Updated on 2024/02/02

写真a

 
SAITOH Yasunori
 
Organization
Research Institute for Interdisciplinary Science Assistant Professor
Position
Assistant Professor
Homepage
https://sites.google.com/view/sugalab/home
External link

Degree

  • 博士（創薬科学） ( 名古屋大学 )

Research Interests

  • ケイ酸チャネル

  • ケイ酸輸送体

  • Tight junction

  • water channel

  • claudin

  • Silicic acid

  • membrane protein

  • Structural analysis

  • frog

  • Rice

Research Areas

  • Life Science / Structural biochemistry  / Structural physiology

Education

  • Nagoya University   大学院 創薬科学研究科   基盤創薬学専攻 （博士課程前期課程および後期課程)

    2012.4 - 2017.3

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    Notes： 修士 (創薬科学), 博士 (創薬科学), 指導教員: 藤吉好則特任教授

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  • Shizuoka University   理学部   生物科学科

    2008.4 - 2012.3

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    Notes： 学士 (理学), 指導教員: 田中滋康教授, 鈴木雅一准教授, 岡田令子講師

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  • TAMANOKONAN high school     Academic course

    2005.4 - 2008.3

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Research History

  • Okayama University   The Research Institute for Interdisciplinary Science   Assistant professor (Tenure Track)

    2023.4

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    Country：Japan

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  • Japan Science and Technology Agency, ACT-X researcher

    2020.12 - 2023.3

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  • Okayama University   Research Institute for Interdisciplinary Science   Assistant Professor （Special Appointment）

    2017.4 - 2023.3

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  • Nagoya University   Graduate school of pharmaceutical sciences   Japan Society for the Promotion of Science Research fellowship for young scientist

    2016.4 - 2017.3

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  • Okayama University   Faculty of Pharmaceutical Sciences

    2015.4 - 2017.3

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    Notes：指導教員: 山下敦子教授

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Papers

  • Oxygen-evolving photosystem II structures during S1-S2-S3 transitions. International journal

    Hongjie Li, Yoshiki Nakajima, Eriko Nango, Shigeki Owada, Daichi Yamada, Kana Hashimoto, Fangjia Luo, Rie Tanaka, Fusamichi Akita, Koji Kato, Jungmin Kang, Yasunori Saitoh, Shunpei Kishi, Huaxin Yu, Naoki Matsubara, Hajime Fujii, Michihiro Sugahara, Mamoru Suzuki, Tetsuya Masuda, Tetsunari Kimura, Tran Nguyen Thao, Shinichiro Yonekura, Long-Jiang Yu, Takehiko Tosha, Kensuke Tono, Yasumasa Joti, Takaki Hatsui, Makina Yabashi, Minoru Kubo, So Iwata, Hiroshi Isobe, Kizashi Yamaguchi, Michihiro Suga, Jian-Ren Shen

    Nature   2024.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0-4) at the Mn4CaO5 cluster1-3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4-7. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca2+ ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O-O bond formation.

    DOI： 10.1038/s41586-023-06987-5

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  • Structure and Function of a Plant Silicic Acid Channel Invited Reviewed

    Yasunori SAITOH, Michihiro SUGA

    Nihon Kessho Gakkaishi   64 ( 4 )   265 - 266   2022.12

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    Authorship：Lead author   Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：The Crystallographic Society of Japan  

    DOI： 10.5940/jcrsj.64.265

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  • Structure and function of a silicic acid channel Lsi1 Invited Reviewed International journal

    Yasunori Saitoh, Michihiro Suga

    Frontiers in Plant Science   13 ( 982068 )   1 - 9   2022.9

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

    Silicon is a beneficial element for plant growth and production, especially in rice. Plant roots take up silicon in the form of silicic acid. Silicic acid channels, which belong to the NIP subfamily of aquaporins, are responsible for silicic acid uptake. Accumulated experimental results have deepened our understanding of the silicic acid channel for its uptake mechanism, physiological function, localization, and other aspects. However, how the silicic acid channel efficiently and selectively permeates silicic acid remains to be elucidated. Recently reported crystal structures of the silicic acid channel enabled us to discuss the mechanism of silicic acid uptake by plant roots at an atomic level. In this mini-review, we focus on the crystal structures of the silicic acid channel and provide a detailed description of the structural determinants of silicic acid permeation and its transport mechanism, which are crucial for the rational creation of secure and sustainable crops.

    DOI： 10.3389/fpls.2022.982068

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  • Structural basis for high selectivity of a rice silicon channel Lsi1 Reviewed International journal

    Yasunori Saitoh, Namiki Mitani-Ueno, Keisuke Saito, Kengo Matsuki, Sheng Huang, Lingli Yang, Naoki Yamaji, Hiroshi Ishikita, Jian-Ren Shen, Jian Feng Ma, Michihiro Suga

    Nature Communications   12 ( 1 )   6236 - 6236   2021.10

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    <title>Abstract</title>Silicon (Si), the most abundant mineral element in the earth’s crust, is taken up by plant roots in the form of silicic acid through Low silicon rice 1 (Lsi1). Lsi1 belongs to the Nodulin 26-like intrinsic protein subfamily in aquaporin and shows high selectivity for silicic acid. To uncover the structural basis for this high selectivity, here we show the crystal structure of the rice Lsi1 at a resolution of 1.8 Å. The structure reveals transmembrane helical orientations different from other aquaporins, characterized by a unique, widely opened, and hydrophilic selectivity filter (SF) composed of five residues. Our structural, functional, and theoretical investigations provide a solid structural basis for the Si uptake mechanism in plants, which will contribute to secure and sustainable rice production by manipulating Lsi1 selectivity for different metalloids.

    DOI： 10.1038/s41467-021-26535-x

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    Other Link： https://www.nature.com/articles/s41467-021-26535-x

  • Morphologic determinant of tight junctions revealed by claudin-3 structures. Reviewed International journal

    Shun Nakamura, Katsumasa Irie, Hiroo Tanaka, Kouki Nishikawa, Hiroshi Suzuki, Yasunori Saitoh, Atsushi Tamura, Sachiko Tsukita, Yoshinori Fujiyoshi

    Nature communications   10 ( 1 )   816 - 816   2019.2

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    Language：English   Publishing type：Research paper (scientific journal)  

    Tight junction is a cell adhesion apparatus functioning as barrier and/or channel in the paracellular spaces of epithelia. Claudin is the major component of tight junction and polymerizes to form tight junction strands with various morphologies that may correlate with their functions. Here we present the crystal structure of mammalian claudin-3 at 3.6 Å resolution. The third transmembrane helix of claudin-3 is clearly bent compared with that of other subtypes. Structural analysis of additional two mutants with a single mutation representing other subtypes in the third helix indicates that this helix takes a bent or straight structure depending on the residue. The presence or absence of the helix bending changes the positions of residues related to claudin-claudin interactions and affects the morphology and adhesiveness of the tight junction strands. These results evoke a model for tight junction strand formation with different morphologies - straight or curvy strands - observed in native epithelia.

    DOI： 10.1038/s41467-019-08760-7

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  • ウェルシュ菌エンテロトキシンとクローディン-19との複合体の構造学的研究 Reviewed

    齊藤恭紀

    名古屋大学 大学院 創薬科学研究科 博士論文   2017.3

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    Authorship：Lead author,　Last author,　Corresponding author   Language：Japanese   Publishing type：Doctoral thesis  

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  • Structural insight into tight junction disassembly by Clostridium perfringens enterotoxin Reviewed

    Yasunori Saitoh, Hiroshi Suzuki, Kazutoshi Tani, Kouki Nishikawa, Katsumasa Irie, Yuki Ogura, Atsushi Tamura, Sachiko Tsukita, Yoshinori Fujiyoshi

    SCIENCE   347 ( 6223 )   775 - 778   2015.2

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER ASSOC ADVANCEMENT SCIENCE  

    The C-terminal region of Clostridium perfringens enterotoxin (C-CPE) can bind to specific claudins, resulting in the disintegration of tight junctions (TJs) and an increase in the paracellular permeability across epithelial cell sheets. Here we present the structure of mammalian claudin-19 in complex with C-CPE at 3.7 angstrom resolution. The structure shows that C-CPE forms extensive hydrophobic and hydrophilic interactions with the two extracellular segments of claudin-19. The claudin-19/C-CPE complex shows no density of a short extracellular helix that is critical for claudins to assemble into TJ strands. The helix displacement may thus underlie C-CPE-mediated disassembly of TJs.

    DOI： 10.1126/science.1261833

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  • Novel Vasotocin-Regulated Aquaporins Expressed in the Ventral Skin of Semiaquatic Anuran Amphibians: Evolution of Cutaneous Water-Absorbing Mechanisms Reviewed

    Yasunori Saitoh, Yuji Ogushi, Yuki Shibata, Reiko Okada, Shigeyasu Tanaka, Masakazu Suzuki

    ENDOCRINOLOGY   155 ( 6 )   2166 - 2177   2014.6

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：ENDOCRINE SOC  

    Until now, it was believed that only one form of arginine vasotocin (AVT)-regulated aquaporin (AQP) existed to control water absorption from the ventral skin of semiaquatic anuran amphibians, eg, AQP-rj3(a) in Rana japonica. In the present study, we have identified a novel form of ventral skin-type AQP, AQP-rj3b, in R. japonica by cDNA cloning. The oocyte swelling assay confirmed that AQP-rj3b can facilitate water permeability. Both AQP-rj3a and AQP-rj3b were expressed abundantly in the ventral hindlimb skin and weakly in the ventral pelvic skin. For the hindlimb skin, water permeability was increased in response to AVT, although the hydroosmotic response was not statistically significant in the pelvic skin. Isoproterenol augmented water permeability of the hindlimb skin, and the response was inhibited by propranolol. These events were well correlated with the intracellular trafficking of the AQPs. Immunohistochemistry showed that both AQP-rj3 proteins were translocated from the cytoplasmic pool to the apical membrane of principal cells in the first-reacting cell layer of the hindlimb skin after stimulation with AVT and/or isoproterenol. The type-b AQP was also found in R. (Lithobates) catesbeiana and R. (Pelophylax) nigromaculata. Molecular phylogenetic analysis indicated that the type-a is closely related to ventral skin-type AQPs from aquatic Xenopus, whereas the type-b is closer to the AQPs from terrestrial Bufo and Hyla, suggesting that the AQPs from terrestrial species are not the orthologue of the AQPs from aquatic species. Based on these results, we propose a model for the evolution of cutaneous water-absorbing mechanisms in association with AQPs.

    DOI： 10.1210/en.2013-1928

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Books

  • Crystal structure elucidation of a complex between Clostridium perfringens food poisoning toxin and its receptor.

    Yasunori Saitoh（ Role： Sole author）

    2015.9 

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MISC

  • 穀物由来ケイ酸チャネルによるケイ酸輸送機構の構造学的研究

    齊藤恭紀, 三谷(上野)奈見季, 斉藤圭亮, 斉藤圭亮, 松木謙悟, 黄勝, 楊霊麗, 山地直樹, 石北央, 石北央, 沈建仁, 沈建仁, 馬建鋒, 菅倫寛, 菅倫寛, 菅倫寛

    膜シンポジウム(CD-ROM)   ( 33 )   2021

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  • Structural basis for silicic acid permeation mechanism by rice silicic acid channel

    齊藤恭紀, 三谷(上野)奈見季, 斉藤圭亮, 斉藤圭亮, 松木謙悟, HUANG Sheng, YANG Lingli, 山地直樹, 石北央, 石北央, SHEN Jian-Ren, SHEN Jian-Ren, MA Jian Feng, 菅倫寛, 菅倫寛, 菅倫寛

    日本分子生物学会年会プログラム・要旨集(Web)   44th   2021

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Presentations

  • Silicic acid permeation mechanism of rice silicic acid channel Invited

    Yasunori Saitoh

    468th Biological Science Seminar, Graduate School of Environmental Life, Natural Science and Technology, Okayama University  2023.12.13 

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    Event date： 2023.12.13

    Language：Japanese   Presentation type：Public lecture, seminar, tutorial, course, or other speech  

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  • Hi rice-san, I want to know how do you eat silicon with a resolution of less than 200 pm. Invited

    Yasunori Saitoh

    2022.12.19 

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    Event date： 2022.12.19 - 2022.12.20

    Language：Japanese   Presentation type：Public lecture, seminar, tutorial, course, or other speech  

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  • Structural study for silicic acid permeation mechanism of rice silicic acid channel

    〇Yasunori Saitoh, Namiki Mitani-Ueno, Keisuke Saito, Kengo Matsuki, Sheng Huang, Lingli Yang, Naoki Yamaji, Hiroshi Ishikita, Jiang-Ren Shen, Jiang Feng Ma, Michihiro Suga

    2022.11.11 

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    Event date： 2022.11.11

    Language：Japanese   Presentation type：Poster presentation  

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  • Structural basis for silicic acid permeation mechanism by rice silicic acid channel

    〇Yasunori Saitoh, Namiki Mitani-Ueno, Keisuke Saito, Kengo Matsuki, Sheng Huang, Lingli Yang, Naoki Yamaji, Hiroshi Ishikita, Jiang-Ren Shen, Jiang Feng Ma, Michihiro Suga

    The 22nd Annual Meeting of the Protein Science Society of Japan. Young Scientist Award Symposium.  2022.6.8 

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    Event date： 2022.6.7 - 2022.6.9

    Language：English   Presentation type：Oral presentation (invited, special)  

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  • Structural basis for silicic acid permeation mechanism by rice silicic acid channel

    Yasunori Saitoh, Namiki Mitani-Ueno, Keisuke Saito, Kengo Matsuki, Sheng Huang, Lingli Yang, Naoki Yamaji, Hiroshi Ishikita, Jian-Ren Shen, Jian Feng Ma, Michihiro Suga

    The 44th Annual Meeting of the Molecular Biology Society of Japan  2021.12.2 

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    Event date： 2021.12.1 - 2021.12.3

    Presentation type：Poster presentation  

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  • Structural basis for high selectivity of a rice silicic acid channel

    〇Yasunori Saitoh, Namiki Mitani-Ueno, Keisuke Saito, Kengo Matsuki, Sheng Huang, Lingli Yang, Naoki Yamaji, Hiroshi Ishikita, Jian-Ren Shen, Jian Feng Ma, Michihiro Suga

    PDB50th Anniversary Symposium in Asia  2021.11.24 

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    Event date： 2021.11.24

    Language：English   Presentation type：Poster presentation  

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  • Structural study on the silicic acid uptake mechanism by grain-derived silicic acid channel

    〇Yasunori Saitoh, Namiki Mitani-Ueno, Keisuke Saito, Kengo Matsuki, Sheng Huang, Lingli Yang, Naoki Yamaji, Hiroshi Ishikita, Jian-Ren Shen, Jian Feng Ma, Michihiro Suga

    The Membrane Society of Japan, Membrane SYMPOSIUM No. 33 (2021)  2021.11.17 

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    Event date： 2021.11.16 - 2021.11.17

    Language：Japanese   Presentation type：Oral presentation (general)  

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  • Structure of a silicon transporter in plant Invited

    Yasunori Saitoh, Kengo Matsuki, Shin-Ichiro Yonekura, Lingli Yang, Namiki Mitani, Naoki Yamaji, Jian-Ren Shen, Jian Feng Ma, Michi Suga

    The 60 th Annual meeting of the Japanese Society of Plant Physiogists, (Nagoya, Japan)  2019.3 

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    Event date： 2019.3.13 - 2019.3.15

    Presentation type：Oral presentation (invited, special)  

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  • ウェルシュ菌エンテロトキシンによる密着結合の解体についての構造学的洞察

    齊藤恭紀, 鈴木博視, 谷一寿, 西川幸希, 入江克雅, 小倉祐輝, 田村淳, 月田早智子, 藤吉好則

    生化学若い研究者の会 中四国支部 冬セミナー  2017.1 

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    Language：Japanese   Presentation type：Poster presentation  

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  • 味覚受容体の発現・精製および高速原子間力顕微鏡観察

    齊藤恭紀, 能代大輔, 芦川雄二, 安藤敏夫, 山下敦子

    第14回 次世代を担う若手のためのフィジカル・ファーマフォーラム (PPF2016)  2016.8 

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    Language：Japanese   Presentation type：Oral presentation (general)  

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  • 味覚受容体T1Rの発現・精製条件の検討

    齊藤恭紀, 山下敦子

    創薬標的膜タンパク質の移ろいを"み (見・診・覧) る" 研究会 リトリート2015)  2015.10 

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    Language：Japanese   Presentation type：Poster presentation  

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  • 食中毒の原因毒素が細胞間隙バリアを崩壊させる仕組み

    齊藤 恭紀

    岡山大学薬学部セミナー  2015.4 

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    Language：Japanese   Presentation type：Public lecture, seminar, tutorial, course, or other speech  

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  • 半水棲ガエルRana Japonicaの下腹部皮膚における2種類ｍのアクアポリンの発現

    齊藤恭紀, 尾串雄次, 岡田令子, 鈴木雅一, 田中滋康

    日本動物学会第82回大会  2011.9 

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    Language：Japanese   Presentation type：Poster presentation  

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  • HPLCによる光合成色素分析の高速システム化とその応用

    齊藤恭紀, 塩井祐三

    文部科学省理数学生応援プロジェクト 研究報告会 リサーチフェスタ  2010.10 

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    Language：Japanese   Presentation type：Poster presentation  

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  • HPLCによる光合成色素分析の高速システム化とその応用

    齊藤恭紀, 塩井祐三

    日本植物学会第74回大会  2010.9 

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    Language：Japanese   Presentation type：Poster presentation  

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Awards

  • Protein Science Society of Japan, Young Scientist Award

    2022.6   Protein Science Society of Japan   Structural basis for silicic acid permeation mechanism by rice silicic acid channel

    Yasunori Saitoh

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  • 第14回 次世代を担う若手のためのフィジカル・ファーマフォーラム(PPF2016) 質問賞

    2016.8   日本薬学会 物理系薬学部会  

    齊藤 恭紀

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  • NAGOYA UNIVERSITY OUTSTANDING GRADUATE STUDENT AWARD

    2015.6   Nagoya University  

    Yasunori Saitoh

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  • Exemption from Repayment of Scholarship Loans for Graduate Students with Particularly Outstanding Academic Achievements

    2014.9   Japan Student Services Organization  

    Yasunori Saitoh

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  • 平成23年度卒業研究発表会 学科長賞

    2012.2   静岡大学 理学部 生物科学科  

    齊藤 恭紀

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  • 理数学生応援プロジェクト「早期研究室配属プログラム」体験報告会優秀発表賞

    2009.12   静岡大学 理学部  

    齊藤 恭紀

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Research Projects

  • 穀物由来ケイ酸排出輸送体のケイ酸輸送機構の解明

    Grant number：23K05656  2023.04 - 2026.03

    日本学術振興会  科学研究費助成事業 基盤研究(C)  基盤研究(C)

    齊藤 恭紀

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    Grant amount：\4810000 （ Direct expense: \3700000 、 Indirect expense：\1110000 ）

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  • 水酸化半金属を結合した穀物由来ケイ酸チャネルの構造解析

    Grant number：21K15029  2021.04 - 2023.03

    日本学術振興会  科学研究費助成事業 若手研究  若手研究

    齊藤 恭紀

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    Grant amount：\4550000 （ Direct expense: \3500000 、 Indirect expense：\1050000 ）

    土壌中に豊富に含まれるケイ素は植物の有益元素として知られており、特にケイ素を良く吸収するイネ科の植物においてその有益性は顕著である。イネ等の穀物はケイ素を土壌中から取り込み、生物的・非生物的ストレスに対して耐性を獲得しているので、ケイ素を取り込む仕組みの理解は穀物の頑健性や生産性の向上に大きく寄与すると期待されている。穀物におけるケイ素の取り込みは、根の外皮細胞の細胞膜上に発現しているケイ酸チャネルが土壌中のケイ酸を取り込むことから始まる。これまでに、研究代表者はイネのケイ酸チャネルの構造を1.8 Å分解能で解明し、詳細なケイ酸透過機構の一端を明らかにしてきた。しかしながら、得られたケイ酸チャネルの結晶構造はチャネル内に水分子のみが占めている状態であり、ケイ酸チャネルとケイ酸がどのような相互作用をしているのかは予測の範囲を出ていない。本研究ではケイ酸を含めた水酸化半金属と相互作用しているケイ酸チャネルの構造を捉え、ケイ酸チャネルの基質認識機構をより詳細に理解できるようにすることを目的とした。
    本年度では、ケイ酸チャネルの結晶を、ケイ酸等を含んだ溶液にソーキングし、X線回折データセットを収集し、これらのデータを解析した。ケイ酸チャネルの結晶の質を向上させるため、結晶パッキングに関わるアミノ酸残基に変異を導入し、精製・結晶化を行った。また、ケイ酸チャネルをクライオ電子顕微鏡で観察し、良い単粒子像が得られることも確認した。本年度はコロナ禍で、活動制限や試薬・物品類の購入難等、様々な面において実験に制限がかかり、当初の研究目的および研究実施計画はやや遅れる結果となった。

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  • Structural analysis of a crop silicic acid transporter.

    2020.12 - 2023.03

    Japan Science and Technology Agency  JST Strategic Basic Research Programs_ACT-X  ACT-X

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    Authorship：Principal investigator 

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  • 穀物由来ケイ酸チャネルの基質選択機構の解明

    2019.04 - 2021.03

    日本学術振興会  若手研究 

    齊藤 恭紀

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    Authorship：Principal investigator  Grant type：Competitive

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  • 穀物アクアポリンのケイ酸取り込み機構の解明

    2017.04 - 2019.03

    Japan Society for the Promotion of Science  Grant-in-Aid for Research Activity Start-up 

    Yasunori Saitoh

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    Authorship：Principal investigator  Grant type：Competitive

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  • 味覚受容体のシグナル変換機構の解明

    2016.04 - 2017.03

    Japan Society for the Promotion of Science  Research Fellowship for Young Scientists 

    Yasunori Saitoh

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    Authorship：Principal investigator  Grant type：Competitive

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Other research activities

  • イネのタンパク質の分子構造解明 岡山大・菅准教授ら、新品種期待

    2021.12

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    山陽新聞デジタル, 山陽新聞2021年12月12日(日), 全県版第２全県

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  • Nature Comm | 马建锋/Michihiro Suga合作揭示水稻硅转运蛋白Lsi1高选择性结构基础

    2021.11

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    BioArt植物

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  • 岡山大と東大、イネの安定多収に欠かせないケイ酸チャネルの構造基盤を解明

    2021.10

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    日本経済新聞 オンライン

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  • Researchers gain better understanding of cellular intestinal barrier structure

    2015.02

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  • 細胞つなぐ仕組みを破壊 名大・阪大解明

    2015.02

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    朝日新聞（２月１３日)

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  • ウェルシュ菌毒素と受容体結合の構造解明 名大阪大 食中毒予防などに応用

    2015.02

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    化学工業日報(２月２６日)

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  • 細胞のバリアー緩む仕組み解明 名大グループ 脳への投薬応用に期待

    2015

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    中日新聞（２月１３日)

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Class subject in charge

  • Experimental Course (Molecular Biology) （2023academic year） Fourth semester  - 木5～8

  • Laboratory Course A （2023academic year） 1st and 2nd semester  - 月5～8,木5～8