Frontiers Media SA Acta Medica Okayama 1664-462X 16 2025 Structural analysis of PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte alga Rhodomonas sp. NIES-2332 1716939 EN Wenyue Zhang Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Nozomi Yonehara Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Mizuki Ishii Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Haowei Jiang Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Romain La Rocca Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Pi-Cheng Tsai Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Hongjie Li Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Koji Kato Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Fusamichi Akita Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Jian-Ren Shen Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Light energy is converted to chemical energy by two photosystems (PSI and PSII) in complex with their light-harvesting complex proteins (LHCI and LHCII) in photosynthesis. Rhodomonas is a member of cryptophyte alga whose LHCs contain unique chlorophyll a/c proteins (ACPs) and phycobiliproteins. We purified PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte Rhodomonas sp. NIES-2332 and analyzed their structures at high resolutions of 2.08 Å and 2.17 Å, respectively, using cryo-electron microscopy. These structures are largely similar to those reported previously from two other species of cryptophytes, but exhibited some differences in both the pigment locations and subunit structures. A part of the antenna subunits of both photosystems is shifted compared with the previously reported structures from other species of cryptophytes, suggesting some differences in the energy transfer rates from the antenna to the PSI and PSII cores. Newly identified lipids are found to occupy the interfaces between the antennae and cores, which may be important for assembly and stabilization of the supercomplexes. Water molecules surrounding three iron-sulfur clusters of the PSI core are found in our high-resolution structure, some of which are conserved from cyanobacteria to higher plants but some are different. In addition, our structure of PSII-ACPII lacks the subunits of oxygen-evolving complex as well as the Mn4CaO5 cluster, suggesting that the cells are in the S-growth phase, yet the PSI-ACPI structure showed the binding of PsaQ, suggesting that it is in an L-phase. These results suggest that the S-phase and L-phase can co-exist in the cryptophytic cells. The high-resolution structures of both PSI-ACPIs and PSII-ACPIIs solved in this study provide a more solid structural basis for elucidating the energy transfer and quenching mechanisms in this group of the organisms. No potential conflict of interest relevant to this article was reported.

Nature Portfolio Acta Medica Okayama 2041-1723 16 1 2025 Structure of a photosystem II-FCPII supercomplex from a haptophyte reveals a distinct antenna organization 4175 EN Romain La Rocca Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Koji Kato Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Pi-Cheng Tsai Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Yoshiki Nakajima Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Fusamichi Akita Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Jian-Ren Shen Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University 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. No potential conflict of interest relevant to this article was reported.

Springer Science and Business Media LLC Acta Medica Okayama 0028-0836 626 7999 2024 Oxygen-evolving photosystem II structures during S1–S2–S3 transitions 670 677 EN Hongjie Li Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Yoshiki Nakajima Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Eriko Nango Institute of Multidisciplinary Research for Advanced Materials, Tohoku University Shigeki Owada Japan Synchrotron Radiation Research Institute Daichi Yamada Department of Picobiology, Graduate School of Life Science, University of Hyogo Kana Hashimoto Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Fangjia Luo Japan Synchrotron Radiation Research Institute Rie Tanaka RIKEN SPring-8 Center Fusamichi Akita Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Koji Kato Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Jungmin Kang RIKEN SPring-8 Center Yasunori Saitoh Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Shunpei Kishi Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Huaxin Yu Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Naoki Matsubara Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Hajime Fujii Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Michihiro Sugahara Japan Synchrotron Radiation Research Institute Mamoru Suzuki Institute for Protein Research, Osaka University Tetsuya Masuda Division of Food and Nutrition, Faculty of Agriculture, Ryukoku University Tetsunari Kimura Department of Chemistry, Graduate School of Science, Kobe University Tran Nguyen Thao Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Shinichiro Yonekura Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Long-Jiang Yu Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Takehiko Tosha RIKEN SPring-8 Center Kensuke Tono Japan Synchrotron Radiation Research Institute Yasumasa Joti Japan Synchrotron Radiation Research Institute Takaki Hatsui Japan Synchrotron Radiation Research Institute Makina Yabashi Japan Synchrotron Radiation Research Institute Minoru Kubo Department of Picobiology, Graduate School of Life Science, University of Hyogo So Iwata RIKEN SPring-8 Center Hiroshi Isobe Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Kizashi Yamaguchi Center for Quantum Information and Quantum Biology, Osaka University Michihiro Suga Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Jian-Ren Shen Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0–4) at the Mn4CaO5 cluster1,2,3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4,5,6,7. 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. No potential conflict of interest relevant to this article was reported.

Elsevier BV Acta Medica Okayama 0010-8545 471 2022 Geometric, electronic and spin structures of the CaMn4O5 catalyst for water oxidation in oxygen-evolving photosystem II. Interplay between experiments and theoretical computations 214742 EN Kizashi Yamaguchi Center for Quantum Information and Quantum Biology, Osaka University Mitsuo Shoji Center of Computational Sciences, Tsukuba University Hiroshi Isobe Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University Takashi Kawakami RIKEN Center for Computational Science Koichi Miyagawa Center of Computational Sciences, Tsukuba University Michihiro Suga Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University Fusamichi Akita Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University Jian-Ren Shen Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University The aim of this review is to elucidate geometric structures of the catalytic CaMn4Ox (x = 5, 6) cluster in the Kok cycle for water oxidation in the oxygen evolving complex (OEC) of photosystem II (PSII) based on the high-resolution (HR) X-ray diffraction (XRD) and serial femtosecond crystallography (SFX) experiments using the X-ray free-electron laser (XFEL). Quantum mechanics (QM) and QM/molecular mechanics (MM) computations are performed to elucidate the electronic and spin structures of the CaMn4Ox (x = 5, 6) cluster in five states S-i (i = 0 similar to 4) on the basis of the X-ray spectroscopy, electron paramagnetic resonance (EPR) and related experiments. Interplay between the experiments and theoretical computations has been effective to elucidate the coordination structures of the CaMn4Ox (x = 5, 6) cluster ligated by amino acid residues of the protein matrix of PSII, valence states of the four Mn ions and total spin states by their exchange-couplings, and proton-shifted isomers of the CaMn4Ox (x = 5, 6) cluster. The HR XRD and SFX XFEL experiments have also elucidated the biomolecular systems structure of OEC of PSII and the hydrogen bonding networks consisting of water molecules, chloride anions, etc., for water inlet and proton release pathways in PSII. Large-scale QM/MM computations have been performed for elucidation of the hydrogen bonding distances and angles by adding invisible hydrogen atoms to the HR XRD structure. Full geometry optimizations by the QM and QM/MM methods have been effective for elucidation of the molecular systems structure around the CaMn4Ox (x = 5, 6) cluster in OEC. DLPNO-CCSD(T-0) method has been applied to elucidate relative energies of possible intermediates in each state of the Kok cycle for water oxidation. Implications of these results are discussed in relation to the blueprint for developments of artificial catalysts for water oxidation. No potential conflict of interest relevant to this article was reported.

Nature Portfolio Acta Medica Okayama 2041-1723 13 1 2022 Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex 1764 EN Ryo Nagao Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Koji Kato Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Minoru Kumazawa Graduate School of Biostudies, Kyoto University Kentaro Ifuku Graduate School of Agriculture, Kyoto University Makio Yokono Institute of Low Temperature Science, Hokkaido University Takehiro Suzuki Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Naoshi Dohmae Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Fusamichi Akita Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Seiji Akimoto Graduate School of Science, Kobe University Naoyuki Miyazaki Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba Jian-Ren Shen Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University 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 angstrom 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. Fucoxanthin chlorophyll a/c-binding proteins (FCPs) harvest light energy in diatoms. The authors analyzed a structure of PSII-FCPII supercomplex at high resolution by cryo-EM, which identified each FCP subunit and pigment network in the supercomplex. No potential conflict of interest relevant to this article was reported.

Nature Portfolio Acta Medica Okayama 2041-1723 13 1 2022 Structure of a tetrameric photosystem I from a glaucophyte alga Cyanophora paradoxa 1679 EN Koji Kato Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Ryo Nagao Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Yoshifumi Ueno Graduate School of Science, Kobe University Makio Yokono Institute of Low Temperature Science, Hokkaido University Takehiro Suzuki Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Jiang Tian-Yi Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Naoshi Dohmae Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Fusamichi Akita Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Seiji Akimoto Graduate School of Science, Kobe University Naoyuki Miyazaki Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba Shen Jian-Ren Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University 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-angstrom 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 degrees, 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. No potential conflict of interest relevant to this article was reported.

Springer Acta Medica Okayama 2399-3642 4 1 2021 High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams 382 EN Koji Kato Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Naoyuki Miyazaki Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba Tasuku Hamaguchi Biostructural Mechanism Laboratory, RIKEN Spring-8 Center Yoshiki Nakajima Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Fusamichi Akita Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Koji Yonekura Institute of Multidisciplinary Research for Advanced Materials, Tohoku University Jian-Ren Shen Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University 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. No potential conflict of interest relevant to this article was reported.

Nature Acta Medica Okayama 2399-3642 3 1 2020 Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins 232 EN Fusamichi Akita Graduate School of Natural Science and Technology, Okayama University Ryo Nagao Research Institute for Interdisciplinary Science, Okayama University Koji Kato Research Institute for Interdisciplinary Science, Okayama University Yoshiki Nakajima Graduate School of Natural Science and Technology, Okayama University Makio Yokono Nippon Flour Mills Co., Ltd., Innovation Center Yoshifumi Ueno Graduate School of Science, Kobe University Takehiro Suzuki Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Naoshi Dohmae Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Jian-Ren Shen Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Seiji Akimoto Graduate School of Science, Kobe University Naoyuki Miyazaki Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba 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-angstrom 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. Akita et al. present the latest approach to solve IsiA-PSI supercomplex molecular structure with increased resolution using cryo-EM and time-resolved fluorescence studies. With 2.7 angstrom resolution, they reveal molecular interactions between PSI and IsiA subunits and that IsiA functions as an energy donor in the supercomplex. No potential conflict of interest relevant to this article was reported.

Nature Research Acta Medica Okayama 2041-1723 11 1 2020 Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex EN Ryo Nagao Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Koji Kato Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Kentaro Ifuku Graduate School of Biostudies, Kyoto University Takehiro Suzuki Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Minoru Kumazawa Faculty of Agriculture, Kyoto University Ikuo Uchiyama National Institute for Basic Biology, National Institutes of Natural Sciences Yasuhiro Kashino Graduate School of Life Science, University of Hyogo Naoshi Dohmae Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Seiji Akimoto Graduate School of Science,Kobe University Jian-Ren Shen Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Naoyuki Miyazaki Institute for Protein Research, Osaka University Fusamichi Akita Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University 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-angstrom 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. One of the major photosynthetic light-harvesting complexes (LHCs) are fucoxanthin chlorophyll a/c-binding proteins (FCPs), which are present in diatoms, a major group of algae. Here, the authors present the cryo-EM structure of the photosystem I-FCP (PSI-FCPI) supercomplex isolated from the marine centric diatom Chaetoceros gracilis that contains 16 FCPI subunits surrounding the PSI core and discuss possible excitation energy transfer pathways. No potential conflict of interest relevant to this article was reported.

Nature Research Acta Medica Okayama 2041-1723 11 1 2020 Structural basis for the adaptation and function of chlorophyll f in photosystem I 238 EN Koji Kato Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Toshiyuki Shinoda Faculty of Science, Tokyo University of Science Ryo Nagao Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Seiji Akimoto Graduate School of Science, Kobe University Takehiro Suzuki Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Naoshi Dohmae Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science Min Chen School of Life and Environmental Sciences, University of Sydney Suleyman I. Allakhverdiev K.A. Timiryazev Institute of Plant Physiology RAS Jian-Ren Shen Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Fusamichi Akita Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Naoyuki Miyazaki Institute for Protein Research, Laboratory of Protein Synthesis and Expression, Osaka University Tatsuya Tomo Faculty of Science, Tokyo University of Science 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. No potential conflict of interest relevant to this article was reported.

SI Acta Medica Okayama 03044165 1864 2 2020 Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA 129466 EN Michihiro Suga Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Atsuhiro Shimada Graduate School of Applied Biological Sciences and Faculty of Applied Biological Sciences, Gifu University Fusamichi Akita Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Jian-Ren Shen Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Takehiko Tosha Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center Hiroshi Sugimoto Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center 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.<br/> 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.<br/> 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.<br/> 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. No potential conflict of interest relevant to this article was reported.

American Association for the Advancement of Science Acta Medica Okayama 0036-8075 366 6463 2019 An oxyl/oxo mechanism for dioxygen bond formation in PSII revealed by X-ray free electron lasers 334 338 EN Michihiro Suga Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Fusamichi Akita Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Keitaro Yamashita RIKEN SPring-8 Center Yoshiki Nakajima Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Go Ueno RIKEN SPring-8 Center Hongjie Li Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Takahiro Yamane Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Kunio Hirata RIKEN SPring-8 Center Yasufumi Umena Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Shinichiro Yonekura Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Long-Jiang Yu Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Hironori Murakami Japan Synchrotron Radiation Research Institute Takashi Nomura RIKEN SPring-8 Center Tetsunari Kimura Department of Chemistry, Graduate School of Science, Kobe University Minoru Kubo RIKEN SPring-8 Center Seiki Baba Japan Synchrotron Radiation Research Institute Takashi Kumasaka Japan Synchrotron Radiation Research Institute Kensuke Tono RIKEN SPring-8 Center Makina Yabashi RIKEN SPring-8 Center Hiroshi Isobe Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Kizashi Yamaguchi The Institute for Scientific and Industrial Research, Osaka University Masaki Yamamoto RIKEN SPring-8 Center Hideo Ago RIKEN SPring-8 Center Jian-Ren Shen Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S0 to S4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S1, S2, and S3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S2, but flipping of D1 Glu189 upon transition to S3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn4CaO6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation. No potential conflict of interest relevant to this article was reported.

Nature Publishing Group Acta Medica Okayama 0028-0836 543 7643 2017 Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL 131 135 EN Michihiro Suga Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Fusamichi Akita Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Michihiro Sugahara RIKEN SPring-8 Center Minoru Kubo Japan Science and Technology Agency, PRESTO Yoshiki Nakajima Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Takanori Nakane Department of Biological Sciences, Graduate School of Science, The University of Tokyo Keitaro Yamashita RIKEN SPring-8 Center Yasufumi Umena Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Makoto Nakabayashi Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Takahiro Yamane Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Takamitsu Nakano Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Mamoru Suzuki Institute for Protein Research, Osaka University Tetsuya Masuda Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University Shigeyuki Inoue Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo Tetsunari Kimura Department of Chemistry, Graduate School of Science, Kobe University Takashi Nomura RIKEN SPring-8 Center Shinichiro Yonekura Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Long-Jiang Yu Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Tomohiro Sakamoto Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Taiki Motomura Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Jing-Hua Chen Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Yuki Kato Division of Material Science, Graduate School of Science, Nagoya University Takumi Noguchi Division of Material Science, Graduate School of Science, Nagoya University Kensuke Tono Japan Synchrotron Radiation Research Institute Yasumasa Joti Japan Synchrotron Radiation Research Institute Takashi Kameshima Japan Synchrotron Radiation Research Institute46 Takaki Hatsui RIKEN SPring-8 Center Eriko Nango RIKEN SPring-8 Center Rie Tanaka RIKEN SPring-8 Center Hisashi Naitow RIKEN SPring-8 Center Yoshinori Matsuura RIKEN SPring-8 Center Ayumi Yamashita RIKEN SPring-8 Center Masaki Yamamoto RIKEN SPring-8 Center Osamu Nureki Department of Biological Sciences, Graduate School of Science, The University of Tokyo Makina Yabashi RIKEN SPring-8 Center Tetsuya Ishikawa RIKEN SPring-8 Center So Iwata RIKEN SPring-8 Center Jian-Ren Shen Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1.9 Å resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn4CaO5 cluster organized in an asymmetric, 'distorted-chair' form. This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the 'radiation damage-free' structure. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures. Here we describe the structural changes in PSII induced by two-flash illumination at room temperature at a resolution of 2.35 Å using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 ångström compact free-electron laser. An isomorphous difference Fourier map between the two-flash and dark-adapted states revealed two areas of apparent changes: around the QB/non-haem iron and the Mn4CaO5 cluster. The changes around the QB/non-haem iron region reflected the electron and proton transfers induced by the two-flash illumination. In the region around the OEC, a water molecule located 3.5 Å from the Mn4CaO5 cluster disappeared from the map upon two-flash illumination. This reduced the distance between another water molecule and the oxygen atom O4, suggesting that proton transfer also occurred. Importantly, the two-flash-minus-dark isomorphous difference Fourier map showed an apparent positive peak around O5, a unique μ4-oxo-bridge located in the quasi-centre of Mn1 and Mn4 (refs 4,5). This suggests the insertion of a new oxygen atom (O6) close to O5, providing an O=O distance of 1.5 Å between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously No potential conflict of interest relevant to this article was reported.

Nature Publishing Group Acta Medica Okayama 0028-0836 517 2015 Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses 99 103 EN Michihiro Suga Fusamichi Akita Kunio Hirata Go Ueno Hironori Murakami Yoshiki Nakajima Tetsuya Shimizu Keitaro Yamashita Masaki Yamamoto Hideo Ago Jian-Ren Shen Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex which catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9-ångström (Å) resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well-defined protein environment1. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation2, and slight differences were found in the Mn–Mn distances between the results of XRD1, EXAFS3–7 and theoretical studies8–14. Here we report a ‘radiation-damage-free’ structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 Å using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and a huge number of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn–Mn distances that are shorter by 0.1–0.2 Å. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn–ligand distances and analysis of the Jahn–Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer Mn–O distances in contrast to the other oxo-oxygen atoms, suggesting that it is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for design of artificial catalysts for water oxidation. No potential conflict of interest relevant to this article was reported.