2025/04/23 更新

写真a

ナカジマ ヨシキ
中島 芳樹
NAKAJIMA Yoshiki
所属
学術研究院先鋭研究領域(異分野基礎) 助教
職名
助教
外部リンク

研究キーワード

  • 光化学系II

  • 構造生物学

  • 光合成

研究分野

  • ライフサイエンス / 構造生物化学

所属学協会

 

論文

  • Biochemical evidence for the diversity of LHCI proteins in PSI-LHCI from the red alga Galdieria sulphuraria NIES-3638. 査読 国際誌

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

    Photosynthesis research   163 ( 1 )   14 - 14   2025年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    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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  • Structural basis for molecular assembly of fucoxanthin chlorophyll a/c-binding proteins in a diatom photosystem I supercomplex 査読

    Koji Kato, Yoshiki Nakajima, Jian Xing, Minoru Kumazawa, Haruya Ogawa, Jian-Ren Shen, Kentaro Ifuku, Ryo Nagao

    eLife   13   2024年10月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:eLife Sciences Publications, Ltd  

    Photosynthetic organisms exhibit remarkable diversity in their light-harvesting complexes (LHCs). LHCs are associated with photosystem I (PSI), forming a PSI-LHCI supercomplex. The number of LHCI subunits, along with their protein sequences and pigment compositions, has been found to differ greatly among the PSI-LHCI structures. However, the mechanisms by which LHCIs recognize their specific binding sites within the PSI core remain unclear. In this study, we determined the cryo-electron microscopy structure of a PSI supercomplex incorporating fucoxanthin chlorophyll a/c-binding proteins (FCPs), designated as PSI-FCPI, isolated from the diatom Thalassiosira pseudonana CCMP1335. Structural analysis of PSI-FCPI revealed five FCPI subunits associated with a PSI monomer; these subunits were identified as RedCAP, Lhcr3, Lhcq10, Lhcf10, and Lhcq8. Through structural and sequence analyses, we identified specific protein–protein interactions at the interfaces between FCPI and PSI subunits, as well as among FCPI subunits themselves. Comparative structural analyses of PSI-FCPI supercomplexes, combined with phylogenetic analysis of FCPs from T. pseudonana and the diatom Chaetoceros gracilis, underscore the evolutionary conservation of protein motifs crucial for the selective binding of individual FCPI subunits. These findings provide significant insights into the molecular mechanisms underlying the assembly and selective binding of FCPIs in diatoms.

    DOI: 10.7554/elife.99858.3

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    その他リンク: https://cdn.elifesciences.org/articles/99858/elife-99858-v1.xml

  • Presence of low-energy chlorophylls d in photosystem I trimer and monomer cores isolated from Acaryochloris sp. NBRC 102871. 査読 国際誌

    Ryo Nagao, Haruki Yamamoto, Haruya Ogawa, Hibiki Ito, Yuma Yamamoto, Takehiro Suzuki, Koji Kato, Yoshiki Nakajima, Naoshi Dohmae, Jian-Ren Shen

    Photosynthesis research   161 ( 3 )   203 - 212   2024年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Acaryochloris species belong to a special category of cyanobacteria possessing chlorophyll (Chl) d. One of the photosynthetic characteristics of Acaryochloris marina MBIC11017 is that the absorption spectra of photosystem I (PSI) showed almost no bands and shoulders of low-energy Chls d over 740 nm. In contrast, the absorption spectra of other Acaryochloris species showed a shoulder around 740 nm, suggesting that low-energy Chls d within PSI are diversified among Acaryochloris species. In this study, we purified PSI trimer and monomer cores from Acaryochloris sp. NBRC 102871 and examined their protein and pigment compositions and spectral properties. The protein bands and pigment compositions of the PSI trimer and monomer of NBRC102871 were virtually identical to those of MBIC11017. The absorption spectra of the NBRC102871 PSIs exhibited a shoulder around 740 nm, whereas the fluorescence spectra of PSI trimer and monomer displayed maximum peaks at 754 and 767 nm, respectively. These spectral properties were different from those of MBIC11017, indicating the presence of low-energy Chls d within the NBRC102871 PSIs. Moreover, we analyzed the NBRC102871 genome to identify amino acid sequences of PSI proteins and compared them with those of the A. marina MBIC11017 and MBIC10699 strains whose genomes are available. The results showed that some of the sequences in NBRC102871 were distinct from those in MBIC11017 and MBIC10699. These findings provide insights into the variety of low-energy Chls d with respect to the protein environments of PSI cores among the three Acaryochloris strains.

    DOI: 10.1007/s11120-024-01108-3

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  • Oxygen-evolving photosystem II structures during S1–S2–S3 transitions 査読

    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年2月

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    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1038/s41586-023-06987-5

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  • Structure of PSI-LHCI fromCyanidium caldariumprovides evolutionary insights into conservation and diversity of red-lineage LHCs 査読 国際誌

    Koji Kato, Tasuku Hamaguchi, Minoru Kumazawa, Yoshiki Nakajima, Kentaro Ifuku, Shunsuke Hirooka, Yuu Hirose, Shin-ya Miyagishima, Takehiro Suzuki, Keisuke Kawakami, Naoshi Dohmae, Koji Yonekura, Jian-Ren Shen, Ryo Nagao

    Proceedings of the National Academy of Sciences of the United States of America   121 ( 11 )   e2319658121   2023年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Cold Spring Harbor Laboratory  

    Abstract

    Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and their structural variety in photosystem I-LHC (PSI-LHCI) supercomplexes has been shown. However, structural and evolutionary correlations of red-lineage LHCs are unknown. Here we determined a 1.92-Å resolution cryo-electron microscopic structure of a PSI-LHCI supercomplex isolated from the red algaCyanidium caldariumRK-1 (NIES-2137) which is an important taxon in the Cyanidiophyceae, and subsequently investigated these correlations through structural comparisons and phylogenetic analysis. The PSI-LHCI structure shows five LHCI subunits together with a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in red-lineage algae showed clear orthology of LHCs betweenC. caldariumandCyanidioschyzon merolae, whereas no orthologous relationships were found betweenC. caldariumLhcr1–3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.

    DOI: 10.1101/2023.10.25.563911

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▼全件表示

書籍等出版物

  • Structure, Electron Transfer Chain of Photosystem II and the Mechanism of Water Splitting

    Jian-Ren Shen, Yoshiki Nakajima, Fusamichi Akita, Michihiro Suga( 担当: 分担執筆)

    Springer  2021年9月 

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MISC

  • 光化学系IIによる水分解・酸素発生機構研究の歩み

    中島 芳樹

    CanAppleニュース 第205号   2021年10月

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    掲載種別:記事・総説・解説・論説等(その他)  

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  • 水分解反応のしくみを観測ー人工光合成触媒開発へ前進ー

    久保稔, 菅原道泰, 中島芳樹

    Chem-station   2017年5月

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    掲載種別:記事・総説・解説・論説等(その他)  

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講演・口頭発表等

  • X線自由電子レーザーが明らかにする光化学系IIの水分解反応の分子機構

    〇菅倫寛, 中島芳樹, Hongjie Li, 沈建仁

    第59回日本生物物理学会年会  2021年11月25日 

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  • X線自由電子レーザーによって明らかになった光合成光化学系IIの水分解反応

    〇菅倫寛, 中島芳樹, 秋田総理, 沈建仁

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共同研究・競争的資金等の研究

  • クライオ電顕構造解析を基盤とした光合成光化学系II表在性タンパク質の分子機能の解明

    研究課題/領域番号:23K14211  2023年04月 - 2025年03月

    日本学術振興会  科学研究費助成事業  若手研究

    中島 芳樹

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    配分額:4680000円 ( 直接経費:3600000円 、 間接経費:1080000円 )

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  • ゆがんだイス型の触媒の立体構造が紐解く光化学系IIの水分解反応

    研究課題/領域番号:20H03226  2020年04月 - 2023年03月

    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)

    菅 倫寛, 中島 芳樹

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    担当区分:研究分担者 

    配分額:17810000円 ( 直接経費:13700000円 、 間接経費:4110000円 )

    光合成での水分解・酸素発生反応は光化学系II(PSII)内部のMn4CaO5クラスターが酸化状態を5段階(S0状態からS4状態へ)に順次変化させて触媒する。このうち,中間体S2状態は電磁性共鳴法により区別されるスピン状態の異なる2つの平衡状態があることが知られているが,構造解析されたのはスピン状態がS=1/2のもののみであり,スピン状態がS=5/2のものは解析されていない。そこで本研究ではPSIIのS=5/2のS2状態を調製して構造解析することを目指している。令和3年度は中間体状態が得ることを目的として,溶液のpHをアルカリ状態にしたものを調製して固定ターゲット法を用いて回折実験を行い,構造解析を進めた。光をあててS状態遷移させたもの、光を当てる前の状態のものなど複数の状態について調製してデータを収集した。解析の結果,溶液状態がアルカリ状態に変化したことに伴う立体構造の変化を確認することができた。また,時間分解シリアルフェムト秒構造解析を行ってS=1/2のものを室温で構造解析した。解析の結果,これまで凍結状態で確認されていたS=1/2状態での構造変化を確認したほか、新たに基質の水分子を取り込むためのチャネルと思われている水素結合のネットワークに変化が見られた。これは構造変化したところが水チャネルであることを示す証拠となるものである。この内容は論文にまとめIUCrJに発表した。

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担当授業科目

  • 基礎生物学2b (2024年度) 第4学期  - 火1~2

  • 教養生物学実験(分子生物) (2024年度) 第4学期  - 木5~8

  • 構造生物学特別演習 (2024年度) 通年  - その他

  • 生体高分子構造学 (2024年度) 後期  - 火3~4