Updated on 2025/06/10

写真a

 
KATOU Kouji
 
Organization
Scheduled update Special-Appointment Associate Professor
Position
Special-Appointment Associate Professor
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Degree

  • 博士(理学) ( 大阪大学 )

Research Interests

  • X線結晶構造解析

  • 核酸-タンパク質複合体

  • 生体超分子複合体

  • タンパク質-核酸複合体

Research Areas

  • Life Science / Structural biochemistry

Education

  • Osaka University   大学院・理学研究科   高分子科学専攻

    2003.4 - 2006.3

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Research History

  • Okayama University   The Research Institute for Interdisciplinary Science

    2023.4

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  • Japan Synchrotron Radiation Research Institute   Structural Biology Division

    2022.4 - 2023.3

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  • Okayama University   The Research Institute for Interdisciplinary Science

    2018.4 - 2022.3

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  • Hokkaido University   Faculty of Advanced Life Science   Assistant Professor

    2013.4 - 2018.3

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  • University of Hyogo   Graduate School

    2012.7 - 2013.3

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Committee Memberships

  • 日本結晶学会   編集幹事  

    2024.4   

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  • 日本結晶学会   編集委員  

    2022.4 - 2024.3   

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Papers

  • Structure of a photosystem I supercomplex from Galdieria sulphuraria close to an ancestral red alga Reviewed

    Koji Kato, Minoru Kumazawa, Yoshiki Nakajima, Takehiro Suzuki, Naoshi Dohmae, Jian-Ren Shen, Kentaro Ifuku, Ryo Nagao

    Science Advances   11 ( 20 )   2025.5

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    Authorship:Lead author   Publishing type:Research paper (scientific journal)   Publisher:American Association for the Advancement of Science (AAAS)  

    Red algae exhibit unique photosynthetic adaptations, characterized by photosystem I (PSI) supercomplexes containing light-harvesting complexes (LHCs), forming PSI-LHCI supercomplexes. In this study, we solved the PSI-LHCI structure of Galdieria sulphuraria NIES-3638 at 2.19-angstrom resolution using cryo–electron microscopy, revealing a PSI monomer core associated with seven LHCI subunits. Structural analysis uncovered the absence of phylloquinones, the common secondary electron acceptor in PSI of photosynthetic organisms, suggesting adaptation to a benzoquinone-like molecule. Phylogenetic analysis suggests that G. sulphuraria retains traits characteristic of an ancestral red alga, including distinctive LHCI binding and interaction patterns. Variations in LHCI composition and interactions across red algae, particularly in red-lineage chlorophyll a / b –binding–like protein and red algal LHCs, highlight evolutionary divergence and specialization. These findings not only deepen our understanding of red algal PSI-LHCI diversification but also enable us to predict features of an ancestral red algal PSI-LHCI supercomplex, providing a framework to explore evolutionary adaptations from an ancestral red alga.

    DOI: 10.1126/sciadv.adv7488

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  • Structure of a photosystem II-FCPII supercomplex from a haptophyte reveals a distinct antenna organization Reviewed

    Romain La Rocca, Koji Kato, Pi-Cheng Tsai, Yoshiki Nakajima, Fusamichi Akita, Jian-Ren Shen

    Nature Communications   16 ( 1 )   2025.5

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    Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    DOI: 10.1038/s41467-025-59512-9

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    Other Link: https://www.nature.com/articles/s41467-025-59512-9

  • Biochemical and structural analysis of the mechanism for the catalysis and specificity of cellobiose 2-epimerase from Rhodothermus marinus. Reviewed International journal

    Wataru Saburi, Hirohiko Muto-Fukiya, Nongluck Jaito, Koji Kato, Jian Yu, Min Yao, Haruhide Mori

    Bioscience, biotechnology, and biochemistry   2025.3

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

    Cellobiose 2-epimerase (CE) catalyzes C-2 epimerization of reducing end d-glucose/d-mannose residue of β-(1→4)-disaccharides, and also slightly catalyzes aldose-ketose conversion. In this study, we investigated the structure-function relationship of Rhodothermus marinus CE (RmCEs). In 2H2O, 2H replaced the 2-H of the reducing end sugar residue, suggesting a proton abstraction-addition mechanism via the cis-enediolate intermediate. The structure of the RmCE-mannobiitol complex showed that His259 was suitable for abstracting 2-H from d-mannose residue, whereas His390 was suitable for the d-glucose residue. H259A and H390A mutations abolished activity for Galβ1-4Man and Galβ1-4Glc formation from Galβ1-4Fru, respectively, and these mutants catalyzed both epimerization and isomerization to Galβ1-4Glc and Galβ1-4Man, respectively. Ala substitution of the residues interacting with the 2-O of the reducing end sugar residue significantly reduced the velocity for epimerization, but not for isomerization. Trp385, stacked onto the non-reducing-end sugar residues of disaccharides, was shown to be important for disaccharide specificity.

    DOI: 10.1093/bbb/zbaf042

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  • Structural study of the chlorophyll between Lhca8 and PsaJ in an Antarctica green algal photosystem I-LHCI supercomplex revealed by its atomic structure Reviewed

    Pi-Cheng Tsai, Koji Kato, Jian-Ren Shen, Fusamichi Akita

    Biochimica et Biophysica Acta (BBA) - Bioenergetics   149543 - 149543   2025.2

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    Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.bbabio.2025.149543

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  • Biochemical evidence for the diversity of LHCI proteins in PSI-LHCI from the red alga Galdieria sulphuraria NIES-3638. Reviewed International journal

    Ryo Nagao, Haruya Ogawa, Takehiro Suzuki, Naoshi Dohmae, Koji Kato, Yoshiki Nakajima, Jian-Ren Shen

    Photosynthesis research   163 ( 1 )   14 - 14   2025.1

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

    Red algae are photosynthetic eukaryotes whose light-harvesting complexes (LHCs) associate with photosystem I (PSI). In this study, we examined characteristics of PSI-LHCI, PSI, and LHCI isolated from the red alga Galdieria sulphuraria NIES-3638. The PSI-LHCI supercomplexes were purified using anion-exchange chromatography followed by hydrophobic-interaction chromatography, and finally by trehalose density gradient centrifugation. PSI and LHCI were similarly prepared following the dissociation of PSI-LHCI with Anzergent 3-16. Polypeptide analysis of PSI-LHCI revealed the presence of PSI and LHC proteins, along with red-lineage chlorophyll a/b-binding-like protein (RedCAP), which is distinct from LHC proteins within the LHC protein superfamily. RedCAP, rather than LHC proteins, exhibited tight binding to PSI. Carotenoid analysis of LHCI identified zeaxanthin, β-cryptoxanthin, and β-carotene, with zeaxanthin particularly enriched, which is consistent with other red algal LHCIs. A Qy peak of chlorophyll a in the LHCI absorption spectrum was blue-shifted compared with those of PSI-LHCI and PSI, and a fluorescence emission peak was similarly shifted to shorter wavelengths. Based on these results, we discuss the diversity of LHC proteins and RedCAP in red algal PSI-LHCI supercomplexes.

    DOI: 10.1007/s11120-024-01134-1

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MISC

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Presentations

  • High-resolution cryo-EM structure of photosystem II from Thermosynechococcus vulcanus

    Koji Kato, Yoshiki Nakajima, Fusamichi Akita, Radostin Danev, Jian-Ren Shen

    2025.3.15 

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    Event date: 2025.3.14 - 2025.3.16

    Language:Japanese   Presentation type:Poster presentation  

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  • Cryo-EM Structure of PSI-LHCI from a Red alga Cyanidium caldarium

    Koji Kato, Tasuku Hamaguchi, Minoru Kumazawa, Yoshiki Nakajima, Kentaro Ifuku, Yuu Hirose, Keisuke Kawakami, Koji Yonekura, Ryo Nagao, Jian-Ren Shen

    13th Asia Pacific Microscopy Congress  2025.2.3 

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    Event date: 2025.2.2 - 2025.2.7

    Language:English   Presentation type:Poster presentation  

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  • クライオ電子顕微鏡によるタンパク質構造解析の原理と解析例 Invited

    加藤公児

    Brainstorming 2024  2024.9.28 

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    Event date: 2024.9.28 - 2024.9.29

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

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  • Cryo-EM structure of PSI-LHCI from a red alga Cyanidium caldarium

    Koji Kato, Tasuku Hamaguchi, Minoru Kumazawa, Yoshiki Nakajima, Kentaro Ifuku, Yuu Hirose, Keisuke Kawakami, Koji Yonekura, Ryo Nagao, Jian-Ren Shen

    2nd Asia-Oceania International Congress on Photosynthesis (AOICP)  2024.9.19 

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    Event date: 2024.9.18 - 2024.9.21

    Language:English   Presentation type:Poster presentation  

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  • Structural analysis of supercomplex Invited

    Koji Kato

    The 32th Annual Meeting of Japan Society of Exercise and Sports Physiology  2024.8.22 

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    Event date: 2024.8.22 - 2024.8.23

    Language:Japanese   Presentation type:Symposium, workshop panel (public)  

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Awards

  • 第27回井上研究奨励賞

    2011.2   井上科学振興財団   3.5Å分解能でのラット肝臓由来vaultの構造解析

    加藤公児

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Research Projects

  • Structural biology of phycobilisome-tetrameric photosystem I supercomplex

    Grant number:20H02914  2020.04 - 2023.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    加藤 公児, 長尾 遼

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    Grant amount:\17940000 ( Direct expense: \13800000 、 Indirect expense:\4140000 )

    光化学系I(PSI)は、シアノバクテリアでは三量体そして植物では単量体であることが広く知られている。近年、研究代表者らはシアノバクテリアであるアナベナから新しいタイプの四量体PSIを精製し、クライオ電子顕微鏡を用いて3.3Å分解能で構造を決定し、これまでにない色素間の相互作用とエネルギー伝達経路を明らかにした。本研究は、この四量体を形成するPSIと光エネルギーを集めるアンテナタンパク質の超複合体を単離し、その構造と機能を解明することを目的とする。
    2021年度は高分解能の解析が困難であることが予想されるアンテナタンパク質サブコンプレックス、フィコシアニンを、陰イオン交換カラム等を用いて精製を行った。その精製標品と市販の結晶化スクリーニングキットを用いて約500条件で結晶化し、いくつかの条件で結晶が得られた。それらの結晶を用いて、SPring-8のビームラインBL41XU及び、BL44XUにて、X線回折実験を行い、1.5Å分解能の回折強度データを収集した。さらに、分子置換法により初期位相を決定することに成功した。
    超複合体の構造解析においては、最終精製ステップに用いたトレハロース密度勾配遠心分離法で得られた複数の画分(複合体)それぞれを、負染色による透過電顕観察を行うことにより粒子の均一性を確認した。その中で最も安定で均一性が高い複合体について、クライオ電顕グリッドの調整条件を検討し、比較的良好な条件で5000枚程度のクライオ電顕画像を撮影し、単粒子解析を行ったところ、分解能が9Å程度のクライオEMマップが得られた。しかしながら分解能が足りないためモデルの構築には至っていない。撮影された電顕画像を確認したところアンテナタンパク質と思われる分子の解離が見られたため、超複合体が不安定で様々な会合状態の超複合体が混在していることが原因で分解能が良いマップが得られなかったと考えられる。

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  • 褐藻由来光化学系アンテナ超複合体の単粒子構造解析

    Grant number:20H03194  2020.04 - 2023.03

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

    秋田 総理, 宮崎 直幸, 加藤 公児

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    Grant amount:\18200000 ( Direct expense: \14000000 、 Indirect expense:\4200000 )

    本研究では、赤色系統の光合成生物である褐藻から光化学系I-フコキサンチンクロロフィルa/cタンパク質超複合体(PSI-FCPI)と光化学系II-フコキサンチンクロロフィルa/cタンパク質超複合体(PSII-FCPII)を単離し、その原子構造をクライオ電子顕微鏡単粒子解析法によって決定する。その構造を基に、複合体中の色素の配置や結合様式、タンパク質サブユニット間の相互作用、エネルギー伝達様式を解明する。さらに、緑色系統の光合成生物が持つPSI-光捕集タンパク質超複合体(PSI-LHCI)やPSII-光捕集タンパク質超複合体(PSII-LHCII)と比較する事で、異なる波長の光を吸収するために、赤色系統の光合成生物がどの様に光合成分子装置を進化させてきたかを明らかにする。今年度はコロナウイルスによって出発材料の褐藻の入手が困難であったため、PSI-FCPIに絞って、精製を行なう事にした。
    褐藻Cladosiphon okamuranusをビーズショッカーで念入りに破砕し、遠心分離でチラコイド膜を分離後、回収したチラコイド膜から界面活性剤を用いてPSI-FCPI可溶化した。チラコイド膜の濃度・界面活性剤の種類・界面活性剤の濃度・温度・可溶化の時間などを検討し、SDS-PAGEで確認した。最適な可溶化条件を用いて、ショ糖密度勾配遠心分離法・陰イオン交換クロマトグラフィーでPSI-FCPIを更に精製し、SDS-PAGE、Native-PAGE、吸光スペクトル解析、ネガティブ染色試料の透過型電子顕微鏡観察等により評価した。

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  • Structural analysis of intermediate of Photosystem II using Cryo-EM

    Grant number:19K22396  2019.06 - 2021.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Research (Exploratory)

    Akita Fusamichi

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    Grant amount:\6500000 ( Direct expense: \5000000 、 Indirect expense:\1500000 )

    In this project, PSII was purified from cyanobacteria and about 2,000 images were collected using CryoARM300 cryo-electron microscope. We analyzed the structure of PSII in solution by cryo-EM at a resolution of 1.95 angstrom.The resolution is almost same as the structure at a 1.9 angstrom by X-ray crystallography. In this map, the PsbY subunits at both sides of PSII appeared in complete form. Therefore, the cryo-EM map was considered to be closer to the in vivo state. However, PSII was damaged at the electron dose used for the measurement. Therefore, we recalculated the map by changing the number of image frames and reducing the electron dose, and succeeded in obtaining a map with less damage while maintaining the high resolution.

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  • Elucidation of a tRNA conversion mechanism of transsulfursome by the structural analysis of quaternary complex

    Grant number:17H03637  2017.04 - 2020.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    Yao Min

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    Grant amount:\17420000 ( Direct expense: \13400000 、 Indirect expense:\4020000 )

    To translate the protein according to the genetic code on the ribosome, the aminoacyl-tRNA (aa-tRNA) must be synthesized correctly. Generally, the aminoacyl-tRNA synthetase (aaRS) directly catalyzes this synthesis. However, in methanogenic archaea, a ternary complex called transsulfursome (SepRS, SepCys, SepCysS) synthesizes Cys-tRNA(Cys) in an indirect pathway.
    In this study, we analyzed the relationship of structure and function of transsulfursome-tRNA complex by using X-ray crystallography, small-angle X-ray scattering, electron microscopic observation, and biochemical methods. Taken results together, we understood the dynamic molecular mechanism for the Cys-tRNA(Cys) synthesis of the transsulfursome.

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  • Molecular mechanism elucidation of multifunctional tRNA ligase in tRNA splicing

    Grant number:16K18498  2016.04 - 2018.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)  Grant-in-Aid for Young Scientists (B)

    Kato Koji, SAKURAI Naofumi, SUZUKI Wakana

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    Grant amount:\4290000 ( Direct expense: \3300000 、 Indirect expense:\990000 )

    Crystal structure of Trl1 ligase domain (Trl1-LD) - GMP complex was determined with 2.75 angstrom resolution. Two molecules of GMP were stacked and bonded near the active center of Trl1-LD. As a result of detailed analysis of the complex structure, basic amino acids were concentrated around two molecules of GMPs. From these facts, it was considered that these GMPs are mimicking tRNA exons in the ligation process. Based on this structure, it was possible to infer the binding mode of tRNA of Trl1-LD.

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Class subject in charge

  • Biophysics I (2024academic year) 1st semester  - 火1~2

  • Biophysics I (2024academic year) 1st semester  - 火1~2

  • Introduction to Interdisciplinary Science 2 (2021academic year) Prophase  - 水1,水2