Elsevier BVActa Medica Okayama0005-2728186732026Multiple structures of photosystem I-FCPI supercomplexes from a coccolithophore alga reveal a modular antenna organization149588ENRomainLa RoccaAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityPi-ChengTsaiAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityKojiKatoAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityYoshikiNakajimaAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityFusamichiAkitaAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityJian-RenShenAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityPhotosystem I (PSI) converts light energy into chemical energy in photosynthesis, and forms supercomplexes with light-harvesting complexes (LHCI) in eukaryotes to enhance energy capture and transfer. Various numbers and organizations of both PSI core and LHCI subunits are observed in various organisms. A subgroup of haptophytes named coccolithophores play a major role in marine carbon cycle and CaCO3 production, and the light-harvesting antennas of them are named FCPs (fucoxanthin-chlorophyll a/c binding protein) because they bind chlorophyll c and fucoxanthin in addition to chlorophyll a. A structure of a large PSI-FCPI supercomplex containing 38 FCPI subunits has been reported from a coccolithophore Emiliania huxleyi recently (L. Shen et al., Science 389, eadv2132, 2025). Here we solved five cryo-electron microscopy (cryo-EM) structures of PSI–FCPI supercomplexes isolated from another coccolithophore Chrysotila roscoffensis with different detergents at resolutions ranging from 2.3 to 1.7 Å. These structures represent discrete PSI-FCPIs containing 1, 4, 6, 8 and 9 FCPI subunits, with FCPIs arranged in a modular fashion. Association of each FCPI module to the PSI core, as well as the arrangement of protein subunits and pigments, are revealed. Contributions of individual antenna modules to excitation energy transfer were calculated and compared with PSI–FCPI supercomplexes from other species of coccolithophores and haptophytes. These results pinpoint the assembly of stable PSI–FCPI supercomplexes in C. roscoffensis and provide insights into how antenna modules contribute to energy transfer in coccolithophores.No potential conflict of interest relevant to this article was reported.Frontiers Media SAActa Medica Okayama1664-462X162025Structural analysis of PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte alga Rhodomonas sp. NIES-23321716939ENWenyueZhangAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityNozomiYoneharaAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityMizukiIshiiAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityHaoweiJiangAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityRomainLa RoccaAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityPi-ChengTsaiAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityHongjieLiAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityKojiKatoAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityFusamichiAkitaAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityJian-RenShenAdvanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityLight 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.American Association for the Advancement of Science (AAAS)Acta Medica Okayama2375-254811442025Structural insights into the divergent evolution of a photosystem I supercomplex in Euglena graciliseaea6241ENKojiKatoResearch Institute for Interdisciplinary Science, Advanced Research Field, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityYoshikiNakajimaResearch Institute for Interdisciplinary Science, Advanced Research Field, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityRunaSakamotoResearch Institute for Interdisciplinary Science, Advanced Research Field, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityMinoruKumazawaInstitute of Low Temperature Science, Hokkaido UniversityKentaroIfukuGraduate School of Agriculture, Kyoto UniversityTakahiroIshikawaInstitute of Agricultural and Life Sciences, Academic Assembly, Shimane UniversityJian-RenShenResearch Institute for Interdisciplinary Science, Advanced Research Field, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityAtsushiTakabayashiInstitute of Low Temperature Science, Hokkaido UniversityRyoNagaoFaculty of Agriculture, Shizuoka UniversityPhotosystem I (PSI) forms supercomplexes with light-harvesting complexes (LHCs) to perform oxygenic photosynthesis. Here, we report a 2.82-angstrom cryo–electron microscopy structure of the PSI-LHCI supercomplex from Euglena gracilis, a eukaryotic alga with secondary green alga-derived plastids. The structure reveals a PSI monomer core with eight subunits and 13 asymmetrically arranged LHCI proteins. Euglena LHCIs bind diadinoxanthin, which is one of the carotenoids typically associated with red-lineage LHCs and is not present in the canonical LHCI belt found in green-lineage PSI-LHCI structures. Phylogenetic analysis shows that the Euglena LHCIs originated from LHCII-related clades rather than from the green-lineage LHCI group and that the nuclear-encoded PSI subunit PsaD likely originated from cyanobacteria via horizontal gene transfer. These observations indicate a mosaic origin of the Euglena PSI-LHCI. Our findings uncover a noncanonical light-harvesting architecture and highlight the structural and evolutionary plasticity of photosynthetic systems, illustrating how endosymbiotic acquisition and lineage-specific adaptation shape divergent light-harvesting strategies.No potential conflict of interest relevant to this article was reported.eLife Sciences Publications, LtdActa Medica Okayama2050-084X132024Structural basis for molecular assembly of fucoxanthin chlorophyll a/c-binding proteins in a diatom photosystem I supercomplexRP99858ENKojiKatoResearch Institute for Interdisciplinary Science and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityYoshikiNakajimaResearch Institute for Interdisciplinary Science and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityJianXingGraduate School of Agriculture, Kyoto UniversityMinoruKumazawaGraduate School of Agriculture, Kyoto UniversityHaruyaOgawaResearch Institute for Interdisciplinary Science and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityJian-RenShenResearch Institute for Interdisciplinary Science and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityKentaroIfukuGraduate School of Agriculture, Kyoto UniversityRyoNagaoFaculty of Agriculture, Shizuoka UniversityPhotosynthetic 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.No potential conflict of interest relevant to this article was reported.American Association for the Advancement of ScienceActa Medica Okayama2375-254811202025Structure of a photosystem I supercomplex from Galdieria sulphuraria close to an ancestral red algaeadv7488ENKojiKatoResearch institute for interdisciplinary Science and Graduate School of environ-mental, life, natural Science and technology, Okayama UniversityMinoruKumazawaGraduate School of Agriculture, Kyoto UniversityYoshikiNakajimaResearch institute for interdisciplinary Science and Graduate School of environ-mental, life, natural Science and technology, Okayama UniversityTakehiroSuzukiBiomolecular characterization Unit, RiKen center for Sustainable Resource ScienceNaoshiDohmaeBiomolecular characterization Unit, RiKen center for Sustainable Resource ScienceJian-RenShenResearch institute for interdisciplinary Science and Graduate School of environ-mental, life, natural Science and technology, Okayama UniversityKentaroIfukuGraduate School of Agriculture, Kyoto UniversityRyoNagaoFaculty of Agriculture, Shizuoka UniversityRed algae exhibit unique photosynthetic adaptations, characterized by photosystem I (PSI) supercomplexes containing light-harvesting complexes (LHCs), forming PSI-LHCI supercomplexes. In this study, we solved the PSI-LHCI structure of Galdieria sulphuraria NIES-3638 at 2.19-angstrom resolution using cryo-electron microscopy, revealing a PSI monomer core associated with seven LHCI subunits. Structural analysis uncovered the absence of phylloquinones, the common secondary electron acceptor in PSI of photosynthetic organisms, suggesting adaptation to a benzoquinone-like molecule. Phylogenetic analysis suggests that G. sulphuraria retains traits characteristic of an ancestral red alga, including distinctive LHCI binding and interaction patterns. Variations in LHCI composition and interactions across red algae, particularly in red-lineage chlorophyll a/b-binding-like protein and red algal LHCs, highlight evolutionary divergence and specialization. These findings not only deepen our understanding of red algal PSI-LHCI diversification but also enable us to predict features of an ancestral red algal PSI-LHCI supercomplex, providing a framework to explore evolutionary adaptations from an ancestral red alga.No potential conflict of interest relevant to this article was reported.Nature PortfolioActa Medica Okayama2041-17231612025Structure of a photosystem II-FCPII supercomplex from a haptophyte reveals a distinct antenna organization4175ENRomainLa RoccaResearch Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityKojiKatoResearch Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityPi-ChengTsaiResearch Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityYoshikiNakajimaResearch Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityFusamichiAkitaResearch Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityJian-RenShenResearch Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityHaptophytes 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.eLife Sciences PublicationsActa Medica Okayama2050-084X132024Structural basis for molecular assembly of fucoxanthin chlorophyll a/c-binding proteins in a diatom photosystem I supercomplexRP99858ENKojiKatoResearch Institute for Interdisciplinary Science and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityYoshikiNakajimaResearch Institute for Interdisciplinary Science and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityJianXingGraduate School of Agriculture, Kyoto UniversityMinoruKumazawaGraduate School of Agriculture, Kyoto UniversityHaruyaOgawaResearch Institute for Interdisciplinary Science and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityJian-RenShenResearch Institute for Interdisciplinary Science and Graduate School of Environmental, Life, Natural Science and Technology, Okayama UniversityKentaroIfukuGraduate School of Agriculture, Kyoto UniversityRyoNagaoFaculty of Agriculture, Shizuoka UniversityPhotosynthetic 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.No potential conflict of interest relevant to this article was reported.Springer Science and Business Media LLCActa Medica Okayama0028-083662679992024Oxygen-evolving photosystem II structures during S1–S2–S3 transitions670677ENHongjieLiResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityYoshikiNakajimaResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityErikoNangoInstitute of Multidisciplinary Research for Advanced Materials, Tohoku UniversityShigekiOwadaJapan Synchrotron Radiation Research InstituteDaichiYamadaDepartment of Picobiology, Graduate School of Life Science, University of HyogoKanaHashimotoResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityFangjiaLuoJapan Synchrotron Radiation Research InstituteRieTanakaRIKEN SPring-8 CenterFusamichiAkitaResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityKojiKatoResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityJungminKangRIKEN SPring-8 CenterYasunoriSaitohResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityShunpeiKishiResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityHuaxinYuResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityNaokiMatsubaraResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityHajimeFujiiResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityMichihiroSugaharaJapan Synchrotron Radiation Research InstituteMamoruSuzukiInstitute for Protein Research, Osaka UniversityTetsuyaMasudaDivision of Food and Nutrition, Faculty of Agriculture, Ryukoku UniversityTetsunariKimuraDepartment of Chemistry, Graduate School of Science, Kobe UniversityTran NguyenThaoResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityShinichiroYonekuraResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityLong-JiangYuResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityTakehikoToshaRIKEN SPring-8 CenterKensukeTonoJapan Synchrotron Radiation Research InstituteYasumasaJotiJapan Synchrotron Radiation Research InstituteTakakiHatsuiJapan Synchrotron Radiation Research InstituteMakinaYabashiJapan Synchrotron Radiation Research InstituteMinoruKuboDepartment of Picobiology, Graduate School of Life Science, University of HyogoSoIwataRIKEN SPring-8 CenterHiroshiIsobeResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityKizashiYamaguchiCenter for Quantum Information and Quantum Biology, Osaka UniversityMichihiroSugaResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityJian-RenShenResearch Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama UniversityPhotosystem 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.Nature PortfolioActa Medica Okayama2041-17231412023Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120920ENRyoNagaoResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityKojiKatoResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityTasukuHamaguchiBiostructural Mechanism Laboratory, RIKEN SPring-8 CenterYoshifumiUenoGraduate School of Science, Kobe UniversityNaokiTsuboshitaResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityShotaShimizuResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityMiyuFurutaniGraduate School of Science, Kobe UniversityShigekiEhiraDepartment of Biological Sciences, Graduate School of Science, Tokyo Metropolitan UniversityYoshikiNakajimaResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityKeisukeKawakamiBiostructural Mechanism Laboratory, RIKEN SPring-8 CenterTakehiroSuzukiBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceNaoshiDohmaeBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceSeijiAkimotoGraduate School of Science, Kobe UniversityKojiYonekura Biostructural Mechanism Laboratory, RIKEN SPring-8 CenterJian-RenShenResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityIron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs.No potential conflict of interest relevant to this article was reported.eLIFE SCIENCES PUBL LTDActa Medica Okayama2050-084X112022Structural basis for the absence of low-energy chlorophylls in a photosystem I trimer from Gloeobacter violaceuse73990ENKojiKatoResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityTasukuHamaguchiBiostructural Mechanism Laboratory, RIKEN SPring-8 CenterRyoNagaoResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityKeisukeKawakamiBiostructural Mechanism Laboratory, RIKEN SPring-8 CenterYoshifumiUenoGraduate School of Science, Kobe UniversityTakehiroSuzukiBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceHirokoUchidaResearch Center for Inland Seas, Kobe UniversityAkioMurakamiGraduate School of Science, Kobe UniversityYoshikiNakajimaResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityMakioYokonoInstitute of Low Temperature Science, Hokkaido UniversitySeijiAkimotoGraduate School of Science, Kobe UniversityNaoshiDohmaeBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceKojiYonekuraBiostructural Mechanism Laboratory, RIKEN SPring-8 CenterJian-RenShenResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityPhotosystem I (PSI) is a multi-subunit pigment-protein complex that functions in light-harvesting and photochemical charge-separation reactions, followed by reduction of NADP to NADPH required for CO2 fixation in photosynthetic organisms. PSI from different photosynthetic organisms has a variety of chlorophylls (Chls), some of which are at lower-energy levels than its reaction center P700, a special pair of Chls, and are called low-energy Chls. However, the sites of low-energy Chls are still under debate. Here, we solved a 2.04-& ANGS; resolution structure of a PSI trimer by cryo-electron microscopy from a primordial cyanobacterium Gloeobacter violaceus PCC 7421, which has no low-energy Chls. The structure shows the absence of some subunits commonly found in other cyanobacteria, confirming the primordial nature of this cyanobacterium. Comparison with the known structures of PSI from other cyanobacteria and eukaryotic organisms reveals that one dimeric and one trimeric Chls are lacking in the Gloeobacter PSI. The dimeric and trimeric Chls are named Low1 and Low2, respectively. Low2 is missing in some cyanobacterial and eukaryotic PSIs, whereas Low1 is absent only in Gloeobacter. These findings provide insights into not only the identity of low-energy Chls in PSI, but also the evolutionary changes of low-energy Chls in oxyphototrophs.No potential conflict of interest relevant to this article was reported.Nature PortfolioActa Medica Okayama2041-17231312022Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex1764ENRyoNagaoResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityKojiKatoResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityMinoruKumazawaGraduate School of Biostudies, Kyoto UniversityKentaroIfukuGraduate School of Agriculture, Kyoto UniversityMakioYokonoInstitute of Low Temperature Science, Hokkaido UniversityTakehiroSuzukiBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceNaoshiDohmaeBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceFusamichiAkitaResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversitySeijiAkimotoGraduate School of Science, Kobe UniversityNaoyukiMiyazakiLife Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of TsukubaJian-RenShenResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityFucoxanthin 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 PortfolioActa Medica Okayama2041-17231312022Structure of a tetrameric photosystem I from a glaucophyte alga Cyanophora paradoxa1679ENKojiKatoResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityRyoNagaoResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityYoshifumiUenoGraduate School of Science, Kobe UniversityMakioYokonoInstitute of Low Temperature Science, Hokkaido UniversityTakehiroSuzukiBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceJiangTian-YiResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityNaoshiDohmaeBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceFusamichiAkitaResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversitySeijiAkimotoGraduate School of Science, Kobe UniversityNaoyukiMiyazakiLife Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of TsukubaShenJian-RenResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityPhotosystem 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.SpringerActa Medica Okayama2399-3642412021High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams382ENKojiKatoResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityNaoyukiMiyazakiLife Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of TsukubaTasukuHamaguchiBiostructural Mechanism Laboratory, RIKEN Spring-8 CenterYoshikiNakajimaResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityFusamichiAkitaResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityKojiYonekuraInstitute of Multidisciplinary Research for Advanced Materials, Tohoku UniversityJian-RenShenResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityPhotosystem 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 Okayama2399-3642312020Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins232ENFusamichiAkitaGraduate School of Natural Science and Technology, Okayama UniversityRyoNagaoResearch Institute for Interdisciplinary Science, Okayama UniversityKojiKatoResearch Institute for Interdisciplinary Science, Okayama UniversityYoshikiNakajimaGraduate School of Natural Science and Technology, Okayama UniversityMakioYokonoNippon Flour Mills Co., Ltd., Innovation CenterYoshifumiUenoGraduate School of Science, Kobe UniversityTakehiroSuzukiBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceNaoshiDohmaeBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceJian-RenShen Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversitySeijiAkimotoGraduate School of Science, Kobe UniversityNaoyukiMiyazakiLife Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of TsukubaIron-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 ResearchActa Medica Okayama2041-17231112020Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplexENRyoNagaoResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityKojiKatoResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityKentaroIfukuGraduate School of Biostudies, Kyoto UniversityTakehiroSuzukiBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceMinoruKumazawaFaculty of Agriculture, Kyoto UniversityIkuoUchiyamaNational Institute for Basic Biology, National Institutes of Natural SciencesYasuhiroKashinoGraduate School of Life Science, University of HyogoNaoshiDohmaeBiomolecular Characterization Unit, RIKEN Center for Sustainable Resource ScienceSeijiAkimotoGraduate School of Science,Kobe UniversityJian-RenShenResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityNaoyukiMiyazakiInstitute for Protein Research, Osaka UniversityFusamichiAkitaResearch Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama UniversityPhotosynthetic 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.