Updated on 2025/12/02

写真a

 
AKITA Fusamichi
 
Organization
Scheduled update Associate Professor
Position
Associate Professor
External link

Degree

  • Ph.D. ( 2007.6   Osaka University )

 

Papers

  • Structure of a photosystem II-FCPII supercomplex from a haptophyte reveals a distinct antenna organization. International journal

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

    Nature communications   16 ( 1 )   4175 - 4175   2025.5

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

    Haptophytes are unicellular algae that produce 30 to 50% of biomass in oceans. Among haptophytes, a subset named coccolithophores is characterized by calcified scales. Despite the importance of coccolithophores in global carbon fixation and CaCO3 production, their energy conversion system is still poorly known. Here we report a cryo-electron microscopic structure of photosystem II (PSII)-fucoxanthin chlorophyll c-binding protein (FCPII) supercomplex from Chyrostila roscoffensis, a representative of coccolithophores. This complex has two sets of six dimeric and monomeric FCPIIs, with distinct orientations. Interfaces of both FCPII/FCPII and FCPII/core differ from previously reported. We also determine the sequence of Psb36, a subunit previously found in diatoms and red algae. The principal excitation energy transfer (EET) pathways involve mainly 5 FCPIIs, where one FCPII monomer mediates EET to CP47. Our findings provide a solid structural basis for EET and energy dissipation pathways occurring in coccolithophores.

    DOI： 10.1038/s41467-025-59512-9

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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

    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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  • 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 of a tetrameric photosystem I from a glaucophyte alga Cyanophora paradoxa

    Koji Kato, Ryo Nagao, Yoshifumi Ueno, Makio Yokono, Takehiro Suzuki, Tian-Yi Jiang, Naoshi Dohmae, Fusamichi Akita, Seiji Akimoto, Naoyuki Miyazaki, Jian-Ren Shen

    Nature Communications   13 ( 1 )   2022.12

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

    Abstract

    Photosystem I (PSI) is one of the two photosystems functioning in light-energy harvesting, transfer, and electron transfer in photosynthesis. However, the oligomerization state of PSI is variable among photosynthetic organisms. We present a 3.8-Å resolution cryo-electron microscopic structure of tetrameric PSI isolated from the glaucophyte alga Cyanophora paradoxa, which reveals differences with PSI from other organisms in subunit composition and organization. The PSI tetramer is organized in a dimer of dimers with a C2 symmetry. Unlike cyanobacterial PSI tetramers, two of the four monomers are rotated around 90°, resulting in a completely different pattern of monomer-monomer interactions. Excitation-energy transfer among chlorophylls differs significantly between Cyanophora and cyanobacterial PSI tetramers. These structural and spectroscopic features reveal characteristic interactions and excitation-energy transfer in the Cyanophora PSI tetramer, suggesting that the Cyanophora PSI could represent a turning point in the evolution of PSI from prokaryotes to eukaryotes.

    DOI： 10.1038/s41467-022-29303-7

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    Other Link： https://www.nature.com/articles/s41467-022-29303-7

  • Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex

    Ryo Nagao, Koji Kato, Minoru Kumazawa, Kentaro Ifuku, Makio Yokono, Takehiro Suzuki, Naoshi Dohmae, Fusamichi Akita, Seiji Akimoto, Naoyuki Miyazaki, Jian-Ren Shen

    Nature Communications   13 ( 1 )   2022.12

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

    Abstract

    Fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) function as light harvesters in diatoms. The structure of a diatom photosystem II-FCPII (PSII-FCPII) supercomplex have been solved by cryo-electron microscopy (cryo-EM) previously; however, the FCPII subunits that constitute the FCPII tetramers and monomers are not identified individually due to their low resolutions. Here, we report a 2.5 Å resolution structure of the PSII-FCPII supercomplex using cryo-EM. Two types of tetrameric FCPs, S-tetramer, and M-tetramer, are identified as different types of hetero-tetrameric complexes. In addition, three FCP monomers, m1, m2, and m3, are assigned to different gene products of FCP. The present structure also identifies the positions of most Chls c and diadinoxanthins, which form a complicated pigment network. Excitation-energy transfer from FCPII to PSII is revealed by time-resolved fluorescence spectroscopy. These structural and spectroscopic findings provide insights into an assembly model of FCPII and its excitation-energy transfer and quenching processes.

    DOI： 10.1038/s41467-022-29294-5

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    Other Link： https://www.nature.com/articles/s41467-022-29294-5

  • Geometric, electronic and spin structures of the CaMn4O5 catalyst for water oxidation in oxygen-evolving photosystem II. Interplay between experiments and theoretical computations

    Kizashi Yamaguchi, Mitsuo Shoji, Hiroshi Isobe, Takashi Kawakami, Koichi Miyagawa, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen

    COORDINATION CHEMISTRY REVIEWS   471   2022.11

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  • High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams Reviewed

    Koji Kato, Naoyuki Miyazaki, Tasuku Hamaguchi, Yoshiki Nakajima, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen

    Communications Biology   4 ( 1 )   2021.12

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

    <title>Abstract</title>Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.

    DOI： 10.1038/s42003-021-01919-3

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    Other Link： http://www.nature.com/articles/s42003-021-01919-3

  • Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer Reviewed

    Huaxin Yu, Tasuku Hamaguchi, Yoshiki Nakajima, Koji Kato, Keisuke Kawakami, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen

    Biochimica et Biophysica Acta (BBA) - Bioenergetics   148471 - 148471   2021.7

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

    DOI： 10.1016/j.bbabio.2021.148471

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  • Capturing structural changes of the S1 to S2 transition of photosystem II using time-resolved serial femtosecond crystallography. Reviewed International journal

    Hongjie Li, Yoshiki Nakajima, Takashi Nomura, Michihiro Sugahara, Shinichiro Yonekura, Siu Kit Chan, Takanori Nakane, Takahiro Yamane, Yasufumi Umena, Mamoru Suzuki, Tetsuya Masuda, Taiki Motomura, Hisashi Naitow, Yoshinori Matsuura, Tetsunari Kimura, Kensuke Tono, Shigeki Owada, Yasumasa Joti, Rie Tanaka, Eriko Nango, Fusamichi Akita, Minoru Kubo, So Iwata, Jian-Ren Shen, Michihiro Suga

    IUCrJ   8 ( Pt 3 )   431 - 443   2021.5

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    Photosystem II (PSII) catalyzes light-induced water oxidation through an S i -state cycle, leading to the generation of di-oxygen, protons and electrons. Pump-probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S1-to-S2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S1-to-S2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.

    DOI： 10.1107/S2052252521002177

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  • High-resolution cryo-EM structure of photosystem II: Effects of electron beam damage

    Koji Kato, Naoyuki Miyazaki, Tasuku Hamaguchi, Yoshiki Nakajima, Fusamichi Akita, Koji Yonekura, Jian-Ren Shen

    2020.10

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    Publisher：Cold Spring Harbor Laboratory  

    Abstract

    Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state, and its final state structure has not been solved because of the low efficiencies of the S-state transitions in the crystals. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, which was reduced by reducing the electron dose. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.

    DOI： 10.1101/2020.10.18.344648

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  • Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex. Reviewed International journal

    Ryo Nagao, Koji Kato, Kentaro Ifuku, Takehiro Suzuki, Minoru Kumazawa, Ikuo Uchiyama, Yasuhiro Kashino, Naoshi Dohmae, Seiji Akimoto, Jian-Ren Shen, Naoyuki Miyazaki, Fusamichi Akita

    Nature communications   11 ( 1 )   2481 - 2481   2020.5

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

    Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c-binding proteins (FCPs) present in diatoms, a group of organisms having important contribution to the global carbon cycle. Here, we report a 2.40-Å resolution structure of the diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The supercomplex is composed of 16 different FCPI subunits surrounding a monomeric PSI core. Each FCPI subunit showed different protein structures with different pigment contents and binding sites, and they form a complicated pigment-protein network together with the PSI core to harvest and transfer the light energy efficiently. In addition, two unique, previously unidentified subunits were found in the PSI core. The structure provides numerous insights into not only the light-harvesting strategy in diatom PSI-FCPI but also evolutionary dynamics of light harvesters among oxyphototrophs.

    DOI： 10.1038/s41467-020-16324-3

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  • Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins. Reviewed International journal

    Fusamichi Akita, Ryo Nagao, Koji Kato, Yoshiki Nakajima, Makio Yokono, Yoshifumi Ueno, Takehiro Suzuki, Naoshi Dohmae, Jian-Ren Shen, Seiji Akimoto, Naoyuki Miyazaki

    Communications biology   3 ( 1 )   232 - 232   2020.5

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    Iron-stress induced protein A (IsiA) is a chlorophyll-binding membrane-spanning protein in photosynthetic prokaryote cyanobacteria, and is associated with photosystem I (PSI) trimer cores, but its structural and functional significance in light harvesting remains unclear. Here we report a 2.7-Å resolution cryo-electron microscopic structure of a supercomplex between PSI core trimer and IsiA from a thermophilic cyanobacterium Thermosynechococcus vulcanus. The structure showed that 18 IsiA subunits form a closed ring surrounding a PSI trimer core. Detailed arrangement of pigments within the supercomplex, as well as molecular interactions between PSI and IsiA and among IsiAs, were resolved. Time-resolved fluorescence spectra of the PSI-IsiA supercomplex showed clear excitation-energy transfer from IsiA to PSI, strongly indicating that IsiA functions as an energy donor, but not an energy quencher, in the supercomplex. These structural and spectroscopic findings provide important insights into the excitation-energy-transfer and subunit assembly mechanisms in the PSI-IsiA supercomplex.

    DOI： 10.1038/s42003-020-0949-6

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  • Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA. Reviewed International journal

    Michihiro Suga, Atsuhiro Shimada, Fusamichi Akita, Jian-Ren Shen, Takehiko Tosha, Hiroshi Sugimoto

    Biochimica et biophysica acta. General subjects   1864 ( 2 )   129466 - 129466   2020.2

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

    BACKGROUND: The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach. SCOPE OF REVIEW: Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described. MAJOR CONCLUSIONS: XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data. GENERAL SIGNIFICANCE: XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.

    DOI： 10.1016/j.bbagen.2019.129466

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  • Structural basis for the adaptation and function of chlorophyll f in photosystem I. Reviewed International journal

    Koji Kato, Toshiyuki Shinoda, Ryo Nagao, Seiji Akimoto, Takehiro Suzuki, Naoshi Dohmae, Min Chen, Suleyman I Allakhverdiev, Jian-Ren Shen, Fusamichi Akita, Naoyuki Miyazaki, Tatsuya Tomo

    Nature communications   11 ( 1 )   238 - 238   2020.1

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

    Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f.

    DOI： 10.1038/s41467-019-13898-5

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  • FTIR Microspectroscopic Analysis of the Water Oxidation Reaction in a Single Photosystem II Microcrystal. Reviewed International journal

    Kato Y, Haniu S, Nakajima Y, Akita F, Shen JR, Noguchi T

    The journal of physical chemistry. B   124 ( 1 )   121 - 127   2019.12

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

    Microcrystals of photosystem II (PSII) have recently been used to investigate the intermediate structures of the water oxidizing complex during water oxidation by serial femtosecond crystallography using X-ray free electron lasers. To clarify the water oxidation mechanism, it is crucial to know whether the reaction proceeds properly in the microcrystals. In this work, we monitored the water oxidation reaction in a single PSII microcrystal using Fourier transform infrared (FTIR) microspectroscopy with the transmission method. Flash-induced micro-FTIR difference spectra of S-state transitions in a PSII microcrystal showed features virtually identical to the corresponding spectra previously obtained using the attenuated total reflection method for multiple microcrystals, representing the reactions near the crystal surface, as well as the spectra in solution. This observation indicates that the reaction processes of water oxidation proceed with relatively high efficiencies retaining native intermediate structures in the entire inside of a PSII microcrystal.

    DOI： 10.1021/acs.jpcb.9b10154

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  • Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy. Reviewed International journal

    Koji Kato, Ryo Nagao, Tian-Yi Jiang, Yoshifumi Ueno, Makio Yokono, Siu Kit Chan, Mai Watanabe, Masahiko Ikeuchi, Jian-Ren Shen, Seiji Akimoto, Naoyuki Miyazaki, Fusamichi Akita

    Nature communications   10 ( 1 )   4929 - 4929   2019.10

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

    Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a tetrameric PSI core isolated from a cyanobacterium, Anabaena sp. PCC 7120, analysed by single-particle cryo-electron microscopy (cryo-EM) at 3.3 Å resolution. The PSI tetramer has a C2 symmetry and is organised in a dimer of dimers form. The structure reveals interactions at the dimer-dimer interface and the existence of characteristic pigment orientations and inter-pigment distances within the dimer units that are important for unique excitation energy transfer. In particular, characteristic residues of PsaL are identified to be responsible for the formation of the tetramer. Time-resolved fluorescence analyses showed that the PSI tetramer has an enhanced excitation-energy quenching. These structural and spectroscopic findings provide insights into the physiological significance of the PSI tetramer and evolutionary changes of the PSI organisations.

    DOI： 10.1038/s41467-019-12942-8

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  • An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser. Reviewed

    Suga M, Akita F, Yamashita K, Nakajima Y, Ueno G, Li H, Yamane T, Hirata K, Umena Y, Yonekura S, Yu LJ, Murakami H, Nomura T, Kimura T, Kubo M, Baba S, Kumasaka T, Tono K, Yabashi M, Isobe H, Yamaguchi K, Yamamoto M, Ago H, Shen JR

    Science (New York, N.Y.)   366 ( 6463 )   334 - 338   2019.10

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

    DOI： 10.1126/science.aax6998

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  • Elucidation of the entire Kok cycle for photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics calculations: Comparison with the experimental results by the recent serial femtosecond crystallography Reviewed

    Shoji Mitsuo, Isobe Hiroshi, Shen Jian-Ren, Suga Michihiro, Akita Fusamichi, Miyagawa Koichi, Shigeta Yasuteru, Yamaguchi Kizashi

    CHEMICAL PHYSICS LETTERS   730   416 - 425   2019.9

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

    DOI： 10.1016/j.cplett.2019.06.026

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  • Structural basis for energy harvesting and dissipation in a diatom PSII–FCPII supercomplex Reviewed

    Ryo Nagao, Koji Kato, Takehiro Suzuki, Kentaro Ifuku, Ikuo Uchiyama, Yasuhiro Kashino, Naoshi Dohmae, Seiji Akimoto, Jian-Ren Shen, Naoyuki Miyazaki, Fusamichi Akita

    Nature Plants   5 ( 8 )   890 - 901   2019.8

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

    DOI： 10.1038/s41477-019-0477-x

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    Other Link： http://www.nature.com/articles/s41477-019-0477-x

  • Structure of the green algal photosystem I supercomplex with a decameric light-harvesting complex I. Reviewed

    Suga M, Ozawa SI, Yoshida-Motomura K, Akita F, Miyazaki N, Takahashi Y

    Nature plants   5 ( 6 )   626 - 636   2019.6

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  • Biochemical characterization of photosystem I complexes having different subunit compositions of fucoxanthin chlorophyll a/c-binding proteins in the diatom Chaetoceros gracilis. Reviewed International journal

    Ryo Nagao, Yoshifumi Ueno, Fusamichi Akita, Takehiro Suzuki, Naoshi Dohmae, Seiji Akimoto, Jian-Ren Shen

    Photosynthesis research   140 ( 2 )   141 - 149   2019.5

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

    Diatoms are dominant phytoplankton in aquatic environments and have unique light-harvesting apparatus, fucoxanthin chlorophyll a/c-binding protein (FCP). Diatom photosystem I (PSI) interacts with specific FCPs (FCPI); however, it remains unclear how PSI cores receive excitation energy from FCPI. To analyze the energy transfer dynamics, it is necessary to isolate both PSI cores and PSI-FCPI complexes. In this study, we prepared three PSI complexes, which are PSI-FCPI membrane fragments, detergent-solubilized PSI-FCPI supercomplexes and PSI core-like complexes, from the marine centric diatom, Chaetoceros gracilis, and examined their biochemical properties. Both the PSI-FCPI membrane fragments and supercomplexes showed similar subunit compositions including FCPI, whereas the PSI complexes were devoid of most FCPI subunits. The purity and homogeneity of the two detergent-solubilized PSI preparations were verified by clear-native PAGE and electron microscopy. The difference of pigment contents among the three PSI samples was shown by absorption spectra at 77 K. The intensity in the whole spectrum of PSI-FCPI membranes was much higher than those of the other two complexes, while the spectral shape of PSI complexes was similar to that of cyanobacterial PSI core complexes. 77-K fluorescence spectra of the three PSI preparations exhibited different spectral shapes, especially peak positions and band widths. Based on these observations, we discuss the merits of three PSI preparations for evaluating excitation energy dynamics in diatom PSI-FCPI complexes.

    DOI： 10.1007/s11120-018-0576-y

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  • Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II in Thermosynechococcus elongatus Reviewed International journal

    Nakajima Yoshiki, Umena Yasufumi, Nagao Ryo, Endo Kaichiro, Kobayashi Koichi, Akita Fusamichi, Suga Michihiro, Wada Hajime, Noguchi Takumi, Shen Jian-Ren

    JOURNAL OF BIOLOGICAL CHEMISTRY   293 ( 38 )   14786 - 14797   2018.9

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

    DOI： 10.1074/jbc.RA118.004304

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  • Fourier Transform Infrared Analysis of the S-State Cycle of Water Oxidation in the Microcrystals of Photosystem II Reviewed

    Yuki Kato, Fusamichi Akita, Yoshiki Nakajima, Michihiro Suga, Yasufumi Umena, Jian-Ren Shen, Takumi Noguchi

    Journal of Physical Chemistry Letters   9 ( 9 )   2121 - 2126   2018.5

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

    DOI： 10.1021/acs.jpclett.8b00638

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  • Structured near-infrared Magnetic Circular Dichroism spectra of the Mn4CaO5 cluster of PSII in T. vulcanus are dominated by Mn(IV) d-d ‘spin-flip’ transitions Reviewed

    Jennifer Morton, Maria Chrysina, Vincent S. J. Craig, Fusamichi Akita, Yoshiki Nakajima, Wolfgang Lubitz, Nicholas Cox, Jian-Ren Shen, Elmars Krausz

    Biochimica et Biophysica Acta - Bioenergetics   1859 ( 2 )   88 - 98   2018.2

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

    DOI： 10.1016/j.bbabio.2017.10.004

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  • Large-scale QM/MM calculations of the CaMn4O5 cluster in the S-3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures Reviewed

    Mitsuo Shoji, Hiroshi Isobe, Takahito Nakajima, Yasuteru Shigeta, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi

    FARADAY DISCUSSIONS   198   83 - 106   2017.6

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

    DOI： 10.1039/c6fd00230g

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  • Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL Reviewed

    Michihiro Suga, Fusamichi Akita, Michihiro Sugahara, Minoru Kubo, Yoshiki Nakajima, Takanori Nakane, Keitaro Yamashita, Yasufumi Umena, Makoto Nakabayashi, Takahiro Yamane, Takamitsu Nakano, Mamoru Suzuki, Tetsuya Masuda, Shigeyuki Inoue, Tetsunari Kimura, Takashi Nomura, Shinichiro Yonekura, Long-Jiang Yu, Tomohiro Sakamoto, Taiki Motomura, Jing-Hua Chen, Yuki Kato, Takumi Noguchi, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Eriko Nango, Rie Tanaka, Hisashi Naitow, Yoshinori Matsuura, Ayumi Yamashita, Masaki Yamamoto, Osamu Nureki, Makina Yabashi, Tetsuya Ishikawa, So Iwata, Jian-Ren Shen

    NATURE   543 ( 7643 )   131 - +   2017.3

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    DOI： 10.1038/nature21400

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  • Electron microscopic imaging revealed the flexible filamentous structure of the cell attachment protein P2 of Rice dwarf virus located around the icosahedral 5-fold axes Reviewed

    Naoyuki Miyazaki, Akifumi Higashiura, Tomoko Higashiura, Fusamichi Akita, Hiroyuki Hibino, Toshihiro Omura, Atsushi Nakagawa, Kenji Iwasaki

    JOURNAL OF BIOCHEMISTRY   159 ( 2 )   181 - 190   2016.2

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

    DOI： 10.1093/jb/mvv092

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  • Structural Biology of Photosynthetic Systems

    SHEN Jian-Ren, AKITA Fusamichi, SUGA Michihiro

    Seibutsu Butsuri   56 ( 2 )   79 - 86   2016

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    Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

    Oxygenic photosynthesis synthesizes sugars from water and carbon dioxide using light energy from the sun, thereby converts light energy into chemical energy and provides oxygen for aerobic life on the earth. The light-harvesting, electron transfer, and water-splitting reactions of photosynthesis are catalyzed by two large membrane-protein complexes photosystem II (PSII) and photosystem I (PSI). Through high-resolution crystal structural analysis by synchrotron X-rays as well as femtosecond X-ray free electron lasers, the mechanisms of these reactions have become understandable at the atomic level. Here we review the recent progresses in analyzing the structures of PSII and PSI as well as their functional implications.

    DOI： 10.2142/biophys.56.079

    CiNii Article

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    Other Link： https://jlc.jst.go.jp/DN/JLC/20021928091?from=CiNii

  • High-resolution native structure analyses of supramacromolecular complexes susceptible to radiation damage Reviewed

    Hideo Ago, Kunio Hirata, Go Ueno, Masaki Yamamoto, Kyoko Shinzawa-Itoh, Tomitake Tsukihara, Shinya Yoshikawa, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen

    Acta Crystallographica Section A Foundations and Advances   71 ( a1 )   s15 - s15   2015.8

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    Publishing type：Research paper (scientific journal)   Publisher：International Union of Crystallography ({IUCr})  

    DOI： 10.1107/s2053273315099751

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  • On the guiding principles for lucid understanding of the damage-free S-1 structure of the CaMn4O5 cluster in the oxygen evolving complex of photosystem II Reviewed

    Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi

    CHEMICAL PHYSICS LETTERS   627   44 - 52   2015.5

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  • Theoretical studies of the damage- free S-1 structure of the CaMn4O5 cluster in oxygen-evolving complex of photosystem II Reviewed

    Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Michihiro Suga, Fusamichi Akita, Jian-Ren Shen, Kizashi Yamaguchi

    CHEMICAL PHYSICS LETTERS   623   1 - 7   2015.3

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

    DOI： 10.1016/j.cplett.2015.01.030

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  • Optical identification of the long-wavelength (700-1700 nm) electronic excitations of the native reaction centre, Mn4CaO5 cluster and cytochromes of photosystem II in plants and cyanobacteria Reviewed

    Jennifer Morton, Fusamichi Akita, Yoshild Nakajima, Jian-Ren Shen, Elmars Krausz

    BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS   1847 ( 2 )   153 - 161   2015.2

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

    DOI： 10.1016/j.bbabio.2014.11.003

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  • Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses Reviewed

    Michihiro Suga, Fusamichi Akita, Kunio Hirata, Go Ueno, Hironori Murakami, Yoshiki Nakajima, Tetsuya Shimizu, Keitaro Yamashita, Masaki Yamamoto, Hideo Ago, Jian-Ren Shen

    NATURE   517 ( 7532 )   99 - U265   2015.1

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

    DOI： 10.1038/nature13991

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  • Crystal Structure of Talaromyces cellulolyticus (Formerly Known as Acremonium cellulolyticus) GH Family 11 Xylanase Reviewed

    Misumi Kataoka, Fusamichi Akita, Yuka Maeno, Benchaporn Inoue, Hiroyuki Inoue, Kazuhiko Ishikawa

    APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY   174 ( 4 )   1599 - 1612   2014.10

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

    DOI： 10.1007/s12010-014-1130-9

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  • X-Ray Crystallographic Structure of RNase Po1 That Exhibits Antitumor Activity Reviewed

    Hiroko Kobayashi, Takuya Katsutani, Yumiko Hara, Naomi Motoyoshi, Tadashi Itagaki, Fusamichi Akita, Akifumi Higashiura, Yusuke Yamada, Norio Inokuchi, Mamoru Suzuki

    BIOLOGICAL & PHARMACEUTICAL BULLETIN   37 ( 6 )   968 - 978   2014.6

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

    DOI： 10.1248/bpb.b13-00929

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  • Determination of the PS I content of PS II core preparations using selective emission: A new emission of PS II at 780 nm Reviewed

    Jennifer Morton, Jeremy Hall, Paul Smith, Fusamichi Akita, Faisal Hammad Mekky Koua, Jian-Ren Shen, Elmars Krausz

    BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS   1837 ( 1 )   167 - 177   2014.1

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

    DOI： 10.1016/j.bbabio.2013.09.008

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  • 2P001 Detailed cell entry mechanism of Rice dwarf virus (RDV)(01A. Protein:Structure,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

    Miyazaki Naoyuki, Higashiura Akifumi, Higashiura Tomoko, Akita Fusamichi, Hibino Hiroyuki, Omura Toshihiro, Nakagawa Atsushi, Iwasaki Kenji

    Seibutsu Butsuri   54 ( 1 )   S195   2014

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.54.S195_1

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  • Cryo-electron tomography: Moving towards revealing the viral life cycle of Rice dwarf virus Reviewed

    Naoyuki Miyazaki, Fusamichi Akita, Atsushi Nakagawa, Kazuyoshi Murata, Toshihiro Omura, Kenji Iwasaki

    Journal of Synchrotron Radiation   20 ( 6 )   826 - 828   2013.11

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

    DOI： 10.1107/S090904951302219X

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  • Assembly of the viroplasm by viral non-structural protein Pns10 is essential for persistent infection of rice ragged stunt virus in its insect vector Reviewed

    Dongsheng Jia, Nianmei Guo, Hongyan Chen, Fusamichi Akita, Lianhui Xie, Toshihiro Omura, Taiyun Wei

    JOURNAL OF GENERAL VIROLOGY   93   2299 - 2309   2012.10

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

    DOI： 10.1099/vir.0.042424-0

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  • Hairpin RNA derived from the gene for Pns9, a viroplasm matrix protein of Rice gall dwarf virus, confers strong resistance to virus infection in transgenic rice plants Reviewed

    Takumi Shimizu, Eiko Nakazono-Nagaoka, Fusamichi Akita, Taiyun Wei, Takahide Sasaya, Toshihiro Omura, Tamaki Uehara-Ichiki

    JOURNAL OF BIOTECHNOLOGY   157 ( 3 )   421 - 427   2012.2

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

    DOI： 10.1016/j.jbiotec.2011.12.015

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  • Crystallographic Analysis Reveals Octamerization of Viroplasm Matrix Protein P9-1 of Rice Black Streaked Dwarf Virus Reviewed

    Fusamichi Akita, Akifumi Higashiura, Takumi Shimizu, Yingying Pu, Mamoru Suzuki, Tamaki Uehara-Ichiki, Takahide Sasaya, Shuji Kanamaru, Fumio Arisaka, Tomitake Tsukihara, Atsushi Nakagawa, Toshihiro Omura

    JOURNAL OF VIROLOGY   86 ( 2 )   746 - 756   2012.1

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

    DOI： 10.1128/JVI.00826-11

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  • Aggregation Ability of Virus-Specific Antibodies is Correlated with their Capacity to Neutralize Rice dwarf virus Reviewed

    Hongyan Chen, Taiyun Wei, Ai Saotome, Kengo Sakaguchi, Yasuo Shikamoto, Hiroshi Mizuno, Fusamichi Akita, Takumi Shimizu, Tamaki Uehara-Ichiki, Toshihiro Omura

    JARQ-JAPAN AGRICULTURAL RESEARCH QUARTERLY   46 ( 1 )   65 - 71   2012.1

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

    DOI： 10.6090/jarq.46.65

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  • Immunity to Rice black streaked dwarf virus, a plant reovirus, can be achieved in rice plants by RNA silencing against the gene for the viroplasm component protein Reviewed

    Takumi Shimizu, Eiko Nakazono-Nagaoka, Fusamichi Akita, Tamaki Uehara-Ichiki, Toshihiro Omura, Takahide Sasaya

    VIRUS RESEARCH   160 ( 1-2 )   400 - 403   2011.9

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

    DOI： 10.1016/j.virusres.2011.05.011

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  • Viroplasm matrix protein Pns9 from rice gall dwarf virus forms an octameric cylindrical structure Reviewed

    Fusamichi Akita, Naoyuki Miyazaki, Hiroyuki Hibino, Takumi Shimizu, Akifumi Higashiura, Tamaki Uehara-Ichiki, Takahide Sasaya, Tomitake Tsukihara, Atsushi Nakagawa, Kenji Iwasaki, Toshihiro Omura

    JOURNAL OF GENERAL VIROLOGY   92   2214 - 2221   2011.9

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

    DOI： 10.1099/vir.0.032524-0

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  • Rice Dwarf Viruses with Dysfunctional Genomes Generated in Plants Are Filtered Out in Vector Insects: Implications for the Origin of the Virus Reviewed

    Yingying Pu, Akira Kikuchi, Yusuke Moriyasu, Masatoshi Tomaru, Yan Jin, Haruhisa Suga, Kyoji Hagiwara, Fusamichi Akita, Takumi Shimizu, Osamu Netsu, Nobuhiro Suzuki, Tamaki Uehara-Ichiki, Takahide Sasaya, Taiyun Wei, Yi Li, Toshihiro Omura

    JOURNAL OF VIROLOGY   85 ( 6 )   2975 - 2979   2011.3

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

    DOI： 10.1128/JVI.02147-10

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  • 3VJJ: Crystal Structure Analysis of the P9-1. Reviewed

    Akita F, Higashiura A, Suzuki M, Tsukihara T, Nakagawa A, Omura T

    Protein Data Bank   (phenix.refine: 1.7_650)   2011

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  • The protruding domain of the coat protein of Melon necrotic spot virus is involved in compatibility with and transmission by the fungal vector Olpidium bornovanus Reviewed

    Takehiro Ohki, Fusamichi Akita, Tomofumi Mochizuki, Ayami Kanda, Takahide Sasaya, Shinya Tsuda

    VIROLOGY   402 ( 1 )   129 - 134   2010.6

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

    DOI： 10.1016/j.virol.2010.03.020

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  • The crystal structure of a virus-like particle from the hyperthermophilic archaeon Pyrococcus furiosus provides insight into the evolution of viruses Reviewed

    Fusamichi Akita, Khoon Tee Chong, Hideaki Tanaka, Eiki Yamashita, Naoyuki Miyazaki, Yuichiro Nakaishi, Mamoru Suzuki, Kazunori Namba, Yasuko Ono, Tomitake Tsukihara, Atsushi Nakagawa

    JOURNAL OF MOLECULAR BIOLOGY   368 ( 5 )   1469 - 1483   2007.5

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

    DOI： 10.1016/j.jmb.2007.02.075

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Presentations

  • Structural study of monomeric and dimeric photosystem I-LHCI supercomplexes from a bryophyte at atomic resolutions

    Pi-Cheng Tsai, Romain La Rocca, Hiroyasu Motose, Jian-Ren Shen, Fusamichi Akita

    2025.11.3 

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    Event date： 2025.11.3 - 2025.11.5

    Language：English   Presentation type：Poster presentation  

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Research Projects

  • Elucidation of the mechanisms for light-induced water-splitting and light energy utilization in photosynthesis

    Grant number：22H04916  2022.04 - 2027.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Specially Promoted Research

    沈 建仁, 庄司 光男, 秋田 総理, 菅 倫寛, 山口 兆

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    Grant amount：\627640000 （ Direct expense: \482800000 、 Indirect expense：\144840000 ）

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