一, 沖宗慶一, バンコペトラ
  • 特願WO2019/102516A1:務細胞タンパク質合成系を用いるヌクレオソームの構築法  2017年11月21日
    遠藤弥重太, 高須賀太一
  • 特願 20130189744:Method and Compositions for Improved Lignocellulosic Material Hydrolysis  
    Taichi E. Takasuka, Brian G. Fox, Adam J. Book, Cameron R. Currie
  • 特願US20140079683 A1:Multifunctional Cellulase And Hemicellulase  
    Taichi E. Takasuka, Brian G. Fox, Christopher M. Bianchetti

共同研究・競争的資金等の研究課題

  • Enzymatic conversion of kelp biomass for biofuels and health beneficial products.
    日本学術振興会:科学研究費助成事業 基盤研究(B)
    研究期間 : 2020年04月 -2024年03月 
    代表者 : FOX BRIAN, 高須賀 太一, 細川 雅史, 栗原 秀幸
  • ワンセルファクトリーによるセルロース系バイオマスのPHAsへの一貫生産技術の確立
    日本学術振興会:科学研究費助成事業 特別研究員奨励費
    研究期間 : 2020年11月 -2023年03月 
    代表者 : 高須賀 太一
  • 糸状菌由来の新規多糖分解酵素の探索と機能・構造解析
    日本学術振興会:科学研究費助成事業 基盤研究(C)
    研究期間 : 2020年04月 -2023年03月 
    代表者 : 志水 元亨, 高須賀 太一
  • 日本学術振興会:科学研究費助成事業 基盤研究(C)
    研究期間 : 2020年04月 -2023年03月 
    代表者 : 高須賀 太一
  • 植物栄養輸送体の細胞膜における偏在の分子基盤
    日本学術振興会:科学研究費助成事業 基盤研究(A)
    研究期間 : 2019年04月 -2023年03月 
    代表者 : 高野 順平, 高須賀 太一
  • 藻類バイオマスから化成品を生産する一貫バイオプロセスの構築
    日本学術振興会:科学研究費助成事業 基盤研究(B)
    研究期間 : 2018年04月 -2023年03月 
    代表者 : 渥美 正太, 高須賀 太一, 堀 千明
     
    効率的な糖化に向けた褐藻分解酵素(糖質分解酵素)の分泌と分解産物の化成品への転換を行える大腸菌の作出を行っており、これまで褐藻の主要成分であるラミナリン、アルギン酸、ならびにマニトール単糖に着目し、研究を行った。 遺伝子組換え対象微生物である大腸菌は、マニトールを単一炭素源として生育する事が確認できた。また、ラミナリン分解酵素として糖質分解酵素ファミリーGH55の褐藻中のラミナリン分解能力の解明とアルギン酸分解のための糖質リアーゼファミリーPL18の褐藻中のアルギン酸分解における機能解析を行っている。GH55については、褐藻中の長鎖ラミナリンをほぼ全て可溶性のオリゴ糖や単糖分解する事を確認した。アルギン酸長鎖については、マヌロン酸で構成されるM-blockとグルロン酸で構成されるG-block、及びそれら2種の糖が混合したM/G-blockから構成されるが、いずれの構成糖成分においても、PL18が加水分解する事を確認した。 これらの酵素を用いた後の、褐藻成分分解物の利用については代謝デザインを行っており、イソブタノール以外の有用化成品についても検討中である。
  • 植物バイオマス利用の実現に向けた昆虫共生細菌の分泌する酵素のプロテオーム解析
    稲盛財団:研究助成
    研究期間 : 2018年04月 -2019年03月 
    代表者 : 高須賀 太一
  • Ecological function of wood insect associated microbes(国際共同研究強化)
    日本学術振興会:科学研究費助成事業 国際共同研究加速基金(国際共同研究強化)
    研究期間 : 2016年 -2018年 
    代表者 : 高須賀 太一, フォックス ブライアン, 吉国 泰男
     
    将来枯渇する事が予想される化石資源の代替資源として, 陸海域のバイオマス資源を利用した持続可能なバイオ燃料やバイオ化成品生産技術の確立が求められている. 本研究では, 酵素学的知見から, 陸域のバイオマス作物や海域の褐藻の効率的な分解方法の開発を目指した. 具体的には植物細胞壁の主要成分であるセルロースやヘミセルロース等を効率的に糖化する多機能性セルラーゼ(GH5_4ファミリー)についての研究を行う事で, セルラーゼの多機能性について本ファミリーに属する243種の酵素の機能・系統樹解析を行った. 褐藻をターゲットとした研究では, 2種類の酵素を組み合わせた褐藻の効率的な分解を実現した.
  • Ecological function of wood insect associated microbes
    日本学術振興会:科学研究費助成事業 若手研究(B)
    研究期間 : 2015年04月 -2017年03月 
    代表者 : 高須賀 太一
     
    本研究では、 欧米で甚大な森林被害をもたらしている事が報告されている森林害虫キバチ(Sirex noctilio)の近縁種であり日本に生育するアカアシクビナガキバチを捕獲し、共生する菌類・バクテリアを含めた微生物相による多糖・リグニン分解機構の解明と、そのバイオマス変換技術への応用を目指した研究を行った。捕獲したアカアシクビナガキバチ共生微生物の単離および生化学的解析を行ったところ、子嚢菌門に属するDaldinia属の単離、および本菌による高い木質成分分解酵素の分泌が確認できた。培養上清プロテオミクス解析から本菌の分泌する木質成分分解酵素を網羅的に同定した。

教育活動情報

主要な担当授業

  • バイオテクノロジー学特論
    開講年度 : 2021年
    課程区分 : 修士課程
    開講学部 : 農学院
    キーワード : バイオテクノロジー、糖質酵素、mRNA分解、植物ウイルスベクター、糖質生合成、酵素改変、木質資源、食品機能、微生物資源、微生物バイオプロセス、技術・データ駆動型
  • バイオテクノロジー学特論演習
    開講年度 : 2021年
    課程区分 : 修士課程
    開講学部 : 農学院
    キーワード : バイオテクノロジー,生物利用・物質生産
  • 大学院共通授業科目(一般科目):自然科学・応用科学
    開講年度 : 2021年
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
    キーワード : バイオテクノロジー、糖質酵素、mRNA分解、植物ウイルスベクター、糖質生合成、酵素改変、木質資源、食品機能、微生物資源、微生物バイオプロセス、技術・データ駆動型
  • 食資源生産論
    開講年度 : 2021年
    課程区分 : 修士課程
    開講学部 : 国際食資源学院
    キーワード : 作物,畜産物,水産物,GAP, バイオテクノロジー,発酵生産,食の安全,HACCP, 機能性食品,健康,エネルギー
  • 食資源特別講義
    開講年度 : 2021年
    課程区分 : 修士課程
    開講学部 : 国際食資源学院
    キーワード : バイオテクノロジー, バイオエネルギー生産技術, 有用酵素, ゲノム編集, 代謝工学,動物生殖工学, クローン動物, 遺伝子組換え家畜
  • 大学院共通授業科目(一般科目):自然科学・応用科学
    開講年度 : 2021年
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
    キーワード : Agroecosystem, Biological diversity, Domestication, Livestock and human, Genetic diversity, Landscape, Useful enzyme,genetic engineering, GMO
  • 食資源特別講義
    開講年度 : 2021年
    課程区分 : 修士課程
    開講学部 : 国際食資源学院
    キーワード : Agroecosystem, Biological diversity, Domestication, Livestock and human, Genetic diversity, Landscape, Useful enzyme,genetic engineering, GMO
  • 分子細胞生物学
    開講年度 : 2021年
    課程区分 : 学士課程
    開講学部 : 農学部
    キーワード : 分子生物学,真核生物,遺伝子発現,クロマチン制御,mRNA・タンパク質分解,非コードRNA,シグナル伝達,細胞内輸送
  • 分子生物学
    開講年度 : 2021年
    課程区分 : 学士課程
    開講学部 : 農学部
    キーワード : 複製,転写,翻訳,遺伝子機能発現
  • 応用生命科学実験
    開講年度 : 2021年
    課程区分 : 学士課程
    開講学部 : 農学部
    キーワード : 遺伝子、核酸、酵素、蛋白質、大腸菌、植物、昆虫

大学運営

委員歴

  • 2015年04月 - 現在   日本生化学会   男女共同参画推進委員


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