Faculty Profiles - SHEN Jian-Ren

Papers - SHEN Jian-Ren

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Aggregation-Induced Excitation-Energy Quenching in Fucoxanthin Chlorophyll a/c-Binding Proteins from the Diatom Phaeodactylum tricornutum

Yoshifumi Ueno, Ou-Yang Li, Jian-Ren Shen, Tatsuya Tomo, Seiji Akimoto, Ryo Nagao

The Journal of Physical Chemistry B 2025.3

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

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

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

Photosynthesis research 163 ( 1 ) 14 - 14 2025.1

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

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

DOI： 10.1007/s11120-024-01134-1

Conformational Flexibility of D1-Glu189: A Crucial Determinant in Substrate Water Selection, Positioning, and Stabilization within the Oxygen-Evolving Complex of Photosystem II

Hiroshi Isobe, Takayoshi Suzuki, Michihiro Suga, Jian-Ren Shen, Kizashi Yamaguchi

ACS OMEGA 9 ( 50 ) 50041 - 50048 2024.12

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Photosynthetic water oxidation is a vital process responsible for producing dioxygen and supplying the energy necessary to sustain life on Earth. This fundamental reaction is catalyzed by the oxygen-evolving complex (OEC) of photosystem II, which houses the Mn4CaO5 cluster as its catalytic core. In this study, we specifically focus on the D1-Glu189 amino acid residue, which serves as a direct ligand to the Mn4CaO5 cluster. Our primary goal is to explore, using density functional theory (DFT), how the conformational flexibility of the D1-Glu189 side chain influences crucial catalytic processes, particularly the selection, positioning, and stabilization of a substrate water molecule within the OEC. Our investigation is based on a hypothesis put forth by Li et al. (Nature, 2024, 626, 670), which suggests that during the transition from the S2 to S3 state, a specific water molecule temporarily coordinating with the Ca ion, referred to as O6*, may exist as a hydroxide ion (OH-). Our results demonstrate a key mechanism by which the detachment of the D1-Glu189 carboxylate group from its coordination with the Ca ion allows the creation of a specialized microenvironment within the OEC that enables the selective attraction of O6* in its deprotonated form (OH-) and stabilizes it at the catalytic metal (MnD) site. Our findings indicate that D1-Glu189 is not only a structural ligand for the Ca ion but may also play an active and dynamic role in the catalytic process, positioning O6* optimally for its subsequent participation in the oxidation sequence during the water-splitting cycle.

DOI： 10.1021/acsomega.4c09981

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

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

eLife 13 2024.10

Publishing type：Research paper (scientific journal) Publisher：eLife Sciences Publications, Ltd

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

DOI： 10.7554/elife.99858.3

Other Link： https://cdn.elifesciences.org/articles/99858/elife-99858-v1.xml

Presence of low-energy chlorophylls d in photosystem I trimer and monomer cores isolated from Acaryochloris sp. NBRC 102871. Reviewed International journal

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

Photosynthesis research 161 ( 3 ) 203 - 212 2024.9

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

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

DOI： 10.1007/s11120-024-01108-3

Structural and spectroscopic insights into fucoxanthin chlorophyll a/c-binding proteins of diatoms in diverse oligomeric states. Reviewed International journal

Cuicui Zhou, Yue Feng, Zhenhua Li, Lili Shen, Xiaoyi Li, Yumei Wang, Guangye Han, Tingyun Kuang, Cheng Liu, Jian-Ren Shen, Wenda Wang

Plant communications 101041 - 101041 2024.7

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

Diatoms, a group of prevalent marine algae, contribute significantly to global primary productivity. Their substantial biomass is linked to enhanced absorption of blue-green light underwater, facilitated by fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs), which exhibit oligomeric diversity across diatom species. Using mild clear native PAGE analysis of solubilized thylakoid membranes, we displayed monomeric, dimeric, trimeric, tetrameric, and pentameric FCPs in diatoms. Mass spectrometry analysis revealed that each oligomeric FCP has a specific protein composition, and together they constitute a large Lhcf family of FCP antennas. In addition, we resolved the structures of the Thalassiosira pseudonana FCP (Tp-FCP) homotrimer and the Chaetoceros gracilis FCP (Cg-FCP) pentamer by cryoelectron microscopy at 2.73-Å and 2.65-Å resolution, respectively. The distinct pigment compositions and organizations of various oligomeric FCPs affect their blue-green light-harvesting, excitation energy transfer pathways. Compared with dimeric and trimeric FCPs, the Cg-FCP tetramer and Cg-FCP pentamer exhibit stronger absorption by Chl c, redshifted and broader Chl a fluorescence emission, and more robust circular dichroism signals originating from Chl a-carotenoid dimers. These spectroscopic characteristics indicate that Chl a molecules in the Cg-FCP tetramer and Cg-FCP pentamer are more heterogeneous than in both dimers and the Tp-FCP trimer. The structural and spectroscopic insights provided by this study contribute to a better understanding of the mechanisms that empower diatoms to adapt to fluctuating light environments.

DOI： 10.1016/j.xplc.2024.101041

Strong interaction of CpcL with photosystem I cores induced in heterocysts of Anabaena sp. PCC 7120 Reviewed

Takehiro Suzuki, Haruya Ogawa, Naoshi Dohmae, Jian-Ren Shen, Shigeki Ehira, Ryo Nagao

microPublication Biology 2024.5

Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll d-containing cyanobacterium. Reviewed International journal

Liangliang Shen, Yuanzhu Gao, Kailu Tang, Ruxi Qi, Lutang Fu, Jing-Hua Chen, Wenda Wang, Xiaomin Ma, Peiyao Li, Min Chen, Tingyun Kuang, Xing Zhang, Jian-Ren Shen, Peiyi Wang, Guangye Han

Science advances 10 ( 8 ) eadk7140 2024.2

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

Acaryochloris marina is a unique cyanobacterium using chlorophyll d (Chl d) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of A. marina associates with a number of prochlorophyte Chl-binding (Pcb) proteins to act as the light-harvesting system. We report here the cryo-electron microscopic structure of a PSII-Pcb megacomplex from A. marina at a 3.6-angstrom overall resolution and a 3.3-angstrom local resolution. The megacomplex is organized as a tetramer consisting of two PSII core dimers flanked by sixteen symmetrically related Pcb proteins, with a total molecular weight of 1.9 megadaltons. The structure reveals the detailed organization of PSII core consisting of 15 known protein subunits and an unknown subunit, the assembly of 4 Pcb antennas within each PSII monomer, and possible pathways of energy transfer within the megacomplex, providing deep insights into energy transfer and dissipation mechanisms within the PSII-Pcb megacomplex involved in far-red light utilization.

DOI： 10.1126/sciadv.adk7140

Structures and organizations of PSI-AcpPCI supercomplexes from red tidal and coral symbiotic photosynthetic dinoflagellates. Reviewed International journal

Xiaoyi Li, Zhenhua Li, Fangfang Wang, Songhao Zhao, Caizhe Xu, Zhiyuan Mao, Jialin Duan, Yue Feng, Yang Yang, Lili Shen, Guanglei Wang, Yanyan Yang, Long-Jiang Yu, Min Sang, Guangye Han, Xuchu Wang, Tingyun Kuang, Jian-Ren Shen, Wenda Wang

Proceedings of the National Academy of Sciences of the United States of America 121 ( 7 ) e2315476121 2024.2

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

Marine photosynthetic dinoflagellates are a group of successful phytoplankton that can form red tides in the ocean and also symbiosis with corals. These features are closely related to the photosynthetic properties of dinoflagellates. We report here three structures of photosystem I (PSI)-chlorophylls (Chls) a/c-peridinin protein complex (PSI-AcpPCI) from two species of dinoflagellates by single-particle cryoelectron microscopy. The crucial PsaA/B subunits of a red tidal dinoflagellate Amphidinium carterae are remarkably smaller and hence losing over 20 pigment-binding sites, whereas its PsaD/F/I/J/L/M/R subunits are larger and coordinate some additional pigment sites compared to other eukaryotic photosynthetic organisms, which may compensate for the smaller PsaA/B subunits. Similar modifications are observed in a coral symbiotic dinoflagellate Symbiodinium species, where two additional core proteins and fewer AcpPCIs are identified in the PSI-AcpPCI supercomplex. The antenna proteins AcpPCIs in dinoflagellates developed some loops and pigment sites as a result to accommodate the changed PSI core, therefore the structures of PSI-AcpPCI supercomplex of dinoflagellates reveal an unusual protein assembly pattern. A huge pigment network comprising Chls a and c and various carotenoids is revealed from the structural analysis, which provides the basis for our deeper understanding of the energy transfer and dissipation within the PSI-AcpPCI supercomplex, as well as the evolution of photosynthetic organisms.

DOI： 10.1073/pnas.2315476121

Oxygen-evolving photosystem II structures during S1-S2-S3 transitions. Reviewed 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

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

Quantifying the Energy Spillover between Photosystems II and I in Cyanobacterial Thylakoid Membranes and Cells. Reviewed

Parveen Akhtar, Fanny Balog-Vig, Wenhui Han, Xingyue Li, Guangye Han, Jian-Ren Shen, Petar H Lambrev

Plant & cell physiology 65 ( 1 ) 95 - 106 2024.1

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

The spatial separation of photosystems I and II (PSI and PSII) is thought to be essential for efficient photosynthesis by maintaining a balanced flow of excitation energy between them. Unlike the thylakoid membranes of plant chloroplasts, cyanobacterial thylakoids do not form tightly appressed grana stacks that enforce strict lateral separation. The coexistence of the two photosystems provides a ground for spillover-excitation energy transfer from PSII to PSI. Spillover has been considered as a pathway of energy transfer from the phycobilisomes to PSI and may also play a role in state transitions as means to avoid overexcitation of PSII. Here, we demonstrate a significant degree of energy spillover from PSII to PSI in reconstituted membranes and isolated thylakoid membranes of Thermosynechococcus (Thermostichus) vulcanus and Synechocystis sp. PCC 6803 by steady-state and time-resolved fluorescence spectroscopy. The quantum yield of spillover in these systems was determined to be up to 40%. Spillover was also found in intact cells but to a considerably lower degree (20%) than in isolated thylakoid membranes. The findings support a model of coexistence of laterally separated microdomains of PSI and PSII in the cyanobacterial cells as well as domains where the two photosystems are energetically connected. The methodology presented here can be applied to probe spillover in other photosynthetic organisms.

DOI： 10.1093/pcp/pcad127

Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana. Reviewed International journal

Songhao Zhao, Lili Shen, Xiaoyi Li, Qiushuang Tao, Zhenhua Li, Caizhe Xu, Cuicui Zhou, Yanyan Yang, Min Sang, Guangye Han, Long-Jiang Yu, Tingyun Kuang, Jian-Ren Shen, Wenda Wang

Nature communications 14 ( 1 ) 8164 - 8164 2023.12

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

Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana.

DOI： 10.1038/s41467-023-44055-8

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

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

2023.10

Publisher：Cold Spring Harbor Laboratory

Abstract

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

DOI： 10.1101/2023.10.25.563911

Structure of a diatom photosystem II supercomplex containing a member of Lhcx family and dimeric FCPII. Reviewed International journal

Yue Feng, Zhenhua Li, Xiaoyi Li, Lili Shen, Xueyang Liu, Cuicui Zhou, Jinyang Zhang, Min Sang, Guangye Han, Wenqiang Yang, Tingyun Kuang, Wenda Wang, Jian-Ren Shen

Science advances 9 ( 43 ) eadi8446 2023.10

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

Diatoms rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We report a unique structure of photosystem II (PSII)-FCPII supercomplex from Thalassiosira pseudonana at 2.68-Å resolution by cryo-electron microscopy. FCPIIs within this PSII-FCPII supercomplex exist in dimers and monomers, and a homodimer and a heterodimer were found to bind to a PSII core. The FCPII homodimer is formed by Lhcf7 and associates with PSII through an Lhcx family antenna Lhcx6_1, whereas the heterodimer is formed by Lhcf6 and Lhcf11 and connects to the core together with an Lhcf5 monomer through Lhca2 monomer. An extended pigment network consisting of diatoxanthins, diadinoxanthins, fucoxanthins, and chlorophylls a/c is revealed, which functions in efficient light harvesting, energy transfer, and dissipation. These results provide a structural basis for revealing the energy transfer and dissipation mechanisms and also for the structural diversity of FCP antennas in diatoms.

DOI： 10.1126/sciadv.adi8446

Structural and functional properties of different types of siphonous LHCII trimers from an intertidal green alga Bryopsis corticulans. Reviewed International journal

Zhenhua Li, Cuicui Zhou, Songhao Zhao, Jinyang Zhang, Xueyang Liu, Min Sang, Xiaochun Qin, Yanyan Yang, Guangye Han, Tingyun Kuang, Jian-Ren Shen, Wenda Wang

Structure (London, England : 1993) 31 ( 10 ) 1247 - 1258 2023.10

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

Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the structure of a siphonous-type LHCII trimer from the intertidal green alga Bryopsis corticulans by X-ray crystallography and cryo-electron microscopy (cryo-EM), and analyzed its functional properties by spectral analysis. The Bryopsis LHCII (Bry-LHCII) structures in both homotrimeric and heterotrimeric form show that green light-absorbing siphonaxanthin and siphonein occupied the sites of lutein and violaxanthin in plant LHCII, and two extra chlorophylls (Chls) b replaced Chls a. Binding of these pigments expands the blue-green light absorption of B. corticulans in the tidal zone. We observed differences between the Bry-LHCII homotrimer crystal and cryo-EM structures, and also between Bry-LHCII homotrimer and heterotrimer cryo-EM structures. These conformational changes may reflect the flexibility of Bry-LHCII, which may be required to adapt to light fluctuations from tidal rhythms.

DOI： 10.1016/j.str.2023.08.001

Tight association of CpcL with photosystem I in Anabaena sp. PCC 7120 grown under iron-deficient conditions. Reviewed International journal

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

Biochimica et biophysica acta. Bioenergetics 148993 - 148993 2023.6

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

Phycobilisomes (PBSs), which are huge pigment-protein complexes displaying distinctive color variations, bind to photosystem cores for excitation-energy transfer. It is known that the isolation of supercomplexes consisting of PBSs and photosystem I (PSI) or PBSs and photosystem II (PSII) is challenging due to weak interactions between PBSs and the photosystem cores. In this study, we succeeded in purifying PSI-monomer-PBS and PSI-dimer-PBS supercomplexes from the cyanobacterium Anabaena sp. PCC 7120 grown under iron-deficient conditions by anion-exchange chromatography, followed by trehalose density gradient centrifugation. The absorption spectra of the two types of supercomplexes showed apparent bands originating from PBSs, and their fluorescence-emission spectra exhibited characteristic peaks of PBSs. Two-dimensional blue-native (BN)/SDS-PAGE of the two samples showed a band of CpcL, which is a linker protein of PBS, in addition to PsaA/B subunits. Since interactions of PBSs with PSI are easily dissociated during BN-PAGE using thylakoids from this cyanobacterium grown under iron-replete conditions, it is suggested that iron deficiency for Anabaena induces tight associations of CpcL with PSI, resulting in the formation of PSI-monomer-PBS and PSI-dimer-PBS supercomplexes. Based on these findings, we discuss interactions of PBSs with PSI in Anabaena in response to growth conditions.

DOI： 10.1016/j.bbabio.2023.148993

Structural insights into the action mechanisms of artificial electron acceptors in photosystem II. Reviewed International journal

Shinji Kamada, Yoshiki Nakajima, Jian-Ren Shen

The Journal of biological chemistry 299 ( 7 ) 104839 - 104839 2023.5

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

Photosystem II (PSII) utilizes light energy to split water, and the electrons extracted from water are transferred to QB, a plastoquinone molecule bound to the D1 subunit of PSII. Many artificial electron acceptors (AEAs) with molecular structures similar to that of plastoquinone can accept electrons from PSII. However, the molecular mechanism by which AEAs act on PSII is unclear. Here, we solved the crystal structure of PSII treated with three different AEAs, 2,5-dibromo-1,4-benzoquinone, 2,6-dichloro-1,4-benzoquinone, and 2-phenyl-1,4-benzoquinone, at 1.95 to 2.10 Å resolution. Our results show that all AEAs substitute for QB and are bound to the QB-binding site (QB site) to receive electrons, but their binding strengths are different, resulting in differences in their efficiencies to accept electrons. The acceptor 2-phenyl-1,4-benzoquinone binds most weakly to the QB site and showed the highest oxygen-evolving activity, implying a reverse relationship between the binding strength and oxygen-evolving activity. In addition, a novel quinone-binding site, designated the QD site, was discovered, which is located in the vicinity of QB site and close to QC site, a binding site reported previously. This QD site is expected to play a role as a channel or a storage site for quinones to be transported to the QB site. These results provide the structural basis for elucidating the actions of AEAs and exchange mechanism of QB in PSII and also provide information for the design of more efficient electron acceptors.

DOI： 10.1016/j.jbc.2023.104839

Isolation and characterization of trimeric and monomeric PSI cores from Acaryochloris marina MBIC11017 Reviewed

Ryo Nagao, Haruya Ogawa, Naoki Tsuboshita, Koji Kato, Reona Toyofuku, Tatsuya Tomo, Jian-Ren Shen

Photosynthesis Research 2023.5

Structural insights into a unique PSI-LHCI-LHCII-Lhcb9 supercomplex from moss Physcomitrium patens. Reviewed International journal

Song Zhang, Kailu Tang, Qiujing Yan, Xingyue Li, Liangliang Shen, Wenda Wang, Yi-Kun He, Tingyun Kuang, Guangye Han, Jian-Ren Shen, Xing Zhang

Nature plants 9 ( 5 ) 832 - 846 2023.5

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

Photosystem I (PSI) possesses a variable supramolecular organization among different photosynthetic organisms to adapt to different light environments. Mosses are evolutionary intermediates that diverged from aquatic green algae and evolved into land plants. The moss Physcomitrium patens (P. patens) has a light-harvesting complex (LHC) superfamily more diverse than those of green algae and higher plants. Here, we solved the structure of a PSI-LHCI-LHCII-Lhcb9 supercomplex from P. patens at 2.68 Å resolution using cryo-electron microscopy. This supercomplex contains one PSI-LHCI, one phosphorylated LHCII trimer, one moss-specific LHC protein, Lhcb9, and one additional LHCI belt with four Lhca subunits. The complete structure of PsaO was observed in the PSI core. One Lhcbm2 in the LHCII trimer interacts with PSI core through its phosphorylated N terminus, and Lhcb9 mediates assembly of the whole supercomplex. The complicated pigment arrangement provided important information for possible energy-transfer pathways from the peripheral antennae to the PSI core.

DOI： 10.1038/s41477-023-01401-4

Development of serial X-ray fluorescence holography for radiation-sensitive protein crystals. Reviewed International journal

Artoni Kevin R Ang, Yasufumi Umena, Ayana Sato-Tomita, Naoya Shibayama, Naohisa Happo, Riho Marumi, Yuta Yamamoto, Koji Kimura, Naomi Kawamura, Yu Takano, Tomohiro Matsushita, Yuji C Sasaki, Jian Ren Shen, Kouichi Hayashi

Journal of synchrotron radiation 30 ( Pt 2 ) 368 - 378 2023.3

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

X-ray fluorescence holography (XFH) is a powerful atomic resolution technique capable of directly imaging the local atomic structure around atoms of a target element within a material. Although it is theoretically possible to use XFH to study the local structures of metal clusters in large protein crystals, the experiment has proven difficult to perform, especially on radiation-sensitive proteins. Here, the development of serial X-ray fluorescence holography to allow the direct recording of hologram patterns before the onset of radiation damage is reported. By combining a 2D hybrid detector and the serial data collection used in serial protein crystallography, the X-ray fluorescence hologram can be directly recorded in a fraction of the measurement time needed for conventional XFH measurements. This approach was demonstrated by obtaining the Mn Kα hologram pattern from the protein crystal Photosystem II without any X-ray-induced reduction of the Mn clusters. Furthermore, a method to interpret the fluorescence patterns as real-space projections of the atoms surrounding the Mn emitters has been developed, where the surrounding atoms produce large dark dips along the emitter-scatterer bond directions. This new technique paves the way for future experiments on protein crystals that aim to clarify the local atomic structures of their functional metal clusters, and for other related XFH experiments such as valence-selective XFH or time-resolved XFH.

DOI： 10.1107/S1600577522011833

Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120. Reviewed International journal

Ryo Nagao, Koji Kato, Tasuku Hamaguchi, Yoshifumi Ueno, Naoki Tsuboshita, Shota Shimizu, Miyu Furutani, Shigeki Ehira, Yoshiki Nakajima, Keisuke Kawakami, Takehiro Suzuki, Naoshi Dohmae, Seiji Akimoto, Koji Yonekura, Jian-Ren Shen

Nature communications 14 ( 1 ) 920 - 920 2023.2

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

Iron-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.

DOI： 10.1038/s41467-023-36504-1

Biochemical and spectroscopic characterization of PSI-LHCI from the red alga Cyanidium caldarium. Reviewed International journal

Ryo Nagao, Yoshifumi Ueno, Miyu Furutani, Koji Kato, Jian-Ren Shen, Seiji Akimoto

Photosynthesis research 2023.2

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

Light-harvesting complexes (LHCs) have been diversified in oxygenic photosynthetic organisms, and play an essential role in capturing light energy which is transferred to two types of photosystem cores to promote charge-separation reactions. Red algae are one of the groups of photosynthetic eukaryotes, and their chlorophyll (Chl) a-binding LHCs are specifically associated with photosystem I (PSI). In this study, we purified three types of preparations, PSI-LHCI supercomplexes, PSI cores, and isolated LHCIs, from the red alga Cyanidium caldarium, and examined their properties. The polypeptide bands of PSI-LHCI showed characteristic PSI and LHCI components without contamination by other proteins. The carotenoid composition of LHCI displayed zeaxanthins, β-cryptoxanthins, and β-carotenes. Among the carotenoids, zeaxanthins were enriched in LHCI. On the contrary, both zeaxanthins and β-cryptoxanthins could not be detected from PSI, suggesting that zeaxanthins and β-cryptoxanthins are bound to LHCI but not PSI. A Qy peak of Chl a in the absorption spectrum of LHCI was shifted to a shorter wavelength than those in PSI and PSI-LHCI. This tendency is in line with the result of fluorescence-emission spectra, in which the emission maxima of PSI-LHCI, PSI, and LHCI appeared at 727, 719, and 677 nm, respectively. Time-resolved fluorescence spectra of LHCI represented no 719 and 727-nm fluorescence bands from picoseconds to nanoseconds. These results indicate that energy levels of Chls around/within LHCIs and within PSI are changed by binding LHCIs to PSI. Based on these findings, we discuss the expression, function, and structure of red algal PSI-LHCI supercomplexes.

DOI： 10.1007/s11120-023-00999-y

Photoinduced chlorophyll charge transfer state identified in the light-harvesting complex II from a marine green alga Bryopsis corticulans. Reviewed International journal

Dan-Hong Li, Wenda Wang, Cuicui Zhou, Yan Zhang, Songhao Zhao, Yi-Ming Zhou, Rong-Yao Gao, Hai-Dan Yao, Li-Min Fu, Peng Wang, Jian-Ren Shen, Tingyun Kuang, Jian-Ping Zhang

iScience 26 ( 1 ) 105761 - 105761 2023.1

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

The light-harvesting complex II of Bryopsis corticulans (B-LHCII), a green alga, differs from that of spinach (S-LHCII) in chlorophyll (Chl) and carotenoid (Car) compositions. We investigated ultrafast excitation dynamics of B-LHCII with visible-to-near infrared time-resolved absorption spectroscopy. Absolute fluorescence quantum yield (Φ FL) of LHCII and spectroelectrochemical (SEC) spectra of Chl a and b were measured to assist the spectral analysis. Red-light excitation at Chl Qy-band, but not Car-band, induced transient features resembling the characteristic SEC spectra of Chl a ⋅+ and Chl b ⋅-, indicating ultrafast photogeneration of Chl-Chl charge transfer (CT) species; Φ FL and 3Car∗ declined whereas CT species increased upon prolonging excitation wavelength, showing positive correlation of 1Chl∗ deactivation with Chl-Chl CT formation. Moreover, ultrafast Chl b-to-Chl a and Car-to-Chl singlet excitation transfer were illustrated. The red-light induction of Chl-Chl CT species, as also observed for S-LHCII, is considered a general occurrence for LHCIIs in light-harvesting form.

DOI： 10.1016/j.isci.2022.105761

Cryo-electron microscopy structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium. Reviewed International journal

Jing-Hua Chen, Weiwei Wang, Chen Wang, Tingyun Kuang, Jian-Ren Shen, Xing Zhang

Journal of integrative plant biology 65 ( 1 ) 223 - 234 2023.1

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

The photosynthetic reaction center complex (RCC) of green sulfur bacteria (GSB) consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna-Matthews-Olson (FMO). Functionally, FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs. In vivo, one RC was found to bind two FMOs, however, the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified. Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9 Å resolution by cryo-electron microscopy. The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously. We also observed two new subunits (PscE and PscF) and the N-terminal transmembrane domain of a cytochrome-containing subunit (PscC) in the structure. These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex. A new bacteriochlorophyll (numbered as 816) was identified at the interspace between PscF and PscA-1, causing an asymmetrical energy transfer from the two FMO trimers to RC core. Based on the structure, we propose an energy transfer network within this photosynthetic apparatus.

DOI： 10.1111/jipb.13367

Characterization of the Rate-Limiting Steps in the Dark-To-Light Transitions of Closed Photosystem II: Temperature Dependence and Invariance of Waiting Times during Multiple Light Reactions. Reviewed International journal

Melinda Magyar, Gábor Sipka, Wenhui Han, Xingyue Li, Guangye Han, Jian-Ren Shen, Petar H Lambrev, Győző Garab

International journal of molecular sciences 24 ( 1 ) 2022.12

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

Rate-limiting steps in the dark-to-light transition of Photosystem II (PSII) were discovered by measuring the variable chlorophyll-a fluorescence transients elicited by single-turnover saturating flashes (STSFs). It was shown that in diuron-treated samples: (i) the first STSF, despite fully reducing the QA quinone acceptor molecule, generated only an F1(<Fm) fluorescence level; (ii) to produce the maximum (Fm) level, additional excitations were required, which, however, (iii) were effective only with sufficiently long Δτ waiting times between consecutive STSFs. Detailed studies revealed the gradual formation of the light-adapted charge-separated state, PSIIL. The data presented here substantiate this assignment: (i) the Δτ1/2 half-increment rise (or half-waiting) times of the diuron-treated isolated PSII core complexes (CCs) of Thermostichus vulcanus and spinach thylakoid membranes displayed similar temperature dependences between 5 and −80 °C, with substantially increased values at low temperatures; (ii) the Δτ1/2 values in PSII CC were essentially invariant on the Fk−to-Fk+1 (k = 1−4) increments both at 5 and at −80 °C, indicating the involvement of the same physical mechanism during the light-adaptation process of PSIIL. These data are in harmony with the earlier proposed role of dielectric relaxation processes in the formation of the light-adapted charge-separated state and in the variable chlorophyll-a fluorescence of PSII.

DOI： 10.3390/ijms24010094

Structure of a tetrameric photosystem I from a glaucophyte alga Cyanophora paradoxa Reviewed

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

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

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 Reviewed

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

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

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

Natural and artificial photosynthesis: fundamentals, progress, and challenges. Reviewed International journal

Mohammad Mahdi Najafpour, Jian-Ren Shen, Suleyman I Allakhverdiev

Photosynthesis research 154 ( 3 ) 229 - 231 2022.12

A Possible Mechanism for Aggregation-Induced Chlorophyll Fluorescence Quenching in Light-Harvesting Complex II from the Marine Green Alga Bryopsis corticulans. Reviewed International journal

Hai-Dan Yao, Dan-Hong Li, Rong-Yao Gao, Cuicui Zhou, Wenda Wang, Peng Wang, Jian-Ren Shen, Tingyun Kuang, Jian-Ping Zhang

The journal of physical chemistry. B 126 ( 46 ) 9580 - 9590 2022.11

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

The light-harvesting complex II of a green alga Bryopsis corticulans (B-LHCII) is peculiar in that it contains siphonein and siphonaxathin as carotenoid (Car). Since the S1 state of siphonein and siphonaxathin lies substantially higher than the Qy state of chlorophyll a (Chl a), the Chl a(Qy)-to-Car(S1) excitation energy transfer is unfeasible. To understand the photoprotective mechanism of algal photosynthesis, we investigated the influence of temperature on the excitation dynamics of B-LHCII in trimeric and aggregated forms. At room temperature, the aggregated form showed a 10-fold decrease in fluorescence intensity and lifetime than the trimeric form. Upon lowering the temperature, the characteristic 680 nm fluorescence (F-680) of B-LHCII in both forms exhibited systematic intensity enhancement and spectral narrowing; however, only the aggregated form showed a red emission extending over 690-780 nm (F-RE) with pronounced blueshift, lifetime prolongation, and intensity boost. The remarkable T-dependence of F-RE is ascribed to the Chl-Chl charge transfer (CT) species involved directly in the aggregation-induced Chl deactivation. The CT-quenching mechanism, which is considered to be crucial for B. corticulans photoprotection, draws strong support from the positive correlation of the Chl deactivation rate with the CT state population, as revealed by comparing the fluorescence dynamics of B-LHCII with that of the plant LHCII.

DOI： 10.1021/acs.jpcb.2c05823

Crystal structures of photosystem II from a cyanobacterium expressing psbA2 in comparison to psbA3 reveal differences in the D1 subunit. Reviewed International journal

Yoshiki Nakajima, Natsumi Ugai-Amo, Naoki Tone, Akiko Nakagawa, Masako Iwai, Masahiko Ikeuchi, Miwa Sugiura, Michihiro Suga, Jian-Ren Shen

The Journal of biological chemistry 298 ( 12 ) 102668 - 102668 2022.11

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

Three psbA genes (psbA1, psbA2, and psbA3) encoding the D1 subunit of photosystem II (PSII) are present in the thermophilic cyanobacterium Thermosynechococcus elongatus and are expressed differently in response to changes in the growth environment. To clarify the functional differences of the D1 protein expressed from these psbA genes, PSII dimers from two strains, each expressing only one psbA gene (psbA2 or psbA3), were crystallized, and we analyzed their structures at resolutions comparable to previously studied PsbA1-PSII. Our results showed that the hydrogen bond between pheophytin/D1 (PheoD1) and D1-130 became stronger in PsbA2- and PsbA3-PSII due to change of Gln to Glu, which partially explains the increase in the redox potential of PheoD1 observed in PsbA3. In PsbA2, one hydrogen bond was lost in PheoD1 due to the change of D1-Y147F, which may explain the decrease in stability of PheoD1 in PsbA2. Two water molecules in the Cl-1 channel were lost in PsbA2 due to the change of D1-P173M, leading to the narrowing of the channel, which may explain the lower efficiency of the S-state transition beyond S2 in PsbA2-PSII. In PsbA3-PSII, a hydrogen bond between D1-Ser270 and a sulfoquinovosyl-diacylglycerol molecule near QB disappeared due to the change of D1-Ser270 in PsbA1 and PsbA2 to D1-Ala270. This may result in an easier exchange of bound QB with free plastoquinone, hence an enhancement of oxygen evolution in PsbA3-PSII due to its high QB exchange efficiency. These results provide a structural basis for further functional examination of the three PsbA variants.

DOI： 10.1016/j.jbc.2022.102668

Roles of the Flexible Primary Coordination Sphere of the Mn4CaOx Cluster: What Are the Immediate Decay Products of the S3 State? Reviewed International journal

Hiroshi Isobe, Mitsuo Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi

The journal of physical chemistry. B 126 ( 38 ) 7212 - 7228 2022.9

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

The primary coordination sphere of the multinuclear cofactor (Mn4CaOx) in the oxygen-evolving complex (OEC) of photosystem II is absolutely conserved to maintain its structure and function. Recent time-resolved serial femtosecond crystallography identified large reorganization of the primary coordination sphere in the S2 to S3 transition, which elicits a cascade of events involving Mn oxidation and water molecule binding to a putative catalytic Mn site. We examined how the crystallographic fields, created by transient conformational states of the OEC at various time points, affect the thermodynamics of various isomers of the Mn cluster using DFT calculations, with an aim of comprehending the functional roles of the flexible primary coordination sphere in the S2 to S3 transition and in the recovery of the S2 state. The results show that the relative movements of surrounding residues change the size and shape of the cavity of the cluster and thereby affect the thermodynamics of various catalytic intermediates as well as the ability to capture a new water molecule at a coordinatively unsaturated site. The implication of these findings is that the protein dynamics may serve to gate the catalytic reaction efficiently by controlling the sequence of Mn oxidation/reduction and water binding/release. This interpretation is consistent with EPR experiments; g ∼ 5 and g ∼ 3 signals obtained after near-infrared (NIR) excitation of the S3 state at 4 K and a g ∼ 5 only signal produced after prolonged incubation of the S3 state at 77 K can be best explained as originating from water-bound S2 clusters (Stotal = 7/2) under a S3 ligand field, i.e., the immediate one-electron reduction products of the oxyl-oxo (Stotal = 6) and hydroxo-oxo (Stotal = 3) species in the S3 state.

DOI： 10.1021/acs.jpcb.2c02596

Simulating the low-temperature, metastable electrochromism of Photosystem I: Applications to Thermosynechococcus vulcanus and Chroococcidiopsis thermalis. Reviewed International journal

J Langley, R Purchase, S Viola, A Fantuzzi, G A Davis, Jian-Ren Shen, A W Rutherford, E Krausz, N Cox

The Journal of chemical physics 157 ( 12 ) 125103 - 125103 2022.9

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

Low-temperature, metastable electrochromism has been used as a tool to assign pigments in Photosystem I (PS I) from Thermosynechococcus vulcanus and both the white light and far-red light (FRL) forms of Chroococcidiopsis thermalis. We find that a minimum of seven pigments is required to satisfactorily model the electrochromism of PS I. Using our model, we provide a short list of candidates for the chlorophyll f pigment in FRL C. thermalis that absorbs at 756 nm, whose identity, to date, has proven to be controversial. Specifically, we propose the linker pigments A40 and B39 and two antenna pigments A26 and B24 as defined by crystal structure 1JB0. The pros and cons of these assignments are discussed, and we propose further experiments to better understand the functioning of FRL C. thermalis.

DOI： 10.1063/5.0100431

Excited-state intermediates in a designer protein encoding a phototrigger caught by an X-ray free-electron laser. Reviewed International journal

Xiaohong Liu, Pengcheng Liu, Hongjie Li, Zhen Xu, Lu Jia, Yan Xia, Minling Yu, Wenqin Tang, Xiaolei Zhu, Chao Chen, Yuanlin Zhang, Eriko Nango, Rie Tanaka, Fangjia Luo, Koji Kato, Yoshiki Nakajima, Shunpei Kishi, Huaxin Yu, Naoki Matsubara, Shigeki Owada, Kensuke Tono, So Iwata, Long-Jiang Yu, Jian-Ren Shen, Jiangyun Wang

Nature chemistry 14 ( 9 ) 1054 - 1060 2022.9

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

One of the primary objectives in chemistry research is to observe atomic motions during reactions in real time. Although X-ray free-electron lasers (XFELs) have facilitated the capture of reaction intermediates using time-resolved serial femtosecond crystallography (TR-SFX), only a few natural photoactive proteins have been investigated using this method, mostly due to the lack of suitable phototriggers. Here we report the genetic encoding of a xanthone amino acid (FXO), as an efficient phototrigger, into a rationally designed human liver fatty-acid binding protein mutant (termed XOM), which undergoes photo-induced C-H bond transformation with high selectivity and quantum efficiency. We solved the structures of XOM before and 10-300 ns after flash illumination, at 1.55-1.70 Å resolutions, and captured the elusive excited-state intermediates responsible for precise C-H bond activation. We expect that most redox enzymes can now be investigated by TR-SFX, using our method, to reveal reaction intermediates key for their efficiency and selectivity.

DOI： 10.1038/s41557-022-00992-3

Exciton quenching by oxidized chlorophyll Z across the two adjacent monomers in a photosystem II core dimer Reviewed

Ahmed Mohamed, Shunsuke Nishi, Keisuke Kawakami, Jian-Ren Shen, Shigeru Itoh, Hiroshi Fukumura, Yutaka Shibata

Photosynthesis Research 2022.8

Excitation relaxation dynamics of carotenoids constituting the diadinoxanthin cycle Reviewed

Kohei Kagatani, Ryo Nagao, Jian-Ren Shen, Yumiko Yamano, Shinichi Takaichi, Seiji Akimoto

Photosynthesis Research 2022.8

Effects of mutations of D1-R323, D1-N322, D1-D319, D1-H304 on the functioning of photosystem II in Thermosynechococcus vulcanus. Reviewed International journal

Qingjun Zhu, Yanyan Yang, Yanan Xiao, Wenhui Han, Xingyue Li, Wenda Wang, Tingyun Kuang, Jian-Ren Shen, Guangye Han

Photosynthesis research 152 ( 2 ) 193 - 206 2022.5

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

Photosystem II (PSII) has a number of hydrogen-bonding networks connecting the manganese cluster with the lumenal bulk solution. The structure of PSII from Thermosynechococcus vulcanus (T. vulcanus) showed that D1-R323, D1-N322, D1-D319 and D1-H304 are involved in one of these hydrogen-bonding networks located in the interfaces between the D1, CP43 and PsbV subunits. In order to investigate the functions of these residues in PSII, we generated seven site-directed mutants D1-R323A, D1-R323E, D1-N322R, D1-D319L, D1-D319R, D1-D319Y and D1-H304D of T. vulcanus and examined the effects of these mutations on the growth and functions of the oxygen-evolving complex. The photoautotrophic growth rates of these mutants were similar to that of the wild type, whereas the oxygen-evolving activities of the mutant cells were decreased differently to 63-91% of that of the wild type at pH 6.5. The mutant cells showed a higher relative activity at higher pH region than the wild type cells, suggesting that higher pH facilitated proton egress in the mutants. In addition, oxygen evolution of thylakoid membranes isolated from these mutants showed an apparent decrease compared to that of the cells. This is due to the loss of PsbU during purification of the thylakoid membranes. Moreover, PsbV was also lost in the PSII core complexes purified from the mutants. Taken together, D1-R323, D1-N322, D1-D319 and D1-H304 are vital for the optimal function of oxygen evolution and functional binding of extrinsic proteins to PSII core, and may be involved in the proton egress pathway mediated by YZ.

DOI： 10.1007/s11120-022-00920-z

Ultrafast excitation quenching by the oxidized photosystem II reaction center. Reviewed International journal

Parveen Akhtar, Gábor Sipka, Wenhui Han, Xingyue Li, Guangye Han, Jian-Ren Shen, Győző Garab, Howe-Siang Tan, Petar H Lambrev

The Journal of chemical physics 156 ( 14 ) 145101 - 145101 2022.4

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

Photosystem II (PSII) is the pigment-protein complex driving the photoinduced oxidation of water and reduction of plastoquinone in all oxygenic photosynthetic organisms. Excitations in the antenna chlorophylls are photochemically trapped in the reaction center (RC) producing the chlorophyll-pheophytin radical ion pair P+ Pheo-. When electron donation from water is inhibited, the oxidized RC chlorophyll P+ acts as an excitation quencher, but knowledge on the kinetics of quenching is limited. Here, we used femtosecond transient absorption spectroscopy to compare the excitation dynamics of PSII with neutral and oxidized RC (P+). We find that equilibration in the core antenna has a major lifetime of about 300 fs, irrespective of the RC redox state. Two-dimensional electronic spectroscopy revealed additional slower energy equilibration occurring on timescales of 3-5 ps, concurrent with excitation trapping. The kinetics of PSII with open RC can be described well with previously proposed models according to which the radical pair P+ Pheo- is populated with a main lifetime of about 40 ps, which is primarily determined by energy transfer between the core antenna and the RC chlorophylls. Yet, in PSII with oxidized RC (P+), fast excitation quenching was observed with decay lifetimes as short as 3 ps and an average decay lifetime of about 90 ps, which is shorter than the excited-state lifetime of PSII with open RC. The underlying mechanism of this extremely fast quenching prompts further investigation.

DOI： 10.1063/5.0086046

Structural basis for the absence of low-energy chlorophylls in a photosystem I trimer from Gloeobacter violaceus Reviewed

Koji Kato, Tasuku Hamaguchi, Ryo Nagao, Keisuke Kawakami, Yoshifumi Ueno, Takehiro Suzuki, Hiroko Uchida, Akio Murakami, Yoshiki Nakajima, Makio Yokono, Seiji Akimoto, Naoshi Dohmae, Koji Yonekura, Jian-Ren Shen

eLife 11 2022.4

Publishing type：Research paper (scientific journal) Publisher：eLife Sciences Publications, Ltd

Photosystem 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-Å 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.

DOI： 10.7554/elife.73990

Other Link： https://cdn.elifesciences.org/articles/73990/elife-73990-v1.xml

Structure, Function, and Variations of the Photosystem I-Antenna Supercomplex from Different Photosynthetic Organisms. Reviewed International journal

Jian-Ren Shen

Sub-cellular biochemistry 99 351 - 377 2022

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

Photosystem I (PSI) is a protein complex functioning in light-induced charge separation, electron transfer, and reduction reactions of ferredoxin in photosynthesis, which finally results in the reduction of NAD(P)- to NAD(P)H required for the fixation of carbon dioxide. In eukaryotic algae, PSI is associated with light-harvesting complex I (LHCI) subunits, forming a PSI-LHCI supercomplex. LHCI harvests and transfers light energy to the PSI core, where charge separation and electron transfer reactions occur. During the course of evolution, the number and sequences of protein subunits and the pigments they bind in LHCI change dramatically depending on the species of organisms, which is a result of adaptation of organisms to various light environments. In this chapter, I will describe the structure of various PSI-LHCI supercomplexes from different organisms solved so far either by X-ray crystallography or by cryo-electron microscopy, with emphasis on the differences in the number, structures, and association patterns of LHCI subunits associated with the PSI core found in different organisms.

DOI： 10.1007/978-3-031-00793-4_11

Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare. Reviewed International journal

Liangliang Shen, Kailu Tang, Wenda Wang, Chen Wang, Hangjun Wu, Zhiyuan Mao, Shaoya An, Shenghai Chang, Tingyun Kuang, Jian-Ren Shen, Guangye Han, Xing Zhang

Nature 2021.12

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

The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET)1-3. The NDH complex associates with PSI to form the PSI-NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI-NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI-NDH is composed of two copies of the PSI-light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI-NDH-dependent CET.

DOI： 10.1038/s41586-021-04277-6

Structural basis for high selectivity of a rice silicon channel Lsi1 Reviewed

Yasunori Saitoh, Namiki Mitani-Ueno, Keisuke Saito, Kengo Matsuki, Sheng Huang, Lingli Yang, Naoki Yamaji, Hiroshi Ishikita, Jian-Ren Shen, Jian Feng Ma, Michihiro Suga

Nature Communications 12 ( 1 ) 2021.12

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

<title>Abstract</title>Silicon (Si), the most abundant mineral element in the earth’s crust, is taken up by plant roots in the form of silicic acid through Low silicon rice 1 (Lsi1). Lsi1 belongs to the Nodulin 26-like intrinsic protein subfamily in aquaporin and shows high selectivity for silicic acid. To uncover the structural basis for this high selectivity, here we show the crystal structure of the rice Lsi1 at a resolution of 1.8 Å. The structure reveals transmembrane helical orientations different from other aquaporins, characterized by a unique, widely opened, and hydrophilic selectivity filter (SF) composed of five residues. Our structural, functional, and theoretical investigations provide a solid structural basis for the Si uptake mechanism in plants, which will contribute to secure and sustainable rice production by manipulating Lsi1 selectivity for different metalloids.

DOI： 10.1038/s41467-021-26535-x

Other Link： https://www.nature.com/articles/s41467-021-26535-x

Molecular phylogeny of fucoxanthin‐chlorophyll a / c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity Reviewed

Minoru Kumazawa, Hiroyo Nishide, Ryo Nagao, Natsuko Inoue‐Kashino, Jian‐Ren Shen, Takeshi Nakano, Ikuo Uchiyama, Yasuhiro Kashino, Kentaro Ifuku

Physiologia Plantarum 174 ( 1 ) 2021.11

Excitation-energy transfer in heterocysts isolated from the cyanobacterium Anabaena sp. PCC 7120 as studied by time-resolved fluorescence spectroscopy. Reviewed International journal

Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Yoshiki Nakajima, Takehiro Suzuki, Ka-Ho Kato, Naoki Tsuboshita, Naoshi Dohmae, Jian-Ren Shen, Shigeki Ehira, Seiji Akimoto

Biochimica et biophysica acta. Bioenergetics 1863 ( 1 ) 148509 - 148509 2021.11

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

Heterocysts are formed in filamentous heterocystous cyanobacteria under nitrogen-starvation conditions, and possess a very low amount of photosystem II (PSII) complexes than vegetative cells. Molecular, morphological, and biochemical characterizations of heterocysts have been investigated; however, excitation-energy dynamics in heterocysts are still unknown. In this study, we examined excitation-energy-relaxation processes of pigment-protein complexes in heterocysts isolated from the cyanobacterium Anabaena sp. PCC 7120. Thylakoid membranes from the heterocysts showed no oxygen-evolving activity under our experimental conditions and no thermoluminescence-glow curve originating from charge recombination of S2QA-. Two dimensional blue-native/SDS-PAGE analysis exhibits tetrameric, dimeric, and monomeric photosystem I (PSI) complexes but almost no dimeric and monomeric PSII complexes in the heterocyst thylakoids. The steady-state fluorescence spectrum of the heterocyst thylakoids at 77 K displays both characteristic PSI fluorescence and unusual PSII fluorescence different from the fluorescence of PSII dimer and monomer complexes. Time-resolved fluorescence spectra at 77 K, followed by fluorescence decay-associated spectra, showed different PSII and PSI fluorescence bands between heterocysts and vegetative thylakoids. Based on these findings, we discuss excitation-energy-transfer mechanisms in the heterocysts.

DOI： 10.1016/j.bbabio.2021.148509

The importance of identifying the true catalyst when using Randles-Sevcik equation to calculate turnover frequency Reviewed

Zahra Abdi, Matthias Vandichel, Alla S. Sologubenko, Marc-Georg Willinger, Jian-Ren Shen, Suleyman I. Allakhverdiev, Mohammad Mahdi Najafpour

International Journal of Hydrogen Energy 46 ( 76 ) 37774 - 37781 2021.11

Language：English Publishing type：Research paper (scientific journal) Publisher：Elsevier Ltd

Water splitting will become important to store excess renewable electrical energy into hydrogen. Although the oxygen-evolution reaction (OER) by water oxidation is a critical reaction for water splitting, further investigations are needed to find the details of the OER mechanism for various electrocatalysts. More in particular for homogeneous electrocatalysts, the Randles-Sevcik equation has been extensively applied to determine the turnover frequency (TOF). Herein, using vitamin B12 as a case study, we show that the dynamical deposition/dissolution of the heterogeneous catalyst during OER makes the Randles-Sevcik equation too complicated to be used for calculating the TOF. Indeed, the conventionally applied post-characterization methods do not provide sufficient accuracy to prove the homogeneity of OER mechanisms
thus, using the Randles-Sevcik equation to calculate the TOF is not necessarily correct.

DOI： 10.1016/j.ijhydene.2021.09.039

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

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

Biochimica et biophysica acta. Bioenergetics 1862 ( 10 ) 148471 - 148471 2021.10

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

Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer.

DOI： 10.1016/j.bbabio.2021.148471

Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI

Koji Kato, Tasuku Hamaguchi, Ryo Nagao, Keisuke Kawakami, Yoshifumi Ueno, Takehiro Suzuki, Hiroko Uchida, Akio Murakami, Yoshiki Nakajima, Makio Yokono, Seiji Akimoto, Naoshi Dohmae, Koji Yonekura, Jian-Ren Shen

2021.10

Publisher：Cold Spring Harbor Laboratory

Abstract

Photosystem I (PSI) of photosynthetic organisms is a multi-subunit pigment-protein complex and functions in light harvesting and photochemical charge-separation reactions, followed by reduction of NADP to NADPH required for CO₂ fixation. 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 site of low-energy Chls is still under debate. Here, we solved a 2.04-Å resolution structure of a PSI trimer by cryo-electron microscopy from a primitive cyanobacterium Gloeobacter violaceus PCC 7421, which has no low-energy Chls. The structure showed absence of some subunits commonly found in other cyanobacteria, confirming the primitive 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 does not exist in some cyanobacterial and eukaryotic PSIs, whereas Low1 is absent only in Gloeobacter. Since Gloeobacter is susceptible to light, this indicates that Low1 serves as a main photoprotection site in most oxyphototrophs, whereas Low2 is involved in either energy transfer or energy quenching in some of the oxyphototrophs. Thus, these findings provide insights into not only the functional significance of low-energy Chls in PSI, but also the evolutionary changes of low-energy Chls responsible for the photoprotection machinery from photosynthetic prokaryotes to eukaryotes.

DOI： 10.1101/2021.09.29.462462

Structural implications for a phycobilisome complex from the thermophilic cyanobacterium Thermosynechococcus vulcanus. Reviewed International journal

Keisuke Kawakami, Ryo Nagao, Yuhei O Tahara, Tasuku Hamaguchi, Takehiro Suzuki, Naoshi Dohmae, Daisuke Kosumi, Jian-Ren Shen, Makoto Miyata, Koji Yonekura, Nobuo Kamiya

Biochimica et biophysica acta. Bioenergetics 1862 ( 9 ) 148458 - 148458 2021.9

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

Phycobilisomes (PBSs) are huge, water-soluble light-harvesting complexes used by oxygenic photosynthetic organisms. The structures of some subunits of the PBSs, including allophycocyanin (APC) and phycocyanin (PC), have been solved by X-ray crystallography previously. However, there are few reports on the overall structures of PBS complexes in photosynthetic organisms. Here, we report the overall structure of the PBS complex isolated from the cyanobacterium Thermosynechococcus vulcanus, determined by negative-staining electron microscopy (EM). Intact PBS complexes were purified by trehalose density gradient centrifugation with a high-concentration phosphate buffer and then subjected to a gradient-fixation preparation using glutaraldehyde. The final map constructed by the single-particle analysis of EM images showed a hemidiscoidal structure of the PBS, consisting of APC cores and peripheral PC rods. The APC cores are composed of five cylinders: A1, A2, B, C1, and C2. Each of the cylinders is composed of three (A1 and A2), four (B), or two (C1 and C2) APC trimers. In addition, there are eight PC rods in the PBS: one bottom pair (Rb and Rb'), one top pair (Rt and Rt'), and two side pairs (Rs1/Rs1' and Rs2/Rs2'). Comparison with the overall structures of PBSs from other organisms revealed structural characteristics of T. vulcanus PBS.

DOI： 10.1016/j.bbabio.2021.148458

Structural insights into cyanobacterial photosystem II intermediates associated with Psb28 and Tsl0063. Reviewed International journal

Yanan Xiao, Guoqiang Huang, Xin You, Qingjun Zhu, Wenda Wang, Tingyun Kuang, Guangye Han, Sen-Fang Sui, Jian-Ren Shen

Nature plants 7 ( 8 ) 1132 - 1142 2021.8

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

Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyses light-induced water oxidation, leading to the conversion of light energy into chemical energy and the release of dioxygen. We analysed the structures of two Psb28-bound PSII intermediates, Psb28-RC47 and Psb28-PSII, purified from a psbV-deletion strain of the thermophilic cyanobacterium Thermosynechococcus vulcanus, using cryo-electron microscopy. Both Psb28-RC47 and Psb28-PSII bind one Psb28, one Tsl0063 and an unknown subunit. Psb28 is located at the cytoplasmic surface of PSII and interacts with D1, D2 and CP47, whereas Tsl0063 is a transmembrane subunit and binds at the side of CP47/PsbH. Substantial structural perturbations are observed at the acceptor side, which result in conformational changes of the quinone (QB) and non-haem iron binding sites and thus may protect PSII from photodamage during assembly. These results provide a solid structural basis for understanding the assembly process of native PSII.

DOI： 10.1038/s41477-021-00961-7

High-light modification of excitation-energy-relaxation processes in the green flagellate Euglena gracilis. Reviewed International journal

Ryo Nagao, Makio Yokono, Ka-Ho Kato, Yoshifumi Ueno, Jian-Ren Shen, Seiji Akimoto

Photosynthesis research 149 ( 3 ) 303 - 311 2021.5

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

Photosynthetic organisms finely tune their photosynthetic machinery including pigment compositions and antenna systems to adapt to various light environments. However, it is poorly understood how the photosynthetic machinery in the green flagellate Euglena gracilis is modified under high-light conditions. In this study, we examined high-light modification of excitation-energy-relaxation processes in Euglena cells. Oxygen-evolving activity in the cells incubated at 300 µmol photons m-2 s-1 (HL cells) cannot be detected, reflecting severe photodamage to photosystem II (PSII) in vivo. Pigment compositions in the HL cells showed relative increases in 9'-cis-neoxanthin, diadinoxanthin, and chlorophyll b compared with the cells incubated at 30 µmol photons m-2 s-1 (LL cells). Absolute fluorescence spectra at 77 K exhibit smaller intensities of the PSII and photosystem I (PSI) fluorescence in the HL cells than in the LL cells. Absolute fluorescence decay-associated spectra at 77 K of the HL cells indicate suppression of excitation-energy transfer from light-harvesting complexes (LHCs) to both PSI and PSII with the time constant of 40 ps. Rapid energy quenching in LHCs and PSII in the HL cells is distinctly observed by averaged Chl-fluorescence lifetimes. These findings suggest that Euglena modifies excitation-energy-relaxation processes in addition to pigment compositions to deal with excess energy. These results provide insights into the photoprotection strategies of this alga under high-light conditions.

DOI： 10.1007/s11120-021-00849-9

A unique photosystem I reaction center from a chlorophyll d-containing cyanobacterium Acaryochloris marina. Reviewed International journal

Caihuang Xu, Qingjun Zhu, Jing-Hua Chen, Liangliang Shen, Xiaohan Yi, Zihui Huang, Wenda Wang, Min Chen, Tingyun Kuang, Jian-Ren Shen, Xing Zhang, Guangye Han

Journal of integrative plant biology 2021.5

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

Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c6 ) and the reduction of ferredoxin. This catalytic reaction is realized by a transmembrane electron transfer chain consisting of primary electron donor (a special chlorophyll (Chl) pair) and electron acceptors A0 , A1 , and three Fe4 S4 clusters, FX , FA , and FB . Here we report the PSI structure from a Chl d-dominated cyanobacterium Acaryochloris marina at 3.3 Å resolution obtained by single-particle cryo-electron microscopy. The A. marina PSI exists as a trimer with three identical monomers. Surprisingly, the structure reveals a unique composition of electron transfer chain in which the primary electron acceptor A0 is composed of two pheophytin a rather than Chl a found in any other well-known PSI structures. A novel subunit Psa27 is observed in the A. marina PSI structure. In addition, 77 Chls, 13 α-carotenes, two phylloquinones, three Fe-S clusters, two phosphatidyl glycerols, and one monogalactosyl-diglyceride were identified in each PSI monomer. Our results provide a structural basis for deciphering the mechanism of photosynthesis in a PSI complex with Chl d as the dominating pigments and absorbing far-red light.

DOI： 10.1111/jipb.13113

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

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

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

Structure of plant photosystem I-light harvesting complex I supercomplex at 2.4 Å resolution. Reviewed International journal

Jie Wang, Long-Jiang Yu, Wenda Wang, Qiujing Yan, Tingyun Kuang, Xiaochun Qin, Jian-Ren Shen

Journal of integrative plant biology 2021.3

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

Photosystem I (PSI) is one of the two photosystems in photosynthesis, and performs a series of electron transfer reactions leading to the reduction of ferredoxin. In higher plants, PSI is surrounded by four light-harvesting complex I (LHCI) subunits, which harvest and transfer energy efficiently to the PSI core. The crystal structure of PSI-LHCI supercomplex has been analyzed up to 2.6 Å resolution, providing much information on the arrangement of proteins and cofactors in this complicated supercomplex. Here we have optimized crystallization conditions, and analyzed the crystal structure of PSI-LHCI at 2.4 Å resolution. Our structure showed some shift of the LHCI, especially the Lhca4 subunit, away from the PSI core, suggesting the indirect connection and inefficiency of energy transfer from this Lhca subunit to the PSI core. We identified five new lipids in the structure, most of them are located in the gap region between the Lhca subunits and the PSI core. These lipid molecules may play important roles in binding of the Lhca subunits to the core, as well as in the assembly of the supercomplex. The present results thus provide novel information for the elucidation of the mechanisms for the light-energy harvesting, transfer and assembly of this supercomplex. This article is protected by copyright. All rights reserved.

DOI： 10.1111/jipb.13095

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

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

COMMUNICATIONS BIOLOGY 4 ( 1 ) 382 - 382 2021.3

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE RESEARCH

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 angstrom 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. Kato, Miyazaki, Hamaguchi et al. report the structure of Photosystem II in solution at 1.95 angstrom resolution by single-particle cryo-electron microscopy. They find that reducing the electron beam dosage decreases the electron beam damage while keeping the resolution of the cryo-EM structure, providing insights into the best practice for the determination of cryo-EM structures.

DOI： 10.1038/s42003-021-01919-3

Structure of photosystem I-LHCI-LHCII from the green alga Chlamydomonas reinhardtii in State 2 Reviewed International journal

Zihui Huang, Liangliang Shen, Wenda Wang, Zhiyuan Mao, Xiaohan Yi, Tingyun Kuang, Jian-Ren Shen, Xing Zhang, Guangye Han

NATURE COMMUNICATIONS 12 ( 1 ) 1100 - 1100 2021.2

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE RESEARCH

Photosystem I (PSI) and II (PSII) balance their light energy distribution absorbed by their light-harvesting complexes (LHCs) through state transition to maintain the maximum photosynthetic performance and to avoid photodamage. In state 2, a part of LHCII moves to PSI, forming a PSI-LHCI-LHCII supercomplex. The green alga Chlamydomonas reinhardtii exhibits state transition to a far larger extent than higher plants. Here we report the cryo-electron microscopy structure of a PSI-LHCI-LHCII supercomplex in state 2 from C. reinhardtii at 3.42 angstrom resolution. The result reveals that the PSI-LHCI-LHCII of C. reinhardtii binds two LHCII trimers in addition to ten LHCI subunits. The PSI core subunits PsaO and PsaH, which were missed or not well-resolved in previous Cr-PSI-LHCI structures, are observed. The present results reveal the organization and assembly of PSI core subunits, LHCI and LHCII, pigment arrangement, and possible pathways of energy transfer from peripheral antennae to the PSI core. Photosystems (PS) I and II undergo state transitions to optimize photosynthesis and photoprotection. Here the authors report a cryo-electron microscopy structure of the state 2 PSI-LHCI-LHCII supercomplex from C. reinhardtii revealing subunit organization and possible pathways of energy transfer.

DOI： 10.1038/s41467-021-21362-6

Structural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium Thermosynechococcus vulcanus Reviewed International journal

Guoqiang Huang, Yanan Xiao, Xiong Pi, Liang Zhao, Qingjun Zhu, Wenda Wang, Tingyun Kuang, Guangye Han, Sen-Fang Sui, Jian-Ren Shen

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 118 ( 5 ) 2021.2

Language：English Publishing type：Research paper (scientific journal) Publisher：NATL ACAD SCIENCES

Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyzes light-driven water oxidation, leading to the conversion of light energy into chemical energy and the release of molecular oxygen. Psb27 is a small thylakoid lumen-localized protein known to serve as an assembly factor for the biogenesis and repair of the PSII complex. The exact location and binding fashion of Psb27 in the intermediate PSII remain elusive. Here, we report the structure of a dimeric Psb27-PSII complex purified from a psbV deletion mutant (Delta PsbV) of the cyanobacterium Thermosynechococcus vulcanus, solved by cryo-electron microscopy. Our structure showed that Psb27 is associated with CP43 at the luminal side, with specific interactions formed between Helix 2 and Helix 3 of Psb27 and a loop region between Helix 3 and Helix 4 of CP43 (loop C) as well as the large, lumen-exposed and hydrophilic E-loop of CP43. The binding of Psb27 imposes some conflicts with the N-terminal region of PsbO and also induces some conformational changes in CP43, CP47, and D2. This makes PsbO unable to bind in the Psb27-PSII. Conformational changes also occurred in D1, PsbE, PsbF, and PsbZ; this, together with the conformational changes occurred in CP43, CP47, and D2, may prevent the binding of PsbU and induce dissociation of PsbJ. This structural information provides important insights into the regulation mechanism of Psb27 in the biogenesis and repair of PSII.

DOI： 10.1073/pnas.2018053118

Antenna arrangement and energy-transfer pathways of PSI-LHCI from the moss Physcomitrella patens Reviewed International journal

Qiujing Yan, Liang Zhao, Wenda Wang, Xiong Pi, Guangye Han, Jie Wang, Lingpeng Cheng, Yi-Kun He, Tingyun Kuang, Xiaochun Qin, Sen-Fang Sui, Jian-Ren Shen

CELL DISCOVERY 7 ( 1 ) 10 - 10 2021.2

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

Plants harvest light energy utilized for photosynthesis by light-harvesting complex I and II (LHCI and LHCII) surrounding photosystem I and II (PSI and PSII), respectively. During the evolution of green plants, moss is at an evolutionarily intermediate position from aquatic photosynthetic organisms to land plants, being the first photosynthetic organisms that landed. Here, we report the structure of the PSI-LHCI supercomplex from the moss Physcomitrella patens (Pp) at 3.23 angstrom resolution solved by cryo-electron microscopy. Our structure revealed that four Lhca subunits are associated with the PSI core in an order of Lhca1-Lhca5-Lhca2-Lhca3. This number is much decreased from 8 to 10, the number of subunits in most green algal PSI-LHCI, but the same as those of land plants. Although Pp PSI-LHCI has a similar structure as PSI-LHCI of land plants, it has Lhca5, instead of Lhca4, in the second position of Lhca, and several differences were found in the arrangement of chlorophylls among green algal, moss, and land plant PSI-LHCI. One chlorophyll, PsaF-Chl 305, which is found in the moss PSI-LHCI, is located at the gap region between the two middle Lhca subunits and the PSI core, and therefore may make the excitation energy transfer from LHCI to the core more efficient than that of land plants. On the other hand, energy-transfer paths at the two side Lhca subunits are relatively conserved. These results provide a structural basis for unravelling the mechanisms of light-energy harvesting and transfer in the moss PSI-LHCI, as well as important clues on the changes of PSI-LHCI after landing.

DOI： 10.1038/s41421-021-00242-9

Enhancement of excitation-energy quenching in fucoxanthin chlorophyll alpha/c-binding proteins isolated from a diatom Phaeodactylum tricornutum upon excess-light illumination Reviewed International journal

Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Takehiro Suzuki, Minoru Kumazawa, Ka-Ho Kato, Naoki Tsuboshita, Naoshi Dohmae, Kentaro Ifuku, Jian-Ren Shen, Seiji Akimoto

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1862 ( 2 ) 148350 - 148350 2021.2

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

Photosynthetic organisms regulate pigment composition and molecular oligomerization of light-harvesting complexes in response to solar light intensities, in order to improve light-harvesting efficiency. Here we report excitation-energy dynamics and relaxation of fucoxanthin chlorophyll alpha/c-binding protein (FCP) complexes isolated from a diatom Phaeodactylum tricornutum grown under high-light (HL) illumination. Two types of FCP complexes were prepared from this diatom under the HL condition, whereas one FCP complex was isolated from the cells grown under a low-light (LL) condition. The subunit composition and oligomeric states of FCP complexes under the HL condition are different from those under the LL condition. Absorption and fluorescence spectra at 77 K of the FCP complexes also vary between the two conditions, indicating modifications of the pigment composition and arrangement upon the HL illumination. Time-resolved fluorescence curves at 77 K of the FCP complexes under the HL condition showed shorter lifetime components compared with the LL condition. Fluorescence decay-associated spectra at 77 K showed distinct excitation-energy-quenching components and alterations of energy-transfer pathways in the FCP complexes under the HL condition. These findings provide insights into molecular and functional mechanisms of the dynamic regulation of FCPs in this diatom under excess-light conditions.

DOI： 10.1016/j.bbabio.2020.148350

An Exciton Dynamics Model of Bryopsis corticulans Light-Harvesting Complex II Reviewed International journal

Hoang Long Nguyen, Thanh Nhut Do, Parveen Akhtar, Thomas L. C. Jansen, Jasper Knoester, Wenda Wang, Jian-Ren Shen, Petar H. Lambrev, Howe-Siang Tan

JOURNAL OF PHYSICAL CHEMISTRY B 125 ( 4 ) 1134 - 1143 2021.2

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Bryopsis corticulans is a marine green macroalga adapted to the intertidal environment. It possesses siphonaxanthin-binding light-harvesting complexes of photosystem II (LHCII) with spectroscopic properties markedly different from the LHCII in plants. By applying a phenomenological fitting procedure to the two-dimensional electronic spectra of the LHCII from B. corticulans measured at 77 K, we can extract information about the excitonic states and energy-transfer processes. The fitting method results in well-converged parameters, including excitonic energy levels with their respective transition dipole moments, spectral widths, energy-transfer rates, and coupling properties. The 2D spectra simulated from the fitted parameters concur very well with the experimental data, showing the robustness of the fitting method. An excitonic energy-transfer scheme can be constructed from the fitting parameters. It shows the rapid energy transfer from chlorophylls (Chls) b to a at subpicosecond time scales and a long-lived state in the Chl b region at around 659 nm. Three weakly connected terminal states are resolved at 671, 675, and 677 nm. The lowest state is higher in energy than that in plant LHCII, which is probably because of the fewer number of Chls a in a B. corticulans LHCII monomer. Modeling based on existing Hamiltonians for the plant LHCII structure with two Chls a switched to Chls b suggests several possible Chl a-b replacements in comparison with those of plant LHCII. The adaptive changes result in a slower energy equilibration in the complex, revealed by the longer relaxation times of several exciton states compared to those of plant LHCII. The strength of our phenomenological fitting method for obtaining excitonic energy levels and energy-transfer network is put to the test in systems such as B. corticulans LHCII, where prior knowledge on exact assignment and spatial locations of pigments are lacking.

DOI： 10.1021/acs.jpcb.0c10634

Light-Adapted Charge-Separated State of Photosystem II: Structural and Functional Dynamics of the Closed Reaction Center. Reviewed International journal

Gábor Sipka, Melinda Magyar, Alberto Mezzetti, Parveen Akhtar, Qingjun Zhu, Yanan Xiao, Guangye Han, Stefano Santabarbara, Jian-Ren Shen, Petar H Lambrev, Győző Garab

The Plant cell 2021.1

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

Photosystem II (PSII) uses solar energy to oxidize water and delivers electrons for life on Earth. The photochemical reaction center of PSII is known to possess two stationary states. In the open state (PSIIO), the absorption of a single photon triggers electron-transfer steps, which convert PSII into the charge-separated closed state (PSIIC). Here, by using steady-state and time-resolved spectroscopic techniques on Spinacia oleracea and Thermosynechococcus vulcanus preparations, we show that additional illumination gradually transforms PSIIC into a light-adapted charge-separated state (PSIIL). The PSIIC-to-PSIIL transition, observed at all temperatures between 80 and 308 K, is responsible for a large part of the variable chlorophyll-a fluorescence (Fv) and is associated with subtle, dark-reversible reorganizations in the core complexes, protein conformational changes at non-cryogenic temperatures and marked variations in the rates of photochemical and photophysical reactions. The build-up of PSIIL requires a series of light-induced events generating rapidly recombining primary radical pairs, spaced by sufficient waiting times between these events - pointing to the roles of local electric-field transients and dielectric relaxation processes. We show that the maximum fluorescence level, Fm, is associated with PSIIL rather than with PSIIC, and thus the Fv/Fm parameter cannot be equated with the quantum efficiency of PSII photochemistry. Our findings resolve the controversies and explain the peculiar features of chlorophyll-a fluorescence kinetics, a tool to monitor the functional activity and the structural-functional plasticity of PSII in different wild-type and mutant organisms and under stress conditions.

DOI： 10.1093/plcell/koab008

Exploring reaction pathways for the structural rearrangements of the Mn cluster induced by water binding in the S-3 state of the oxygen evolving complex of photosystem II Reviewed

Hiroshi Isobe, Mitsuo Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi

JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY 405 2021.1

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE SA

Photosynthetic oxidation of water to dioxygen is catalyzed by the Mn4CaO5 cluster in the protein-cofactor complex photosystem II. The light-driven catalytic cycle consists of four observable intermediates (S-0, S-1, S-2, and S-3) and one transient S-4 state. Recently, using X-ray free-electron laser crystallography, two experimental groups independently observed incorporation of one additional oxygen into the cluster during the S-2 to S-3 transition, which is likely to represent a substrate. The present study implicates two competing reaction routes encountered during the structural rearrangement of the catalyst induced by the water binding and immediately preceding the formation of final stable forms in the S-3 state. This mutually exclusive competition involves concerted versus stepwise conformational changes between two isomers, called open and closed cubane structures, which have different consequences on the immediate product in the S-3 state. The concerted pathway involves a one-step conversion between two isomeric hydroxo forms without changes to the metal oxidation and total spin (S-total = 3) states. Alternatively, in the stepwise process, the bound waters are oxidized and transformed into an oxyl-oxo form in a higher spin (S-total = 6) state. Here, density functional calculations are used to characterize all relevant intermediates and transition structures and demonstrate that the stepwise pathway to the substrate activation is substantially favored over the concerted one, as evidenced by comparison of the activation barriers (11.1 and 20.9 kcal mol(-1), respectively). Only after formation of the oxyl-oxo precursor can the hydroxo species be generated; this occurs with a slow kinetics and an activation barrier of 17.8 kcal mol(-1). The overall thermodynamic driving force is likely to be controlled by the movements of two glutamate ligands, D1-Glu189 and CP43-Glu354, in the active site and ranges from very weak (+0.4 kcal mol(-1)) to very strong (-23.5 kcal mol(-1)).

DOI： 10.1016/j.jphotochem.2020.112905

Molecular organizations and function of iron-stress-induced-A protein family in Anabaena sp. PCC 7120 Reviewed International journal

Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Takehiro Suzuki, Koji Kato, Ka-Ho Kato, Naoki Tsuboshita, Tian-Yi Jiang, Naoshi Dohmae, Jian-Ren Shen, Shigeki Ehira, Seiji Akimoto

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1862 ( 1 ) 148327 - 148327 2021.1

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

Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions, and surround photosystem I (PSI) trimer with a ring formation. A cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, it is unknown how the IsiAs are associated with PSI. Here we report on molecular organizations and function of the IsiAs in this cyanobacterium. A deletion mutant of the isiA1 gene was constructed, and the four types of thylakoids were prepared from the wild-type (WT) and Delta isiA1 cells under iron-replete (+Fe) and iron-deficient (-Fe) conditions. Immunoblotting analysis exhibits a clear expression of the IsiA1 in the WT-Fe. The PSI-IsiA1 supercomplex is found in the WT-Fe, and excitation-energy transfer from IsiA1 to PSI is verified by time-resolved fluorescence analyses. Instead of the IsiA1, both IsiA2 and IsiA3 are bound to PSI monomer in the Delta isiA1-Fe. These findings provide insights into multiple-expression system of the IsiA family in this cyanobacterium.

DOI： 10.1016/j.bbabio.2020.148327

Basic pH-induced modification of excitation-energy dynamics in fucoxanthin chlorophyll a/c-binding proteins isolated from a pinguiophyte, Glossomastix chrysoplasta Reviewed International journal

Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Ka-Ho Kato, Naoki Tsuboshita, Jian-Ren Shen, Seiji Akimoto

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1862 ( 1 ) 148306 - 148306 2021.1

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

Photosynthetic organisms have diversified light-harvesting complexes (LHCs) to collect solar energy efficiently, leading to an acquisition of their ecological niches. Herein we report on biochemical and spectroscopic characterizations of fucoxanthin chlorophyll a/c-binding protein (FCP) complexes isolated from a marine pinguiophyte Glossomastix chrysoplasta. The pinguiophyte FCP showed one subunit band in SDS-PAGE and one protein-complex band with a molecular weight at around 66 kDa in clear-native PAGE. By HPLC analysis, the FCP possesses chlorophylls a and c, fucoxanthin, and violaxanthin. To clarify excitation-energy-relaxation processes in the FCP, we measured time-resolved fluorescence spectra at 77 K of the FCP adapted to pH 5.0, 6.5, and 8.0. Fluorescence curves measured at pH 5.0 and 8.0 showed shorter lifetime components compared with those at pH 6.5. The rapid decay components at pH 5.0 and 8.0 are unveiled by fluorescence decay-associated (FDA) spectra; fluorescence decays occur in the 270 and 160-ps FDA spectra only at pH 5.0 and 8.0, respectively. In addition, energy-transfer pathways with time constants of tens of picoseconds are altered under the basic pH condition but not the acidic pH condition. These findings provide novel insights into pH-dependent energy-transfer and energy-quenching machinery in not only FCP family but also photosynthetic LHCs.

DOI： 10.1016/j.bbabio.2020.148306

Structural elucidation of vascular plant photosystem I and its functional implications Reviewed International journal

Xiuxiu Li, Gongxian Yang, Xinyi Yuan, Fenghua Wu, Wenda Wang, Jian-Ren Shen, Tingyun Kuang, Xiaochun Qin

Functional Plant Biology 2021

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

In vascular plants, bryophytes and algae, the photosynthetic light reaction takes place in the thylakoid membrane where two transmembrane supercomplexes PSII and PSI work together with cytochrome b6f and ATP synthase to harvest the light energy and produce ATP and NADPH. Vascular plant PSI is a 600-kDa protein-pigment supercomplex, the core complex of which is partly surrounded by peripheral light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core to be used for charge separation. PSI is unique mainly in absorption of longer-wavelengths than PSII, fast excitation energy transfer including uphill energy transfer, and an extremely high quantum efﬁciency. From the early 1980s, a lot of effort has been dedicated to structural and functional studies of PSI-LHCI, leading to the current understanding of how more than 200 cofactors are kept at the correct distance and geometry to facilitate fast energy transfer in this supercomplex at an atomic level. In this review, we review the history of studies on vascular plant PSI-LHCI, summarise the present research progress on its structure, and present some new and further questions to be answered in future studies.

DOI： 10.1071/fp21077

Adaptation of light-harvesting and energy-transfer processes of a diatomPhaeodactylum tricornutumto different light qualities Reviewed International journal

Kumiko Oka, Yoshifumi Ueno, Makio Yokono, Jian-Ren Shen, Ryo Nagao, Seiji Akimoto

PHOTOSYNTHESIS RESEARCH 146 ( 1-3 ) 227 - 234 2020.12

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

Fucoxanthin-chlorophyll (Chl)a/c-binding proteins (FCPs) are light-harvesting pigment-protein complexes found in diatoms and brown algae. Due to the characteristic pigments, such as fucoxanthin and Chlc, FCPs can capture light energy in blue-to green regions. A pennate diatomPhaeodactylum tricornutumsynthesizes a red-shifted form of FCP under weak or red light, extending a light-absorption ability to longer wavelengths. In the present study, we examined changes in light-harvesting and energy-transfer processes ofP. tricornutumcells grown under white- and single-colored light-emitting diodes (LEDs). The red-shifted FCP appears in the cells grown under the green, yellow, and red LEDs, and exhibited a fluorescence peak around 714 nm. Additional energy-transfer pathways are established in the red-shifted FCP; two forms (F713 and F718) of low-energy Chlawork as energy traps at 77 K. Averaged fluorescence lifetimes are prolonged in the cells grown under the yellow and red LEDs, whereas they are shortened in the blue-LED-grown cells. Based on these results, we discussed the light-adaptation machinery ofP. tricornutumcells involved in the red-shifted FCP.

DOI： 10.1007/s11120-020-00714-1

Adaptation of light-harvesting and energy-transfer processes of a diatom Chaetoceros gracilis to different light qualities Reviewed International journal

Seiji Akimoto, Yoshifumi Ueno, Makio Yokono, Jian-Ren Shen, Ryo Nagao

PHOTOSYNTHESIS RESEARCH 146 ( 1-3 ) 87 - 93 2020.12

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

Diatoms are a major group of microalgae in marine and freshwater environments. To utilize the light energy in blue to green region, diatoms possess unique antenna pigment-protein complexes, fucoxanthin chlorophyll a/c-binding proteins (FCPs). Depending on light qualities and quantities, diatoms form FCPs with different energies: normal-type and red-shifted FCPs. In the present study, we examined changes in light-harvesting and energy-transfer processes of a diatom Chaetoceros gracilis cells grown using white- and single-colored light-emitting diodes (LEDs), by means of time-resolved fluorescence spectroscopy. The blue LED, which is harvested by FCPs, modified energy transfer involving CP47, and suppressed energy transfer to PSI. Under the red-LED conditions, which is absorbed by both FCPs and PSs, energy transfer to PSI was enhanced, and the red-shifted FCP appeared. The red-shifted FCP was also recognized under the green- and yellow-LEDs, suggesting that lack of the shorter-wavelength light induces the red-shifted FCP. Functions of the red-shifted FCPs are discussed.

DOI： 10.1007/s11120-020-00713-2

Effects of CO2 and temperature on photosynthetic performance in the diatom Chaetoceros gracilis Reviewed International journal

Ryo Nagao, Yoshifumi Ueno, Seiji Akimoto, Jian-Ren Shen

PHOTOSYNTHESIS RESEARCH 146 ( 1-3 ) 189 - 195 2020.12

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

CO2 concentration and temperature for growth of photosynthetic organisms are two important factors to ensure better photosynthetic performance. In this study, we investigated the effects of CO2 concentration and temperature on the photosynthetic performance in a marine centric diatom Chaetoceros gracilis. Cells were grown under four different conditions, namely, at 25 degrees C with air bubbling, at 25 degrees C with a supplementation of 3% CO2, at 30 degrees C with air bubbling, and at 30 degrees C with the CO2 supplementation. It was found that the growth rate of cells at 30 degrees C with the CO2 supplementation is faster than those at other three conditions. The pigment compositions of cells grown under the different conditions are altered, and fluorescence spectra measured at 77 K also showed different peak positions. A novel fucoxanthin chlorophyll a/c-binding protein complex is observed in the cells grown at 30 degrees C with the CO2 supplementation but not in the other three types of cells. Since oxygen-evolving activities of the four types of cells are almost unchanged, it is suggested that the CO2 supplementation and growth temperature are involved in the regulation of photosynthetic light-harvesting apparatus in C. gracilis at different degrees. Based on these observations, we discuss the favorable growth conditions for C. gracilis.

DOI： 10.1007/s11120-020-00729-8

Changes in excitation relaxation of diatoms in response to fluctuating light, probed by fluorescence spectroscopies Reviewed International journal

Miyuki Tanabe, Yoshifumi Ueno, Makio Yokono, Jian-Ren Shen, Ryo Nagao, Seiji Akimoto

PHOTOSYNTHESIS RESEARCH 146 ( 1-3 ) 143 - 150 2020.12

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

A marine pennate diatom Phaeodactylum tricornutum (Pt) and a marine centric diatom Chaetoceros gracilis (Cg) possess unique light-harvesting complexes, fucoxanthin chlorophyll a/c-binding proteins (FCPs). FCPs have dual functions: light harvesting in the blue to green regions and quenching of excess energy. So far, excitation dynamics including FCPs have been studied by altering continuous light conditions. In the present study, we examined responses of the diatom cells to fluctuating light (FL) conditions. Excitation dynamics in the cells incubated under the FL conditions were analyzed by time-resolved fluorescence measurements followed by global analysis. As responses common to the Pt and Cg cells, quenching behaviors were observed in photosystem (PS) II with time constants of hundreds of picoseconds. The PSII -> PSI energy transfer was modified only in the Pt cells, whereas quenching in FCPs was suggested only in the Cg cells, indicating different strategy for the dissipation of excess energy under the FL conditions.

DOI： 10.1007/s11120-020-00720-3

Regulation of photosystem I-light-harvesting complex I from a red algaCyanidioschyzon merolaein response to light intensities Reviewed International journal

Lijing Chang, Lirong Tian, Fei Ma, Zhiyuan Mao, Xiaochi Liu, Guangye Han, Wenda Wang, Yanyan Yang, Tingyun Kuang, Jie Pan, Jian-Ren Shen

PHOTOSYNTHESIS RESEARCH 146 ( 1-3 ) 287 - 297 2020.12

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

Photosynthetic organisms use different means to regulate their photosynthetic activity in respond to different light conditions under which they grow. In this study, we analyzed changes in the photosystem I (PSI) light-harvesting complex I (LHCI) supercomplex from a red algaCyanidioschyzon merolae, upon growing under three different light intensities, low light (LL), medium light (ML), and high light (HL). The results showed that the red algal PSI-LHCI is separated into two bands on blue-native PAGE, which are designated PSI-LHCI-A and PSI-LHCI-B, respectively, from cells grown under LL and ML. The former has a higher molecular weight and binds more Lhcr subunits than the latter. They are considered to correspond to the two types of PSI-LHCI identified by cryo-electron microscopic analysis recently, namely, the former with five Lhcrs and the latter with three Lhcrs. The amount of PSI-LHCI-A is higher in the LL-grown cells than that in the ML-grown cells. In the HL-grown cells, PSI-LHCI-A completely disappeared and only PSI-LHCI-B was observed. Furthermore, PSI core complexes without Lhcr attached also appeared in the HL cells. Fluorescence decay kinetics measurement showed that Lhcrs are functionally connected with the PSI core in both PSI-LHCI-A and PSI-LHCI-B obtained from LL and ML cells; however, Lhcrs in the PSI-LHCI-B fraction from the HL cells are not coupled with the PSI core. These results indicate that the red algal PSI not only regulates its antenna size but also adjusts the functional connection of Lhcrs with the PSI core in response to different light intensities.

DOI： 10.1007/s11120-020-00778-z

Function of PsbO-Asp158 in photosystem II: effects of mutation of this residue on the binding of PsbO and function of PSII in Thermosynechococcus vulcanus Reviewed International journal

Qingjun Zhu, Yanyan Yang, Yanan Xiao, Wenda Wang, Tingyun Kuang, Jian-Ren Shen, Guangye Han

PHOTOSYNTHESIS RESEARCH 146 ( 1-3 ) 29 - 40 2020.12

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

PsbO-D158 is a highly conserved residue of the PsbO protein in photosystem II (PSII), and participates in one of the hydrogen-bonding networks connecting the manganese cluster with the lumenal surface. In order to examine the role of PsbO-D158, we mutated it to E, N or K in Thermosynechococcus vulcanus and characterized photosynthetic properties of the mutants obtained. The growth rates of these three mutants were similar to that of the wild type, whereas the oxygen-evolving activity of the three mutant cells decreased to 60-64% of the wild type. Fluorescence kinetics showed that the mutations did not affect the electron transfer from Q(A) to Q(B), but slightly affected the donor side of PSII. Moreover, all of the three mutant cells were more sensitive to high light and became slower to recover from photoinhibition. In the isolated thylakoid membranes from the three mutants, the PsbU subunit was lost and the oxygen-evolving activity was reduced to a lower level compared to that in the respective cells. PSII complexes isolated from these mutants showed no oxygen-evolving activity, which was found to be due to large or complete loss of PsbO, PsbV and PsbU during the process of purification. Moreover, PSII cores purified from the three mutants contained Psb27, an assembly co-factor of PSII. These results suggest that PsbO-D158 is required for the proper binding of the three extrinsic proteins to PSII and plays an important role in maintaining the optimal oxygen-evolving activity, and its mutation caused incomplete assembly of the PSII complex.

DOI： 10.1007/s11120-020-00715-0

Role of PsbV-Tyr137 in photosystem II studied by site-directed mutagenesis in the thermophilic cyanobacterium Thermosynechococcus vulcanus Reviewed International journal

Yanan Xiao, Qingjun Zhu, Yanyan Yang, Wenda Wang, Tingyun Kuang, Jian-Ren Shen, Guangye Han

PHOTOSYNTHESIS RESEARCH 146 ( 1-3 ) 41 - 54 2020.12

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

PsbV (cytochrome c(550)) is one of the three extrinsic proteins of photosystem II (PSII) and functions to maintain the stability and activity of the Mn4CaO5 cluster, the catalytic center for water oxidation. PsbV-Y137 is the C-terminal residue of PsbV and is located at the exit of a hydrogen-bond network mediated by the D1-Y161-H190 residue pair. In order to examine the function of PsbV-Y137, four mutants, PsbV-Y137A, PsbV-Y137F, PsbV-Y137G, and PsbV-Y137W, were generated with Thermosynechococcus vulcanus (T. vulcanus). These mutants showed growth rates similar to that of the wild-type strain (WT); however, their oxygen-evolving activities were different. At pH 6.5, the oxygen evolution rates of Y137F and Y137W were almost identical to that of WT, whereas the oxygen evolution rates of the Y137A, Y137G mutants were 64% and 61% of WT, respectively. However, the oxygen evolution in the latter two mutants decreased less at higher pHs, suggesting that higher pHs facilitated oxygen evolution probably by facilitating proton egress in these two mutants. Furthermore, thylakoid membranes isolated from the PsbV-Y137A, PsbV-Y137G mutants exhibited much lower levels of oxygen-evolving activity than that of WT, which was found to be caused by the release of PsbV. In addition, PSII complexes purified from the PsbV-Y137A and PsbV-Y137G mutants lost all of the three extrinsic proteins but instead bind Psb27, an assembly cofactor of PSII. These results demonstrate that the PsbV-Tyr137 residue is required for the stable binding of PsbV to PSII, and the hydrogen-bond network mediated by D1-Y161-H190 is likely to function in proton egress during water oxidation.

DOI： 10.1007/s11120-020-00753-8

Architecture of the photosynthetic complex from a green sulfur bacterium Reviewed International journal

Jing-Hua Chen, Hangjun Wu, Caihuang Xu, Xiao-Chi Liu, Zihui Huang, Shenghai Chang, Wenda Wang, Guangye Han, Tingyun Kuang, Jian-Ren Shen, Xing Zhang

SCIENCE 370 ( 6519 ) 931 - + 2020.11

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER ASSOC ADVANCEMENT SCIENCE

The photosynthetic apparatus of green sulfur bacteria (GSB) contains a peripheral antenna chlorosome, light-harvesting Fenna-Matthews-Olson proteins (FMO), and a reaction center (GsbRC). We used cryo-electron microscopy to determine a 2.7-angstrom structure of the FMO-GsbRC supercomplex from Chlorobaculum tepidum. The GsbRC binds considerably fewer (bacterio) chlorophylls [(B)Chls] than other known type I RCs do, and the organization of (B)Chls is similar to that in photosystem II. Two BChl layers in GsbRC are not connected by Chls, as seen in other RCs, but associate with two carotenoid derivatives. Relatively long distances of 22 to 33 angstroms were observed between BChls of FMO and GsbRC, consistent with the inefficient energy transfer between these entities. The structure contains common features of both type I and type II RCs and provides insight into the evolution of photosynthetic RCs.

DOI： 10.1126/science.abb6350

Reply to "Comment on 'Acidic pH-Induced Modification of Energy Transfer in Diatom Fucoxanthin Chlorophyll a/c-Binding Proteins'" Reviewed International journal

Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Jian-Ren Shen, Seiji Akimoto

JOURNAL OF PHYSICAL CHEMISTRY B 124 ( 46 ) 10588 - 10589 2020.11

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

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

Formation of the High-Spin S-2 State Related to the Extrinsic Proteins in the Oxygen Evolving Complex of Photosystem II Reviewed International journal

Shota Taguchi, Liangliang Shen, Guangye Han, Yasufumi Umena, Jian-Ren Shen, Takumi Noguchi, Hiroyuki Mino

JOURNAL OF PHYSICAL CHEMISTRY LETTERS 11 ( 20 ) 8908 - 8913 2020.10

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

The high-spin S-2 state was investigated with photosystem II (PSII) from spinach, Thermosynechococcus vulcanus, and Cyanidioschyzon merolae. In extrinsic protein-depleted PSII, high-spin electron paramagnetic resonance (EPR) signals were not detected in either species, whereas all species showed g similar to 5 signals in the presence of a high concentration of Ca2+ instead of the multiline signal. In the intact and PsbP/Qdepleted PSII from spinach, the g = 4.1 EPR signal was detected. These results show that formation of the high-spin S-2 state of the manganese cluster is regulated by the extrinsic proteins through a charge located near the Mn4 atom in the Mn4CaO5 cluster but is independent of the intrinsic proteins. The shift to the g similar to 5 state is caused by tilting of the z-axis in the Mn4 coordinates through hydrogen bonds or external divalent cations. The structural modification may allow insertion of an oxygen atom during the S-2-to-S-3 transition.

DOI： 10.1021/acs.jpclett.0c02411

Structural basis for energy transfer in a huge diatom PSI-FCPI supercomplex Reviewed International journal

Caizhe Xu, Xiong Pi, Yawen Huang, Guangye Han, Xiaobo Chen, Xiaochun Qin, Guoqiang Huang, Songhao Zhao, Yanyan Yang, Tingyun Kuang, Wenda Wang, Sen-Fang Sui, Jian-Ren Shen

NATURE COMMUNICATIONS 11 ( 1 ) 5081 - 5081 2020.10

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE RESEARCH

Diatom is an important group of marine algae and contributes to around 20% of the global photosynthetic carbon fixation. Photosystem I (PSI) of diatoms is associated with a large number of fucoxanthin-chlorophyll a/c proteins (FCPIs). We report the structure of PSI-FCPI from a diatom Chaetoceros gracilis at 2.38 angstrom resolution by single-particle cryo-electron microscopy. PSI-FCPI is a monomeric supercomplex consisting of 12 core and 24 antenna subunits (FCPIs), and 326 chlorophylls a, 34 chlorophylls c, 102 fucoxanthins, 35 diadinoxanthins, 18 beta -carotenes and some electron transfer cofactors. Two subunits designated PsaR and PsaS were found in the core, whereas several subunits were lost. The large number of pigments constitute a unique and huge network ensuring efficient energy harvesting, transfer and dissipation. These results provide a firm structural basis for unraveling the mechanisms of light-energy harvesting, transfer and quenching in the diatom PSI-FCPI, and also important clues to evolutionary changes of PSI-LHCI. Diatoms are marine algae with an important role in global photosynthetic carbon fixation. Here, the authors present the 2.38 angstrom cryo-EM structure of photosystem I (PSI) in complex with its 24 fucoxanthin chlorophyll a/c-binding (FCPI) antenna proteins from the diatom Chaetoceros gracilis, which provides mechanistic insights into light-energy harvesting, transfer and quenching of the PSI-FCPI supercomplex.

DOI： 10.1038/s41467-020-18867-x

Structural variations of photosystem I-antenna supercomplex in response to adaptations to different light environments Reviewed International journal

Michihiro Suga, Jian-Ren Shen

CURRENT OPINION IN STRUCTURAL BIOLOGY 63 10 - 17 2020.8

Language：English Publishing type：Research paper (scientific journal) Publisher：CURRENT BIOLOGY LTD

Photosystem I (PSI) is one of the two photosystems in photosynthesis, and generates reducing power required for carbon dioxide fixation. PSI exists as a reaction center core in cyanobacteria but is surrounded by light-harvesting antenna complexes (LHCI) to form PSI-LHCI supercomplexes in eukaryotic organisms. The structures of PSI core and PSI-LHCI have been reported from various organisms. We compare these structures and highlight the differences among different organisms. While the PSI core is more conserved, there are differences in its subunit composition and organization. Larger differences are found in the subunit composition, organization, and pigment binding in LHCI. All these changes can be explained in the framework of better adaptation to different light environment that each photosynthetic organism inhabits.

DOI： 10.1016/j.sbi.2020.02.005

Spectral tuning of light-harvesting complex II in the siphonous alga Bryopsis corticulans and its effect on energy transfer dynamics Reviewed International journal

Parveen Akhtar, Pawel J. Nowakowski, Wenda Wang, Thanh Nhut Do, Songhao Zhao, Giuliano Siligardi, Gyozo Garab, Jian-Ren Shen, Howe-Siang Tan, Petar H. Lambrev

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1861 ( 7 ) 148191 - 148191 2020.7

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

Light-harvesting complex II (LHCII) from the marine green macroalga Bryopsis corticulans is spectroscopically characterized to understand the structural and functional changes resulting from adaptation to intertidal environment. LHCII is homologous to its counterpart in land plants but has a different carotenoid and chlorophyll (Chl) composition. This is reflected in the steady-state absorption, fluorescence, linear dichroism, circular dichroism and anisotropic circular dichroism spectra. Time-resolved fluorescence and two-dimensional electronic spectroscopy were used to investigate the consequences of this adaptive change in the pigment composition on the excited-state dynamics. The complex contains additional Chl b spectral forms - absorbing at around 650 nm and 658 nm - and lacks the red-most Chl a forms compared with higher-plant LHCII. Similar to plant LHCII, energy transfer between Chls occurs on timescales from under hundred fs (mainly from Chl b to Chl a) to several picoseconds (mainly between Chl a pools). However, the presence of long-lived, weakly coupled Chl b and Chl a states leads to slower exciton equilibration in LHCII from B. corticulans. The finding demonstrates a trade-off between the enhanced absorption of blue-green light and the excitation migration time. However, the adaptive change does not result in a significant drop in the overall photochemical efficiency of Photosystem II. These results show that LHCII is a robust adaptable system whose spectral properties can be tuned to the environment for optimal light harvesting.

DOI： 10.1016/j.bbabio.2020.148191

Acidic pH-Induced Modification of Energy Transfer in Diatom Fucoxanthin Chlorophyll a/c-Binding Proteins Reviewed International journal

Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Jian-Ren Shen, Seiji Akimoto

JOURNAL OF PHYSICAL CHEMISTRY B 124 ( 24 ) 4919 - 4923 2020.6

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

pH influences excitation-energy-relaxation processes in photosynthetic light-harvesting complexes. Here, we report the excitation-energy dynamics by pH changes in fucoxanthin chlorophyll a/c-binding proteins (FCPs) isolated from a diatom Phaeodactylum tricornutum, probed by time-resolved fluorescence spectroscopy at 77 K. The fluorescence curve measured at pH 5.0 showed a shorter lifetime component than that measured at pH 6.5 and 8.0. The rapid decay component at pH 5.0 is supported by fluorescence decay-associated (FDA) spectra, where strong fluorescence decays relative to fluorescence rises appear in the pH-5.0 FDA spectrum with 70 ps. These results indicate that the diatom FCPs switch their function from light-harvesting to energy-quenching via arrangements of the energy-transfer pathways under acidic pHs. Based on the crystal structure of the diatom FCPs, we propose a model for the energy-quenching machinery through structural changes of the pigment environments, thus providing insights into the pH-dependent light-harvesting strategy in the diatom FCPs.

DOI： 10.1021/acs.jpcb.0c04231

Structural features of the diatom photosystem II-light-harvesting antenna complex Reviewed International journal

Wenda Wang, Songhao Zhao, Xiong Pi, Tingyun Kuang, Sen-Fang Sui, Jian-Ren Shen

FEBS JOURNAL 287 ( 11 ) 2191 - 2200 2020.6

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

In photosynthesis, light energy is captured by pigments bound to light-harvesting antenna proteins (LHC) that then transfer the energy to the photosystem (PS) cores to initiate photochemical reactions. The LHC proteins surround the PS cores to form PS-LHC supercomplexes. In order to adapt to a wide range of light environments, photosynthetic organisms have developed a large variety of pigments and antenna proteins to utilize the light energy efficiently under different environments. Diatoms are a group of important eukaryotic algae and possess fucoxanthin (Fx) chlorophyll a/c proteins (FCP) as antenna which have exceptional capabilities of harvesting blue-green light under water and dissipate excess energy under strong light conditions. We have solved the structure of a PSII-FCPII supercomplex from a centric diatom Chaetoceros gracilis by cryo-electron microscopy, and also the structure of an isolated FCP dimer from a pennate diatom Phaeodactylum tricornutum by X-ray crystallography at a high resolution. These results revealed the oligomerization states of FCPs distinctly different from those of LHCII found in the green lineage organisms, the detailed binding patterns of Chl c and Fxs, a huge pigment network, and extensive protein-protein, pigment-protein, and pigment-pigment interactions within the PSII-FCPII supercomplex. These results therefore provide a solid structural basis for examining the detailed mechanisms of the highly efficient energy transfer and quenching processes in diatoms.

DOI： 10.1111/febs.15183

Excitation dynamics and relaxation in the major antenna of a marine green alga Bryopsis corticulans Reviewed International journal

Dan-Hong Li, Wenda Wang, Cuicui Zhou, Yan Zhang, Peng Wang, Jian-Ren Shen, Tingyun Kuang, Jian-Ping Zhang

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1861 ( 5-6 ) 148186 - 148186 2020.6

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

The light-harvesting complexes II (LHCIIs) of spinach and Bryopsis corticulans as a green alga are similar in structure, but differ in carotenoid (Car) and chlorophyll (Chl) compositions. Carbonyl Cars siphonein (Spn) and siphonaxanthin (Spx) bind to B. corticulans LHCII likely in the sites as a pair of lutein (Lut) molecules bind to spinach LHCII in the central domain. To understand the light-harvesting and photoprotective properties of the algal LHCII, we compared its excitation dynamics and relaxation to those of spinach LHCII been well documented. It was found that B. corticulans LHCII exhibited a substantially longer chlorophyll (Chl) fluorescence lifetime (4.9 ns vs 4.1 ns) and a 60% increase of the fluorescence quantum yield. Photoexcitation populated (3)Car* equally between Spn and Spx in B. corticulans LHCII, whereas predominantly at Lut620 in spinach LHCII. These results prove the functional differences of the LHCIIs with different Car pairs and Chl a/b ratios: B. corticulans LHCII shows the enhanced blue-green light absorption, the alleviated quenching of 1 Chl*, and the dual sites of quenching (3)Chl*, which may facilitate its light-harvesting and photoprotection functions. Moreover, for both types of LHCIIs, the triplet excitation profiles revealed the involvement of extra (3)Car* formation mechanisms besides the conventional Chl-to-Car triplet transfer, which are discussed in relation to the ultrafast processes of (1)Chl* quenching. Our experimental findings will be helpful in deepening the understanding of the light harvesting and photoprotection functions of B. corticulans living in the intertidal zone with dramatically changing light condition.

DOI： 10.1016/j.bbabio.2020.148186

Water-oxidizing complex in Photosystem II: Its structure and relation to Manganese-oxide based catalysts Reviewed

Mohammad Mandi Najafpour, Ivelina Zaharieva, Zahra Zand, Seyedeh Maedeh Hosseini, Margarita Kouzmanova, Malgorzata Holynska, Ionut Tranca, Anthony W. Larkum, Jian-Ren Shen, Suleyman Allakhverdiev

COORDINATION CHEMISTRY REVIEWS 409 213183 - 213183 2020.5

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE SA

Cyanobacteria, green algae, and higher plants provide the major part of molecular O-2 of Earth atmosphere via water oxidation of oxygenic photosynthesis. The water-oxidizing complex is a manganese-calcium oxide-based cluster embedded in Photosystem II that oxidizes water with high turnover frequency. The atomic structure and analysis of the Mn-Ca cluster are important in understanding the mechanism of water oxidation and for the design of efficient artificial water-oxidizing catalysts. With this short review, we aim to introduce the basic features of the biological water oxidation to the new-comers in the field. Taking into account the recent structural studies, including a high-resolution, radiation-damage-free structure of the water-oxidizing complex, and structures of intermediate S-states revealed by femtosecond X-ray free electron lasers, we discuss the structure and functions of the biologically active site and its implications for the development of inorganic catalysts for solar fuels production. (C) 2020 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.ccr.2020.213183

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

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

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.

DOI： 10.1038/s42003-020-0949-6

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

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

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.

DOI： 10.1038/s41467-020-16324-3

Liquid-Liquid Phase Transition Drives Intra-chloroplast Cargo Sorting. Reviewed International journal

Min Ouyang, Xiaoyi Li, Jing Zhang, Peiqiang Feng, Hua Pu, Lingxi Kong, Zechen Bai, Liwei Rong, Xiumei Xu, Wei Chi, Qiang Wang, Fan Chen, Congming Lu, Jianren Shen, Lixin Zhang

Cell 180 ( 6 ) 1144 - 1159 2020.3

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

In eukaryotic cells, organelle biogenesis is pivotal for cellular function and cell survival. Chloroplasts are unique organelles with a complex internal membrane network. The mechanisms of the migration of imported nuclear-encoded chloroplast proteins across the crowded stroma to thylakoid membranes are less understood. Here, we identified two Arabidopsis ankyrin-repeat proteins, STT1 and STT2, that specifically mediate sorting of chloroplast twin arginine translocation (cpTat) pathway proteins to thylakoid membranes. STT1 and STT2 form a unique hetero-dimer through interaction of their C-terminal ankyrin domains. Binding of cpTat substrate by N-terminal intrinsically disordered regions of STT complex induces liquid-liquid phase separation. The multivalent nature of STT oligomer is critical for phase separation. STT-Hcf106 interactions reverse phase separation and facilitate cargo targeting and translocation across thylakoid membranes. Thus, the formation of phase-separated droplets emerges as a novel mechanism of intra-chloroplast cargo sorting. Our findings highlight a conserved mechanism of phase separation in regulating organelle biogenesis.

DOI： 10.1016/j.cell.2020.02.045

pH-Induced Regulation of Excitation Energy Transfer in the Cyanobacterial Photosystem I Tetramer Reviewed International journal

Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Tian-Yi Jiang, Jian-Ren Shen, Seiji Akimoto

JOURNAL OF PHYSICAL CHEMISTRY B 124 ( 10 ) 1949 - 1954 2020.3

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Excitation energy-transfer processes in pigment-protein complexes in photosynthetic organisms are often changed under different pH conditions. However, it is unclear how the pH changes affect excitation energy relaxations in photosystem I (PSI) cores. In this study, we examined the pH sensitivity of energy dynamics in the PSI tetramer, dimer, and monomer isolated from a cyanobacterium, Anabaena sp. PCC 7120, by means of time-resolved fluorescence spectroscopy. Each PSI was adapted to pH 5.0, 6.5, and 8.0. Fluorescence decay-associated (FDA) spectra of the pH 8.0 PSI dimer and monomer showed positive and negative peaks within 5 ps, whereas the FDA spectra of the PSI tetramer did not show such a 5 ps fluorescence component. Mean lifetimes of the fluorescence at pH 6.5 are shorter in the PSI tetramer than in the PSI dimer and monomer, indicating an accelerated energy quenching in the tetramer. The effects of the acidic and basic pHs on the energy-transfer processes differ significantly among the three types of PSIs, suggesting different pH-sensing sites around pigment molecules in the three PSIs. Based on these results, together with our recent structural finding of the PSI tetramer, we discuss functional implications for the pH-sensing regulation of the excitation energy transfer in the PSI tetramer.

DOI： 10.1021/acs.jpcb.0c01136

Excitation-Energy Transfer and Quenching in Diatom PSI-FCPI upon P700 Cation Formation Reviewed International journal

Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Jian-Ren Shen, Seiji Akimoto

JOURNAL OF PHYSICAL CHEMISTRY B 124 ( 8 ) 1481 - 1486 2020.2

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Excitation-energy transfer in photosystem I (PSI) is changed by a cation formation of a special pair chlorophyll P700 in the PSI core; however, it remains unclear how light-harvesting pigment-protein complexes are involved in the P700-related energy-transfer mechanisms. Here, we report effects of the redox changes of P700 on excitation-energy dynamics in diatom PSI-fucoxanthin chlorophyll a/c-binding protein (PSI-FCPI) and PSI core complexes by means of time-resolved fluorescence (TRF) spectroscopy. For the TRF measurements, the PSI-FCPI and PSI were adapted under P700 neutral and cation conditions using chemical reagents. Upon the P700(+) formation, fluorescence decay-associated (FDA) spectra constructed from the TRF spectra exhibit a larger fluorescence decay amplitude relative to a fluorescence rise magnitude within 100 ps in each of the PSI-FCPI and PSI. The decay components are shifted to lower wavelengths in each of the P700-cation PSI-FCPI and PSI than in the P700-neutral PSIs. The rapid fluorescence decays upon the P700(+) formation are clearly verified by mean lifetimes reconstructed from the FDA spectra. Because the P700-cation PSI does not cause charge-separation reactions, the relatively strong decay components and rapid fluorescence decays observed are likely attributed to excitation-energy quenching. These observations suggest that chlorophylls in PSI and around/within FCPI are involved in the energy-quenching events by the redox changes of P700.

DOI： 10.1021/acs.jpcb.0c00715

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

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

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, damagefree 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

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

Yuki Kato, Satoshi Haniu, Yoshiki Nakajima, Fusamichi Akita, Jian-Ren Shen, Takumi Noguchi

JOURNAL OF PHYSICAL CHEMISTRY B 124 ( 1 ) 121 - 127 2020.1

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

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

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

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

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

Influence of osmolytes on the stability of thylakoid-based dye-sensitized solar cells Reviewed

Roman A. Voloshin, Nathan G. Brad, Sergey K. Zharmukhamedov, Yashar M. Feyziyev, Irada M. Huseynova, Mohammad Mandi Najafpour, Jian-Ren Shen, T. Nejat Veziroglu, Barry D. Bruce, Suleyman Allakhverdiev

INTERNATIONAL JOURNAL OF ENERGY RESEARCH 43 ( 14 ) 8878 - 8889 2019.11

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

In recent years, there has been considerable interest in incorporating naturally occurring components of the photosynthetic apparatus into man-made solar cells, because of the high quantum efficiency of photosynthetic reaction centers. One hurdle to overcome regarding the use of native membranes in these devices is their limited lifespans. In this study, we used stabilizers to increase the long-term viability of biomolecules in vitro, thereby alleviating this challenge. In this regard, it is known that osmolytes, such as glycine betaine (GB) and sucrose, preserve photosynthetic activity in isolated photosystems. Upon investigation of the thermal protection properties of GB and sucrose in thylakoid-based dye-sensitized solar cells, we report that the addition of GB and sucrose to the thylakoid photosensitizer maintains nonzero photocurrent in the thylakoid-based solar cell upon heating to 50 degrees C. At 50 degrees C, the GB-containing cell displayed about a fourfold increase in photocurrent than the control cell, in which the photocurrent was decreased to nearly zero. The addition of 0.5M and 1M sucrose has respectively caused nearly 40% and 70% increases in photoinduced electron transfer activity over the control at 35 degrees C. Similarly, though to a lesser extent, 1M GB caused an approximate 40% increase in electron transfer activity as well. Moving forward, this approach will be extended to alternative membrane protein isolation strategies, allowing for an accurate comparison with traditional detergent-isolated complexes, with the ultimate goal of developing a cost-effective and sustainable solar cell.

DOI： 10.1002/er.4866

An alternative plant-like cyanobacterial ferredoxin with unprecedented structural and functional properties Reviewed International journal

Taiki Motomura, Lidia Zuccarello, Pierre Setif, Alain Boussac, Yasufumi Umena, David Lemaire, Jatindra N. Tripathy, Miwa Sugiura, Rainer Hienerwadel, Jian-Ren Shen, Catherine Berthomieu

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1860 ( 11 ) 148084 - 148084 2019.11

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

Photosynthetic [2Fe-2S] plant-type ferredoxins have a central role in electron transfer between the photosynthetic chain and various metabolic pathways. Several genes are coding for [2Fe-2S] ferredoxins in cyanobacteria, with four in the thermophilic cyanobacterium Thermosynechococcus elongatus. The structure and functional properties of the major ferredoxin Fd1 are well known but data on the other ferredoxins are scarce. We report the structural and functional properties of a novel minor type ferredoxin, Fd2 of T. elongatus, homologous to Fed4 from Synechocystis sp. PCC 6803. Remarkably, the midpoint potential of Fd2, Em = -440 mV, is lower than that of Fd1, Em = -372 mV. However, while Fd2 can efficiently react with photosystem I or nitrite reductase, time-resolved spectroscopy shows that Fd2 has a very low capacity to reduce ferredoxin-NADP(+) oxidoreductase (FNR). These unique Fd2 properties are discussed in relation with its structure, solved at 1.38 angstrom resolution. The Fd2 structure significantly differs from other known ferredoxins structures in loop 2, N-terminal region, hydrogen bonding networks and surface charge distributions. UV-Vis, EPR, and Mid- and Far-IR data also show that the electronic properties of the [2Fe2S] cluster of Fd2 and its interaction with the protein differ from those of Fd1 both in the oxidized and reduced states. The structural analysis allows to propose that valine in the motif Cys(53)ValAsnCys(56) of Fd2 and the specific orientation of Phe72, explain the electron transfer properties of Fd2. Strikingly, the nature of these residues correlates with different phylogenetic groups of cyanobacterial Fds. With its low redox potential and its discrimination against FNR, Fd2 exhibits a unique capacity to direct efficiently photosynthetic electrons to metabolic pathways not dependent on FNR.

DOI： 10.1016/j.bbabio.2019.148084

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

Michihiro Suga, Fusamichi Akita, Keitaro Yamashita, Yoshiki Nakajima, Go Ueno, Hongjie Li, Takahiro Yamane, Kunio Hirata, Yasufumi Umena, Shinichiro Yonekura, Long-Jiang Yu, Hironori Murakami, Takashi Nomura, Tetsunari Kimura, Minoru Kubo, Seiki Baba, Takashi Kumasaka, Kensuke Tono, Makina Yabashi, Hiroshi Isobe, Kizashi Yamaguchi, Masaki Yamamoto, Hideo Ago, Jian-Ren Shen

SCIENCE 366 ( 6463 ) 334 - + 2019.10

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER ASSOC ADVANCEMENT SCIENCE

Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S-0 to S-4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S-1, S-2, and S-3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S-2, but flipping of D1 Glu(189) upon transition to S-3 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.

DOI： 10.1126/science.aax6998

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

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

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 A 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

Structure of a C2S2M2N2 type PSII-LHCII supercomplex from the green alga Chlamydomonas reinhardtii Reviewed International journal

Liangliang Shen, Zihui Huang, Shenghai Chang, Wenda Wang, Jingfen Wang, Tingyun Kuang, Guangye Han, Jian-Ren Shen, Xing Zhang

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 116 ( 42 ) 21246 - 21255 2019.10

Language：English Publishing type：Research paper (scientific journal) Publisher：NATL ACAD SCIENCES

Photosystem II (PSII) in the thylakoid membranes of plants, algae, and cyanobacteria catalyzes light-induced oxidation of water by which light energy is converted to chemical energy and molecular oxygen is produced. In higher plants and most eukaryotic algae, the PSII core is surrounded by variable numbers of light-harvesting antenna complex II (LHCII), forming a PSII-LHCII supercomplex. In order to harvest energy efficiently at low-light-intensity conditions under water, a complete PSII-LHCII supercomplex (C2S2M2N2) of the green alga Chlamydomonas reinhardtii (Cr) contains more antenna subunits and pigments than the dominant PSII-LHCII supercomplex (C2S2M2) of plants. The detailed structure and energy transfer pathway of the Cr-PSII-LHCII remain unknown. Here we report a cryoelectron microscopy structure of a complete, C2S2M2N2-type PSIILHCII supercomplex from C. reinhardtii at 3.37-A resolution. The results show that the Cr-C2S2M2N2 supercomplex is organized as a dimer, with 3 LHCII trimers, 1 CP26, and 1 CP29 peripheral antenna subunits surrounding each PSII core. The N-LHCII trimer partially occupies the position of CP24, which is present in the higher-plant PSII-LHCII but absent in the green alga. The M trimer is rotated relative to the corresponding M trimer in plant PSII-LHCII. In addition, some unique features were found in the green algal PSII core. The arrangement of a huge number of pigments allowed us to deduce possible energy transfer pathways from the peripheral antennae to the PSII core.

DOI： 10.1073/pnas.1912462116

Spectral Properties and Excitation Relaxation of Novel Fucoxanthin Chlorophyll a/c-Binding Protein Complexes Reviewed International journal

Yoshifumi Ueno, Ryo Nagao, Jian-Ren Shen, Seiji Akimoto

JOURNAL OF PHYSICAL CHEMISTRY LETTERS 10 ( 17 ) 5148 - 5152 2019.9

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Fucoxanthin chlorophyll a/c-binding proteins (FCPs) are unique light harvesters for some photosynthetic organisms. There were several reports for the alterations of FCPs in response to light conditions. Here, we present the spectral profiles and excitation dynamics of novel FCP complexes isolated from the diatom Chaetoceros gracilis. Under a red-light condition, C. gracilis cells expressed three types of FCP complexes, two of which are very similar to FCP complexes found in the white-light grown cells, and one of which is the novel FCP complex. The combination of steady-state absorption and fluorescence spectra and time-resolved fluorescence spectra revealed that, compared to other types of FCP complexes, the novel FCP complexes exhibited red-shifted absorption and fluorescence spectra and fast decay of excitation. This finding will provide new insights into not only the light-harvesting strategies of diatoms but also the diversity of light adaptation machinery for photosynthetic organisms.

DOI： 10.1021/acs.jpclett.9b02093

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

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

CHEMICAL PHYSICS LETTERS 730 416 - 425 2019.9

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

The fully optimized geometrical structures of the CaMn4Ox (x = 5, 6) clusters in the Si (i = 0-3) states of the Kok cycle of photosynthetic water oxidation by the large-scale quantum mechanics/molecular mechanics (QM/MM) calculations were compared to recent experimental results based on serial femtosecond crystallography (SFX). The Mn-Mn and Ca-Mn distances obtained by the QM/MM calculations were found to be totally comparable to the SFX experiments, elucidating the entire Kok cycle involving the S-4 transition state during the O-O bond formation for water oxidation in the oxygen evolving complex (OEC) of photosystem II (PSII).

DOI： 10.1016/j.cplett.2019.06.026

Effects of excess light energy on excitation-energy dynamics in a pennate diatom Phaeodactylum tricornutum Reviewed International journal

Ryo Nagao, Yoshifumi Ueno, Makio Yokono, Jian-Ren Shen, Seiji Akimoto

PHOTOSYNTHESIS RESEARCH 141 ( 3 ) 355 - 365 2019.9

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

Controlling excitation energy flow is a fundamental ability of photosynthetic organisms to keep a better performance of photosynthesis. Among the organisms, diatoms have unique light-harvesting complexes, fucoxanthin chlorophyll (Chl) a/c-binding proteins. We have recently investigated light-adaptation mechanisms of a marine centric diatom, Chaetoceros gracilis, by spectroscopic techniques. However, it remains unclear how pennate diatoms regulate excitation energy under different growth light conditions. Here, we studied light-adaptation mechanisms in a marine pennate diatom Phaeodactylum tricornutum grown at 30 mu mol photons m(-2) s(-1) and further incubated for 24 h either in the dark, or at 30 or 300 mu mol photons m(-2) s(-1) light intensity, by time-resolved fluorescence (TRF) spectroscopy. The high-light incubated cells showed no detectable oxygen-evolving activity of photosystem II, indicating the occurrence of a severe photodamage. The photodamaged cells showed alterations of steady-state absorption and fluorescence spectra and TRF spectra compared with the dark and low-light adapted cells. In particular, excitation-energy quenching is significantly accelerated in the photodamaged cells as shown by mean lifetime analysis of the Chl fluorescence. These spectral changes by the high-light treatment may result from arrangements of pigment-protein complexes to maintain the photosynthetic performance under excess light illumination. These growth-light dependent spectral properties in P. tricornutum are largely different from those in C. gracilis, thus providing insights into the different light-adaptation mechanisms between the pennate and centric diatoms.

DOI： 10.1007/s11120-019-00639-4

Novel Mechanism of Cl-Dependent Proton Dislocation in Photosystem II (PSII): Hybrid Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation Reviewed

Atsushi Nakamura, Jiyoung Kang, Ryu-ichiro Terada, Hiori Kino, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Masaru Tateno

JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN 88 ( 8 ) 2019.8

Language：English Publishing type：Research paper (scientific journal) Publisher：PHYSICAL SOC JAPAN

The photosynthetic water oxidation reaction in photosystem II (PSII) causes the ejection of four protons (H+) and electrons from the substrate water bound to the Mn4CaO5 cluster, denoting the catalytic center of the system. Two Cl+ ions, Cl1 and Cl2 sites, were found in the vicinity of the Mn4CaO5 moiety. Herein, a novel H+ transfer mechanism (amide H+ exchange-driven scheme) was identified to operate in the Cl2 pathway based on the hybrid ab initio quantum mechanics (QM) molecular dynamics (MD) simulations of PSII. The analysis revealed that H+ can be displaced across the peptide bond of the D1-His337 and D1-Asn338 backbones, interrupting the hydrogen bond network spanning to the lumenal side in the crystal structure. The estimated energy barrier was consistent with the previous kinetic data. This is the first report to address unidirectional H+ transfer through a peptide bond based on the theoretical analysis involving the environmental protein structure.

DOI： 10.7566/JPSJ.88.084802

Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex Reviewed International journal

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

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. Diatoms are one of the important groups of oxyphototrophs and possess fucoxanthin chlorophyll a/c-binding proteins (FCPs) as light harvesters. The organization and association pattern of FCP with the photosystem II (PSII) core are unknown. Here we solved the structure of PSII-FCPII supercomplexes isolated from a diatom, Chaetoceros gracilis, by single-particle cryoelectron microscopy. The PSII-FCPII forms a homodimer. In each monomer, two FCP homotetramers and three FCP monomers are associated with one PSII core. The structure reveals a highly complicated protein-pigment network that is different from the green-type light-harvesting apparatus. Comparing these two systems allows the identification of energy transfer and quenching pathways. These findings provide structural insights into not only excitation-energy transfer mechanisms in the diatom PSII-FCPII, but also changes of light harvesters between the red-and green-lineage oxyphototrophs during evolution.

DOI： 10.1038/s41477-019-0477-x

A manganese(ii) phthalocyanine under water-oxidation reaction: new findings Reviewed International journal

Younes Mousazade, Mohammad Mahdi Najafpour, Robabeh Bagheri, Zvonko Jaglicic, Jitendra Pal Singh, Keun Hwa Chae, Zhenlun Song, Margarita V. Rodionova, Roman A. Voloshin, Jian-Ren Shen, Seeram Ramakrishna, Suleyman I. Allakhverdiev

DALTON TRANSACTIONS 48 ( 32 ) 12147 - 12158 2019.8

Language：English Publishing type：Research paper (scientific journal) Publisher：ROYAL SOC CHEMISTRY

Phthalocyanines are a promising class of ligands for manganese because of their high binding affinity. This effect is suggested to be an important factor because phthalocyanines tightly bind manganese and stabilize it under moderate conditions. The strong donor power of phthalocyanine is also suggested as a critical factor to stabilize high-valent manganese phthalocyanine. Herein, a manganese(ii) phthalocyanine, which is stable under moderate conditions, was investigated under harsh electrochemical water oxidation. By scanning electron microscopy, transmission electron microscopy, energy dispersive spectrometry, X-ray diffraction, extended X-ray absorption fine structure analysis, X-ray absorption near edge structure analysis, chronoamperometry, magnetic measurements, Fourier-transform infrared spectroscopy, and electrochemical methods, it is shown that manganese phthalocyanine, a known molecular complex showing good stability under moderate conditions, could not withstand water oxidation catalysis and ultimately is altered to form catalytic oxide particles. Such nanosized Mn oxides are the true catalyst for water oxidation. Besides, we try to go a step forward to find an answer as to how Mn oxides form on the surface of the electrode.

DOI： 10.1039/c9dt01790a

The pigment-protein network of a diatom photosystem II-light-harvesting antenna supercomplex Reviewed International journal

Xiong Pi, Songhao Zhao, Wenda Wang, Desheng Liu, Caizhe Xu, Guangye Han, Tingyun Kuang, Sen-Fang Sui, Jian-Ren Shen

SCIENCE 365 ( 6452 ) 463 - + 2019.8

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER ASSOC ADVANCEMENT SCIENCE

Diatoms play important roles in global primary productivity and biogeochemical cycling of carbon, in part owing to the ability of their photosynthetic apparatus to adapt to rapidly changing light intensity. We report a cryo-electron microscopy structure of the photosystem II ( PSII)-fucoxanthin ( Fx) chlorophyll ( Chl) a/c binding protein ( FCPII) supercomplex from the centric diatom Chaetoceros gracilis. The supercomplex comprises two protomers, each with two tetrameric and three monomeric FCPIIs around a PSII core that contains five extrinsic oxygen-evolving proteins at the lumenal surface. The structure reveals the arrangement of a huge pigment network that contributes to efficient light energy harvesting, transfer, and dissipation processes in the diatoms.

DOI： 10.1126/science.aax4406

pH-Sensing Machinery of Excitation Energy Transfer in Diatom PSI-FCPI Complexes Reviewed International journal

Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Jian-Ren Shen, Seiji Akimoto

JOURNAL OF PHYSICAL CHEMISTRY LETTERS 10 ( 13 ) 3531 - 3535 2019.7

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Excitation energy-transfer processes in photosynthetic light-harvesting complexes are strongly affected by the surrounding environments of pigments. Here we report on the effects of pH changes on excitation energy dynamics in both diatom photosystem I-fucoxanthin chlorophyll a/c-binding protein (PSI-FCPI) and PSI core complexes by means of fluorescence spectroscopies. The steady-state fluorescence spectra of the PSI-FCPI showed similar features among three samples at pH 5.0, 6.5, and 8.0. However, fluorescence decay-associated spectra of the pH 5.0- and 8.0-adapted PSI-FCPI within 100 ps exhibit peak shifts to longer and shorter wavelengths, respectively, than the peaks in the pH 6.5 spectra. Because such spectral changes hardly occur in the PSI complexes, the peak shifts at pH 5.0 and 8.0 in the PSI-FCPI can be ascribed to alterations of pigment pigment and/or pigment protein interactions around/within FCPI caused by the pH changes. These findings provide novel physical insights into the pH-sensing light-harvesting strategy in diatom PSI-FCPI.

DOI： 10.1021/acs.jpclett.9b01314

Proton-Coupled Electron Transfer of Plastoquinone Redox Reactions in Photosystem II: A Pump-Probe Ultraviolet Resonance Raman Study Reviewed International journal

Jun Chen, Jinfan Chen, Ying Liu, Yang Zheng, Qingjun Zhu, Guangye Han, Jian-Ren Shen

JOURNAL OF PHYSICAL CHEMISTRY LETTERS 10 ( 12 ) 3240 - 3247 2019.6

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Plastoquinones (PQs) act as electron and proton mediators in photosystem II (PSII) for solar-to-chemical energy conversion. It is known that the redox potential of PQ varies in a wide range spanning hundreds of millivolts; however, its structural origin is not known yet. Here, by developing a pump-probe ultraviolet resonance Raman technique, we measured the vibrational structures of PQs including Q(A) and Q(B) in cyanobacterial PSII directly The conversion of Q(A) to Q(A)(center dot-) in the Mn-depleted PSII is verified by direct observation of the distinct Q(A)(center dot-) vibrational bands. A frequency upshift of the ring C=O/C=C stretch band at 1565 cm(-1) for Q(A)(center dot-) was observed, which suggests a pi-pi interaction between the quinone ring and Trp253. In contrast, proton-coupled reduction of Q(A) to Q(A)H upon light-driven electron transfer is demonstrated in PSII without Q(B) bound. The H-bond between Q(A) and His214 is likely the proton origin of this proton-coupled electron transfer.

DOI： 10.1021/acs.jpclett.9b00959

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

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

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 77K. 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

Redox transients of P680 associated with the incremental chlorophyll-a fluorescence yield rises elicited by a series of saturating flashes in diuron-treated photosystem II core complex of Thermosynechococcus vulcanus Reviewed International journal

Gabor Sipka, Pavel Mueller, Klaus Brettel, Melinda Magyar, Laszlo Kovacs, Qingjun Zhu, Yanan Xiao, Guangye Han, Petar H. Lambrev, Jian-Ren Shen, Gyozo Garab

PHYSIOLOGIA PLANTARUM 166 ( 1 ) 22 - 32 2019.5

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

Recent chlorophyll-a fluorescence yield measurements, using single-turnover saturating flashes (STSFs), have revealed the involvement of a rate-limiting step in the reactions following the charge separation induced by the first flash. As also shown here, in diuron-inhibited PSII core complexes isolated from Thermosynechococcus vulcanus the fluorescence maximum could only be reached by a train of STSFs. In order to elucidate the origin of the fluorescence yield increments in STSF series, we performed transient absorption measurements at 819nm, reflecting the photooxidation and re-reduction kinetics of the primary electron donor P680. Upon single flash excitation of the dark-adapted sample, the decay kinetics could be described with lifetimes of 17ns (approximate to 50%) and 167ns (approximate to 30%), and a longer-lived component (approximate to 20%). This kinetics are attributed to re-reduction of P680(center dot+) by the donor side of PSII. In contrast, upon second-flash (with t between 5s and 100ms) or repetitive excitation, the 819nm absorption changes decayed with lifetimes of about 2ns (approximate to 60%) and 10ns (approximate to 30%), attributed to recombination of the primary radical pair P680(center dot+)Pheo(center dot-), and a small longer-lived component (approximate to 10%). These data confirm that only the first STSF is capable of generating stable charge separation-leading to the reduction of Q(A); and thus, the fluorescence yield increments elicited by the consecutive flashes must have a different physical origin. Our double-flash experiments indicate that the rate-limiting steps, detected by chlorophyll-a fluorescence, are not correlated with the turnover of P680.

DOI： 10.1111/ppl.12945

Blocking backward reaction on hydrogen evolution cocatalyst in a photosystem II hybrid Z-scheme water splitting system Reviewed

Zhen Li, Yu Qi, Wangyin Wang, Deng Li, Zheng Li, Yanan Xiao, Guangye Han, Jian-Ren Shen, Can Li

CHINESE JOURNAL OF CATALYSIS 40 ( 4 ) 486 - 494 2019.4

Language：English Publishing type：Research paper (scientific journal) Publisher：SCIENCE PRESS

Photocatalytic Z-scheme water splitting is considered as a promising approach to produce solar hydrogen. However, the forward hydrogen production reaction is often impeded by backward reactions. In the present study, in a photosystem II-integrated hybrid Z-scheme water splitting system, the backward hydrogen oxidation reaction was significantly suppressed by loading a PtCrOx cocatalyst on a ZrO2/TaON photocatalyst. Due to the weak chemisorption and activation of molecular hydrogen on PtCrOx, where Pt is stabilized in the oxidized forms, POII and Pt-IV, hydrogen oxidation is inhibited. However, it is remarkably well-catalyzed by the metallic Pt cocatalyst, thereby rapidly consuming the produced hydrogen. This work describes an approach to inhibit the backward reaction in the photosystem II-integrated hybrid Z-scheme water splitting system using Fe(CN)(6)(3-)/Fe(CN)(6)(4-) redox couple as an electron shuttle. (C) 2019, Dalian Institute of Chemical Physics, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

DOI： 10.1016/S1872-2067(19)63311-5

Phospholipid distributions in purple phototrophic bacteria and LH1-RC core complexes Reviewed

S. Nagatsuma, K. Gotou, T. Yamashita, L.-J. Yu, J.-R. Shen, M.T. Madigan, Y. Kimura, Z.-Y. Wang-Otomo

Biochimica Biophysica Acta 1860 461 - 468 2019.4

Spin, Valence, and Structural Isomerism in the S-3 State of the Oxygen-Evolving Complex of Photosystem II as a Manifestation of Multimetallic Cooperativity Reviewed International journal

Hiroshi Isobe, Mitsuo Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi

JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15 ( 4 ) 2375 - 2391 2019.4

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Photosynthetic water oxidation is catalyzed by a Mn4CaO5-cluster in photosystem II through an S-state cycle. Understanding the roles of heterogeneity in each S-state, as identified recently by the EPR spectroscopy, is very important to gain a complete description of the catalytic mechanism. We performed herein hybrid DFT calculations within the broken-symmetry formalism and associated analyses of Heisenberg spin models to study the electronic and spin structures of various isomeric structural motifs (hydroxo-oxo, oxyl-oxo, peroxo, and superoxo species) in the S(3 )state. Our extensive study reveals several factors that affect the spin ground state: (1) (formal) Mn oxidation state; (2) metal-ligand covalency; (3) coordination geometry; and (4) structural change of the Mn cluster induced by alternations in Mn...Mn distances. Some combination of these effects could selectively stabilize/destabilize some spin states. We found that the high spin state (S-total= 6) of the oxyl-oxo species can be causative for catalytic function, which manifests through mixing of the metal-ligand character in magnetic orbitals at relatively short 05...06 distances (<2.0 angstrom) and long Mn-A center dot center dot center dot O5 distances (>2.0 angstrom). These results will serve as a basis to conceptually identify and rationalize the physicochemical synergisms that can be evoked by the unique "distorted chair" topology of the cluster through cooperative Jahn-Teller effects on multimetallic centers.

DOI： 10.1021/acs.jctc.8b01055

Cobalt/Cobalt Oxide Surface for Water Oxidation Reviewed

Hadi Feizi, Robabeh Bagheri, Zhenlun Song, Jian-Ren Shen, Suleyman I. Allakhverdiev, Mohammad Mahdi Najafpour

ACS SUSTAINABLE CHEMISTRY & ENGINEERING 7 ( 6 ) 6093 - 6105 2019.3

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Water splitting to produce molecular hydrogen is an essential method to store sustainable energies. One of the bottlenecks for water splitting is the availability of an efficient and stable water-oxidizing catalyst. Herein, metallic cobalt foil, after the treatment under high potential (10-60.0 V), was used for water oxidation. The cobalt/ cobalt oxide surface was characterized by various spectroscopic, microscopy, X-ray diffraction, and electrochemical methods. Diffuse reflectance infrared Fourier transform spectroscopy showed peaks for Co oxide at 489 and 595 cm(-1) attributed to the stretching of Co-O and bending of O-Co-O bonds in the CoO6 octahedra. Small aggregated particles (ca. 50-100 nm) with a spherical morphology were detected by scanning electron microscopy, and high-resolution transmission electron microscopy from the mechanically separated particles indicated spacings of 2.5-2.6 angstrom corresponding to the interplanar spacings of the (011) plane for Co3O4. Selected area (electron) diffraction showed concentric rings centered on a bright central spot, indicating a polycrystalline material. Each ring is related to planes of different orientation and different interplanar spacing, attributed to metallic cobalt and cobalt oxides. X-ray diffraction resulted in patterns corresponding to Co3O4 and CoO(OH), and X-ray photoelectron spectroscopy could confirm the formation of metallic cobalt, Co(II) and Co(III) oxides on the surface of the electrode. These results suggest that the oxide on the surface of foil could be a mixture of different phases of Co oxide containing Co3O4 and CoO(OH). Under overpotentials of 460 and 780 mV, current densities of 0.144 and 0.5 A/cm(2) were observed at pH-14 without dropping of IR. To the best of our knowledge, the three-dimensional electrode obtained here is among the most efficient cobalt-based water-oxidizing electrodes under alkaline conditions reported so far and may be applied in large scale water-splitting systems.

DOI： 10.1021/acssuschemeng.8b06269

Site-directed mutagenesis of two amino acid residues in cytochrome b(559) subunit that interact with a phosphatidylglycerol molecule (PG772) induces quinone-dependent inhibition of photosystem II activity Reviewed International journal

Kaichiro Endo, Koichi Kobayashi, Hsing-Ting Wang, Hsiu-An Chu, Jian-Ren Shen, Hajime Wada

PHOTOSYNTHESIS RESEARCH 139 ( 1-3 ) 267 - 279 2019.3

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

X-ray crystallographic analysis (1.9-angstrom resolution) of the cyanobacterial photosystem II (PSII) dimer showed the presence of five phosphatidylglycerol (PG) molecules per reaction center. One of the PG molecules, PG772, is located in the vicinity of the Q(B)-binding site. To investigate the role of PG772 in PSII, we performed site-directed mutagenesis in the cytochrome (Cyt) b(559) subunit of Synechocystis sp. PCC 6803 to change two amino acids, Thr-5 and Ser-11, which interact with PG772. The photosynthetic activity of intact cells was slightly lower in all mutants than that of cells in the control strain; however, the oxygen-evolving PSII activity was decreased markedly in cells of mutants, as measured using artificial quinones (such as p-benzoquinone). Furthermore, electron transport from Q(A) to Q(B) was inhibited in mutants incubated with quinones, particularly under high-intensity light conditions. Lipid analysis of purified PSII showed approximately one PG molecule per reaction center, presumably PG772, was lost in the PSII dimer from the T5A and S11A mutants compared with that in the PSII dimer from the control strain. In addition, protein analysis of monomer and dimer showed decreased levels of PsbV and PsbU extrinsic proteins in the PSII monomer purified from T5A and S11A mutants. These results suggest that site-directed mutagenesis of Thr-5 and Ser-11, which presumably causes the loss of PG772, induces quinone-dependent inhibition of PSII activity under high-intensity light conditions and destabilizes the binding of extrinsic proteins to PSII.

DOI： 10.1007/s11120-018-0555-3

Ultrafast Excitation Energy Dynamics in a Diatom Photosystem I-Antenna Complex: A Femtosecond Fluorescence Upconversion Study Reviewed International journal

Ryo Nagao, Kohei Kagatani, Yoshifumi Ueno, Jian-Ren Shen, Seiji Akimoto

JOURNAL OF PHYSICAL CHEMISTRY B 123 ( 12 ) 2673 - 2678 2019.3

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) are unique light-harvesting antennas in diatoms. Recent time-resolved fluorescence analysis of photosystem I with FCP associated (PSI-FCPI) has mainly shown excitation energy transfer among Chls a from FCPI to PSI in tens of picoseconds. However, it remains unclear how each pigment, especially carotenoids and Chl c, in the FCPI is functionally related to the energy transfer in a femtosecond time range. Here, we reveal ultrafast excitation energy transfer mechanism in the PSI-FCPI preparations isolated from a diatom, Chaetoceros gracilis, by means of femtosecond time-resolved fluorescence spectroscopy with an upconversion system. Compared with the fluorescence lifetime components of PSI core-like complexes, the energy transfer of Chl c -> Chl a in the FCPI was observed within hundreds of femtoseconds, and the energy in the FCPI was transferred to PSI in similar to 2 ps. The comparative fluorescence analyses provide physical insights into the energy transfer machinery within FCPI and from FCPI to PSI.

DOI： 10.1021/acs.jpcb.8b12086

Structure of a green algal photosystem I in complex with a large number of light-harvesting complex I subunits Reviewed International journal

Xiaochun Qin, Xiong Pi, Wenda Wang, Guangye Hang, Lixia Zhu, Mingmei Liu, Linpeng Cheng, Jian-Ren Shen, Tingyun Kuang, Sen-Fang Sui

NATURE PLANTS 5 ( 3 ) 263 - 272 2019.3

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

Photosystem I (PSI) is a highly efficient natural light-energy converter, and has diverse light-harvesting antennas associated with its core in different photosynthetic organisms. In green algae, an extremely large light-harvesting complex I (LHCI) captures and transfers energy to the PSI core. Here, we report the structure of PSI-LHCI from a green alga Bryopsis corticulans at 3.49 angstrom resolution, obtained by single-particle cryo-electron microscopy, which revealed 13 core subunits including subunits characteristic of both prokaryotes and eukaryotes, and 10 light-harvesting complex a (Lhca) antennas that form a double semi-ring and an additional Lhca dimer, including a novel four-transmembrane-helix Lhca. In total, 244 chlorophylls were identified, some of which were located at key positions for the fast energy transfer. These results provide a firm structural basis for unravelling the mechanisms of light-energy harvesting, transfer and quenching in the green algal PSI-LHCI, and important clues as to how PSI-LHCI has changed during evolution.

DOI： 10.1038/s41477-019-0379-y

Properties and structure of a low-potential, penta-heme cytochrome c(552) from a thermophilic purple sulfur photosynthetic bacterium Thermochromatium tepidum Reviewed International journal

Jing-Hua Chen, Long-Jiang Yu, Alain Boussac, Zheng-Yu Wang-Otomo, Tingyun Kuang, Jian-Ren Shen

PHOTOSYNTHESIS RESEARCH 139 ( 1-3 ) 281 - 293 2019.3

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

The thermophilic purple sulfur bacterium Thermochromatium tepidum possesses four main water-soluble redox proteins involved in the electron transfer behavior. Crystal structures have been reported for three of them: a high potential iron-sulfur protein, cytochrome c, and one of two low-potential cytochrome c(552) (which is a flavocytochrome c) have been determined. In this study, we purified another low-potential cytochrome c(552) (LPC), determined its N-terminal amino acid sequence and the whole gene sequence, characterized it with absorption and electron paramagnetic spectroscopy, and solved its high-resolution crystal structure. This novel cytochrome was found to contain five c-type hemes. The overall fold of LPC consists of two distinct domains, one is the five heme-containing domain and the other one is an Ig-like domain. This provides a representative example for the structures of multiheme cytochromes containing an odd number of hemes, although the structures of multiheme cytochromes with an even number of hemes are frequently seen in the PDB database. Comparison of the sequence and structure of LPC with other proteins in the databases revealed several characteristic features which may be important for its functioning. Based on the results obtained, we discuss the possible intracellular function of this LPC in Tch. tepidum.

DOI： 10.1007/s11120-018-0507-y

Structural basis for blue-green light harvesting and energy dissipation in diatoms Reviewed International journal

Wenda Wang, Long-Jiang Yu, Caizhe Xu, Takashi Tomizaki, Songhao Zhao, Yasufumi Umena, Xiaobo Chen, Xiaochun Qin, Yueyong Xin, Michihiro Suga, Guangye Han, Tingyun Kuang, Jian-Ren Shen

SCIENCE 363 ( 6427 ) 598 - + 2019.2

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER ASSOC ADVANCEMENT SCIENCE

Diatoms are abundant photosynthetic organisms in aquatic environments and contribute 40% of its primary productivity. An important factor that contributes to the success of diatoms is their fucoxanthin chlorophyll a/c-binding proteins (FCPs), which have exceptional light-harvesting and photoprotection capabilities. Here, we report the crystal structure of an FCP from the marine diatom Phaeodactylum tricornutum, which reveals the binding of seven chlorophylls (Chls) a, two Chls c, seven fucoxanthins (Fxs), and probably one diadinoxanthin within the protein scaffold. Efficient energy transfer pathways can be found between Chl a and c, and each Fx is surrounded by Chls, enabling the energy transfer and quenching via Fx highly efficient. The structure provides a basis for elucidating the mechanisms of blue-green light harvesting, energy transfer, and dissipation in diatoms.

DOI： 10.1126/science.aav0365

Low-Energy Chlorophylls in Fucoxanthin Chlorophyll a/c-Binding Protein Conduct Excitation Energy Transfer to Photosystem I in Diatoms Reviewed International journal

Ryo Nagao, Makio Yokono, Yoshifumi Ueno, Jian-Ren Shen, Seiji Akimoto

JOURNAL OF PHYSICAL CHEMISTRY B 123 ( 1 ) 66 - 70 2019.1

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Photosynthetic organisms handle solar energy precisely to achieve efficient photochemical reactions. Because there are a wide variety of light-harvesting antennas in oxyphototrophs, the excitation energy transfer mechanisms are thought to differ significantly. In this study, we compared excitation energy dynamics between photosystem I (PSI) cores and a complex between PSI and fucoxanthin chlorophyll (Chl) a/c-binding protein I (PSI FCPI) isolated from a diatom, Chaetoceros gracilis, by means of picosecond time-resolved fluorescence analyses. Time-resolved spectra measured at 77 K clearly show that low-energy Chls in the FCPI transfer not only most of the excitation energy to the reaction center Chls in the PSI cores but also the remaining energy to carotenoids for quenching. Under room-temperature conditions, the energy in the low-energy Chls is rapidly equilibrated on Chls in the PSI cores by uphill energy transfer within a few tens of picoseconds. These findings provide solid evidence that the low-energy Chls in the FCPI contribute to the photochemical reactions in PSI.

DOI： 10.1021/acs.jpcb.8b09253

A transparent electrode with water-oxidizing activity Reviewed

Gouhar Azadi, Robabeh Bagheri, Rahman Bikas, Younes Mousazade, Junfeng Cui, Zhenlun Song, Vasyl Kinzhybalo, Jian-Ren Shen, Suleyman I. Allakhverdiev, Mohammad Mahdi Najafpour

INTERNATIONAL JOURNAL OF HYDROGEN ENERGY 43 ( 51 ) 22896 - 22904 2018.12

Language：English Publishing type：Research paper (scientific journal) Publisher：PERGAMON-ELSEVIER SCIENCE LTD

Hydrogen production by water splitting is a promising method to store energy. Water-oxidation reaction is a bottleneck in water-splitting systems. Herein, a mononuclear nickel(II) phosphine complex with 1,2-bis(dicyclohexylphosphino)ethane ligand, was synthesized and characterized by X-ray crystallography method. The water-oxidizing catalyst under the electrochemical condition was studied. The role of Ni compound for the water-oxidation reaction on the surface of fluorine-doped tin oxide as one of the true catalysts was investigated by the electrochemical methods and Scanning Electron Microscopy coupled with Energy Dispersive X-ray (SEM/EDX) Spectroscopy. The big ligand around the Ni ion causes a very small size of Ni-based particles on the surface of the electrode, which are the active catalysts for the water-oxidation reaction. Such small nanosized Ni-based compounds are transparent and have no effect on the transparency of the obtained fluorine-doped tin oxide. Thus, it is a promising method to synthesize a transparent fluorine-doped tin oxide with water-oxidizing activity. (C) 2018 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.ijhydene.2018.10.146

Novel features of LH1-RC from Thermochromatium tepidum revealed from its atomic resolution structure Reviewed International journal

Long-Jiang Yu, Michihiro Suga, Zheng-Yu Wang-Otomo, Jian-Ren Shen

FEBS JOURNAL 285 ( 23 ) 4359 - 4366 2018.12

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

Light-harvesting-1 (LH1)-reaction center (RC) super-complex is a membrane protein-pigment complex existing in purple photosynthetic bacteria, where LH1 absorbs light energy and transfers them rapidly and efficiently to RC to initiate the charge separation and electron transfer reactions. The structure of LH1-RC has been reported at relatively low resolutions from several different species of bacteria previously, but was solved at an atomic resolution recently from a thermophilic photosynthetic bacterium Thermochromatium tepidum. This high-resolution structure revealed the detailed organization of the super-complex including a number of unique features that are important for its functioning, such as a more intact RC structure, transporting routes for quinones to replace the bound Q(B) as well as for the in-and-out of the closed LH1 ring, detailed coordinating environment of the Ca2+ ions in LH1 important for the remarkable red shift of the absorption spectrum, as well as for the enhanced thermostability. These results thus greatly advance our understanding on the mechanisms of energy transfer, quinone exchange, the red shift in the LH1-Qy transition and the enhanced thermal stability, in this super-complex.

DOI： 10.1111/febs.14679

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

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

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

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC

Sulfoquinovosyl-diacylglycerol (SQDG) is one of the four lipids present in the thylakoid membranes. Depletion of SQDG causes different degrees of effects on photosynthetic growth and activities in different organisms. Four SQDG molecules bind to each monomer of photosystem II (PSII), but their role in PSII function has not been characterized in detail, and no PSII structure without SQDG has been reported. We analyzed the activities of PSII from an SQDG-deficient mutant of the cyanobacterium Thermosynechococcus elongatus by various spectroscopic methods, which showed that depletion of SQDG partially impaired the PSII activity by impairing secondary quinone (Q(B)) exchange at the acceptor site. We further solved the crystal structure of the PSII dimer from the SQDG deletion mutant at 2.1 angstrom resolution and found that all of the four SQDG-binding sites were occupied by other lipids, most likely PG molecules. Replacement of SQDG at a site near the head of Q(B) provides a possible explanation for the Q(B) impairment. The replacement of two SQDGs located at the monomer-monomer interface by other lipids decreased the stability of the PSII dimer, resulting in an increase in the amount of PSII monomer in the mutant. The present results thus suggest that although SQDG binding in all of the PSII-binding sites is necessary to fully maintain the activity and stability of PSII, replacement of SQDG by other lipids can partially compensate for their functions.

DOI： 10.1074/jbc.RA118.004304

Alterations of pigment composition and their interactions in response to different light conditions in the diatom Chaetoceros gracilis probed by time-resolved fluorescence spectroscopy Reviewed International journal

Ryo Nagao, Yoshifumi Ueno, Makio Yokono, Jian-Ren Shen, Seiji Akimoto

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1859 ( 7 ) 524 - 530 2018.7

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

Maintenance of energy balance under changeable light conditions is an essential function of photosynthetic organisms to achieve efficient photochemical reactions. Among the photosynthetic organisms, diatoms possess light-harvesting fucoxanthin chlorophyll (Chl) a/c-binding protein (FCP) as peripheral antennas. However, how diatoms regulate excitation-energy distribution between FCP and the two photosystem cores during light adaptation is poorly understood. In this study, we examined spectroscopic properties of a marine diatom Chaetoceros gracilis adapted in the dark and at photosynthetic photon flux density at 30 and 300 mu mol photons m(-2)s(-1). Absorption spectra at 77 K showed significant changes in the Soret region, and 77-K steady-state fluorescence spectra showed significant differences in the spectral shape and relative fluorescence intensity originating from both PSII and PSI, among the cells grown under different light conditions. These results suggest alterations of pigment composition and their interactions under the different light conditions. These alterations affected the excitation-energy dynamics monitored by picosecond time-resolved fluorescence analyses at 77 K significantly. The contributions of Chls having lower energy levels than the reaction center Chls in the two photosystems to the energy dynamics were clearly identified in the three cells but with presumably different roles. These findings provide insights into the regulatory mechanism of excitation-energy balance in diatoms under various light conditions.

DOI： 10.1016/j.bbabio.2018.04.003

A siphonous morphology affects light-harvesting modulation in the intertidal green macroalga Bryopsis corticulans (Ulvophyceae) Reviewed International journal

Vasco Giovagnetti, Guangye Han, Maxwell A. Ware, Petra Ungerer, Xiaochun Qin, Wen-Da Wang, Tingyun Kuang, Jian-Ren Shen, Alexander V. Ruban

PLANTA 247 ( 6 ) 1293 - 1306 2018.6

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

Main conclusion The macroalga Bryopsis corticulans relies on a sustained protective NPQ and a peculiar body architecture to efficiently adapt to the extreme light changes of intertidal shores.During low tides, intertidal algae experience prolonged high light stress. Efficient dissipation of excess light energy, measured as non-photochemical quenching (NPQ) of chlorophyll fluorescence, is therefore required to avoid photodamage. Light-harvesting regulation was studied in the intertidal macroalga Bryopsis corticulans, during high light and air exposure. Photosynthetic capacity and NPQ kinetics were assessed in different filament layers of the algal tufts and in intact chloroplasts to unravel the nature of NPQ in this siphonous green alga. We found that the morphology and pigment composition of the B. corticulans body provides functional segregation between surface sunlit filaments (protective state) and those that are underneath and undergo severe light attenuation (light-harvesting state). In the surface filaments, very high and sustained NPQ gradually formed. NPQ induction was triggered by the formation of transthylakoid proton gradient and independent of the xanthophyll cycle. PsbS and LHCSR proteins seem not to be active in the NPQ mechanism activated by this alga. Our results show that B. corticulans endures excess light energy pressure through a sustained protective NPQ, not related to photodamage, as revealed by the unusually quick restoration of photosystem II (PSII) function in the dark. This might suggest either the occurrence of transient PSII photoinactivation or a fast rate of PSII repair cycle.

DOI： 10.1007/s00425-018-2854-5

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

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

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Photosynthetic water oxidation is performed in photosystem II (PSII) through a light-driven cycle of intermediates called S states (S-0-S-4) at the water oxidizing center. Time-resolved serial femtosecond crystallography (SFX) has recently been applied to the microcrystals of PSII to obtain the structural information on these intermediates. However, it remains unanswered whether the reactions efficiently proceed throughout the S-state cycle retaining the native structures of the intermediates in PSII crystals. We investigated the water oxidation reactions in the PSII microcrystals using flash-induced Fourier transform infrared (FTIR) difference spectroscopy. In comparison with the FTIR spectra in solution, it was shown that all of the metastable intermediates in the microcrystals retained their native structures, and the efficiencies of the S-state transitions remained relatively high, although those of the S-2 -> S-3 and S-3 -> S-0 transitions were slightly lowered possibly due to some restriction of water movement in the crystals.

DOI： 10.1021/acs.jpclett.8b00638

Structure of photosynthetic LH1-RC supercomplex at 1.9 angstrom resolution Reviewed International journal

Long-Jiang Yu, Michihiro Suga, Zheng-Yu Wang-Otomo, Jian-Ren Shen

NATURE 556 ( 7700 ) 209 - + 2018.4

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

Light-harvesting complex 1 (LH1) and the reaction centre (RC) form a membrane-protein supercomplex that performs the primary reactions of photosynthesis in purple photosynthetic bacteria. The structure of the LH1-RC complex can provide information on the arrangement of protein subunits and cofactors; however, so far it has been resolved only at a relatively low resolution. Here we report the crystal structure of the calcium-ion-bound LH1-RC supercomplex of Thermochromatium tepidum at a resolution of 1.9 angstrom. This atomic-resolution structure revealed several new features about the organization of protein subunits and cofactors. We describe the loop regions of RC in their intact states, the interaction of these loop regions with the LH1 subunits, the exchange route for the bound quinone QB with free quinone molecules, the transport of free quinones between the inside and outside of the LH1 ring structure, and the detailed calcium-ionbinding environment. This structure provides a solid basis for the detailed examination of the light reactions that occur during bacterial photosynthesis.

DOI： 10.1038/s41586-018-0002-9

Vyacheslav (Slava) Klimov (1945-2017): A scientist par excellence, a great human being, a friend, and a Renaissance man Reviewed International journal

Suleyman I. Allakhverdiev, Sergey K. Zharmukhamedov, Margarita V. Rodionova, Vladimir A. Shuvalov, Charles Dismukes, Jian-Ren Shen, James Barber, Goran Samuelsson, Govindjee

PHOTOSYNTHESIS RESEARCH 136 ( 1 ) 1 - 16 2018.4

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

Vyacheslav Vasilevich (V.V.) Klimov (or Slava, as most of us called him) was born on January 12, 1945 and passed away on May 9, 2017. He began his scientific career at the Bach Institute of Biochemistry of the USSR Academy of Sciences (Akademy Nauk (AN) SSSR), Moscow, Russia, and then, he was associated with the Institute of Photosynthesis, Pushchino, Moscow Region, for about 50 years. He worked in the field of biochemistry and biophysics of photosynthesis. He is known for his studies on the molecular organization of photosystem II (PSII). He was an eminent scientist in the field of photobiology, a well-respected professor, and, above all, an outstanding researcher. Further, he was one of the founding members of the Institute of Photosynthesis in Pushchino, Russia. To most, Slava Klimov was a great human being. He was one of the pioneers of research on the understanding of the mechanism of light energy conversion and of water oxidation in photosynthesis. Slava had many collaborations all over the world, and he is (and will be) very much missed by the scientific community and friends in Russia as well as around the World. We present here a brief biography and some comments on his research in photosynthesis. We remember him as a friendly and enthusiastic person who had an unflagging curiosity and energy to conduct outstanding research in many aspects of photosynthesis, especially that related to PSII.

DOI： 10.1007/s11120-017-0440-5

Unique organization of photosystem I-light-harvesting supercomplex revealed by cryo-EM from a red alga Reviewed International journal

Xiong Pi, Lirong Tian, Huai-En Dai, Xiaochun Qin, Lingpeng Cheng, Tingyun Kuang, Sen-Fang Sui, Jian-Ren Shen

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 115 ( 17 ) 4423 - 4428 2018.4

Language：English Publishing type：Research paper (scientific journal) Publisher：NATL ACAD SCIENCES

Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic algae and higher plants, PSI consists of a core surrounded by variable species and numbers of light-harvesting complex (LHC)I proteins, forming a PSI-LHCI supercomplex. Here, we report cryo-EM structures of PSI-LHCR from the red alga Cyanidioschyzon merolae in two forms, one with three Lhcr subunits attached to the side, similar to that of higher plants, and the other with two additional Lhcr subunits attached to the opposite side, indicating an ancient form of PSI-LHCI. Furthermore, the red algal PSI core showed features of both cyanobacterial and higher plant PSI, suggesting an intermediate type during evolution from prokaryotes to eukaryotes. The structure of PsaO, existing in eukaryotic organisms, was identified in the PSI core and binds three chlorophylls a and may be important in harvesting energy and in mediating energy transfer from LHCII to the PSI core under state-2 conditions. Individual attaching sites of LHCRs with the core subunits were identified, and each Lhcr was found to contain 11 to 13 chlorophylls a and 5 zeaxanthins, which are apparently different from those of LHCs in plant PSI-LHCI. Together, our results reveal unique energy transfer pathways different from those of higher plant PSI-LHCI, its adaptation to the changing environment, and the possible changes of PSI-LHCI during evolution from prokaryotes to eukaryotes.

DOI： 10.1073/pnas.1722482115

Rate-limiting steps in the dark-to-light transition of Photosystem II - revealed by chlorophyll-a fluorescence induction Reviewed International journal

Melinda Magyar, Gabor Sipka, Laszlo Kovacs, Bettina Ughy, Qingjun Zhu, Guangye Han, Vladimir Spunda, Petar H. Lambrev, Jian-Ren Shen, Gyozo Garab

SCIENTIFIC REPORTS 8 ( 1 ) 2755 - 2755 2018.2

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

Photosystem II (PSII) catalyses the photoinduced oxygen evolution and, by producing reducing equivalents drives, in concert with PSI, the conversion of carbon dioxide to sugars. Our knowledge about the architecture of the reaction centre (RC) complex and the mechanisms of charge separation and stabilisation is well advanced. However, our understanding of the processes associated with the functioning of RC is incomplete: the photochemical activity of PSII is routinely monitored by chlorophyll-a fluorescence induction but the presently available data are not free of controversy. In this work, we examined the nature of gradual fluorescence rise of PSII elicited by trains of singleturnover saturating flashes (STSFs) in the presence of a PSII inhibitor, permitting only one stable charge separation. We show that a substantial part of the fluorescence rise originates from lightinduced processes that occur after the stabilisation of charge separation, induced by the first STSF; the temperature-dependent relaxation characteristics suggest the involvement of conformational changes in the additional rise. In experiments using double flashes with variable waiting times (Delta tau) between them, we found that no rise could be induced with zero or short Delta tau, the value of which depended on the temperature -revealing a previously unknown rate-limiting step in PSII.

DOI： 10.1038/s41598-018-21195-2

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 International journal

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

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

Photosystem II passes through four metastable S-states in catalysing light-driven water oxidation. Variable temperature variable field (VTVH) Magnetic Circular Dichroism (MCD) spectra in PSII of Thermosynochococcus (T.) volcanos for each S-state are reported. These spectra, along with assignments, provide a new window into the electronic and magnetic structure of Mn4CaO5. VTVH MCD spectra taken in the S-2 state provide a clear g = 2, S = 1/2 paramagnetic characteristic, which is entirely consistent with that known by EPR. The three features, seen as positive (+) at 749 nm, negative (-) at 773 nm and (+) at 808 nm are assigned as (4)A -> E-2 spin-flips within the d(3) configuration of the Mn(IV) centres present. This assignment is supported by comparison(s) to spin flips seen in a range of Mn(IV) materials. S-3 exhibits a more intense (-) MCD peak at 764 nm and has a stronger MCD saturation characteristic. This S-3 MCD saturation behaviour can be accurately modelled using parameters taken directly from analyses of EPR spectra. We see no evidence for Mn(III) d-d absorption in the near-IR of any S-state. We suggest that Mn(IV)-based absorption may be responsible for the well-known near-IR induced changes induced in S-2 EPR spectra of T. volcanos and not Mn(Ill)-based, as has been commonly assumed. Through an analysis of the nephelauxetic effect, the excitation energy of S-state dependent spin-flips seen may help identify coordination characteristics and changes at each Mn(IV). A prospectus as to what more detailed S state dependent MCD studies promise to achieve is outlined.

DOI： 10.1016/j.bbabio.2017.10.004

Purification of fully active and crystallizable photosystem II from thermophilic cyanobacteria Reviewed

Keisuke Kawakami, Jian-Ren Shen

Methods in Enzymology 613 1 - 16 2018.1

Language：English Publishing type：Part of collection (book) Publisher：Academic Press Inc.

Photosystem II (PSII) is a membrane protein complex which functions to catalyze light-induced water oxidation in oxygenic photosynthesis. Through the water-splitting reaction of PSII, light energy is converted into biologically useful chemical energy, and molecular oxygen is formed which transformed the atmosphere into an aerobic one and sustained aerobic life on the Earth. The PSII core complex from cyanobacteria consists of 17 transmembrane subunits and 3 extrinsic subunits with a total molecular mass of approximately 350 kDa per monomer, and PSII exists predominately in a dimeric form in vivo. This chapter describes the purification procedures leading to highly pure, homogenous, and highly active PSII core dimers from a thermophilic cyanobacterium, Thermosynechococcus vulcanus (T. vulcanus), that are used for successful crystallization and diffraction at atomic resolution. The purity and homogeneity of the PSII dimers thus obtained are characterized by absorption spectra, low-temperature fluorescence spectra, SDS-PAGE, clear native PAGE, blue native PAGE, gel filtration chromatography, and oxygen-evolving activity measurements. Finally, high-quality crystals obtained from the purified PSII dimers are shown.

DOI： 10.1016/bs.mie.2018.10.002

An aluminum/cobalt/iron/nickel alloy as a precatalyst for water oxidation Reviewed

Mohammad Mandi Najafpour, Somayeh Mehrabani, Robabeh Bagheri, Zhenlun Song, Jian-Ren Shen, Suleyman I. Allakhverdiev

INTERNATIONAL JOURNAL OF HYDROGEN ENERGY 43 ( 4 ) 2083 - 2090 2018.1

Language：English Publishing type：Research paper (scientific journal) Publisher：PERGAMON-ELSEVIER SCIENCE LTD

Among different strategies, water splitting toward hydrogen production is a promising process to store energy from intermittent sources. However, the anodic water oxidation is a bottleneck for water splitting. In this paper, we report an aluminum/cobalt/iron/nickel alloy as a precatalyst for the electrochemical water oxidation. The alloy electrode contains different metal ions including cobalt, iron, and nickel which all are efficient for water oxidation is tested. We characterized this electrode using scanning electron microscopy, transmission electron microscopy, diffuse reflectance infrared Fourier transform spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy and electrochemical methods. After stabilization, the electrode shows an onset overpotential of 200.0 mV and affords a current density of 3.5 mA cm(-2) at an overpotential of 600.0 mV in KOH solution at pH 13. (C) 2017 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.ijhydene.2017.12.025

Probing structure-function relationships in early events in photosynthesis using a chimeric photocomplex Reviewed International journal

Kenji V. P. Nagashima, Mai Sasaki, Kanako Hashimoto, Shinichi Takaichi, Sakiko Nagashima, Long-Jiang Yu, Yuto Abe, Kenta Gotou, Tomoaki Kawakami, Mizuki Takenouchi, Yuuta Shibuya, Akira Yamaguchi, Takashi Ohno, Jian-Ren Shen, Kazuhito Inoue, Michael T. Madigan, Yukihiro Kimura, Zheng-Yu Wang-Otomo

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114 ( 41 ) 10906 - 10911 2017.10

Language：English Publishing type：Research paper (scientific journal) Publisher：NATL ACAD SCIENCES

The native core light-harvesting complex (LH1) from the thermophilic purple phototrophic bacterium Thermochromatium tepidum requires Ca2+ for its thermal stability and characteristic absorption maximum at 915 nm. To explore the role of specific amino acid residues of the LH1 polypeptides in Ca-binding behavior, we constructed a genetic system for heterologously expressing the Tch. tepidum LH1 complex in an engineered Rhodobacter sphaeroides mutant strain. This system contained a chimeric pufBALM gene cluster (pufBA from Tch. tepidum and pufLM from Rba. sphaeroides) and was subsequently deployed for introducing site-directed mutations on the LH1 polypeptides. All mutant strains were capable of phototrophic (anoxic/light) growth. The heterologously expressed Tch. tepidum wild-type LH1 complex was isolated in a reaction center (RC)-associated form and displayed the characteristic absorption properties of this thermophilic phototroph. Spheroidene (the major carotenoid in Rba. sphaeroides) was incorporated into the Tch. tepidum LH1 complex in place of its native spirilloxanthins with one carotenoid molecule present per alpha beta-subunit. The hybrid LH1-RC complexes expressed in Rba. sphaeroides were characterized using absorption, fluorescence excitation, and resonance Raman spectroscopy. Site-specific mutagenesis combined with spectroscopic measurements revealed that alpha-D49, beta-L46, and a deletion at position 43 of the alpha-polypeptide play critical roles in Ca binding in the Tch. tepidum LH1 complex; in contrast, alpha-N50 does not participate in Ca2+ coordination. These findings build on recent structural data obtained from a high-resolution crystallographic structure of the membrane integrated Tch. tepidum LH1-RC complex and have unambiguously identified the location of Ca2+ within this key antenna complex.

DOI： 10.1073/pnas.1703584114

Functional role of Lys residues of Psb31 in electrostatic interactions with diatom photosystem II Reviewed International journal

Ryo Nagao, Takehiro Suzuki, Naoshi Dohmae, Jian-Ren Shen, Tatsuya Tomo

FEBS LETTERS 591 ( 20 ) 3259 - 3264 2017.10

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

We recently revealed that positively charged amino acids of Psb31, an extrinsic subunit found in diatom photosystem II (PSII), are involved in electrostatic interactions with PSII intrinsic subunits. However, the molecular interactions of Psb31 with PSII remain unclear. Here, we report the functional contribution of Lys residues in the binding of Psb31 to PSII using site-directed mutants of Psb31. Each of the K33A, K39A, K54A, K56A, K57A, and K69A mutants exhibits decreased binding affinities to PSII concomitantly with decreases in the O-2 evolution activity. Conversely, each of the K24A, K76A, K80A, and K117A mutants functionally binds to PSII in a manner similar to wild-type Psb31. These results provide evidence that some Lys residues of Psb31 are responsible for electrostatic interactions with PSII.

DOI： 10.1002/1873-3468.12830

Isolation and characterization of PSI-LHCI super-complex and their sub-complexes from a red alga Cyanidioschyzon merolae Reviewed International journal

Lirong Tian, Zheyi Liu, Fangjun Wang, Liangliang Shen, Jinghua Chen, Lijing Chang, Songhao Zhao, Guangye Han, Wenda Wang, Tingyun Kuang, Xiaochun Qin, Jian-Ren Shen

PHOTOSYNTHESIS RESEARCH 133 ( 1-3 ) 201 - 214 2017.9

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

Photosystem I (PSI)-light-harvesting complex I (LHCI) super-complex and its sub-complexes PSI core and LHCI, were purified from a unicellular red alga Cyanidioschyzon merolae and characterized. PSI-LHCI of C. merolae existed as a monomer with a molecular mass of 580 kDa. Mass spectrometry analysis identified 11 subunits (PsaA, B, C, D, E, F, I, J, K, L, O) in the core complex and three LHCI subunits, CMQ142C, CMN234C, and CMN235C in LHCI, indicating that at least three Lhcr subunits associate with the red algal PSI core. PsaG was not found in the red algae PSI-LHCI, and we suggest that the position corresponding to Lhca1 in higher plant PSI-LHCI is empty in the red algal PSI-LHCI. The PSI-LHCI complex was separated into two bands on native PAGE, suggesting that two different complexes may be present with slightly different protein compositions probably with respective to the numbers of Lhcr subunits. Based on the results obtained, a structural model was proposed for the red algal PSI-LHCI. Furthermore, pigment analysis revealed that the C. merolae PSI-LHCI contained a large amount of zeaxanthin, which is mainly associated with the LHCI complex whereas little zeaxanthin was found in the PSI core. This indicates a unique feature of the carotenoid composition of the Lhcr proteins and may suggest an important role of Zea in the light-harvesting and photoprotection of the red algal PSI-LHCI complex.

DOI： 10.1007/s11120-017-0384-9

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 International journal

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

FARADAY DISCUSSIONS 198 83 - 106 2017.6

Language：English Publishing type：Research paper (scientific journal) Publisher：ROYAL SOC CHEMISTRY

Large-scale QM/MM calculations were performed to elucidate an optimized geometrical structure of a CaMn4O5 cluster with and without water insertion in the S-3 state of the oxygen evolving complex (OEC) of photosystem II (PSII). The left (L)-opened structure was found to be stable under the assumption of no hydroxide anion insertion in the S-3 state, whereas the right (R)-opened structure became more stable if one water molecule is inserted to the Mn4Ca cluster. The optimized Mn-a(4)-Mn-d(1) distance determined by QM/MM was about 5.0 angstrom for the S-3 structure without an inserted hydroxide anion, but this is elongated by 0.2-0.3 angstrom after insertion. These computational results are discussed in relation to the possible mechanisms of O-O bond formation in water oxidation by the OEC of PSII.

DOI： 10.1039/c6fd00230g

Biological approaches to artificial photosynthesis, fundamental processes and theoretical approaches: general discussion Reviewed International journal

Vincent Artero, Leif Hammarstrom, Fengtao Fan, Dong Ryeol Whang, Jose Martinez, Anthony Harriman, Takumi Noguchi, Joshua Karlsson, Peter Summers, Shigeru Itoh, Richard Cogdell, Alexander Kibler, Johannes Ehrmaier, Hitoshi Tamiaki, Etsuko Fujita, Seigo Shima, Shunya Yoshino, Haruo Inoue, Michael Wasielewski, Thomas Corry, Devens Gust, Flavia Cassiola, Hitoshi Ishida, Katsuhiko Takagi, Sang Ook Kang, Can Li, Licheng Sun, Hyunwoong Park, Hideki Hashimoto, Yutaka Amao, Eun Jin Son, Nobuo Kamiya, Jian-Ren Shen, Kizashi Yamaguchi

FARADAY DISCUSSIONS 198 147 - 168 2017.6

Molecular catalysts for artificial photosynthesis: general discussion Reviewed International journal

Mei Wang, Vincent Artero, Leif Hammarstrom, Jose Martinez, Joshua Karlsson, Devens Gust, Peter Summers, Charles Machan, Peter Brueggeller, Christopher D. Windle, Yosuke Kageshima, Richard Cogdell, Kristine Rodulfo Tolod, Alexander Kibler, Dogukan Hazar Apaydin, Etsuko Fujita, Johannes Ehrmaier, Seigo Shima, Elizabeth Gibson, Ferdi Karadas, Anthony Harriman, Haruo Inoue, Akihiko Kudo, Tomoaki Takayama, Michael Wasielewski, Flavia Cassiola, Masayuki Yagi, Hitoshi Ishida, Federico Franco, Sang Ook Kang, Daniel Nocera, Can Li, Fabio Di Fonzo, Hyunwoong Park, Licheng Sun, Tohru Setoyama, Young Soo Kang, Osamu Ishitani, Jian-Ren Shen, Ho-Jin Son, Shigeyuki Masaoka

FARADAY DISCUSSIONS 198 353 - 395 2017.6

Crystal structure and redox properties of a novel cyanobacterial heme protein with a His/Cys heme axial ligation and a Per-Arnt-Sim (PAS)-like domain Reviewed International journal

Taiki Motomura, Michihiro Suga, Rainer Hienerwadel, Akiko Nakagawa, Thanh-Lan Lai, Wolfgang Nitschke, Takahiro Kuma, Miwa Sugiura, Alain Boussac, Jian-Ren Shen

JOURNAL OF BIOLOGICAL CHEMISTRY 292 ( 23 ) 9599 - 9612 2017.6

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC

Photosystem II catalyzes light-induced water oxidation leading to the generation of dioxygen indispensable for sustaining aerobic life on Earth. The Photosystem II reaction center is composed of D1 and D2 proteins encoded by psbA and psbD genes, respectively. In cyanobacteria, different psbA genes are present in the genome. The thermophilic cyanobacterium Thermosynechococcus elongatus contains three psbA genes: psbA1, psbA2, and psbA3, and a new c-type heme protein, Tll0287, was found to be expressed in a strain expressing the psbA2 gene only, but the structure and function of Tll0287 are unknown. Here we solved the crystal structure of Tll0287 at a 2.0 angstrom resolution. The overall structure of Tll0287 was found to be similar to some kinases and sensor proteins with a Per-Arnt-Sim-like domain rather than to other c-type cytochromes. The fifth and sixth axial ligands for the heme were Cys and His, instead of the His/Met or His/His ligand pairs observed for most of the c-type hemes. The redox potential, E-1/2, of Tll0287 was -255 +/- 20 mV versus normal hydrogen electrode at pH values above 7.5. Below this pH value, the E1/2 increased by approximate to 57 mV/pH unit at 15 degrees C, suggesting the involvement of a protonatable group with a pK(red) = 7.2 +/- 0.3. Possible functions of Tll0287 as a redox sensor under microaerobic conditions or a cytochrome subunit of an H2S-oxidizing system are discussed in view of the environmental conditions in which psbA2 is expressed, as well as phylogenetic analysis, structural, and sequence homologies.

DOI： 10.1074/jbc.M116.746263

Ultrafast energy transfer within the photosystem II core complex Reviewed International journal

Jie Pan, Andrius Gelzinis, Vladimir Chorosajev, Mikas Vengris, S. Seckin Senlik, Jian-Ren Shen, Leonas Valkunas, Darius Abramavicius, Jennifer P. Ogilvie

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 19 ( 23 ) 15356 - 15367 2017.6

Language：English Publishing type：Research paper (scientific journal) Publisher：ROYAL SOC CHEMISTRY

We report 2D electronic spectroscopy on the photosystem II core complex (PSII CC) at 77 K under different polarization conditions. A global analysis of the high time-resolution 2D data shows rapid, sub-100 fs energy transfer within the PSII CC. It also reveals the 2D spectral signatures of slower energy equilibration processes occurring on several to hundreds of picosecond time scales that are consistent with previous work. Using a recent structure-based model of the PSII CC [Y. Shibata, S. Nishi, K. Kawakami, J. R. Shen and T. Renger, J. Am. Chem. Soc., 2013, 135, 6903], we simulate the energy transfer in the PSII CC by calculating auxiliary time-resolved fluorescence spectra. We obtain the observed sub-100 fs evolution, even though the calculated electronic energy shows almost no dynamics at early times. On the other hand, the electronic-vibrational interaction energy increases considerably over the same time period. We conclude that interactions with vibrational degrees of freedom not only induce population transfer between the excitonic states in the PSII CC, but also reshape the energy landscape of the system. We suggest that the experimentally observed ultrafast energy transfer is a signature of excitonic-polaron formation.

DOI： 10.1039/c7cp01673e

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

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

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

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)(1-3). The structure of PSII has been analysed at 1.9 angstrom resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn4CaO5 cluster organized in an asymmetric, `distorted-chair' form(4). This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the `radiation damage-free'(5) 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 angstrom using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 angstrom 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 angstrom 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 mu 4-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 angstrom between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously(6,7.)

DOI： 10.1038/nature21400

RESOLUTION BEYOND THE DIFFRACTION LIMIT Reviewed

Jian-Ren Shen, Stephen D. Bartlett, Amro Zayed, Abigail C. Allwood, Barbara Mazzolai, Virgilio Mattoli, Matthias Minderer, Christopher D. Harvey, Flavio Donato, Edvard I. Moser, M. Coleman Miller, Susan L. Williams

NATURE 540 ( 7634 ) 536 - 537 2016.12

Probing the Lysine Proximal Microenvironments within Membrane Protein Complexes by Active Dimethyl Labeling and Mass Spectrometry Reviewed International journal

Ye Zhou, Yue Wu, Mingdong Yao, Zheyi Liu, Jin Chen, Jun Chen, Lirong Tian, Guangye Han, Jian-Ren Shen, Fangjun Wang

ANALYTICAL CHEMISTRY 88 ( 24 ) 12060 - 12065 2016.12

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Positively charged lysines are crucial to maintaining the native structures of proteins and protein complexes by forming hydrogen bonds and electrostatic interactions with their proximal amino acid residues. However, it is still a challenge to develop an efficient method for probing the active proximal microenvironments of lysines without changing their biochemical/physical properties. Herein, we developed an active covalent labeling strategy combined with mass spectrometry to systematically probe the lysine proximal microenvironments within membrane protein complexes (similar to 700 kDa) with high throughput. Our labeling strategy has the advantages of high labeling efficiency and stability, preservation of the active charge states, as well as biological activity of the labeled proteins. In total, 121 lysines with different labeling levels were obtained for the photosystem II complexes from cyanobacteria, red algae, and spinach and provided important insights for understanding the conserved and nonconserved local structures of PSII complexes among evolutionarily divergent species that perform photosynthesis.

DOI： 10.1021/acs.analchem.6b02502

Spatially Separated Photosystem II and a Silicon Photoelectrochemical Cell for Overall Water Splitting: A Natural-Artificial Photosynthetic Hybrid Reviewed International journal

Wangyin Wang, Hong Wang, Qingjun Zhu, Wei Qin, Guangye Han, Jian-Ren Shen, Xu Zong, Can Li

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 55 ( 32 ) 9229 - 9233 2016.8

Language：English Publishing type：Research paper (scientific journal) Publisher：WILEY-V C H VERLAG GMBH

Integrating natural and artificial photosynthetic platforms is an important approach to developing solar-driven hybrid systems with exceptional function over the individual components. A natural-artificial photosynthetic hybrid platform is formed by wiring photosystem II (PSII) and a platinum-decorated silicon photoelectrochemical (PEC) cell in a tandem manner based on a photocatalytic-PEC Z-scheme design. Although the individual components cannot achieve overall water splitting, the hybrid platform demonstrated the capability of unassisted solar-driven overall water splitting. Moreover, H-2 and O-2 evolution can be separated in this system, which is ascribed to the functionality afforded by the unconventional Z-scheme design. Furthermore, the tandem configuration and the spatial separation between PSII and artificial components provide more opportunities to develop efficient natural-artificial hybrid photosynthesis systems.

DOI： 10.1002/anie.201604091

Structure and energy transfer pathways of the plant photosystem I-LHCI supercomplex Reviewed International journal

Michihiro Suga, Xiaochun Qin, Tingyun Kuang, Jian-Ren Shen

CURRENT OPINION IN STRUCTURAL BIOLOGY 39 46 - 53 2016.8

Language：English Publishing type：Research paper (scientific journal) Publisher：CURRENT BIOLOGY LTD

Photosystem I (PSI) is one of the two photosystems in oxygenic photosynthesis, and absorbs light energy to generate reducing power for the reduction of NADP+ to NADPH with a quantum efficiency close to 100%. The plant PSI core forms a supercomplex with light-harvesting complex I (LHCI) with a total molecular weight of over 600 kDa. Recent X-ray structure analysis of the PSI-LHCI membrane-protein supercomplex has revealed detailed arrangement of the light-harvesting pigments and other cofactors especially within LHCI. Here we introduce the overall structure of the PSI-LHCI supercomplex, and then focus on the excited energy transfer (EET) pathways from LHCI to the PSI core and photoprotection mechanisms based on the structure obtained.

DOI： 10.1016/j.sbi.2016.04.004

Oxygen-Evolving Porous Glass Plates Containing the Photosynthetic Photosystem II Pigment-Protein Complex Reviewed International journal

Tomoyasu Noji, Keisuke Kawakami, Jian-Ren Shen, Takehisa Dewa, Mamoru Nango, Nobuo Kamiya, Shigeru Itoh, Tetsuro Jin

LANGMUIR 32 ( 31 ) 7796 - 7805 2016.8

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

The development of artificial photosynthesis has focused on the efficient coupling of reaction at photoanode and cathode, wherein the production of hydrogen (or energy carriers) is coupled to the electrons derived from water splitting reactions. The natural photosystem II (PSII) complex splits water efficiently using light energy. The PSII complex is a large pigment protein complex (20 nm in diameter) containing a manganese cluster. A new photoanodic device was constructed incorporating stable PSII purified from a cyanobacterium Thermosynechococcus vulcanus through immobilization within 20 or 50 nm nanopores contained in porous glass plates (PGPs). PSII in the nanopores retained its native structure and high photoinduced water splitting activity. The photocatalytic rate (turnover frequency) of PSII in PGP was enhanced 11-fold compared to that in solution, yielding a rate of 50-300 mol e(-) /(mol PSII.s) with 2,6-dichloroindophenol (DCIP) as an electron acceptor. The PGP system realized high local concentrations of PSII and DCIP to enhance the collisional reactions in nanotubes with low disturbance of light penetration. The system allows direct visualization/determination of the reaction inside the nanotubes, which contributes to optimize the local reaction condition. The PSII/PGP device will substantively contribute to the construction of artificial photosynthesis using water as the ultimate electron source.

DOI： 10.1021/acs.langmuir.6b02106

Crystal structure of plant PSI-LHCI supercomplex and its energy transfer mechanism

Xiaochun Qin, Michihiro Suga, Tingyun Kuang, Jianren Shen

Kexue Tongbao/Chinese Science Bulletin 61 ( 19 ) 2163 - 2175 2016.7

Language：Chinese Publishing type：Research paper (scientific journal) Publisher：Chinese Academy of Sciences

Photosynthesis uses light energy from the sun to convert CO2 and water into carbohydrates and oxygen, thus sustaining all aerobic life forms on Earth. Energy conversion in photosynthesis is carried out by two large membrane-protein complexes: photosystemI(PSI) and photosystemII(PSII). In higher plants, the PSIcore is surrounded by a belt of 4 light-harvestingIsubunits (LHCIor Lhca), forming a PSI-LHCIsupercomplex. The PSI-LHCIsupercomplex is an extremely efficient solar energy converter with a quantum efficiency close to 100%. In order to reveal the mechanism of energy harvesting and transfer within this large pigment-protein complex, it is essential to solve its crystal structure. The structure of the PSI-LHCIsupercomplex has been analyzed at a resolution up to 3.3 Å previously. However, this resolution was not enough to elucidate the detailed mechanism of light-harvesting and energy transfer in this complex. Recently we succeeded in analyzing the structure of the PSI-LHCIsupercomplex from pea at 2.8 Å resolution (1). Our studies showed that the PSI-LHCIsupercomplex contains 16 different subunits (including 12 core subunits PsaA-L and 4 LHCIsubunits Lhca1-4) and 205 cofactors (143 chlorophylls a, 12 chlorophylls b, 26 β-carotenes, 5 luteins, 4 violaxanthin, 10 lipids), with a total molecular mass of 600 kD. Our results identified chlorophyll a, chlorophyll b, and some carotenoids in the 4 LHCIsubunits for the first time, and revealed the differences in the structures of the 4 LHCI subunits, their interactions, and the interactions between them and the PSIcore subunits. Comparison among the available six structures of the Lhc family members (Lhca1 to Lhca4, LHCIIand CP29) revealed that, although all these Lhc proteins have a highly conserved second protein structure, notable differences were found in the two loop regions AC and BC as well as the N-terminal region. Most pigments are arranged at the same position except some distinct differences among different Lhc subunits in the position of several Chls bound at the interface between adjacent Lhca complexes, and between Lhca and PSIcore complex. Based on the structure resolved, 4 plausible energy transfer pathways (1Bs, 1Fl, 2Js, 3As/l) from LHCIto the PSIcore complex were deduced. Red forms of Chls were found to be involved in energy transfer from each Lhca to PSIcore. Our structure revealed that each Lhca binds a red chlorophyll dimer of Chl a3-Chl a9, which contribute to red-shifted spectra of Lhca complexes and have a pronounced effect on the energy transfer and trapping in the whole PSI-LHCIcomplex. All the four red dimers locate at the interface between LHCIand PSIcore complex, which looks like four bridges connecting Lhca with the core. The Chl-Chl interactions between each Lhca and the core complex suggested that excitation energy from the LHCIbelt to the PSIcore would mainly flow via Lhca1 and Lhca3. In this review, we discuss the detailed structure of the PSI-LHCIsupercomplex and the possible energy transfer mechanism within it. Taken together, this structure provides a solid structural basis for our understanding on energy transfer and photoprotection mechanisms within PSI-LHCIsupercomplex, and thus will be a big step forward toward understanding the mechanisms of photosynthesis.

DOI： 10.1360/N972016-00217

Current Insights to Enhance Hydrogen Production by Photosynthetic Organisms

Roshan Sharma Poudyal, Indira Tiwari, Mohammad Mahdi Najafpour, Dmitry A. Los, Robert Carpentier, Jian-Ren Shen, Suleyman I. Allakhverdiev

Hydrogen Science and Engineering: Materials, Processes, Systems and Technology 1 461 - 487 2016.4

Language：English Publishing type：Part of collection (book) Publisher：Wiley-VCH Verlag

Hydrogen gas (H 2) is considered to be one of the most important gases on earth
it can be used as an important alternative source of renewable energy. Although the amount of this gas in the Earth's atmosphere is far less compared to other gases, H 2 can be produced in different ways either by physical, chemical, or biological reactions, or obtained from fossil fuels. It can be produced biologically by lower or higher organisms, and this can contribute as an alternative source of H 2 for future generations. For biological H 2 production, bacteria, cyanobacteria, algae, and higher plants are the major organisms that can produce pure H 2 for sustainable usage. In this chapter, we briefly review different methods of production of H 2 and focus on modern studies devoted to photosynthetic production of H 2 by algae and microorganisms.

DOI： 10.1002/9783527674268.ch20

Polypeptide and Mn-Ca oxide: Toward a biomimetic catalyst for water-splitting systems Reviewed

Mohammad Mahdi Najafpour, Mohadeseh Zarei Ghobadi, Bahram Sarvi, Sepideh Madadkhani, Davood Jafarian Sedigh, Parvin Rafighi, Mojtaba Tavahodi, Jian-Ren Shen, Suleyman I. Allakhverdiev

INTERNATIONAL JOURNAL OF HYDROGEN ENERGY 41 ( 12 ) 5504 - 5512 2016.4

Language：English Publishing type：Research paper (scientific journal) Publisher：PERGAMON-ELSEVIER SCIENCE LTD

Water oxidation is the bottleneck for hydrogen production by water-splitting systems using sunlight or other sustainable energies. Herein we report nano-sized Mn-Ca oxide in an engineered polypeptide (Glu-Glu-Glu-Glu-Glu-Glu-Glu-His-Val-Val-Val-Val-Val-Val-Val-Val) as a structural model for biological water-oxidizing site in plants, algae, and cyanobacteria. The compound was synthesized by a simple procedure and characterized by transmission electron microscopy, atomic absorption spectroscopy, scanning electron microscopy, energy-dispersive spectroscopy, X-ray diffraction spectrometry, UV-Visible spectroscopy, dynamic light scattering, and some electrochemical methods. Using hydrogen to store sustainable energies is a promising strategy in near future and such nano-sized Mn-Ca oxide/polypeptide is a promising strategy in water-splitting systems to provide cheap electrons from water toward hydrogen production. Copyright (C) 2016, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.ijhydene.2016.01.131

Geometric and electronic structures of the synthetic Mn4CaO4 model compound mimicking the photosynthetic oxygen-evolving complex Reviewed International journal

Mitsuo Shoji, Hiroshi Isobe, Jian-Ren Shen, Kizashi Yamaguchi

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18 ( 16 ) 11330 - 11340 2016.4

Language：English Publishing type：Research paper (scientific journal) Publisher：ROYAL SOC CHEMISTRY

Water oxidation by photosystem II (PSII) converts light energy into chemical energy with the concomitant production of molecular oxygen, both of which are indispensable for sustaining life on Earth. This reaction is catalyzed by an oxygen-evolving complex (OEC) embedded in the huge PSII complex, and its mechanism remains elusive in spite of the extensive studies of the geometric and electronic structures. In order to elucidate the water-splitting mechanism, synthetic approaches have been extensively employed to mimic the native OEC. Very recently, a synthetic complex [Mn4CaO4(ButCOO)(8)(py)(ButCOOH)(2)] (1) closely mimicking the structure of the native OEC was obtained. In this study, we extensively examined the geometric, electronic and spin structures of 1 using the density functional theory method. Our results showed that the geometric structure of 1 can be accurately reproduced by theoretical calculations, and revealed many similarities in the ground valence and spin states between 1 and the native OEC. We also revealed two different valence states in the one-electron oxidized state of 1 (corresponding to the S-2 state), which lie in the lower and higher ground spin states (S = 1/2 and S = 5/2), respectively. One remarkable difference between 1 and the native OEC is the presence of a non-negligible antiferromagnetic interaction between the Mn1 and Mn4 sites, which slightly influenced their ground spin structures (spin alignments). The major reason causing the difference can be attributed to the short Mn1-O5 and Mn1-Mn4 distances in 1. The introduction of the missing O4 atom and the reorientation of the Ca coordinating ligands improved the Mn1-O5 and Mn1-Mn4 distances comparable to the native OEC. These modifications will therefore be important for the synthesis of further advanced model complexes more closely mimicking the native OEC beyond 1.

DOI： 10.1039/c5cp07226c

Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga Reviewed International journal

Hideo Ago, Hideyuki Adachi, Yasufumi Umena, Takayoshi Tashiro, Keisuke Kawakami, Nobuo Kamiya, Lirong Tian, Guangye Han, Tingyun Kuang, Zheyi Liu, Fangjun Wang, Hanfa Zou, Isao Enami, Masashi Miyano, Jian-Ren Shen

JOURNAL OF BIOLOGICAL CHEMISTRY 291 ( 11 ) 5676 - 5687 2016.3

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC

Photosystem II (PSII) catalyzes light-induced water splitting, leading to the evolution of molecular oxygen indispensible for life on the earth. The crystal structure of PSII from cyanobacteria has been solved at an atomic level, but the structure of eukaryotic PSII has not been analyzed. Because eukaryotic PSII possesses additional subunits not found in cyanobacterial PSII, it is important to solve the structure of eukaryotic PSII to elucidate their detailed functions, as well as evolutionary relationships. Here we report the structure of PSII from a red alga Cyanidium caldarium at 2.76 resolution, which revealed the structure and interaction sites of PsbQ, a unique, fourth extrinsic protein required for stabilizing the oxygen-evolving complex in the lumenal surface of PSII. The PsbQ subunit was found to be located underneath CP43 in the vicinity of PsbV, and its structure is characterized by a bundle of four up-down helices arranged in a similar way to those of cyanobacterial and higher plant PsbQ, although helices I and II of PsbQ were kinked relative to its higher plant counterpart because of its interactions with CP43. Furthermore, two novel transmembrane helices were found in the red algal PSII that are not present in cyanobacterial PSII; one of these helices may correspond to PsbW found only in eukaryotic PSII. The present results represent the first crystal structure of PSII from eukaryotic oxygenic organisms, which were discussed in comparison with the structure of cyanobacterial PSII.

DOI： 10.1074/jbc.M115.711689

Manganese Compounds as Water-Oxidizing Catalysts: From the Natural Water-Oxidizing Complex to Nanosized Manganese Oxide Structures Reviewed International journal

Mohammad Mahdi Najafpour, Gernot Renger, Malgorzata Holynska, Atefeh Nemati Moghaddam, Eva-Mari Aro, Robert Carpentier, Hiroshi Nishihara, Julian J. Eaton-Rye, Jian-Ren Shen, Suleyman I. Allakhverdiev

CHEMICAL REVIEWS 116 ( 5 ) 2886 - 2936 2016.3

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

All cyanobacteria, algae, and plants use a similar water-oxidizing catalyst for water oxidation. This catalyst is housed in Photosystem II, a membrane-protein complex that functions as a light-driven water oxidase in oxygenic photosynthesis. Water oxidation is also an important reaction in artificial photosynthesis because it has the potential to provide cheap electrons from water for hydrogen production or for the reduction of carbon dioxide on an industrial scale. The water-oxidizing complex of Photosystem II is a Mn-Ca cluster that oxidizes water with a low overpotential and high turnover frequency number of up to 25-90 molecules of O-2 released per second. In this Review, we discuss the atomic structure of the Mn-Ca cluster of the Photosystem II water-oxidizing complex from the viewpoint that the underlying mechanism can be informative when designing artificial water-oxidizing catalysts. This is followed by consideration of functional Mn-based model complexes for water oxidation and the issue of Mn complexes decomposing to Mn oxide. We then provide a detailed assessment of the chemistry of Mn oxides by considering how their bulk and nanoscale properties contribute to their effectiveness as water-oxidizing catalysts.

DOI： 10.1021/acs.chemrev.5b00340

CRYSTALLOGRAPHY Resolution beyond the diffraction limit Reviewed International journal

Jian-Ren Shen

NATURE 530 ( 7589 ) 168 - 169 2016.2

Chemical Equilibrium Models for the S-3 State of the Oxygen-Evolving Complex of Photosystem II Reviewed International journal

Hiroshi Isobe, Mitsuo Shoji, Jian-Ren Shen, Kizashi Yamaguchi

INORGANIC CHEMISTRY 55 ( 2 ) 502 - 511 2016.1

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

We have performed hybrid density functional theory (DFT) calculations to investigate how chemical equilibria can be described in the S-3 state of the oxygen-evolving complex in photosystem II. For a chosen 340-atom model, 1 stable and 11 metastable intermediates have been identified within the range of 13 kcal mol(1) that differ in protonation, charge, spin, and conformational states. The results imply that reversible interconversion of these intermediates gives rise to dynamic equilibria that involve processes with relocations of protons and electrons residing in the Mn4CaO5 cluster, as well as bound water ligands, with concomitant large changes in the cluster geometry. Such proton tautomerism and redox isomerism are responsible for reversible activation/deactivation processes of substrate oxygen species, through which MnO and OO bonds are transiently ruptured and formed. These results may allow for a tentative interpretation of kinetic data on substrate water exchange on the order of seconds at room temperature, as measured by time-resolved mass spectrometry. The reliability of the hybrid DFT method for the multielectron redox reaction in such an intricate system is also addressed.

DOI： 10.1021/acs.inorgchem.5b02471

The effect of lanthanum(III) and cerium(III) ions between layers of manganese oxide on water oxidation Reviewed International journal

Mohammad Mahdi Najafpour, Mohsen Abbasi Isaloo, Malgorzata Holynska, Jian-Ren Shen, Suleyman Allakhverdiev

PHOTOSYNTHESIS RESEARCH 126 ( 2-3 ) 489 - 498 2015.12

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

Manganese oxide structure with lanthanum(III) or cerium(III) ions between the layers was synthesized by a simple method. The ratio of Mn to Ce or La in samples was 0.00, 0.04, 0.08, 0.16, 0.32, 0.5, 0.82, or 1.62. The compounds were characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction studies, and atomic absorption spectroscopy. The compounds show efficient catalytic activity of water oxidation in the presence of cerium(IV) ammonium nitrate with a turnover frequency of 1.6 mmol O-2/mol Mn.s. In contrast to the water-oxidizing complex in Photosystem II, calcium(II) has no specific role to enhance the water-oxidizing activity of the layered manganese oxides and other cations can be replaced without any significant decrease in water-oxidizing activities of these layered Mn oxides. Based on this and previously reported results from oxygen evolution in the presence of H (2) (18) O, we discuss the mechanism and the important factors influencing the water-oxidizing activities of the manganese oxides.

DOI： 10.1007/s11120-015-0098-9

Special issue on Regulation of the Photosynthetic Systems in honor of Tingyun Kuang International journal

Congming Lu, Jian-Ren Shen, Lixin Zhang

PHOTOSYNTHESIS RESEARCH 126 ( 2-3 ) 185 - 188 2015.12

The effect of lanthanum(III) and cerium(III) ions between layers of manganese oxide on water oxidation (vol 126, pg 489, 2015) Reviewed International journal

Mohammad Mahdi Najafpour, Mohsen Abbasi Isaloo, Malgorzata Holynska, Jian-Ren Shen, Suleyman I. Allakhverdiev

PHOTOSYNTHESIS RESEARCH 126 ( 2-3 ) 499 - 499 2015.12

Site-directed mutagenesis of amino acid residues of D1 protein interacting with phosphatidylglycerol affects the function of plastoquinone Q(B) in photosystem II Reviewed International journal

Kaichiro Endo, Naoki Mizusawa, Jian-Ren Shen, Masato Yamada, Tatsuya Tomo, Hirohisa Komatsu, Masami Kobayashi, Koichi Kobayashi, Hajime Wada

PHOTOSYNTHESIS RESEARCH 126 ( 2-3 ) 385 - 397 2015.12

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

Recent X-ray crystallographic analysis of photosystem (PS) II at 1.9- resolution identified 20 lipid molecules in the complex, five of which are phosphatidylglycerol (PG). In this study, we mutagenized amino acid residues S232 and N234 of D1, which interact with two of the PG molecules (PG664 and PG694), by site-directed mutagenesis in Synechocystis sp. PCC 6803 to investigate the role of the interaction in PSII. The serine and asparagine residues at positions 232 and 234 from the N-terminus were mutagenized to alanine and aspartic acid, respectively, and a mutant carrying both amino acid substitutions was also produced. Although the obtained mutants, S232A, N234D, and S232AN234D, exhibited normal growth, they showed decreased photosynthetic activities and slower electron transport from Q(A) to Q(B) than the control strain. Thermoluminescence analysis suggested that this slower electron transfer in the mutants was caused by more negative redox potential of Q(B), but not in those of Q(A) and S-2. In addition, the levels of extrinsic proteins, PsbV and PsbU, were decreased in PSII monomer purified from the S232AN234D mutant, while that of Psb28 was increased. In the S232AN234D mutant, the content of PG in PSII was slightly decreased, whereas that of monogalactosyldiacylglycerol was increased compared with the control strain. These results suggest that the interactions of S232 and N234 with PG664 and PG694 are important to maintain the function of Q(B) and to stabilize the binding of extrinsic proteins to PSII.

DOI： 10.1007/s11120-015-0150-9

Proton Matrix ENDOR Studies on Ca2+-depleted and Sr2+-substituted Manganese Cluster in Photosystem II Reviewed International journal

Hiroki Nagashinna, Yoshiki Nakajima, Jian-Ren Shen, Hiroyuki Mino

JOURNAL OF BIOLOGICAL CHEMISTRY 290 ( 47 ) 28166 - 28174 2015.11

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC

Proton matrix ENDOR spectra were measured for Ca2+-depleted and Sr2+-substituted photosystem II (PSII) membrane samples from spinach and core complexes from Theymosynechococcus vulcanus in the S-2 state. The ENDOR spectra obtained were similar for untreated PSII from T. vulcanus and spinach, as well as for Ca2+-containing and Sr2+-substituted PSII, indicating that the proton arrangements around the manganese cluster in cyanobacterial and higher plant PSII and Ca2+-containing and Sr2+-substituted are similar in the S-2 state, in agreement with the similarity of the crystal structure of both Ca2+-containing and Sr2+-substituted PSII in the Si state. Nevertheless, slightly different hyperfine separations were found between Ca2+-containing and Sr2+-substituted PSII because of modifications of the water protons ligating to the Sr2+ ion. Importantly, Ca2+ depletion caused the loss of ENDOR signals with a 1.36-MHz separation because of the loss of the water proton W4 connecting Ca2+ and Y, directly. With respect to the crystal structure and the functions of Ca2+ in oxygen evolution, it was concluded that the roles of Ca2+ and Sr2+ involve the maintenance of the hydrogen bond network near the Ca2+ site and electron transfer pathway to the manganese cluster.

DOI： 10.1074/jbc.M115.675496

Strong Coupling between the Hydrogen Bonding Environment and Redox Chemistry during the S-2 to S-3 Transition in the Oxygen-Evolving Complex of Photosystem II Reviewed International journal

Hiroshi Isobe, Mitsuo Shoji, Jian-Ren Shen, Kizashi Yamaguchi

JOURNAL OF PHYSICAL CHEMISTRY B 119 ( 43 ) 13922 - 13933 2015.10

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

We have studied the early phase of the S-2 -> S-3 transition in the oxygen-evolving complex (OEC) of photosystem II using the hybrid density functional theory with a quantum mechanical model composed of 338-341 atoms. Special attention is given to the vital role of water molecules in the vicinity of the Mn4CaO5 core. Our results demonstrate how important the dynamic behavior of surrounding water molecules is in mediating critical chemical transformations such as binding and deprotonation of substrates and hydration of the catalytic site and identify a strong coupling of water-chain relocation near the redox-active tyrosine residue Tyr161 (Tyr(Z)) with oxidation of the Mn4CaO5 cluster by Tyr(Z)center dot(+). The oxidation reaction is further promoted when the catalytic site is more solvated by water. These results indicate the importance of surrounding water molecules in biological catalysts as they ultimately lead to effective catalytic function and/or favorable electron-transfer dynamics.

DOI： 10.1021/acs.jpcb.5b05740

The biological water-oxidizing complex at the nano-bio interface Reviewed International journal

Mohammad Mahdi Najafpour, Mohadeseh Zarei Ghobadi, Anthony W. Larkum, Jian-Ren Shen, Suleyman I. Alliakhverdiev

TRENDS IN PLANT SCIENCE 20 ( 9 ) 559 - 568 2015.9

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE LONDON

Photosynthesis is one of the most important processes on our planet, providing food and oxygen for the majority of living organisms on Earth. Over the past 30 years scientists have made great strides in understanding the central photosynthetic process of oxygenic photosynthesis, whereby water is used to provide the hydrogen and reducing equivalents vital to CO2 reduction and sugar formation. A recent crystal structure at 1.9-1.95 angstrom has made possible an unparalleled map of the structure of photosystem II (PSII) and particularly the manganese-calcium (Mn-Ca) cluster, which is responsible for splitting water. Here we review how knowledge of the water-splitting site provides important criteria for the design of artificial Mn-based water-oxidizing catalysts, allowing the development of clean and sustainable solar energy technologies.

DOI： 10.1016/j.tplants.2015.06.005

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

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

Language：English Publisher：ELSEVIER

Several key concepts and geometrical rules for the Mn-Mn and Mn-O distances of the CaMn4O5 cluster in the oxygen evolving complex (OEC) of photosystem II (PSII) by previous and present theoretical calculations were examined for a clear understanding of the damage-free Si structure revealed by X-ray free electron laser (XFEL). A simple equation to estimate the Mn-a-Mn-b distance in relation to the Mn-a-O(5) distance was derived taking into consideration the Jahn-Teller (JT) effects for Mn centers, indicating that the XFEL structure is regarded as a slightly right-elongated quasi-central structure in contradiction to a right-opened structure proposed by the EXAFS measurements. (C) 2015 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2015.03.033

Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex Reviewed International journal

Xiaochun Qin, Michihiro Suga, Tingyun Kuang, Jian-Ren Shen

SCIENCE 348 ( 6238 ) 989 - 995 2015.5

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER ASSOC ADVANCEMENT SCIENCE

Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core with extremely high efficiency. We report the structure of PSI-LHCI, a 600-kilodalton membrane protein supercomplex, from Pisum sativum (pea) at a resolution of 2.8 angstroms. The structure reveals the detailed arrangement of pigments and other cofactors-especially within LHCI-as well as numerous specific interactions between the PSI core and LHCI. These results provide a firm structural basis for our understanding on the energy transfer and photoprotection mechanisms within the PSI-LHCI supercomplex.

DOI： 10.1126/science.aab0214

A synthetic Mn4Ca-cluster mimicking the oxygen-evolving center of photosynthesis Reviewed International journal

Chunxi Zhang, Changhui Chen, Hongxing Dong, Jian-Ren Shen, Holger Dau, Jingquan Zhao

SCIENCE 348 ( 6235 ) 690 - 693 2015.5

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER ASSOC ADVANCEMENT SCIENCE

Photosynthetic splitting of water into oxygen by plants, algae, and cyanobacteria is catalyzed by the oxygen-evolving center (OEC). Synthetic mimics of the OEC, which is composed of an asymmetric manganese-calcium-oxygen cluster bound to protein groups, may promote insight into the structural and chemical determinants of biological water oxidation and lead to development of superior catalysts for artificial photosynthesis. We synthesized a Mn4Ca-cluster similar to the native OEC in both the metal-oxygen core and the binding protein groups. Like the native OEC, the synthetic cluster can undergo four redox transitions and shows two magnetic resonance signals assignable to redox and structural isomerism. Comparison with previously synthesized Mn3CaO4-cubane clusters suggests that the fourth Mn ion determines redox potentials and magnetic properties of the native OEC.

DOI： 10.1126/science.aaa6550

Damage Management in Water-Oxidizing Catalysts: From Photosystem II to Nanosized Metal Oxides Reviewed

Mohammad Mahdi Najafpour, Monika Fekete, Davood Jafarian Sedigh, Eva-Mari Aro, Robert Carpentier, Julian J. Eaton-Rye, Hiroshi Nishihara, Jian-Ren Shen, Suleyman I. Allakhverdiev, Leone Spiccia

ACS CATALYSIS 5 ( 3 ) 1499 - 1512 2015.3

Language：English Publisher：AMER CHEMICAL SOC

Current energy resources largely rely on fossil fuels that are expected to be depleted in 50-200 years. On a global scale, the intensive use of this energy source has resulted in highly detrimental effects to the environment. Hydrogen production by water splitting, with sunlight as the main energy source, is a promising way to augment the production of renewable energy; however, the development of an efficient and stable water-oxidizing catalyst remains a key task before a technological breakthrough based on water splitting can be realized. A main issue hampering the development of commercially viable, non-precious-metal-based catalysts is their susceptibility to degradation. To efficiently address this major drawback, self-healing catalysts that can repair their structure without human intervention will be necessary. In this review, we focus on water oxidation by natural and artificial Mn-, Co-, and Ni-based catalysts and then discuss the self-healing properties that contribute to sustaining their catalytic activity.

DOI： 10.1021/cs5015157

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

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

The structure of the oxygen evolving complex (OEC) of photosystem II (PSII) was recently analyzed by crystallography at 1.95 angstrom resolution using X-ray free electron laser (XFEL), but the positions of hydrogen atoms were not determined. We have examined the XFEL structure theoretically under the assumption off our protonation cases. The spin densities obtained by the high-spin UB3LYP revealed that a partial internal reduction of the high-valent Mn ions in the CaMn4O4X(H2O)(3)Y cluster occurs for the O-(5)(=X) = O2- case, entailing its protonation (X = OH-) in the XFEL structure. (C) 2015 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2015.01.030

Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II Reviewed

Mitsuo Shoji, Hiroshi Isobe, Shusuke Yamanaka, Yasufumi Umena, Keisuke Kawakami, Nobuo Kamiya, Jian-Ren Shen, Takahito Nakajima, Kizashi Yamaguchi

MOLECULAR PHYSICS 113 ( 3-4 ) 359 - 384 2015.2

Language：English Publishing type：Research paper (scientific journal) Publisher：TAYLOR & FRANCIS LTD

Quantum mechanical (QM)/molecular mechanics (MM) calculations by the use of a large-scale QM model (QM Model V) have been performed to elucidate hydrogen-bonding networks and proton wires for proton release pathways (PRP) of water oxidation reaction in the oxygen evolving complex (OEC) of photosystem II (PSII). Full geometry optimisations of PRP by the QM/MM model have been carried out starting from the geometry of heavy atoms determined by the recent high-resolution X-ray diffraction (XRD) experiment of PSII refined to 1.9 angstrom resolution. Computational results by the QM/MM calculations have elucidated the hydrogen-bonding O center dot center dot center dot O(N) and O center dot center dot center dot H distances and O(N)-H center dot center dot center dot O angles in PRP, together with the Cl-O(N) and Cl center dot center dot center dot H distances and O(N)-H center dot center dot center dot Cl angles for chloride anions. The optimised hydrogen-bonding networks are well consistent with the XRD results and available experiments such as extended X-ray absorption fine structure, showing the reliability of channel structures of OEC of PSII revealed by the XRD experiment. The QM/MM computations have elucidated possible roles of chloride anions in the OEC of PSII. The QM/MM computational results have provided useful information for understanding and explanation of accumulated mutation experiments of key amino acid residues in the OEC of PSII. Implications of the present results are discussed in relation to three steps for theoretical modelling of water oxidation in the OEC of PSII and bio-inspired working hypotheses for developments of artificial water oxidation systems by use of 3d transition-metal complexes.

DOI： 10.1080/00268976.2014.960021

Biochemical and structural study of Arabidopsis hexokinase 1 Reviewed International journal

Juan Feng, Shun Zhao, Xuemin Chen, Wenda Wang, Wei Dong, Jinghua Chen, Jian-Ren Shen, Lin Liu, Tingyun Kuang

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 71 ( Pt 2 ) 367 - 375 2015.2

Language：English Publishing type：Research paper (scientific journal) Publisher：WILEY-BLACKWELL

Hexokinase 1 from Arabidopsis thaliana (AtHXK1) plays a dual role in glycolysis and sugar sensing for vital metabolic and physiological processes. The uncoupling of glucose signalling from glucose metabolism was demonstrated by the analysis of two mutants (AtHXK1(G104D) and AtHXK1(S177A)) that are catalytically inactive but still functional in signalling. In this study, substrate-binding experiments indicate that the two catalytically inactive mutants have a high affinity for glucose, and an ordered substrate-binding mechanism has been observed for wild-type AtHXK1. The structure of AtHXK1 was determined both in its inactive unliganded form and in its active glucose-bound form at resolutions of 1.8 and 2.0 angstrom, respectively. These structures reveal a domain rearrangement of AtHXK1 upon glucose binding. The 2.1 angstrom resolution structure of AtHXK1(S177A) in the glucose-bound form shows similar glucose-binding interactions as the wild type. A glucose-sensing network has been proposed based on these structures. Taken together, the results provide a structural explanation for the dual functions of AtHXK1.

DOI： 10.1107/S1399004714026091

Comparison of nano-sized Mn oxides with the Mn cluster of photosystem II as catalysts for water oxidation Reviewed International journal

Mohammad Mandi Najafpour, Mohadeseh Zarei Ghobadi, Behzad Haghighi, Tatsuya Tomo, Jian-Ren Shen, Suleyman I. Allakhverdiey

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1847 ( 2 ) 294 - 306 2015.2

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

"Back to Nature" is a promising way to solve the problems that we face today, such as air pollution and shortage of energy supply based on conventional fossil fuels. A Mn cluster inside photosystem II catalyzes light-induced water-splitting leading to the generation of protons, electrons and oxygen in photosynthetic organisms, and has been considered as a good model for the synthesis of new artificial water-oxidizing catalysts. Herein, we surveyed the structural and functional details of this cluster and its surrounding environment. Then, we review the mechanistic findings concerning the cluster and compare this biological catalyst with nano-sized Mn oxides, which are among the best artificial Mn-based water-oxidizing catalysts. (C) 2014 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2014.11.006

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 International journal

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

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

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

Visible/UV absorption in PS II core complexes is dominated by the chl-a absorptions, which extend to similar to 700 nm. A broad 700-730 nm PS II core complex absorption in spinach has been assigned [1] to a charge transfer excitation between Chl(D1) and Chl(D2). Emission from this state, which peaks at 780 nm, has been seen [2] for both plant and cyanobacterial samples. We show that Thermosynechococcus vulcanus PS II core complexes have parallel absorbance in the 700-730 nm region and similar photochemical behaviour to that seen in spinach. This establishes the low energy charge transfer state as intrinsic to the native PS II reaction centre. High-sensitivity MCD measurements made in the 700-1700 nm region reveal additional electronic excitations at similar to 770 nm and similar to 1550 nm. The temperature and field dependence of MCD spectra establish that the system peaking near 1550 nm is a heme-to-Fe(III) charge transfer excitation. These transitions have not previously been observed for cyt b(559) or cyt C-550. The distinctive characteristics of the MCD signals seen at 770 nm allow us to assign absorption in this region to a d(z)(2) -> d(x2) (-) (y2) transition of Mn(III) in the Ca-Mn4O5 cluster of the oxygen evolving centre. Current measurements were performed in the S-1 state. Detailed analyses of this spectral region, especially in higher S states, promise to provide a new window on models of water oxidation. (C) 2014 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2014.11.003

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

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

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

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 that 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 angstrom resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment(1). However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation(2), and slight differences were found in the Mn-Mn distances determined by XRD1, EXAFS(3-7) and theoretical studies(8-14). Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanus in the S-1 state at a resolution of 1.95 angstroms using femtosecond X-ray pulses of the SPring-8 angstrom compact free-electron laser (SACLA) and hundreds 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 angstroms. 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 distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 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 the design of artificial catalysts for water oxidation.

DOI： 10.1038/nature13991

Isolation and characterization of a PSI-LHCI super-complex and its sub-complexes from a siphonaceous marine green alga, Bryopsis Corticulans Reviewed International journal

Xiaochun Qin, Wenda Wang, Lijing Chang, Jinghua Chen, Peng Wang, Jianping Zhang, Yikun He, Tingyun Kuang, Jian-Ren Shen

PHOTOSYNTHESIS RESEARCH 123 ( 1 ) 61 - 76 2015.1

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

A novel super-complex of photosystem I (PSI)-light-harvesting complex I (LHCI) was isolated from a siphonaceous marine green alga, Bryopsis corticulans. The super-complex contained 9-10 Lhca antennas as external LHCI bound to the core complex. The super-complex was further disintegrated into PSI core and LHCI sub-complexes, and analysis of the pigment compositions by high-performance liquid chromatography revealed unique characteristics of the B. corticulans PSI in that one PSI core contained around 14 a-carotenes and 1-2 e-carotenes. This is in sharp contrast to the PSI core from higher plants and most cyanobacteria where only beta-carotenes were present, and is the first report for an alpha-carotenetype PSI core complex among photosynthetic eukaryotes, suggesting a structural flexibility of the PSI core. Lhca antennas from B. corticulans contained seven kinds of carotenoids (siphonaxanthin, all-trans neoxanthin, 9'-cis neoxanthin, violaxanthin, siphonein, e-carotene, and acarotene) and showed a high carotenoid: chlorophyll ratio of around 7.5: 13. PSI-LHCI super-complex and PSI core showed fluorescence emission peaks at 716 and 718 nm at 77 K, respectively; whereas two Lhca oligomers had fluorescence peaks at 681 and 684 nm, respectively. By comparison with spinach PSI preparations, it was found that B. corticulans PSI had less red chlorophylls, most of them are present in the core complex but not in the outer light-harvesting systems. These characteristics may contribute to the fine tuning of the energy transfer network, and to acclimate to the ever-changing light conditions under which the unique green alga inhabits.

DOI： 10.1007/s11120-014-0039-z

Direct electron transfer from photosystem II to hematite in a hybrid photoelectrochemical cell Reviewed International journal

Wangyin Wang, Zhiliang Wang, Qingjun Zhu, Guangye Han, Chunmei Ding, Jun Chen, Jian-Ren Shen, Can Li

CHEMICAL COMMUNICATIONS 51 ( 95 ) 16952 - 16955 2015

Language：English Publishing type：Research paper (scientific journal) Publisher：ROYAL SOC CHEMISTRY

A hybrid photoanode integrating the cyanobacterial photosystem II (PSII) with a hematite film for water oxidation is constructed. Direct electron transfer from PSII to the excited Ti/Fe2O3 electrode occurs under light irradiation, resulting in a significant improvement of the photocurrent.

DOI： 10.1039/c5cc06900a

The Structure of Photosystem II and the Mechanism of Water Oxidation in Photosynthesis Reviewed International journal

Jian-Ren Shen

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 66 66 23 - 48 2015

Language：English Publishing type：Part of collection (book) Publisher：ANNUAL REVIEWS

Oxygenic photosynthesis forms the basis of aerobic life on earth by converting light energy into biologically useful chemical energy and by splitting water to generate molecular oxygen. The water-splitting and oxygen-evolving reaction is catalyzed by photosystem II (PSII), a huge, multisubunit membrane-protein complex located in the thylakoid membranes of organisms ranging from cyanobacteria to higher plants. The structure of PSII has been analyzed at 1.9-angstrom resolution by X-ray crystallography, revealing a clear picture of the Mn4CaO5 cluster, the catalytic center for water oxidation. This article provides an overview of the overall structure of PSII followed by detailed descriptions of the specific structure of the Mn4CaO5 cluster and its surrounding protein environment. Based on the geometric organization of the Mn4CaO5 cluster revealed by the crystallographic analysis, in combination with the results of a vast number of experimental studies involving spectroscopic and other techniques as well as various theoretical studies, the article also discusses possible mechanisms for water splitting that are currently under consideration.

DOI： 10.1146/annurev-arplant-050312-120129

Durability of oxygen evolution of photosystem II incorporated into lipid bilayers Reviewed

Tomoyasu Noji, Masaharu Kondo, Keisuke Kawakami, Jian-Ren Shen, Mamoru Nango, Takehisa Dewa

RESEARCH ON CHEMICAL INTERMEDIATES 40 ( 9 ) 3231 - 3241 2014.11

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

Photosystem II (PSII) has attracted a lot of attention for use in the construction of artificial photosynthetic materials due to its high activity of oxidation of water molecules. However, the robustness of PSII needs to be improved for in vitro application. In this study, we incorporated PSII (Thermosynechococcus vulcanus) into various phospholipid membranes to examine the activity and durability of oxygen evolution. PSII was incorporated into anionic 1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (PSII-DOPG), zwitterionic 1,2-dioleoyl-sn-glycero-3-phosphocholine (PSII-DOPC), and cationic 1,2-dioleoyl-sn-glycero-3-ethylphosphocholine (PSII-EDOPC). Structural integrity of PSII was examined by absorption and fluorescence spectroscopy. Compared with PSII dissolved in a micellar solution of n-dodecyl-beta-d-maltoside (PSII-micelle), durability of PSII-DOPC and PSII-DOPG were enhanced by 1.3- and 1.5-fold, respectively. The activity and durability of PSII-EDOPC was significantly low. Lipid-dependent activity and durability were discussed in terms of kinetic parameters of V (max) and K (m), and inhibition of the electron acceptor, phenyl-p-benzoquinone.

DOI： 10.1007/s11164-014-1829-9

Water exchange in manganese-based water-oxidizing catalysts in photosynthetic systems: From the water-oxidizing complex in photosystem II to nano-sized manganese oxides Reviewed International journal

Mohammad Mahdi Najafpour, Mohsen Abbasi Isaloo, Julian J. Eaton-Rye, Tatsuya Tomo, Hiroshi Nishihara, Kimiyuki Satoh, Robert Carpentier, Jian-Ren Shen, Suleyman I. Allakhverdiev

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1837 ( 9 ) 1395 - 1410 2014.9

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

The water-oxidizing complex (WOC), also known as the oxygen-evolving complex (OEC), of photosystem II in oxygenic photosynthetic organisms efficiently catalyzes water oxidation. It is, therefore, responsible for the presence of oxygen in the Earth's atmosphere. The WOC is a manganese-calcium (Mn4CaO5(H2O)(4)) cluster housed in a protein complex. In this review, we focus on water exchange chemistry of metal hydrates and discuss the mechanisms and factors affecting this chemical process. Further, water exchange rates for both the biological cofactor and synthetic manganese water splitting are discussed. The importance of fully unveiling the water exchange mechanism to understand the chemistry of water oxidation is also emphasized here. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy. (C) 2014 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2014.03.008

Photosynthesis research for sustainability: Keys to produce clean energy Reviewed International journal

Suleyman I. Allakhverdiev, Jian-Ren Shen

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1837 ( 9 ) 1377 - 1383 2014.9

Two new C-type cytochromes found in cyanobacteria: Tll0287 and PsbV2 Reviewed

Thanh-Lan Lai, Miwa Sugiura, Michihiro Suga, Jian-Ren Shen, Alain Boussac

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY 19 S838 - S838 2014.8

A nano-sized manganese oxide in a protein matrix as a natural water-oxidizing site Reviewed International journal

Mohammad Mandi Najafpour, Mohadeseh Zarei Ghobadi, Behzad Haghighi, Tatsuya Tomo, Robert Carpentier, Jian-Ren Shen, Suleyman I. Allakhverdiev

PLANT PHYSIOLOGY AND BIOCHEMISTRY 81 3 - 15 2014.8

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER

The purpose of this review is to present recent advances in the structural and functional studies of water-oxidizing center of Photosystem II and its surrounding protein matrix in order to synthesize artificial catalysts for production of clean and efficient hydrogen fuel. (C) 2014 Elsevier Masson SAS. All rights reserved.

DOI： 10.1016/j.plaphy.2014.01.020

Unraveling the Molecular Dynamics of Thylakoids Under Light Stress Reviewed

Yasusi Yamamoto, Jian-Ren Shen, Yuichiro Takahashi

PLANT AND CELL PHYSIOLOGY 55 ( 7 ) 1203 - 1205 2014.7

Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL Reviewed International journal

Kunio Hirata, Kyoko Shinzawa-Itoh, Naomine Yano, Shuhei Takemura, Koji Kato, Miki Hatanaka, Kazumasa Muramoto, Takako Kawahara, Tomitake Tsukihara, Eiki Yamashita, Kensuke Tono, Go Ueno, Takaaki Hikima, Hironori Murakami, Yuichi Inubushi, Makina Yabashi, Tetsuya Ishikawa, Masaki Yamamoto, Takashi Ogura, Hiroshi Sugimoto, Jian-Ren Shen, Shinya Yoshikawa, Hideo Ago

NATURE METHODS 11 ( 7 ) 734 - U174 2014.7

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

We report a method of femtosecond crystallography for solving radiation damage-free crystal structures of large proteins at sub-angstrom spatial resolution, using a large single crystal and the femtosecond pulses of an X-ray free-electron laser (XFEL). We demonstrated the performance of the method by determining a 1.9-angstrom radiation damage-free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.

DOI： 10.1038/NMETH.2962

Water Oxidation Chemistry of a Synthetic Dinuclear Ruthenium Complex Containing Redox-Active Quinone Ligands Reviewed International journal

Hiroshi Isobe, Koji Tanaka, Jian-Ren Shen, Kizashi Yamaguchi

INORGANIC CHEMISTRY 53 ( 8 ) 3973 - 3984 2014.4

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

We investigated theoretically the catalytic mechanism of electrochemical water oxidation in aqueous solution by a dinuclear ruthenium complex containing redox-active quinone ligands, [Ru-2(X)(Y)(3,6-tBu(2)Q)(2)(btpyan)](m+) [X, Y = H2O, OH, O, O-2; 3,6-tBu(2)Q = 3,6-di-tert-butyl-1,2-benzoquinone; btpyan = 1,8-bis(2,2':6',2"-terpyrid-4'-yl)anthracene] (m = 2, 3, 4) (1). The reaction involves a series of electron and proton transfers to achieve redox leveling, with intervening chemical transformations in a mesh scheme, and the entire molecular structure and motion of the catalyst 1 work together to drive the catalytic cycle for water oxidation. Two substrate water molecules can bind to 1 with simultaneous loss of one or two proton(s), which allows pH-dependent variability in the proportion of substrate-bound structures and following pathways for oxidative activation of the aqua/hydroxo ligands at low thermodynamic and kinetic costs. The resulting bis-oxo intermediates then undergo endothermic O-O radical coupling between two Ru(III)-O-center dot units in an anti-coplanar conformation leading to bridged mu-peroxo or mu-superoxo intermediates. The mu-superoxo species can liberate oxygen with the necessity for the preceding binding of a water molecule, which is possible only after four-electron oxidation is completed. The magnitude of catalytic current would be limited by the inherent sluggishness of the hinge-like bending motion of the bridged mu-superoxo complex that opens up the compact, hydrophobic active site of the catalyst and thereby allows water entry under dynamic conditions. On the basis of a newly proposed mechanism, we rationalize the experimentally observed behavior of electrode kinetics with respect to potential and discuss what causes a high overpotential for water oxidation by 1.

DOI： 10.1021/ic402340d

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

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

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

Routinely prepared PS II core samples are often contaminated by a significant (similar to 1-5%) fraction of PSI, as well as related proteins. This contamination is of little importance in many experiments, but masks the optical behaviour of the deep red state in PS II, which absorbs in the same spectral range (700-730 nm) as PS I (Hughes et al. 2006). When contamination levels are less than similar to 1%, it becomes difficult to quantify the PS I related components by gelbased, chromatographic, circular dichroism or EPR techniques. We have developed a fluorescence-based technique, taking advantage of the distinctively different low-temperature emission characteristics of PS II and PS I when excited near 700 nm. The approach has the advantage of providing the relative concentration of the two photosystems in a single spectral measurement. A sensitivity limit of 0.01% PS I (or better) can be achieved. The procedure is applied to PS II core preparations from spinach and Thermosynechococcus volcanos. Measurements made of T. vulcanus PS II preparations prepared by re-dissolving crystallised material indicate a low but measurable PS I related content. The analysis provides strong evidence for a previously unreported fluorescence of PS II cores peaking near 780 nm. The excitation dependence of this emission as well as its appearance in both low PS I cyanobacterial and plant based PS II core preparations suggests its association with the deep red state of PS II. (C) 2013 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2013.09.008

The structure and activation of substrate water molecules in Sr2+-substituted photosystem II Reviewed International journal

Ruchira Chatterjee, Sergey Milikisiyants, Christopher S. Coates, Faisal H. M. Koua, Jian-Ren Shen, K. V. Lakshmi

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 16 ( 38 ) 20834 - 20843 2014

Language：English Publishing type：Research paper (scientific journal) Publisher：ROYAL SOC CHEMISTRY

The mechanism of solar water oxidation by photosystem II (PSII) is of fundamental interest and it is the object of extensive studies both in the past and present. The solar water oxidation reaction of PSII occurs in the oxygen-evolving complex (OEC). The OEC consists of a tetranuclear manganese calcium-oxo (Mn4Ca-oxo) cluster that is surrounded by amino acid residues and inorganic cofactors. The role of the Ca2+ ion in the water oxidation reaction is one of the most interesting questions that is yet to be answered. In this study, we probe the structural and functional differences induced by metal ion substitution in the Mn4Ca-oxo cluster by substituting the Ca2+ ion in the OEC by a Sr2+ ion. We apply two-dimensional (2D) hyperfine sublevel correlation (HYSCORE) spectroscopy to detect weak magnetic interactions between the paramagnetic Mn4Sr-oxo cluster and the surrounding protons in the S-2 state of the OEC of Sr2+-substituted PSII. We identify three groups of protons that are magnetically interacting with the Mn4Sr-oxo cluster. Using the recently reported 1.9 angstrom resolution X-ray structure of the OEC in the S-1 state [Umena et al.] and the high-resolution 2D HYSCORE spectroscopy studies of the S-2 state of the OEC of Ca2+-containing PSII [Milikisiyants et al., Energy Environ. Sci., 2012, 5, 7747], we discuss the assignments of the three groups of protons that are magnetically coupled to the Mn4Sr-oxo cluster. Since hyperfine interactions are highly sensitive to small perturbations in the electronic and geometric structure of paramagnetic centers, a comparison of the 2D HYSCORE spectra of Sr2+-substituted and Ca2+-containing PSII allows us to draw important conclusions with respect to the structure of the substrate water molecules in the OEC and the role of the Ca2+ ion in the water oxidation reaction. In addition, for the first time, we determine the experimental value of the spin projection factor for the Mn(III) ion of the Mn4Ca-oxo cluster as rho(1) = +/- 1.7 from the assignment of the hyperfine interaction of the paramagnetic cluster with the protons of the D1-His332 residue of PSII.

DOI： 10.1039/c4cp03082f

Hydration of the oxygen-evolving complex of photosystem II probed in the dark-stable S-1 state using proton NMR dispersion profiles Reviewed International journal

Guangye Han, Yang Huang, Faisal Hammad Mekky Koua, Jian-Ren Shen, Per-Olof Westlund, Johannes Messinger

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 16 ( 24 ) 11924 - 11935 2014

Language：English Publishing type：Research paper (scientific journal) Publisher：ROYAL SOC CHEMISTRY

The hydration of the oxygen-evolving complex (OEC) was characterized in the dark stable S-1 state of photosystem II using water R-1(omega) NMR dispersion (NMRD) profiles. The R-1(omega) NMRD profiles were recorded over a frequency range from 0.01 MHz to 40 MHz for both intact and Mn-depleted photosystem II core complexes from Thermosynechococcus vulcanus (T. vulcanus). The intact-minus-(Mn)-depleted difference NMRD profiles show a characteristic dispersion from approximately 0.03 MHz to 1 MHz, which is interpreted on the basis of the Solomon-Bloembergen-Morgan (SBM) and the slow motion theories as being due to a paramagnetic enhanced relaxation (PRE) of water protons. Both theories are qualitatively consistent with the S-T = 1, g = 4.9 paramagnetic state previously described for the S-1 state of the OEC; however, an alternative explanation involving the loss of a separate class of long-lived internal waters due to the Mn-depletion procedure can presently not be ruled out. Using a point-dipole approximation the PRE-NMRD effect can be described as being caused by 1-2 water molecules that are located about 10 angstrom away from the spin center of the Mn4CaO5 cluster in the OEC. The application of the SBM theory to the dispersion observed for PSII in the S-1 state is questionable, because the parameters extracted do not fulfil the presupposed perturbation criterion. In contrast, the slow motion theory gives a consistent picture indicating that the water molecules are in fast chemical exchange with the bulk (tau(w) < 1 mu s). The modulation of the zero-field splitting (ZFS) interaction suggests a (restricted) reorientation/ structural equilibrium of the Mn4CaO5 cluster with a characteristic time constant of tau(ZFS) = 0.6-0.9 mu s.

DOI： 10.1039/c3cp55232b

Photosynthesis: from natural to artificial International journal

Johannes Messinger, Wolfgang Lubitz, Jian-Ren Shen

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 16 ( 24 ) 11810 - 11811 2014

2P257 Theoretical investigation on the conformation-charge relationship of the photosystem II oxygen evolving complex (PSII-OEC)(18B. Photobiology:Photosynthesis,Poster)

Shoji Mitsuo, Isobe Hiroshi, Yamanaka Shusuke, Shen Jian-Ren, Yamaguchi Kizashi

Seibutsu Butsuri 54 ( 1 ) S237 2014

2P258 ENDOR studies on Ca depleted and Sr substituted Mn cluster in photosystem II(18B. Photobiology:Photosynthesis,Poster)

Nagashima Hiroki, Nakajima Yoshiki, Shen Jian-Ren, Mino Hiroyuki

Seibutsu Butsuri 54 ( 1 ) S237 2014

Generalized approximate spin projection calculations of effective exchange integrals of the CaMn4O5 cluster in the S1 and S3 states of the oxygen evolving complex of photosystem II Reviewed

H. Isobe, M. Shoji, S. Yamanaka, H. Mino, Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen, K. Yamaguchi

Phys. Chem. Chem. Phys. 16 ( 24 ) 11911 - 11923 2014

Evidence for an Unprecedented Histidine Hydroxyl Modification on D2-His336 in Photosystem II of Thermosynechoccocus vulcanus and Thermosynechoccocus elongatus Reviewed International journal

Miwa Sugiura, Kazumi Koyama, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Alain Boussac

BIOCHEMISTRY 52 ( 52 ) 9426 - 9431 2013.12

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

The electron density map of the 3D crystal of Photosystem II from Thermosynechococcus vulcanus with a 1.9 angstrom resolution (PDB: 3ARC) exhibits, in the two monomers in the asymmetric unit cell, an, until now, unidentified and uninterpreted strong difference in electron density centered at a distance of around 1.5 angstrom from the nitrogen N delta of the imidazole ring of D2-His336. By MALDI-TOF/MS upon tryptic digestion, it is shown that similar to 20-30% of the fragments containing the D2-His336 residue of Photosystem II from both Thermosynechococcus vulcanus and Thermosynechococcus elongatus bear an extra mass of +16 Da. Such an extra mass likely corresponds to an unprecedented post-translational or chemical hydroxyl modification of histidine.

DOI： 10.1021/bi401213m

Spectral and functional studies on siphonaxanthin-type light-harvesting complex of photosystem II from Bryopsis corticulans Reviewed International journal

Wenda Wang, Xiaochun Qin, Min Sang, Dongqin Chen, Kebin Wang, Rongchen Lin, Congming Lu, Jian-Ren Shen, Tingyun Kuang

PHOTOSYNTHESIS RESEARCH 117 ( 1-3 ) 267 - 279 2013.11

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

Carotenoids with conjugated carbonyl groups possess special photophysical properties which have been studied in some water-soluble light-harvesting proteins (Polivka and Sundstrom, Chem Rev 104:2021-2071, 2004). However, siphonaxanthin-type light-harvesting complexes of photosystem II (LHCII) in siphonous green alga have received fewer studies. In the present study, we determined sequences of genes for several Bryopsis corticulans Lhcbm proteins, which showed that they belong to the group of major LHCII and diverged early from green algae and higher plants. Analysis of pigment composition indicated that this siphonaxanthin-type LHCII contained in total 3 siphonaxanthin and siphonein but no lutein and violaxanthin. In addition, 2 chlorophylls a in higher plant LHCII were replaced by chlorophyll b. These changes led to an increased absorption in green and blue-green light region compared with higher plant LHCII. The binding sites for chlorophylls, siphonaxanthin, and siphonein were suggested based on the structural comparison with that of higher plant LHCII. All of the ligands for the chlorophylls were completely conserved, suggesting that the two chlorophylls b were replaced by chlorophyll a without changing their binding sites in higher plant LHCII. Comparisons of the absorption spectra of isolated siphonaxanthin and siphonein in different organic solutions and the effect of heat treatment suggested that these pigments existed in a low hydrophobic protein environment, leading to an enhancement of light harvesting in the green light region. This low hydrophobic protein environment was maintained by the presence of more serine and threonine residues in B. corticulans LHCII. Finally, esterization of siphonein may also contribute to the enhanced harvesting of green light.

DOI： 10.1007/s11120-013-9808-3

Gold or silver deposited on layered manganese oxide: a functional model for the water-oxidizing complex in photosystem II Reviewed International journal

Mohammad Mahdi Najafpour, Fahimeh Rahimi, Davood Jafarian Sedigh, Robert Carpentier, Julian J. Eaton-Rye, Jian-Ren Shen, Suleyman I. Allakhverdiev

PHOTOSYNTHESIS RESEARCH 117 ( 1-3 ) 423 - 429 2013.11

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

In this report, gold or silver deposited on layered manganese oxide has been synthesized by a simple method and characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction spectrometry, atomic absorption spectroscopy, and energy-dispersive X-ray mapping. The gold deposited on layered manganese oxide showed efficient catalytic activity toward water oxidation in the presence of cerium(IV) ammonium nitrate. The properties associated with this compound suggest it is a functional model for the water-oxidizing complex in photosystem II.

DOI： 10.1007/s11120-013-9899-x

Crystal structure at 1.5 angstrom resolution of the PsbV2 cytochrome from the cyanobacterium Thermosynechococcus elongatus Reviewed International journal

Michihiro Suga, Thanh-Lan Lai, Miwa Sugiura, Jian-Ren Shen, Alain Boussac

FEBS LETTERS 587 ( 19 ) 3267 - 3272 2013.10

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

PsbV2 is a c-type cytochrome present in a very low abundance in the thermophilic cyanobacterium Thermosynechococcus elongatus. We purified this cytochrome and solved its crystal structure at a resolution of 1.5 angstrom. The protein existed as a dimer in the crystal, and has an overall structure similar to other c-type cytochromes like Cytc(6) and Cytc(550), for example. However, the 5th and 6th heme iron axial ligands were found to be His51 and Cys101, respectively, in contrast to the more common bis-His or His/Met ligands found in most cytochromes. Although a few other c-type cytochromes were suggested to have this axial coordination, this is the first crystal structure reported for a c-type heme with this unusual His/Cys axial coordination. Previous spectroscopic characterizations of PsbV2 are discussed in relation to its structural properties. (C) 2013 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.

DOI： 10.1016/j.febslet.2013.08.023

Special issues on Photosynthesis Education honoring Govindjee International journal

Suleyman I. Allakhverdiev, Jian-Ren Shen, Gerald E. Edwards

PHOTOSYNTHESIS RESEARCH 116 ( 2-3 ) 107 - 110 2013.10

Crystal Structure of Psb31, a Novel Extrinsic Protein of Photosystem II from a Marine Centric Diatom and Implications for Its Binding and Function Reviewed International journal

Ryo Nagao, Michihiro Suga, Ayako Niikura, Akinori Okumura, Faisal Hammad Mekky Koua, Takehiro Suzuki, Tatsuya Tomo, Isao Enami, Jian-Ren Shen

BIOCHEMISTRY 52 ( 38 ) 6646 - 6652 2013.9

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Psb31 is a fifth extrinsic protein found in photosystem II (PSII) of a centric diatom, Chaetoceros gracilis. The protein has been shown to bind directly to PSII in the absence of other extrinsic proteins and serves in part as a substitute for PsbO in supporting oxygen evolution. We report here the crystal structure of Psb31 at a resolution of 1.55 angstrom. The structure of Psb31 was composed of two domains, one major, N-terminal four helical domain and one minor, flexible C-terminal domain. The four helices in the N-terminal domain were arranged in an up down-up-down-fold, which appeared unexpectedly to be similar to the structure of spinach PsbQ in spite of their low sequence homology. This suggests that the centric diatom PSII contains another PsbQ- type extrinsic protein in addition to the original PsbQ protein found in the organism. On the other hand, the C-terminal domain of Psb31 has a unique structure composed of one loop and one short helix. Based on these structural analysis and chemical cross-linking experiments, residues responsible for the binding of Psb31 to PSII intrinsic proteins were suggested. The results are discussed in relation to the copy number of extrinsic proteins in higher plant PSII.

DOI： 10.1021/bi400770d

Application of Peptide Gemini Surfactants as Novel Solubilization Surfactants for Photosystems I and II of Cyanobacteria Reviewed International journal

Shuhei Koeda, Katsunari Umezaki, Tomoyasu Noji, Atsushi Ikeda, Keisuke Kawakami, Masaharu Kondo, Yasushi Yamamoto, Jian-Ren Shen, Keijiro Taga, Takehisa Dewa, Shigeru Ito, Mamoru Nango, Toshiki Tanaka, Toshihisa Mizuno

LANGMUIR 29 ( 37 ) 11667 - 11680 2013.9

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

We designed novel peptide gemini surfactants (PG-surfactants), DKDKC12K and DKDKC12D, which can solubilize Photosystem I (PSI) of Thermosynecoccus elongatus and Photosystem II (PRI) of Thermosynecoccus vulcanus in an aqueous buffer solution. To assess the detailed effects of PC-surfactants on the original supramolecular membrane protein complexes and functions of PSI and PSII, we applied the surfactant exchange method to the isolated PSI and PSII. Spectroscopic properties, light-induced electron transfer activity, and dynamic light scattering measurements showed that PSI and PSII could be solubilized not only with retention of the original supramolecular protein complexes and functions but also without forming aggregates. Furthermore, measurement of the lifetime of light-induced charge-separation state in PSI revealed that both surfactants, especially DKDKC12D, displayed slight improvement against thermal denaturation below 60 degrees C compared with that using beta-DDM. This degree of improvement in thermal resistance still seems low, implying that the peptide moieties did not interact directly with membrane protein surfaces. By conjugating an electron mediator such as methyl viologen (MV2+) to DKDKC12K (denoted MV-DKDKC12K), we obtained derivatives that can trap the generated reductive electrons from the light-irradiated PSI. After immobilization onto an indium tin oxide electrode, a cathodic photocurrent from the electrode to the PSI/MV-DKDKC12K conjugate was observed in response to the interval of light irradiation. These findings indicate that the PG-surfactants DKDKC12K and DKDKC12D provide not only a new class of solubilization surfactants but also insights into designing other derivatives that confer new functions on PSI and PSII.

DOI： 10.1021/la402167v

Photosystem II Does Not Possess a Simple Excitation Energy Funnel: Time-Resolved Fluorescence Spectroscopy Meets Theory Reviewed International journal

Yutaka Shibata, Shunsuke Nishi, Keisuke Kawakami, Jian-Ren Shen, Thomas Renger

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 135 ( 18 ) 6903 - 6914 2013.5

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

The experimentally obtained time-resolved fluorescence spectra of photosystem H (PS II) core complexes, purified from a thermophilic cyanobacterium Thermosynechococcus vulcanus, at 5-180 K are compared with simulations. Dynamic localization effects of excitons are treated implicitly by introducing exciton domains of strongly coupled pigments. Exciton relaxations within a domain and exciton transfers between domains are treated on the basis of Redfield theory and generalized Forster theory, respectively. The excitonic couplings between the pigments are calculated by a quantum chemical/electrostatic method (Poisson-TrEsp). Starting with previously published values, a refined set of site energies of the pigments is obtained through optimization cycles of the fits of stationary optical spectra of PS II. Satisfactorily agreement between the experimental and simulated spectra is obtained for the absorption spectrum including its temperature dependence and the linear dichroism spectrum of PS II core complexes (PS II-CC). Furthermore, the refined site energies well reproduce the temperature dependence of the time-resolved fluorescence spectrum of PS II-CC, which is characterized by the emergence of a 695 nm fluorescence peak upon cooling down to 77 K and the decrease of its relative intensity upon further cooling below 77 K. The blue shift of the fluorescence band upon cooling below 77 K is explained by the existence of two red-shifted chlorophyll pools emitting at around 685 and 695 nm. The former pool is assigned to Chl45 or Chl43 in CP43 (Chl numbering according to the nomenclature of Loll et al. Nature 2005, 438, 1040) while the latter is assigned to Chl29 in CP47. The 695 nm emitting chlorophyll is suggested to attract excitations from the peripheral light-harvesting complexes and might also be involved in photoprotection.

DOI： 10.1021/ja312586p

Electronic structure of S-2 state of the oxygen-evolving complex of photosystem II studied by PELDOR Reviewed International journal

Mizue Asada, Hiroki Nagashima, Faisal Hammad Mekky Koua, Jian-Ren Shen, Asako Kawamori, Hiroyuki Mino

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1827 ( 3 ) 438 - 445 2013.3

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

Photosynthetic water splitting is catalyzed by a Mn4CaO5 cluster in photosystem II, whose structure was recently determined at a resolution of 1.9 angstrom [Umena, Y. et al. 2011, Nature, 473:55-60]. To determine the electronic structure of the Mn4CaO5 cluster, pulsed electron-electron double resonance (PELDOR) measurements were performed for the tyrosine residue Y-D(center dot) and S-2 state signals with non-oriented and oriented photosystem II (PS H) samples. Based on these measurements, the spin density distributions were calculated by comparing with the experimental results. The best fitting parameters were obtained with a model in which Mn1 has a large positive projection, Mn3 has a small positive projection, and Mn2 and Mn4 have negative projections (the numbering of Mni (i=1-4) is based on the crystal structure at a 1.9 angstrom resolution), which yielded spin projections of 1.97, -120, 1.19 and -0.96 for Mn1-4 ions. The results show that the Mn1 ion, which is coordinated by H332, 0342 and E189, has a valence of Mn(III) in the S-2 state. The sign of the exchange interactions J(13) is positive, and the other signs are negative. 2(C) 013 Els,evier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2012.12.011

Structure of Sr-substituted photosystem II at 2.1 angstrom resolution and its implications in the mechanism of water oxidation Reviewed International journal

Faisal Hammad Mekky Koua, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 110 ( 10 ) 3889 - 3894 2013.3

Language：English Publishing type：Research paper (scientific journal) Publisher：NATL ACAD SCIENCES

Oxygen-evolving complex of photosystem II ( PSII) is a tetra-manganese calcium penta-oxygenic cluster (Mn4CaO5) catalyzing light-induced water oxidation through several intermediate states (S-states) by a mechanism that is not fully understood. To elucidate the roles of Ca2+ in this cluster and the possible location of water substrates in this process, we crystallized Sr2+-substituted PSII from Thermosynechococcus vulcanus, analyzed its crystal structure at a resolution of 2.1 angstrom, and compared it with the 1.9 angstrom structure of native PSII. Our analysis showed that the position of Sr was moved toward the outside of the cubane structure of the Mn4CaO5-cluster relative to that of Ca2+, resulting in a general elongation of the bond distances between Sr and its surrounding atoms compared with the corresponding distances in the Ca-containing cluster. In particular, we identified an apparent elongation in the bond distance between Sr and one of the two terminal water ligands of Ca2+, W3, whereas that of the Sr-W4 distance was not much changed. This result may contribute to the decrease of oxygen evolution upon Sr2+-substitution, and suggests a weak binding and rather mobile nature of this particular water molecule (W3), which in turn implies the possible involvement of this water molecule as a substrate in the O-O bond formation. In addition, the PsbY subunit, which was absent in the 1.9 angstrom structure of native PSII, was found in the Sr-PSII structure.

DOI： 10.1073/pnas.1219922110

Water oxidation and water-oxidizing complex in cyanobacteria Reviewed

Mohammad Mahdi Najafpour, Atefeh Nemati Moghaddam, Jian-Ren Shen, Govindjee

Stress Biology of Cyanobacteria: Molecular Mechanisms to Cellular Responses 41 - 60 2013.1

Language：English Publishing type：Part of collection (book) Publisher：CRC Press

Cyanobacteria, or blue-green algae as they were called, are a group of bacteria that obtain their energy through oxygenic photosynthesis (for a perspective, see [1]
for evolution, see [2]).Cyanobacteria converted the early reducing atmosphere into an oxidizing one and changed the composition of life forms on Earth. The consensus is that chloroplasts in plants and eukaryotic algae have evolved from cyanobacterial ancestors via endosymbiosis [3]. In this chapter, we will discuss the structure and function of the water-oxidizing complex (WOC) in cyanobacteria [4,5].

DOI： 10.1201/b13853

Structural Basis of Photosynthetic Water-Splitting

Jian-Ren Shen, Yasufumi Umena, Keisuke Kawakami, Nobuo Kamiya

SOLAR CHEMICAL ENERGY STORAGE (SOLCHES) 1568 31 - 34 2013

Language：English Publishing type：Research paper (international conference proceedings) Publisher：AMER INST PHYSICS

Photosynthetic water-splitting takes place in photosystem II (PSII), a membrane protein complex consisting of 20 subunits with an overall molecular mass of 350 kDa. The light-induced water-splitting reaction catalyzed by PSII not only converts light energy into biologically useful chemical energy, but also provides us with oxygen indispensible for sustaining oxygenic life on the earth. We have solved the structure of PSII at a 1.9 angstrom resolution, from which, the detailed structure of the Mn4CaO5-cluster, the catalytic center for water-splitting, became clear. Based on the structure of PSII at the atomic resolution, possible mechanism of light-induced water-splitting was discussed.

DOI： 10.1063/1.4848085

1SAA-03 QM/MM study on the photosystem II oxygen evolving complex at the S1 state(1SAA Molecular mechanism of light-driven water oxidation : photosystem II and artificial photosynthesis,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)

Shoji Mitsuo, Isobe Hiroshi, Yamanaka Shusuke, Kamiya Nobuo, Shen Jian-Ren, Yamaguchi Kizashi

Seibutsu Butsuri 53 ( 1 ) S82 2013

The position and orientation of active carotenoid in photosystem II

Asako Kawamori, Hiroyuki Mino, Jianren Shen

Advanced Topics in Science and Technology in China 64 - 66 2013

Language：English Publishing type：Part of collection (book) Publisher：Springer

The distances between YD and active carotenoid have been determined in cyanobacterium (synecochoccus vulcanus) and spinach PSII by pulsed electron double resonance (PELDOR). The observed spectra were analyzed taking into spin distribution of over 30 carbon atoms in the carotenoid molecule. The result of simulations based on the recent crystal structure fitted well with the spectra. The observed spectra for spinach PSII was different, showing the crystal structure of spinach PSII is slightly different from that of cyanobacteria. The ELDOR spectra of YD-YZ radical pair were observed in a cyanobacterium. The result showed the different distance from Spinach PSII.

DOI： 10.1007/978-3-642-32034-7_13

Electronic structure of the CaMn4O5 cluster in the PSII system refined to the 1.9 Å X-ray resolution. Possible mechanisms of photosynthetic water splitting

S. Yamanaka, K. Kanda, H. Isobe, K. Nakata, Y. Umena, K. Kawakami, J. R. Shen, N. Kamiya, M. Okumura, T. Takada, H. Nakamura, K. Yamaguchi

Advanced Topics in Science and Technology in China 250 - 254 2013

Language：English Publishing type：Part of collection (book) Publisher：Springer

Broken-symmetry (BS) UB3LYP calculations have been performed for the CaMn4O5 cluster (1) in the oxygen-evolving complex (OEC) of the PSII system refined to 1.9 Å resolution by Umena, Kawakami, Kamiya, Shen to elucidate its electronic structure that is crucial for consideration of possible mechanisms of photosynthetic water splitting. Our UB3LYP computations have elucidated the position of protonated oxygen of the CaMn(III)2Mn(IV)2O4(OH) cluster (1a) at the S1 stage of Kok cycle. Starting from the newly elucidated S1 structure of 1a, we have calculated the electronic structure of proton and electron released CaMn(IV)4O5 cluster (1b) that mimics the S4 stage of the cycle. The LUMOs of 1b are depicted for pictorial understanding of electrophilic oxygen sites that are responsible for nucleophilic attack of hydroxide anion (or water) for the O-O bond formation. Implications of present computational results are discussed in relation to possible mechanisms of photosynthetic water splitting.

DOI： 10.1007/978-3-642-32034-7_52

Photosystem II and the unique role of bicarbonate: A historical perspective Reviewed International journal

Dmitriy Shevela, Julian J. Eaton-Rye, Jian-Ren Shen, Govindjee

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1817 ( 8 ) 1134 - 1151 2012.8

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

In photosynthesis, cyanobacteria, algae and plants fix carbon dioxide (CO2) into carbohydrates; this is necessary to support life on Earth. Over 50 years ago, Otto Heinrich Warburg discovered a unique stimulatory role of CO2 in the Hill reaction (i.e., O-2 evolution accompanied by reduction of an artificial electron acceptor), which, obviously, does not include any carbon fixation pathway; Warburg used this discovery to support his idea that O-2 in photosynthesis originates in CO2. During the 1960s, a large number of researchers attempted to decipher this unique phenomenon, with limited success. In the 1970s, Alan Stemler, in Govindjee's lab, perfected methods to get highly reproducible results, and observed, among other things, that the turnover of Photosystem II (PSII) was stimulated by bicarbonate ions (hydrogen carbonate): the effect would, be on the donor or the acceptor, or both sides of PSII. In 1975, Thomas Wydrzynski, also in Govindjee's lab, discovered that there was a definite bicarbonate effect on the electron acceptor (the plastoquinone) side of PSII. The most recent 1.9 angstrom crystal structure of PSII, unequivocally shows HCO3- bound to the non-heme iron that sits in-between the bound primary quinone electron acceptor, Q(A), and the secondary quinone electron acceptor Q(B). In this review, we focus on the historical development of our understanding of this unique bicarbonate effect on the electron acceptor side of PSII, and its mechanism as obtained by biochemical, biophysical and molecular biological approaches in many laboratories around the World. We suggest an atomic level model in which HCO3-/CO32- plays a key role in the protonation of the reduced Q(B). In addition, we make comments on the role of bicarbonate on the donor side of PSII, as has been extensively studied in the labs of Alan Stemler (USA) and Vyacheslav Klimov (Russia). We end this review by discussing the uniqueness of bicarbonate's role in oxygenic photosynthesis and its role in the evolutionary development of O-2-evolving PSII. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial. (C) 2012 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2012.04.003

Cationic state distribution over the chlorophyll d-containing P-D1/P-D2 Pair in photosystem II Reviewed International journal

Keisuke Saito, Jian-Ren Shen, Hiroshi Ishikita

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1817 ( 8 ) 1191 - 1195 2012.8

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

Most of the chlorophyll (Chl) cofactors in photosystem II (PSII) from Acaryochloris marina are Chld, although a few Chla molecules are also present. To evaluate the possibility that Chla may participate in the P-D1/P-D2 Chl pair in PSII from A marina, the P-D1(.+)/P-D2(.+) charge ratio was investigated using the PSII crystal structure analyzed at 1.9-angstrom resolution, while considering all possibilities for the Chld-containing P-D1/P-D2 pair, i.e., Chld/Chld, Chla/Chld, and Chld/Chla pairs. Chld/Chld and Chla/Chld pairs resulted in a large P-D1(.+) population relative to P-D2(.+) as identified in Chla/Chla homodimer pairs in PSII from other species. e.g. Thermosynechococcus elongatus PSII. However, the Chld/Chla pair possessed a P-D1(.+)/P-D2(.+) ratio of approximately 50/50, which is in contrast to previous spectroscopic studies on A. marina PSII. The present results strongly exclude the possibility that the Chld/Chla pair serves as P-D1/P-D2 in A marina PSII. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2011.12.003

The structure and activation of substrate water molecules in the S-2 state of photosystem II studied by hyperfine sublevel correlation spectroscopy Reviewed

Sergey Milikisiyants, Ruchira Chatterjee, Christopher S. Coates, Faisal H. M. Koua, Jian-Ren Shen, K. V. Lakshmi

ENERGY & ENVIRONMENTAL SCIENCE 5 ( 7 ) 7747 - 7756 2012.7

Language：English Publishing type：Research paper (scientific journal) Publisher：ROYAL SOC CHEMISTRY

The water-splitting protein, photosystem II, catalyzes the light-driven oxidation of water to dioxygen. The solar water oxidation reaction takes place at the catalytic center, referred to as the oxygen-evolving complex, of photosystem II. During the catalytic cycle, the oxygen-evolving complex cycles through five distinct intermediate states, S-0-S-4. In this study, we trap the oxygen-evolving complex in the S-2 intermediate state by low temperature illumination of photosystem II isolated from three different species, Thermosynechococcus vulcanus, the PsbB variant of Synechocystis PCC 6803 and spinach. We apply two-dimensional hyperfine sublevel correlation spectroscopy to detect weak magnetic interactions between the paramagnetic tetra-nuclear manganese cluster of the S-2 state of the OEC and the surrounding protons. We identify five groups of protons that are interacting with the tetra-nuclear manganese cluster. From the values of hyperfine interactions and using the recently reported 1.9 angstrom resolution X-ray structure of the OEC in the S-1 state [Umena et al., Nature, 2011, 473, 55], we discuss the assignments of the five groups of protons and draw important conclusions on the structure of the oxygen-evolving complex in the S-2 state. In addition, we conclude that the structure of OEC is nearly identical in photosystem II from Thermosynechococcus vulcanus, the PsbB variant of Synechocystis PCC 6803 and spinach.

DOI： 10.1039/c2ee21210b

Influence of the Axial Ligand on the Cationic Properties of the Chlorophyll Pair in Photosystem II from Thermosynechococcus vulcanus Reviewed International journal

Keisuke Saito, Jian-Ren Shen, Hiroshi Ishikita

BIOPHYSICAL JOURNAL 102 ( 11 ) 2634 - 2640 2012.6

Language：English Publishing type：Research paper (scientific journal) Publisher：CELL PRESS

Influence of the axial ligand of P-D1 chlorophyll (D1-His-198) on the E-m of monomer chlorophylls P-D1 and P-D2, and the P-D1(center dot+)/P-D2(center dot+) charge ratio was investigated by theoretical calculations using the PSII crystal structure of Thermosynechococcus vulcanus analyzed at 1.9-angstrom resolution. It was found that the Em(P-D1)/E-m(P-D2) values and P-D1(center dot+)/P-D2(center dot+) ratio remained unchanged upon D1-H198Q mutation. However, Em(PD1) was increased in the D1-H198A mutant, resulting in a more even distribution of the positive charge over P-D1/P-D2. Introduction of a water molecule as an axial ligand resulted in equal E-m values and P-D1(center dot+)/P-D2(center dot+) ratios between the mutant and wild-type, thus confirming the presence of the water ligand in the mutant.

DOI： 10.1016/j.bpj.2012.04.016

Deformation of Chlorin Rings in the Photosystem II Crystal Structure Reviewed International journal

Keisuke Saito, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Hiroshi Ishikita

BIOCHEMISTRY 51 ( 21 ) 4290 - 4299 2012.5

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

The crystal structure of Photosystem II (PSII) analyzed at a resolution of 1.9 angstrom revealed deformations of chlorin rings in the chlorophylls for the first time. We investigated the degrees of chlorin ring deformation and factors that contributed to them in the PSII crystal structure, using a normal-coordinate structural decomposition procedure. The out-of-plane distortion of the Pm chlorin ring can be described predominantly by a large "doming mode" arising from the axial ligand, D1-His198, as well as the chlorophyll side chains and PSII protein environment. In contrast, the deformation of P-D2 was caused by a "saddling mode" arising from the D2-Trp191 ring and the doming mode arising from D2-His197. Large ruffling modes, which were reported to lower the redox potential in heme proteins, were observed in P-D1 and Chl(D1), but not in P-D2 and ChlD(2). Furthermore, as P-D1 possessed the largest doming mode among the reaction center chlorophylls, the corresponding bacteriochlorophyll P-L possessed the largest doming mode in bacterial photosynthetic reaction centers. However, the majority of the redox potential shift in the protein environment was determined by the electrostatic environment. The difference in the chlorin ring deformation appears to directly refer to the difference in "the local steric protein environment" rather than the redox potential value in PSII.

DOI： 10.1021/bi300428s

3D1022 Determination of magnetic couplings of S_2 state Mn-cluster in Photosystem II studied by PELDOR measurement(Photobiology:Photosynthesis,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Asada Mizue, Nagashima Hiroki, Koua Faisal Hammad Mekky, Shen Jian-Ren, Mino Hiroyuki

Seibutsu Butsuri 52 S63 2012

3D0948 Possible non-photochemical quenching mechanism within pohotosystem II core complex(Photobiology:Photosynthesis,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Shibata Yutaka, Nishi Shunsuke, Kawakami Keisuke, Shen Jian-Ren, Renger Thomas

Seibutsu Butsuri 52 S62 2012

Theoretical illumination of water-inserted structures of the CaMn4O5 cluster in the S2 and S3 states of oxygen-evolving complex of photosystem II: full geometry optimizations by B3LYP hybrid density functional Reviewed

H. Isobe, M. Shoji, S. Yamanaka, Y. Umena, K. Kawakami, N. Kamiya, J.-R. Shen, K. Yamaguchi

Dalton Transactions 41 ( 44 ) 13727 - 13727 2012

Short Hydrogen Bond between Redox-Active Tyrosine Y-z and D1-His190 in the Photosystem II Crystal Structure Reviewed International journal

Keisuke Saito, Jian-Ren Shen, Toyokazu Ishida, Hiroshi Ishikita

BIOCHEMISTRY 50 ( 45 ) 9836 - 9844 2011.11

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

The crystal structure of photosystem IT (PSII) analyzed at a resolution of 1.9 A revealed a remarkably short H-bond between redox-active tyrosine Y-z and D1-His190 (2.46 angstrom donor-acceptor distance). Using large-scale quantum mechanical/molecular mechanical (QM/MM) calculations with the explicit PSII protein environment, we were able to reproduce this remarkably short H-bond in the original geometry of the crystal structure in the neutral [YzO center dot center dot center dot H center dot center dot center dot N-e-His-N delta H center dot center dot center dot O=Asn] state, but not in the oxidized states, indicating that the neutral state was the one observed in the crystal structure. In addition to the appropriate redox/protonation state of Y-z and D1-His190, we found that the presence of a cluster of water molecules played a key role in shortening the distance between Y-z and D1-His190. The orientations of the water molecules in the cluster were energetically stabilized by the highly polarized PSII protein environment, where the Ca ion of the oxygen-evolving complex (OEC) and the OEC ligand D1-Glu189 were also involved.

DOI： 10.1021/bi201366j

Distribution of the Cationic State over the Chlorophyll Pair of the Photosystem II Reaction Center Reviewed International journal

Keisuke Saito, Toyokazu Ishida, Miwa Sugiura, Keisuke Kawakami, Yasufumi Umena, Nobuo Kamiya, Jian-Ren Shen, Hiroshi Ishikita

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 133 ( 36 ) 14379 - 14388 2011.9

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

The reaction center chlorophylls a (Chla) of photosystem II (PSII) are composed of six Chla molecules including the special pair Chla P-D1/P-D2 harbored by the D1/D2 heterodimer. They serve as the ultimate electron abstractors for water oxidation in the oxygen-evolving Mn4CaO5 cluster. Using the PSII crystal structure analyzed at 1.9 angstrom resolution, the redox potentials of P-D1/center dot P-D2 for one-electron oxidation (E-m) were calculated by considering all PSII subunits and the protonation pattern of all titratable residues. The Em(Chla) values were calculated to be 1015-1132 mV for P-D1 and 1141-1201 mV for P-D2, depending on the protonation state of the Mn4CaO5 cluster. The results showed that Em(P-D1) was lower than E-m(P-D2) P-D2 favoring localization of the charge of the cationic state more on P-D1. The P-D1(center dot+)/P-D2(center dot+) charge ratio determined by the large-scale QM/MM calculations with the explicit PS II protein environment yielded a P-D1(center dot+)/P-D2(center dot+) ratio of similar to 80/similar to 20, which was found to be due to the asymmetry in electrostatic characters of several conserved D1/D2 residue pairs that cause the E-m(P-D1)/E-m(P-D2) difference, e.g., Dl -Asn181/D2-Argl 80, D1-Asn298/D2-Arg294, D1-Asp61/D2-His61, D1-Glu189/D2-Phe188, and D1-Asp170/D2-Phe169. The larger P-D1(center dot+) population than P-D2(center dot+) appears to be an inevitable fate of the intact PSII that possesses water oxidation activity.

DOI： 10.1021/ja203947k

Structure of the catalytic, inorganic core of oxygen-evolving photosystem II at 1.9 angstrom resolution Reviewed

Keisuke Kawakami, Yasufumi Umena, Nobuo Kamiya, Jian-Ren Shen

JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 104 ( 1-2 ) 9 - 18 2011.7

Language：English Publisher：ELSEVIER SCIENCE SA

The catalytic center for photosynthetic water-splitting consists of 4 Mn atoms and 1 Ca atom and is located near the lumenal surface of photosystem II. So far the structure of the Mn4Ca-cluster has been studied by a variety of techniques including X-ray spectroscopy and diffraction, and various structural models have been proposed. However, its exact structure is still unknown due to the limited resolution of crystal structures of PSII achieved so far, as well as possible radiation damages that might have occurred. Very recently, we have succeeded in solving the structure of photosystem II at 1.9 angstrom. which yielded a detailed picture of the Mn4CaO5-cluster for the first time. In the high resolution structure, the Mn4CaO5-cluster is arranged in a distorted chair form, with a cubane-like structure formed by 3 Mn and 1 Ca, 4 oxygen atoms as the distorted base of the chair, and 1 Mn and 1 oxygen atom outside of the cubane as the back of the chair. In addition, four water molecules were associated with the cluster, among which, two are associated with the terminal Mn atom and two are associated with the Ca atom. Some of these water molecules may therefore serve as the substrates for water-splitting. The high resolution structure of the catalytic center provided a solid basis for elucidation of the mechanism of photosynthetic water splitting. We review here the structural features of the Mn4CaO5-cluster analyzed at 1.9 angstrom resolution, and compare them with the structures reported previously. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.jphotobiol.2011.03.017

S-1-State Model of the O-2-Evolving Complex of Photosystem II Reviewed International journal

Sandra Luber, Ivan Rivalta, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Gary W. Brudvig, Victor S. Batista

BIOCHEMISTRY 50 ( 29 ) 6308 - 6311 2011.7

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

We introduce a quantum mechanics/molecular mechanics model of the oxygen-evolving complex of photosystem II in the S-1 Mn-4(IV,III,IV,III) state, where Ca2+ is bridged to manganese centers by the carboxylate moieties of D170 and A344 on the basis of the new X-ray diffraction (XRD) model recently reported at 1.9 angstrom resolution. The model is also consistent with high-resolution spectroscopic data, including polarized extended X-ray absorption fine structure data of oriented single crystals. Our results provide refined intermetallic distances within the Mn cluster and suggest that the XRD model most likely corresponds to a mixture of oxidation states, including species more reduced than those observed in the catalytic cycle of water splitting.

DOI： 10.1021/bi200681q

Structural-Functional Role of Chloride in Photosystem II Reviewed International journal

Ivan Rivalta, Muhamed Amin, Sandra Luber, Serguei Vassiliev, Ravi Pokhrel, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Doug Bruce, Gary W. Brudvig, M. R. Gunner, Victor S. Batista

BIOCHEMISTRY 50 ( 29 ) 6312 - 6315 2011.7

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Chloride binding in photosystem II (PSII) is essential for photosynthetic water oxidation. However, the functional roles of chloride and possible binding sites, during oxygen evolution, remain controversial. This paper examines the functions of chloride based on its binding site revealed in the X-ray crystal structure of PSII at 1.9 angstrom resolution. We find that chloride depletion induces formation of a salt bridge between D2-K317 and D1-D61 that could suppress the transfer of protons to the lumen.

DOI： 10.1021/bi200685w

Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 angstrom Reviewed International journal

Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya

NATURE 473 ( 7345 ) 55 - U65 2011.5

Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP

Photosystem II is the site of photosynthetic water oxidation and contains 20 subunits with a total molecular mass of 350 kDa. The structure of photosystem II has been reported at resolutions from 3.8 to 2.9 angstrom. These resolutions have provided much information on the arrangement of protein subunits and cofactors but are insufficient to reveal the detailed structure of the catalytic centre of water splitting. Here we report the crystal structure of photosystem II at a resolution of 1.9 angstrom. From our electron density map, we located all of the metal atoms of the Mn4CaO5 cluster, together with all of their ligands. We found that five oxygen atoms served as oxo bridges linking the five metal atoms, and that four water molecules were bound to the Mn4CaO5 cluster; some of them may therefore serve as substrates for dioxygen formation. We identified more than 1,300 water molecules in each photosystem II monomer. Some of them formed extensive hydrogen-bonding networks that may serve as channels for protons, water or oxygen molecules. The determination of the high-resolution structure of photosystem II will allow us to analyse and understand its functions in great detail.

DOI： 10.1038/nature09913

Labile electronic and spin states of the CaMn4O5 cluster in the PSII system refined to the 1.9 angstrom X-ray resolution. UB3LYP computational results Reviewed

Keita Kanda, Shusuke Yamanaka, Tohru Saito, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Mitsutaka Okumura, Haruki Nakamura, Kizashi Yamaguchi

CHEMICAL PHYSICS LETTERS 506 ( 1-3 ) 98 - 103 2011.4

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

UB3LYP calculations were first performed to elucidate electronic and spin structures of the CaMn4O5 cluster in the oxygen-evolving-complex of the PSII system refined to the 1.9 angstrom X-ray resolution by Kamiya, Shen, and their collaborators. Eight different UB3LYP solutions with axial spin structures were constructed to obtain the energy levels of the cluster on the basis of their X-ray structure. The energy diagrams were analyzed in terms of the Heisenberg model that involves six effective-exchange integrals between manganese ions. Several characteristic features of the electronic states of the cluster are revealed from these theoretical investigations based on the UB3LYP calculations. (C) 2011 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2011.02.030

Proton-Coupled Electron-Transfer Processes in Photosystem II Probed by Highly Resolved g-Anisotropy of Redox-Active Tyrosine Y-Z Reviewed International journal

Hideto Matsuoka, Jian-Ren Shen, Asako Kawamori, Kei Nishiyama, Yasunori Ohba, Seigo Yamauchi

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 133 ( 12 ) 4655 - 4660 2011.3

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

The oxidation of a redox-active tyrosine residue Y-Z in photosystem II (PSII) is coupled with proton transfer to a hydrogen-bonded D1-His190 residue. Because of the apparent proximity of Y-Z to: the water-oxidizing complex and its redox activity, it is believed that Y-Z plays a significant role in water oxidation in PSII. We investigated the g-anisotropy of the tyrosine radical Y-Z(center dot) to provide insight into the mechanism of Y-Z(center dot) proton-coupled electron transfer in Nth-depleted PSII. The anisotropy was highly resolved by electron paramagnetic resonance spectroscopy at the W-band (94.9 GHz) using PSII single crystals. The g(x)-component along the phenolic C-O bond of Y-Z(center dot) was calculated by density functional theory (DFT). It was concluded from the highly resolved g-anisotropy that Y-Z loses a phenol proton to D1-His190 upon tyrosine oxidation, and D1-His190 redonates the same proton back to Y-Z(center dot) upon reduction.

DOI： 10.1021/ja2000566

Roles of PsbI and PsbM in photosystem II dimer formation and stability studied by deletion mutagenesis and X-ray crystallography Reviewed International journal

Keisuke Kawakami, Yasufumi Umena, Masako Iwai, Yousuke Kawabata, Masahiko Ikeuchi, Nobuo Kamiya, Jian-Ren Shen

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1807 ( 3 ) 319 - 325 2011.3

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

PsbM and PsbI are two low molecular weight subunits of photosystem II (PSII), with PsbM being located in the center, and PsbI in the periphery, of the PSII dimer. In order to study the functions of these two subunits from a structural point of view, we crystallized and analyzed the crystal structure of PSII dimers from two mutants lacking either PsbM or PsbI. Our results confirmed the location of these two subunits in the current crystal structure, as well as their absence in the respective mutants. The relative contents of PSII dimers were found to be decreased in both mutants, with a concomitant increase in the amount of PSII monomers, suggesting a destabilization of PSII dimers in both of the mutants. On the other hand, the accumulation level of the overall PSII complexes in the two mutants was similar to that in the wild-type strain. Treatment of purified PSII dimers with lauryldimethylamine N-oxide at an elevated temperature preferentially disintegrated the dimers from the PsbM deletion mutant into monomers and CP43-less monomers, whereas no significant degradation of the dimers was observed from the PsbI deletion mutant. These results indicate that although both PsbM and PsbI are required for the efficient formation and stability of PSII dimers in vivo, they have different roles, namely, PsbM is required directly for the formation of dimers and its absence led to the instability of the dimers accumulated. On the other hand, PsbI is required in the assembly process of PSII dimers in vivo: once the dimers are formed. PsbI was no longer required for its stability. (C) 2010 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2010.12.013

Photosynthetic Oxygen Evolution in Mesoporous Silica Material: Adsorption of Photosystem II Reaction Center Complex into 23 nm Nanopores in SBA Reviewed International journal

Tomoyasu Noji, Chihiro Kamidaki, Keisuke Kawakami, Jian-Ren Shen, Tsutomu Kajino, Yoshiaki Fukushima, Takeshi Sekitoh, Shigeru Itoh

LANGMUIR 27 ( 2 ) 705 - 713 2011.1

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

An oxygen-evolving photosynthetic reaction center complex (PSII) was adsorbed into nanopores in SBA, a mesoporous silica compound. We purified the dimer of PSII complex from a thermophilic cyanobacterium, Thermosynechococcus vulcanus, which grows optimally at 57 degrees C. The thermally stable PSII dimeric complex has a diameter of 20 nm and a molecular mass of 756 kDa and binds more than 60 chlorophylls. The SBA particles, with average internal pore diameters of 15 nm (SBA(15)) and 23 nm (SBA(23)), adsorbed 4.7 and 15 mg of PSII/g SBA, respectively. Measurement with a confocal laser-scanning microscope indicated the adsorption of PSII to the surface and the inner space of the SBA(23) particles, indicating the adsorption of PSII into the 23 nm silica nanopores. PSII did not bind to the inner pores of SBA(15). PSII bound to SBA(23) showed the high and stable activity of a photosynthetic oxygen-evolving reaction, indicating the light-driven electron transport from water to the quinone molecules added in the outer medium. The PSII-SBA conjugate can be a new material for photosensors and artificial photosynthetic systems.

DOI： 10.1021/la1032916

Isolation of photosystem II-enriched membranes and the oxygen-evolving complex subunit proteins from higher plants. Reviewed International journal

Yasusi Yamamoto, Jing Leng, Jian-Ren Shen

Methods in molecular biology (Clifton, N.J.) 684 1 - 10 2011

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

We describe methods to isolate highly active oxygen-evolving photosystem II (PSII) membranes and core complexes from higher plants, and to purify subunits of the oxygen-evolving complex (OEC). The membrane samples used as the material for various in vitro studies of PSII are prepared by solubilizing thylakoid membranes with the nonionic detergent Triton X-100, and the core complexes are prepared by further solubilization of the PSII membranes with n-dodecyl-β-D-maltoside (β-DDM). The OEC subunit proteins are dissociated from the PSII-enriched membranes by alkaline or salt treatment, and are then purified by ion-exchange chromatography using an automated high performance liquid chromatography system.

DOI： 10.1007/978-1-60761-925-3_1

Purification and crystallization of oxygen-evolving photosystem II core complex from thermophilic cyanobacteria. Reviewed International journal

Jian-Ren Shen, Keisuke Kawakami, Hiroyuki Koike

Methods in molecular biology (Clifton, N.J.) 684 41 - 51 2011

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

This chapter describes the purification and crystallization of oxygen-evolving photosystem II core dimer complex from a thermophilic cyanobacterium Thermosynechococcus vulcanus. Procedures used for purification of photosystem II from the cyanobacterium involves cultivation of cells, isolation of thylakoid membranes, purification of crude and pure photosystem II core complexes by detergent solubilization, followed by differential centrifugation and column chromatography. The purified core dimer particles were successfully used for crystallization, and the methods and conditions used for crystallization are presented. These purification and crystallization procedures can be applied for another thermophilic cyanobacterium T. elongatus.

DOI： 10.1007/978-1-60761-925-3_5

2L1412 Crystal structure of oxygen evolving Photosystem II complex at an atomic resolution(Photobiology: Photosynthesis,The 48th Annual Meeting of the Biophysical Society of Japan)

Umena Yasufumi, Kawakami Keisuke, Kamiya Nobuo, Shen Jian-Ren

Seibutsu Butsuri 51 S95 2011

1SL-02 Atomic structure of photosystem II that enables photosynthetic water-splitting(1SL The leading edge of photosynthesis research and energy creation,The 49th Annual Meeting of the Biophysical Society of Japan)

Shen Jian-Ren, Umena Yasufumi, Kawakami Keisuke, Kamiya Nobuo

Seibutsu Butsuri 51 S10 2011

Binding and Functional Properties of Five Extrinsic Proteins in Oxygen-evolving Photosystem II from a Marine Centric Diatom, Chaetoceros gracilis Reviewed International journal

Ryo Nagao, Akira Moriguchi, Tatsuya Tomo, Ayako Niikura, Saori Nakajima, Takehiro Suzuki, Akinori Okumura, Masako Iwai, Jian-Ren Shen, Masahiko Ikeuchi, Isao Enami

JOURNAL OF BIOLOGICAL CHEMISTRY 285 ( 38 ) 29191 - 29199 2010.9

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC

Oxygen-evolving photosystem II (PSII) isolated from a marine centric diatom, Chaetoceros gracilis, contains a novel extrinsic protein (Psb31) in addition to four red algal type extrinsic proteins of PsbO, PsbQ', PsbV, and PsbU. In this study, the five extrinsic proteins were purified from alkaline Tris extracts of the diatom PSII by anion and cation exchange chromatographic columns at different pH values. Reconstitution experiments in various combinations with the purified extrinsic proteins showed that PsbO, PsbQ', and Psb31 rebound directly to PSII in the absence of other extrinsic proteins, indicating that these extrinsic proteins have their own binding sites in PSII intrinsic proteins. On the other hand, PsbV and PsbU scarcely rebound to PSII alone, and their effective bindings required the presence of all of the other extrinsic proteins. Interestingly, PSII reconstituted with Psb31 alone considerably restored the oxygen evolving activity in the absence of PsbO, indicating that Psb31 serves as a substitute in part for PsbO in supporting oxygen evolution. A significant difference found between PSIIs reconstituted with Psb31 and with PsbO is that the oxygen evolving activity of the former is scarcely stimulated by Cl- and Ca2+ ions but that of the latter is largely stimulated by these ions, although rebinding of PsbV and PsbU activated oxygen evolution in the absence of Cl- and Ca2+ ions in both the former and latter PSIIs. Based on these results, we proposed a model for the association of the five extrinsic proteins with intrinsic proteins in diatom PSII and compared it with those in PSIIs from the other organisms.

DOI： 10.1074/jbc.M110.146092

Topological Analysis of the Extrinsic PsbO, PsbP and PsbQ Proteins in a Green Algal PSII Complex by Cross-Linking with a Water-Soluble Carbodiimide Reviewed

Ryo Nagao, Takehiro Suzuki, Akinori Okumura, Ayako Niikura, Masako Iwai, Naoshi Dohmae, Tatsuya Tomo, Jian-Ren Shen, Masahiko Ikeuchi, Isao Enami

PLANT AND CELL PHYSIOLOGY 51 ( 5 ) 718 - 727 2010.5

Language：English Publishing type：Research paper (scientific journal) Publisher：OXFORD UNIV PRESS

The close association of the extrinsic PsbO, PsbP and PsbQ proteins with PSII core subunits in oxygen-evolving PSII complexes from a green alga, Chlamydomonas reinhardtii, was examined by cross-linking experiments with a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC). The green algal PSII complexes treated with EDC were washed with alkaline Tris to remove the non-cross-linked extrinsic proteins, and then applied to Blue-Native-PAGE to prepare PSII core complexes. The extrinsic proteins cross-linked with PSII core complexes were detected by immunoblotting analysis using antibodies against extrinsic proteins and PSII core subunits. The results showed that the PsbO, PsbP and PsbQ proteins directly associated with CP47, the subunit of cytochrome b559 and a small subunit in PSII core complexes, respectively, through electrostatic interactions. In addition, a cross-linked product between the PsbP and PsbQ proteins was found in alkaline Tris extracts of EDC-treated PSII complexes, and its cross-linked site was examined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS) after digestions with trypsin and endoproteinase Asp-N. The results demonstrated that the positively charged amino group of K176 on the PsbP protein electrostatically interacts with the negatively charged carboxyl group of D28 on the PsbQ protein. These binding properties of the extrinsic proteins in the green algal PSII were compared with those in higher plant PSII.

DOI： 10.1093/pcp/pcq042

Structural and functional studies on Ycf12 (Psb30) and PsbZ-deletion mutants from a thermophilic cyanobacterium Reviewed International journal

Kenji Takasaka, Masako Iwai, Yasufumi Umena, Keisuke Kawakami, Yukari Ohmori, Masahiko Ikeuchi, Yuichiro Takahashi, Nobuo Kamiya, Jian-Ren Shen

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1797 ( 2 ) 278 - 284 2010.2

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

Ycf12 (Psb30) and PsbZ are two low molecular weight subunits of photosystem II (PSII), with one and two trans-membrane helices, respectively. In order to study the functions of these two subunits from a structural point of view, we constructed deletion mutants lacking either Ycf12 or PsbZ from Thermosynechococcus elongatus, and purified, crystallized and analyzed the structure of PSII dimer from the two mutants. Our results showed that Ycf12 is located in the periphery of PSII, close to PsbK, PsbZ and PsbJ, and corresponded to the unassigned helix XI reported previously, in agreement with the recent structure at 2.9 angstrom resolution (A. Guskov, J. Kern. A. Gabdulkhakov, M. Broser, A. Zouni, W. Saenger, Cyanobacterial photosystem II at 2.9 angstrom resolution: role of quinones, lipids, channels and chloride, Nat Struct. Mol. Biol. 16 (2009) 334-342). On the other hand, crystals of PsbZ-deleted PSII showed a remarkably different unit cell constants from those of wild-type PSII, indicating a role of PsbZ in the interactions between PSII dimers within the crystal. This is the first example for a different arrangement of PSII dimers within the cyanobacterial PSII crystals. PSII dimers had a lower oxygen-evolving activity from both mutants than that from the wild type. In consistent with this, the relative content of PSII in the thylakoid membranes was lower in the two mutants than that in the wild type. These results suggested that deletion of both subunits affected the PSII activity, thereby destabilized PSII, leading to a decrease in the PSII content in vivo. While PsbZ was present in PSII purified from the Ycf12-deletion mutant, Ycf12 was present in crude PSII but absent in the finally purified PSII from the PsbZ-deletion mutant, indicating a preferential, stabilizing role of PsbZ for the binding of Ycf12 to PSII. These results were discussed in terms of the PSII crystal structure currently available. (C) 2009 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2009.11.001

Crystal structure of oxygen evolving Photosystem II at atomic resolution. Reviewed

Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 66 S124 - S125 2010

Mechanisms of Acido-Tolerance and Characteristics of Photosystems in an Acidophilic and Thermophilic Red Alga, Cyanidium Caldarium Reviewed

Enami Isao, Adachi Hideyuki, Shen Jian-Ren

Red Algae in the Genomic Age 13 373 - 389 2010

Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography Reviewed International journal

Keisuke Kawakami, Yasufumi Umena, Nobuo Kamiya, Jian-Ren Shen

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 106 ( 21 ) 8567 - 8572 2009.5

Language：English Publishing type：Research paper (scientific journal) Publisher：NATL ACAD SCIENCES

The chloride ion, Cl-, is an essential cofactor for oxygen evolution of photosystem II (PSII) and is closely associated with the Mn4Ca cluster. Its detailed location and function have not been identified, however. We substituted Cl- with a bromide ion (Br-) or an iodide ion (I-) in PSII and analyzed the crystal structures of PSII with Br- and I- substitutions. Substitution of Cl- with Br- did not inhibit oxygen evolution, whereas substitution of Cl- with I- completely inhibited oxygen evolution, indicating the efficient replacement of Cl- by I-. PSII with Br- and I- substitutions were crystallized, and their structures were analyzed. The results showed that there are 2 anion-binding sites in each PSII monomer; they are located on 2 sides of the Mn4Ca cluster at equal distances from the metal cluster. Anion-binding site 1 is close to the main chain of D1-Glu-333, and site 2 is close to the main chain of CP43-Glu-354; these 2 residues are coordinated directly with the Mn4Ca cluster. In addition, site 1 is located in the entrance of a proton exit channel. These results indicate that these 2 Cl- anions are required to maintain the coordination structure of the Mn4Ca cluster as well as the proposed proton channel, thereby keeping the oxygen-evolving complex fully active.

DOI： 10.1073/pnas.0812797106

Probing tyrosine Z oxidation in Photosystem II core complex isolated from spinach by EPR at liquid helium temperatures. Reviewed International journal

Yanan Ren, Chunxi Zhang, Han Bao, Jianren Shen, Jingquan Zhao

Photosynthesis research 99 ( 2 ) 127 - 38 2009.2

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

Tyrosine Z (Tyr(Z)) oxidation observed at liquid helium temperatures provides new insights into the structure and function of Tyr(Z) in active Photosystem II (PSII). However, it has not been reported in PSII core complex from higher plants. Here, we report Tyr(Z) oxidation in the S(1) and S(2) states in PSII core complex from spinach for the first time. Moreover, we identified a 500 G-wide symmetric EPR signal (peak position g = 2.18, trough position g = 1.85) together with the g = 2.03 signal induced by visible light at 10 K in the S(1) state in the PSII core complex. These two signals decay with a similar rate in the dark and both disappear in the presence of 6% methanol. We tentatively assign this new feature to the hyperfine structure of the S(1)Tyr(Z)(*) EPR signal. Furthermore, EPR signals of the S(2) state of the Mn-cluster, the oxidation of the non-heme iron, and the S(1)Tyr(Z)(*) in PSII core complexes and PSII-enriched membranes from spinach are compared, which clearly indicate that both the donor and acceptor sides of the reaction center are undisturbed after the removal of LHCII. These results suggest that the new spinach PSII core complex is suitable for the electron transfer study of PSII at cryogenic temperatures.

DOI： 10.1007/s11120-009-9410-x

Towards structural elucidation of eukaryotic photosystem II: Purification, crystallization and preliminary X-ray diffraction analysis of photosystem II from a red alga Reviewed International journal

Hideyuki Adachi, Yasufumi Umena, Isao Enami, Takahiro Henmi, Nobuo Kamiya, Jian-Ren Shen

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1787 ( 2 ) 121 - 128 2009.2

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

Crystal structure of photosystem II (PSII) has been reported from prokaryotic cyanobacteria but not from any eukaryotes. In the present study, we improved the purification procedure of PSII dimers from an acidophilic, thermophilic red alga Cyanidium caldarium, and crystallized them in two forms tinder different crystallization conditions. One had a space group of P222(1) with unit cell constants of a = 146.8 angstrom, b = 176.9 angstrom, and c = 353.7 angstrom. and the other one had a space group of P2(1)2(1)2(1) with unit cell constants of a = 209.2 angstrom, b = 237.5 angstrom, and c = 299.8 angstrom. The unit cell constants of both crystals and the space group of the first-type crystals are different from those of cyanobacterial crystals, which may reflect the structural differences between the red algal and cyanobacterial PSII, as the former contains a fourth extrinsic protein of 20 kDa. X-ray diffraction data were collected and processed to a 3.8 angstrom resolution with the first type crystal. For the second type crystal, a post-crystallization treatment of dehydration was employed to improve the resolution, resulting in a diffraction data of 3.5 angstrom resolution. Analysis of this type of crystal revealed that there are 2 PSII dimers in each asymmetric unit, giving rise to 16 PSII monomers in each unit cell, which contrasts to 4 dimers per unit cell in cyanobacterial crystals. The molecular packing of PSII within the unit cell was constructed with the molecular replacement method and compared with that of the cyanobacterial crystals. (C) 2008 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2008.11.004

2P-223 Comparision of energy-transfer process between photosystem II monomer and dimer from Thermosynechococcus vulucanus studied by time-resolved fluorescence measurement at cryogenic temperature(Photobiology:Photosynthesis,The 47th Annual Meeting of the Biophysical Society of Japan)

Nishi Shunsuke, Komura Masayuki, Noji Tomoyasu, Kawakami Keisuke, Shen Jian-Ren, Shibata Yutaka, Itoh Shigeru

Seibutsu Butsuri 49 S142 2009

3TP2-03 Function of photosystem II core complexes of a thermophilic cyanobacterium introduced into silica mesoporous materials(The 47th Annual Meeting of the Biophysical Society of Japan)

Noji Tomoyasu, Kamidaki Chihiro, Kawakami Keisuke, Shen Jian-Ren, Kajino Tsutomu, Fukushima Yoshiaki, Sekitoh Takeshi, Itoh Shigeru

Seibutsu Butsuri 49 S60 2009

Effects of phospholipase and lipase treatments on photosystem II core dimer from a thermophilic cyanobacterium Reviewed

Jing Leng, Isamu Sakurai, Hajime Wada, Jian-Ren Shen

PHOTOSYNTHESIS RESEARCH 98 ( 1-3 ) 469 - 478 2008.10

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

Lipids are important components of transmembrane protein complexes. In order to study the roles of lipids in photosystem II (PSII), we treated the PSII core dimer complex from a thermophilic cyanobacterium Thermosynechococcus vulcanus with phospholipase A(2) (PLA(2)) and lipase, and examined their effects on PSII structure and function. PLA(2)-treatment decreased the content of phospholipid, phosphatidylglycerol (PG) by 59%, leading to a decrease of oxygen evolution by 40%. On the other hand, although treatment with lipase specifically decreased the content of monogalactosyldiacylglycerol (MGDG) by 52%, it decreased oxygen evolution only by 16%. This indicates that PG plays a more important role in PSII than MGDG. Both PLA(2)- and lipase-treatments induced neither the dissociation of PSII dimer, nor any loss of polypeptides. The degradation of PG resulted in a damage to the Q(B)-binding site as demonstrated from photoreduction activity of 2,6-dichlorophenolindophenol and chlorophyll fluorescence yields in the absence or presence of 3-(3,4-dichlorophenyl)1,1-dimethylurea, and the dependencies of oxygen evolution on various electron acceptors before and after PLA(2)- or lipase-treatments. However, there were approximately three and five molecules of PG and MGDG per PSII reaction center left in the PSII dimeric complex after the PLA(2)- and lipase-treatments. These lipids are therefore bound to the interior of the protein matrix and resistant to the lipase treatments. The resistance of these lipids against PLA(2)- and lipase-treatments may be a specific feature of PSII from the thermophilic cyanobacterium, suggesting a possible correlation between binding of lipids and thermostability of PSII.

DOI： 10.1007/s11120-008-9335-9

Structures and functions of the extrinsic proteins of photosystem II from different species Reviewed

Isao Enami, Akinori Okumura, Ryo Nagao, Takehiro Suzuki, Masako Iwai, Jian-Ren Shen

PHOTOSYNTHESIS RESEARCH 98 ( 1-3 ) 349 - 363 2008.10

Language：English Publisher：SPRINGER

This minireview presents a summary of information available on the variety and binding properties of extrinsic proteins that form the oxygen-evolving complex of photosystem II (PSII) of cyanobacteria, red alga, diatom, green alga, euglena, and higher plants. In addition, the structure and function of extrinsic PsbO, PsbV, and PsbU proteins are summarized based on the crystal structure of thermophilic cyanobacterial PSII together with biochemical and genetic studies from various organisms.

DOI： 10.1007/s11120-008-9343-9

Structure and Function of Photosystem II Reviewed

Jian-Ren Shen, Takahiro Henmi, Nobuo Kamiya

Photosynthetic Protein Complexes: A Structural Approach 83 - 106 2008.9

Acceptor side effects on the electron transfer at cryogenic temperatures in intact photosystem II Reviewed International journal

Han Bao, Chunxi Zhang, Keisuke Kawakami, Yanan Ren, Jian-Ren Shen, Jingquan Zhao

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1777 ( 9 ) 1109 - 1115 2008.9

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

In intact PSII, both the secondary electron donor (Tyrz) and side-path electron donors (Car/Chl(Z)/Cyt(b559)) can be oxidized by P-680(+center dot) at cryogenic temperatures. In this paper, the effects of acceptor side, especially the redox state of the non-heme iron, on the donor side electron transfer induced by visible light at cryogenic temperatures were studied by EPR spectroscopy. We found that the formation and decay of the S(1)Tyr(Z). EPR signal were independent of the treatment of K3Fe(CN)(6), whereas formation and decay of the Car(+center dot)/Chl(Z)(+center dot) EPR signal correlated with the reduction and recovery of the Fe3+ EPR signal of the non-heme iron in K3Fe(CN)(6) pre-treated PSII, respectively. Based on the observed correlation between Car/Chl(Z) oxidation and Fe3+ reduction, the oxidation of non-heme iron by K3Fe(CN)(6) at 0 degrees C was quantified, which showed that around 50-60% fractions of the reaction centers gave rise to the Fe3+ EPR signal. In addition, we found that the presence of phenyl-p-benzoquinone significantly enhanced the yield of Tyr(Z) oxidation. These results indicate that the electron transfer at the donor side can be significantly modified by changes at the acceptor side, and indicate that two types of reaction centers are present in intact PSII, namely, one contains unoxidizable non-heme iron and another one contains oxidizable non-heme iron. Tyrz oxidation and side-path reaction occur separately in these two types of reaction centers, instead of competition with each other in the same reaction centers. In addition, our results show that the non-heme iron has different properties in active and inactive PSII. The oxidation of non-heme iron by K3Fe(CN)(6) takes place only in inactive PSII, which implies that the Fe3+ state is probably not the intermediate species for the turnover of quinone reduction. (C) 2008 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.bbabio.2008.04.044

X-ray crystallographic and biochemical characterizations of a mutant photosystem II complex from Thermosynechococcus vulcanus with the psbTc gene inactivated by an insertion mutation Reviewed International journal

Takahiro Henmi, Masako Iwai, Masahiko Ikeuchi, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya

JOURNAL OF SYNCHROTRON RADIATION 15 ( Pt 3 ) 304 - 307 2008.5

Language：English Publishing type：Research paper (scientific journal) Publisher：INT UNION CRYSTALLOGRAPHY

The crystal structure of a photosystem II (PSII) dimer from Thermosynechococcus vulcanus with its psbTc gene inactivated by insertion mutation of an antibiotic cassette in a site in the C-terminal region was analyzed at 3.8 angstrom resolution. In the crystal structure of the mutant PSII, the transmembrane helix of PsbTc remains, whereas the C-terminal loop of PsbTc has disappeared. In addition, the PsbM subunit, which seemed to be lost in a PsbTc-deletion mutant PSII of T. elongatus, is still present. The deletion of the C-terminal loop of PsbTc in the mutant PSII was verified by mass spectrometry. Thus, the insertion mutation of psbTc eliminated only the C-terminal loop of this subunit. Nevertheless, some features of the mutant PSII, namely a destabilization of the dimeric form and a slight decrease of the oxygen-evolving activity, were observed in the mutant, indicating that the C-terminal loop of PsbTc functions to maintain the stability of the PSII dimer and the activity of oxygen evolution.

DOI： 10.1107/S0909049508002458

Identification of functional domains of PsbU in red algal PSII by site-directed mutagenesis Reviewed

Masanori Sano, Akinori Okumura, Takehiro Suzuki, Masako Iwai, Hideyuki Adachi, Jian-Ren Shen, Isao Enami

Photosynthesis. Energy from the Sun 487 - 490 2008

3S4-3 Recent progress on the structural studies of Photosystem II oxygen- evolving complex(3S4 New trend of photosynthesis =New energy innovation based on the photosynthesis=,The 46th Annual Meeting of the Biophysical Society of Japan)

Shen Jian-Ren

Seibutsu Butsuri 48 S18 2008

Aromatic structure of Tyrosine-92 in the extrinsic PsbU protein of red algal Photosystem II is important for its functioning Reviewed International journal

Akinori Okumura, Masanori Sano, Takehiro Suzuki, Hiroyasu Tanaka, Ryo Nagao, Katsuyoshi Nakazato, Masako Iwai, Hideyuki Adachi, Jian-Ren Shen, Isao Enami

FEBS LETTERS 581 ( 27 ) 5255 - 5258 2007.11

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

PsbU is one of the extrinsic proteins in red algal Photosystem II (PSII) and functions to optimize the availability of Ca2+ and Cl- cofactors for water oxidation. To determine the functional residue of PsbU, we constructed various PsbU mutants from a red alga Cyanidium caldarium and reconstituted these mutants with the red algal PSII. The results revealed that Tyr-92 of PsbU, especially its aromatic ring, was essential for maintaining its function. From the crystal structure of PSII, Tyr-92 is located close to Pro-340 of D1, suggesting that the aromatic ring of Tyr-92 interacts with the CH group of Pro-340 of D1, and this CH/pi interaction is important for the optimal function of the Mn4Ca-cluster. (C) 2007 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.

DOI： 10.1016/j.febslet.2007.10.015

Location of PsbY in oxygen-evolving photosystem II revealed by mutagenesis and X-ray crystallography. Reviewed International journal

Keisuke Kawakami, Masako Iwai, Masahiko Ikeuchi, Nobuo Kamiya, Jian-Ren Shen

FEBS letters 581 ( 25 ) 4983 - 7 2007.10

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

PsbY is one of the low molecular mass subunits of oxygen-evolving photosystem II (PSII). Its location, however, has not been identified in the current crystal structure of PSII. We constructed a PsbY-deletion mutant of Thermosynechococcus elongatus, crystallized, and analyzed the crystal structure of the mutant PSII dimer. The results obtained showed that PsbY is located in the periphery of PSII close to the alpha- and beta-subunits of cytochrome b559, which corresponded to an unassigned helix in the 3.7A structure of T. vulcanus or helix X2 in the 3.0A structure of T. elongatus. Our results also indicated that the C-terminal loop of PsbY is protruded toward the stromal side, instead of the lumenal side predicted previously.

DOI： 10.1016/j.febslet.2007.09.036

Self-assembling peptide inspired by a barnacle underwater adhesive protein Reviewed International journal

Masahiro Nakano, Jian-Ren Shen, Kei Kamino

BIOMACROMOLECULES 8 ( 6 ) 1830 - 1835 2007.6

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

An underwater bioadhesive generally comprises a multiprotein complex that provides a molecular basis for self-assembly. We report here a new class of self-assembling peptide inspired by a 20 kDa barnacle cement protein. Studies on the chemically synthesized 24-residue peptide have revealed that (1) it underwent irreversible self-assembly upon the addition of salt, (2) the self-assembly was started at a salt concentration close to that of seawater with noncovalent intermolecular interactions, (3) the self-assembled material resembled a macroscopic membrane of interwoven nanofilaments, (4) incubation in an alkaline pH range formed the intramolecular disulfide bond of a peptide molecule, thus triggering a conformation change of the molecule, and (5) conformational change of the building block promoted the formation of a nanofiber, resulting in the display of a three-dimensional meshlike mesoscopic structure with defined pores having a diameter of approximately 200 nm. The peptide is likely to provide a suitable basis for further development of peptide-based materials.

DOI： 10.1021/bm0612236

2P330 Introduction of the photosystem II photosynthetic reaction center complex into the silica mesoporous materials(Photobiology-photosynthesis,Poster Presentations)

Noji Tomoyasu, Kawakami Keisuke, Shen Jian-Ren, Kajino Tsutomu, Fukushima Yoshiaki, Sekitoh Takeshi, Itoh Shigeru

Seibutsu Butsuri 47 S195 2007

Lipids in oxygen-evolving photosystem II complexes of cyanobacteria and higher plants Reviewed International journal

Isamu Sakurai, Jian-Ren Shen, Jing Leng, Shunsuke Ohashi, Masami Kobayashi, Hajime Wada

JOURNAL OF BIOCHEMISTRY 140 ( 2 ) 201 - 209 2006.8

Language：English Publishing type：Research paper (scientific journal) Publisher：OXFORD UNIV PRESS

Lipids in dimeric photosystem II complexes prepared from two species of cyanobacteria, Thermosynechococcus vulcanus and Synechocystis sp. PCC6803, and two higher plants, spinach and rice, were analyzed to determine how many lipid molecules and what class of lipids are present in the photosystem Il complexes. It was estimated that 27, 20, 8, and 7 lipid molecules per monomer are bound to the dimeric photosystem Il complexes of T. vulcanus, Synechocystis, spinach, and rice, respectively. In each of the organisms, the lipid composition of the photosystem 11 complexes was quite different from that of the thylakoid membranes used for preparation of the complexes. The content of phosphatidylglycerol. in the photosystem 11 complexes of each organism was much higher than that in the thylakoid membranes. Phospholipase A(2) treatment of the photosystem 11 complexes of Synechocystis that degraded phosphatidylglycerol resulted in impairment of Q(B)-mediated but not Q(A)-mediated electron transport. These findings suggest that phosphatidylglycerol plays important roles in the electron transport at the Q(B)-binding site in photosystem 11 complexes.

DOI： 10.1093/jb/mvj141

Anisotropy of the S-2-state manganese cluster in single crystals of cyanobacterial photosystem II studied by W-band electron paramagnetic resonance spectroscopy Reviewed International journal

Hideto Matsuoka, Ko Furukawa, Tatsuhisa Kato, Hiroyuki Mino, Jian-Ren Shen, Asako Kawamori

JOURNAL OF PHYSICAL CHEMISTRY B 110 ( 26 ) 13242 - 13247 2006.7

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

The multiline signal from the S-2-state manganese cluster in the oxygen evolving complex of photosystem II (PSII) was observed in single crystals of a thermophilic cyanobacterium Thermosynechococcus Vulcanus for the first time by W-band (94 GHz) electron paramagnetic resonance (EPR). At W- band, spectra were characterized by the g-anisotropy, which enabled the precise determination of the tensor. Distinct hyperfine splittings (hfs's) as seen in frozen solutions of PSII at X-band (9.5 GHz) were detected in most of the crystal orientations relative to the magnetic field. In some orientations, however, the hfs's disappeared due to overlapping of a large number of EPR lines from eight crystallographic symmetry-related sites of the manganese cluster within the unit cell of the crystal. Analysis of the orientation-dependent spectral features yielded the following g-tensor components: g(x) = 1.988, g(y) = 1.981, g(z) = 1.965. The principal values suggested an approximate axial symmetry around the Mn(III) ion in the cluster.

DOI： 10.1021/jp055008f

Quality control of Photosystem II: an FtsH protease plays an essential role in the turnover of the reaction center D1 protein in Synechocystis PCC 6803 under heat stress as well as light stress conditions. Reviewed International journal

Takashi Kamata, Hideki Hiramoto, Noriko Morita, Jian-Ren Shen, Nicholas H Mann, Yasusi Yamamoto

Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology 4 ( 12 ) 983 - 90 2005.12

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

The role of an AAA protease FtsH (slr0228) in the turnover of the D1 protein was studied under moderate heat stress conditions using wild-type cells of the cyanobacterium Synechocystis PCC 6803 and the mutant cells lacking a homologue of FtsH (slr0228). When the growth temperature of the wild-type was shifted from 30 degrees C to 40 degrees C, growth and oxygen-evolving activity were partially inhibited. Under the same heat stress, growth of the mutant was inhibited more significantly (63% inhibition after 5 days heat stress, compared with 26% inhibition with the wild-type cells) and the oxygen-evolving activity was also impaired in parallel. With heat stress at 42 degrees C, the level of the D1 protein of wild type cells was decreased, whereas that in mutant cells was not. The responses of cyanobacterial cells to heat stress observed here are quite similar to those to light stress that were reported previously. From these results, we suggest that the FtsH protease (slr0228) is responsible for both the heat-induced and light-induced degradation of the D1 protein. Notably, the amount of FtsH increased when the wild-type cells were exposed to heat stress or light stress, indicating that the up-regulation of the FtsH protease in the thylakoids is crucial for the cyanobacterial cells to cope with these abiotic stresses.

Distribution of the extrinsic proteins as a potential marker for the evolution of photosynthetic oxygen-evolving photosystem II. Reviewed International journal

Isao Enami, Takehiro Suzuki, Osamu Tada, Yoshiko Nakada, Kumi Nakamura, Akihiko Tohri, Hisataka Ohta, Isao Inoue, Jian-Ren Shen

The FEBS journal 272 ( 19 ) 5020 - 30 2005.10

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

Distribution of photosystem II (PSII) extrinsic proteins was examined using antibodies raised against various extrinsic proteins from different sources. The results showed that a glaucophyte (Cyanophora paradoxa) having the most primitive plastids contained the cyanobacterial-type extrinsic proteins (PsbO, PsbV, PsbU), and the primitive red algae (Cyanidium caldarium) contained the red algal-type extrinsic proteins (PsO, PsbQ', PsbV, PsbU), whereas a prasinophyte (Pyraminonas parkeae), which is one of the most primitive green algae, contained the green algal-type ones (PsbO, PsbP, PsbQ). These suggest that the extrinsic proteins had been diverged into cyanobacterial-, red algal- and green algal-types during early phases of evolution after a primary endosymbiosis. This study also showed that a haptophyte, diatoms and brown algae, which resulted from red algal secondary endosymbiosis, contained the red algal-type, whereas Euglena gracilis resulted from green algal secondary endosymbiosis contained the green algal-type extrinsic proteins, suggesting that the red algal- and green algal-type extrinsic proteins have been retained unchanged in the different lines of organisms following the secondary endosymbiosis. Based on these immunological analyses, together with the current genome data, the evolution of photosynthetic oxygen-evolving PSII was discussed from a view of distribution of the extrinsic proteins, and a new model for the evolution of the PSII extrinsic proteins was proposed.

Key cofactors of photosystem II cores from four organisms identified by 1.7-K absorption, CD and MCD. Reviewed International journal

Sindra Peterson Arsköld, Paul J Smith, Jian-Ren Shen, Ron J Pace, Elmars Krausz

Photosynthesis research 84 ( 1-3 ) 309 - 16 2005.6

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

Active Photosystem II (PS II) cores were prepared from spinach, pea, Synechocystis PCC 6803, and Thermosynechococcus vulcanus, the latter of which has been structurally determined [Kamiya and Shen (2003) Proc Natl Acad Sci USA 100: 98-103]. Electrochromic shifts resulting from QA reduction by 1.7-K illumination were recorded, and the Qx and Qy absorption bands of the redox-active pheophytin a thus identified in the different organisms. The Qx transition is approximately 3 nm (100 cm-1) to higher energy in cyanobacteria than in the plants. The predominant Qy shift appears in the range 683-686 nm depending on species, and does not appear to have a systematic shift. Low-temperature absorption, circular dichroism (CD) and magnetic circular dichroism (MCD) spectra of the chlorophyll Qy region are very similar in spinach and pea, but vary in cyanobacteria. We assigned CP43 and CP47 trap-chlorophyll absorption features in all species, as well as a P680 transition. Each absorption identified has an area of one chlorophyll a. The MCD deficit, introduced previously for spinach as an indicator of P680 activity, occurs in the same spectral region and has the same area in all species, pointing to a robustness of this as a signature for P680. MCD and CD characteristics point towards a significant variance in P680 structure between cyanobacteria, thermophilic cyanobacteria, and higher plants.

Pressure equilibrium and jump study on unfolding of 23-kDa protein from spinach photosystem II. Reviewed International journal

Cui-Yan Tan, Chun-He Xu, Jun Wong, Jian-Ren Shen, Shinsuke Sakuma, Yasusi Yamamoto, Reinhard Lange, Claude Balny, Kang-Cheng Ruan

Biophysical journal 88 ( 2 ) 1264 - 75 2005.2

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

Pressure-induced unfolding of 23-kDa protein from spinach photosystem II has been systematically investigated at various experimental conditions. Thermodynamic equilibrium studies indicate that the protein is very sensitive to pressure. At 20 degrees C and pH 5.5, 23-kDa protein shows a reversible two-state unfolding transition under pressure with a midpoint near 160 MPa, which is much lower than most natural proteins studied to date. The free energy (DeltaG(u)) and volume change (DeltaV(u)) for the unfolding are 5.9 kcal/mol and -160 ml/mol, respectively. It was found that NaCl and sucrose significantly stabilize the protein from unfolding and the stabilization is associated not only with an increase in DeltaG(u) but also with a decrease in DeltaV(u). The pressure-jump studies of 23-kDa protein reveal a negative activation volume for unfolding (-66.2 ml/mol) and a positive activation volume for refolding (84.1 ml/mol), indicating that, in terms of system volume, the protein transition state lies between the folded and unfolded states. Examination of the temperature effect on the unfolding kinetics indicates that the thermal expansibility of the transition state and the unfolded state of 23-kDa protein are closer to each other and they are larger than that of the native state. The diverse pressure-refolding pathways of 23-kDa protein in some conditions were revealed in pressure-jump kinetics.

High frequency EPR of the Mn-cluster in single crystals of cyanobacterial photosystem II Reviewed

Asako Kawamori, Jian-Ren Shen, Hiroyuki Mino, Ko Furukawa, Hideto Matsuoka, Tatsuhisa Kato

Photosynthesis: Fundamental Aspects to Global Perspectives 406 - 408 2005

An icosahedral assembly of the light-harvesting chlorophyll a/b protein complex from pea chloroplast thylakoid membranes. Reviewed International journal

Tomoya Hino, Eiji Kanamori, Jian-Ren Shen, Tsutomu Kouyama

Acta crystallographica. Section D, Biological crystallography 60 ( Pt 5 ) 803 - 9 2004.5

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

When the light-harvesting chlorophyll a/b protein complex (LHC-II) from pea thylakoid membranes is co-crystallized with native lipids, an octahedral crystal that exhibits no birefringence is obtained. Cryogenic electron micrographs of a crystal edge showed the crystal to be made up of hollow spherical assemblies with a diameter of 250 A. X-ray diffraction data at 9.5 A resolution revealed the spherical shell of LHC-II to have icosahedral symmetry. A T = 1 icosahedral model of LHC-II, in which the stromal surface of the protein faces outward, was constructed using the previously reported structure of the LHC-II trimer [Kühlbrandt et al. (1994), Nature (London), 367, 614-621]. The present result shows the first example of a well ordered three-dimensional crystal of icosahedral proteoliposomes.

pH-induced conformational changes in the soluble manganese-stabilizing protein of photosystem II. Reviewed International journal

Jun Weng, Cuiyan Tan, Jian-Ren Shen, Yong Yu, Xiaomei Zeng, Chunhe Xu, Kangcheng Ruan

Biochemistry 43 ( 16 ) 4855 - 61 2004.4

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

In this paper, we analyzed the pH-induced changes in the conformational states of the manganese-stabilizing protein (MSP) of photosystem II. Distinct conformational states of MSP were identified using fluorescence spectra, far-UV circular dichroism, and pressure-induced unfolding at varying suspension pH values, and four different conformational states of MSP were clearly distinguished using the center of fluorescence spectra mass when suspension pH was altered from 2 to 12. MSP was completely unfolded at a suspension pH above 11 and partly unfolded below a pH of 3. Analysis of the center of fluorescence spectral mass showed that the MSP structure appears stably folded around pH 6 and 4. The conformational state of MSP at pH 4 seems more stable than that at pH 6. Studies of peak positions of tryptophan fluorescence and MSP-bound 1-anilinonaphthalene-8-sulfonic acid fluorescence spectra supported this observation. A decrease in the suspension pH to 2 resulted in significant alterations in the MSP structure possibly because of protonation of unprotonated residues at lower pH, suggesting the existence of a large number of unprotonated amino acid residues at neutral pH possibly useful for proton transport in oxygen evolution. The acidic pH-induced conformational changes of MSP were reversible upon increase of pH to neutral pH; however, N-bromosuccinimide modification of tryptophan (Trp241) blocks the recovery of pH-induced conformational changes in MSP, implying that Trp241 is a key residue for the unfolded protein to form a functional structure. Thus, pH-induced structural changes of stable MSP (pH 6-4) may be utilized to analyze its functionality as a cofactor for oxygen evolution.

The orientations of core antenna chlorophylls in photosystem II are optimized to maximize the quantum yield of photosynthesis. Reviewed International journal

Sergei Vasil'ev, Jian-Ren Shen, Nobuo Kamiya, Doug Bruce

FEBS letters 561 ( 1-3 ) 111 - 6 2004.3

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

In photosystem II (PSII) the probability that energy absorbed by core antenna chlorophyll (Chl) is transferred to the reaction center (RC) is extremely high. Although close proximity between antenna Chl ensures a high transfer efficiency, relative pigment orientation can fractionally modify it. This level of refinement has often been assumed to be superfluous as so many subsequent processes limit the overall efficiency of photosynthesis. Nevertheless, did natural selection act on the most efficient step of energy conversion in PSII by optimizing the orientation of antenna Chl? Our Monte Carlo simulations sampled the orientation space of Chls in kinetic models for excitation energy transfer based on the X-ray structures of PSII from Thermosynechococcus vulcanus and Synechocystis elongatus. Our results revealed that the orientations of key antenna Chls are optimized to maximize photosynthesis while the orientations of the two peripheral RC Chls (Chl(Z)) are not.

Isolation of photosystem II-enriched membranes and the oxygen-evolving complex subunit proteins from higher plants. Reviewed International journal

Yasusi Yamamoto, Shinsuke Sakuma, Jian-Ren Shen

Methods in molecular biology (Clifton, N.J.) 274 29 - 36 2004

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

Methods for the isolation of highly active oxygen-evolving photosystem (PS)II membranes from higher plants and the purification of the oxygen-evolving complex (OEC) subunits are described. Membrane samples used as the material for various in vitro studies of PSII are prepared by solubilization of thylakoid membranes with the non-ionic detergent Triton X-100. The OEC subunit proteins are dissociated from the PSII-enriched membranes by alkaline treatment or salt treatment, and then purified by ion-exchange chromatography using an automated high-performance liquid chromatography system.

1SD52 Functional implications of photosystem II from its crystal structural analysis

Shen J.-R., Kamiya N.

Seibutsu Butsuri 44 S12 2004

Extrinsic proteins of photosystem II: an intermediate member of PsbQ protein family in red algal PS II. Reviewed International journal

Hisataka Ohta, Takehiro Suzuki, Masaji Ueno, Akinori Okumura, Shizue Yoshihara, Jian-Ren Shen, Isao Enami

European journal of biochemistry 270 ( 20 ) 4156 - 63 2003.10

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

The oxygen-evolving photosystem II (PS II) complex of red algae contains four extrinsic proteins of 12 kDa, 20 kDa, 33 kDa and cyt c-550, among which the 20 kDa protein is unique in that it is not found in other organisms. We cloned the gene for the 20-kDa protein from a red alga Cyanidium caldarium. The gene consists of a leader sequence which can be divided into two parts: one for transfer across the plastid envelope and the other for transfer into thylakoid lumen, indicating that the gene is encoded by the nuclear genome. The sequence of the mature 20-kDa protein has low but significant homology with the extrinsic 17-kDa (PsbQ) protein of PS II from green algae Volvox Carteri and Chlamydomonas reinhardtii, as well as the PsbQ protein of higher plants and PsbQ-like protein from cyanobacteria. Cross-reconstitution experiments with combinations of the extrinsic proteins and PS IIs from the red alga Cy. caldarium and green alga Ch. reinhardtii showed that the extrinsic 20-kDa protein was functional in place of the green algal 17-kDa protein on binding to the green algal PS II and restoration of oxygen evolution. From these results, we conclude that the 20-kDa protein is the ancestral form of the extrinsic 17-kDa protein in green algal and higher plant PS IIs. This provides an important clue to the evolution of the oxygen-evolving complex from prokaryotic cyanobacteria to eukaryotic higher plants. The gene coding for the extrinsic 20-kDa protein was named psbQ' (prime).

Comparison of binding and functional properties of two extrinsic components, Cyt c550 and a 12 kDa protein, in cyanobacterial PSII with those in red algal PSII. Reviewed

Isao Enami, Masako Iwai, Ai Akiyama, Takehiro Suzuki, Akinori Okumura, Takara Katoh, Osamu Tada, Hisataka Ohta, Jian-Ren Shen

Plant & cell physiology 44 ( 8 ) 820 - 7 2003.8

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

Cyt c550 and 12 kDa protein are two extrinsic proteins of photosystem II (PSII) found in cyanobacteria and some eukaryotic algae. The binding patterns of these two extrinsic proteins are different between cyanobacterial (Thermosynechococcus vulcanus) and red algal (Cyanidium caldarium) PSIIs [Shen and Inoue (1993) Biochemistry 32: 1825; Enami et al. (1998) Biochemistry 39: 2787]. In order to elucidate the possible causes responsible for these differences, we first cloned the psbV gene encoding Cyt c550 from a red alga, Cyanidium caldarium, which was compared with the homologous sequences from other organisms. Cross-reconstitution experiments were then performed with different combinations of the extrinsic proteins and the cyanobacterial or red algal PSII. (1). Both the cyanobacterial and red algal Cyt c550 bound directly to the cyanobacterial PSII, whereas none of them bound directly to the red algal PSII, indicating that direct binding of Cyt c550 to PSII principally depends on the structure of PSII intrinsic proteins but not that of Cyt c550 itself. (2). Cyt c550 was functionally exchangeable between the red algal and the cyanobacterial PSII, and the red algal 12 kDa protein functionally bound to the cyanobacterial PSII, whereas the cyanobacterial 12 kDa protein did not bind to the red algal PSII. (3). The antibody against the cyanobacterial or red algal 12 kDa protein reacted with its original one but not with the homologous protein from the other organism, whereas the antibody against the red algal Cyt c550 reacted with both cyanobacterial and red algal Cyt c550. These results imply that the structure and function of Cyt c550 have been largely conserved, whereas those of the 12 kDa protein have been changed, in the two organisms studied here.

Dynamic Interaction between the D1 protein, CP43 and OEC33 at the lumenal side of photosystem II in spinach chloroplasts: evidence from light-induced cross-Linking of the proteins in the donor-side photoinhibition. Reviewed

Takahiro Henmi, Hitoshi Yamasaki, Shinsuke Sakuma, Yuka Tomokawa, Noriaki Tamura, Jian-Ren Shen, Yasusi Yamamoto

Plant & cell physiology 44 ( 4 ) 451 - 6 2003.4

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

During the donor-side photoinhibition of spinach photosystem II, the reaction center D1 protein cross-linked with the antenna chlorophyll binding protein CP43 of photosystem II lacking the oxygen-evolving complex (OEC) subunit proteins. The cross-linking did not occur upon illumination of photosystem II samples that retained the OEC33, nor when OEC33-depleted photosystem II samples were reconstituted with the OEC33 prior to illumination. These results suggest that the D1 protein, CP43 and the OEC33 are located in close proximity at the lumenal side of photosystem II, and that the OEC33 suppresses the unnecessary contact between the D1 protein and CP43. Previously we presented data showing the D1 protein located adjacent to CP43 on the stromal side of photosystem II [Ishikawa et al. (1999) BIOCHIM: Biophys. Acta 1413: 147]. The present data suggest that the spatial arrangement of the D1 protein and CP43 at the lumenal side of photosystem II in spinach chloroplasts is similar to that at the stromal side of photosystem II and is consistent with the assignment of these proteins recently proposed on the crystal structures of the photosystem II complexes from cyanobacteria [Zouni et al. (2001) Nature 409: 739, Kamiya and Shen 2003 PROC: Natl. Acad. Sci. USA, 100: 98]. Moreover, the data suggest that the binding condition and positioning of the OEC33 in the photosystem II complex from higher plants may be different from those in cyanobacteria.

Near-IR irradiation of the S2 state of the water oxidizing complex of photosystem II at liquid helium temperatures produces the metalloradical intermediate attributed to S1Y(Z*). Reviewed International journal

Dionysios Koulougliotis, Jian-Ren Shen, Nikolaos Ioannidis, Vasili Petrouleas

Biochemistry 42 ( 10 ) 3045 - 53 2003.3

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

Near-IR (NIR) excitation at liquid He temperatures of photosystem II (PSII) membranes from the cyanobacterium Synechococcus vulcanus or from spinach poised in the S2 state results in the production of a g = 2.035 EPR resonance, reminiscent of metalloradical signals. The signal is smaller in the spinach preparations, but it is significantly enhanced by the addition of exogenous quinones. Ethanol (2-3%, v/v) eliminates the ability to trap the signal. The g = 2.035 signal is identical to the one recently obtained by Nugent et al. by visible-light illumination of the S1 state, and preferably assigned to S1Y(Z*) [Nugent, J. H. A., Muhiuddin, I. P., and Evans, M. C. W. (2002) Biochemistry 41, 4117-4126]. The production of the g = 2.035 signal by liquid He temperature NIR excitation of the S2 state is paralleled by a significant reduction (typically 40-45% in S. vulcanus) of the S2 state multiline signal. This is in part due to the conversion of the Mn cluster to higher spin states, an effect documented by Boussac et al. [Boussac, A., Un, S., Horner, O., and Rutherford, A. W. (1998) Biochemistry 37, 4001-4007], and in part due to the conversion to the g = 2.035 configuration. Following the decay of the g = 2.035 signal at liquid helium temperatures (decay halftimes in the time range of a few to tens of minutes depending on the preparation), annealing at elevated temperatures (-80 degrees C) results in only partial restoration of the S2 state multiline signal. The full size of the signal can be restored by visible-light illumination at -80 degrees C, implying that during the near-IR excitation and subsequent storage at liquid helium temperatures recombination with Q(A-) (and therefore decay of the S2 state to the S1 state) occurred in a fraction of centers. In support of this conclusion, the g = 2.035 signal remains stable for several hours (at 11 K) in centers poised in the S2...Q(A) configuration before the NIR excitation. The extended stability of the signal under these conditions has allowed the measurement of the microwave power saturation and the temperature dependence in the temperature range of 3.8-11 K. The signal intensity follows Curie law temperature dependence, which suggests that it arises from a ground spin state, or a very low-lying excited spin state. The P1/2 (microwave power at half-saturation) value is 1.7 mW at 3.8 K and increases to 96 mW at 11 K. The large width of the g = 2.035 signal and its relatively fast relaxation support the assignment to a radical species in the proximity of the Mn cluster. The whole phenomenology of the g = 2.035 signal production is analogous to the effects of NIR excitation on the S3 state [Ioannidis, N., Nugent, J. H. A., and Petrouleas, V. (2002) Biochemistry 41, 9589-9600] producing an S2'Y(Z*) intermediate. In the present case, the intermediate is assigned to S1Y(Z*). The NIR-induced increase in the oxidative capability of the Mn cluster is discussed in relation to the photochemical properties of a Mn(III) ion that exists in both S2 and S3 states. The EPR properties of the S1Y(Z*) intermediate cannot be reconciled easily with our current understanding of the magnetic properties of the S1 state. It is suggested that oxidation of tyr Z alters the magnetic properties of the Mn cluster via exchange of a proton.

ATP-induced hexameric ring structure of the cyanobacterial circadian clock protein KaiC. Reviewed International journal

Fumio Hayashi, Hirofumi Suzuki, Ryo Iwase, Tatsuya Uzumaki, Asako Miyake, Jian-Ren Shen, Katsumi Imada, Yukio Furukawa, Koji Yonekura, Keiichi Namba, Masahiro Ishiura

Genes to cells : devoted to molecular & cellular mechanisms 8 ( 3 ) 287 - 96 2003.3

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

BACKGROUND: KaiA, KaiB and KaiC are cyanobacterial circadian clock proteins. KaiC contains two ATP/GTP-binding Walker's motif As, and mutations in these regions affect the clock oscillations. RESULTS: ATP induced the hexamerization of KaiC. The Km value for the ATP for the hexamerization was 1.9 micro m. Triphosphate nucleotides bound to the two Walker's motif As, and their binding functioned cooperatively for the hexamerization. An unhydrolysable substrate, 5'-adenylylimidodiphosphate (AMPPNP), also induced the hexamerization, indicating that nucleotide binding, but not its hydrolysis, is essential for the hexamerization. Mutations in each of the two Walker's motif As that affect the clock phenotype increased the Km value for ATP and inhibited the hexamerization. Thus, the KaiC hexamerization seems to be necessary for its clock function. The KaiC hexamer has the shape of a hexagonal pot with a diameter and height of approximately 100 A and with a relatively large cavity (73 A deep and 18-34 A wide) inside. This pot-shaped structure suggests that KaiC functions in a similar manner to F1-ATPase, helicase or ATP-dependent protease/chaperon, all of which have dynamic activities inside the central cavity of their hexameric rings. CONCLUSION: ATP-induced KaiC hexamerization is necessary for the clock function of KaiC.

Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-A resolution. Reviewed International journal

Nobuo Kamiya, Jian-Ren Shen

Proceedings of the National Academy of Sciences of the United States of America 100 ( 1 ) 98 - 103 2003.1

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

Photosystem II (PSII) is a multisubunit membrane protein complex performing light-induced electron transfer and water-splitting reactions, leading to the formation of molecular oxygen. The first crystal structure of PSII from a thermophilic cyanobacterium Thermosynechococcus elongatus was reported recently [Zouni, A., Witt, H. T., Kern, J., Fromme, P., Krauss, N., Saenger, W. & Orth, P. (2001) Nature 409, 739-743)] at 3.8-A resolution. To analyze the PSII structure in more detail, we have obtained the crystal structure of PSII from another thermophilic cyanobacterium, Thermosynechococcus vulcanus, at 3.7-A resolution. The present structure was built on the basis of the sequences of PSII large subunits D1, D2, CP47, and CP43; extrinsic 33- and 12-kDa proteins and cytochrome c550; and several low molecular mass subunits, among which the structure of the 12-kDa protein was not reported previously. This yielded much information concerning the molecular interactions within this large protein complex. We also show the arrangement of chlorophylls and cofactors, including two beta-carotenes recently identified in a region close to the reaction center, which provided important clues to the secondary electron transfer pathways around the reaction center. Furthermore, possible ligands for the Mn-cluster were determined. In particular, the C terminus of D1 polypeptide was shown to be connected to the Mn cluster directly. The structural information obtained here provides important insights into the mechanism of PSII reactions.

Comparison of the structure of the extrinsic 33 kDa protein from different organisms. Reviewed

Akihiko Tohri, Takehiro Suzuki, Satoshi Okuyama, Kei Kamino, Akihiro Motoki, Masahiko Hirano, Hisataka Ohta, Jian-Ren Shen, Yasushi Yamamoto, Isao Enami

Plant & cell physiology 43 ( 4 ) 429 - 39 2002.4

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

The psbO gene encoding the extrinsic 33 kDa protein of oxygen-evolving photosystem II (PSII) complex was cloned and sequenced from a red alga, Cyanidium caldarium. The gene encodes a polypeptide of 333 residues, of which the first 76 residues served as transit peptides for transfer across the chloroplast envelope and thylakoid membrane. The mature protein consists of 257 amino acids with a calculated molecular mass of 28,290 Da. The sequence homology of the mature 33 kDa protein was 42.9-50.8% between the red alga and cyanobacteria, and 44.7-48.6% between the red alga and higher plants. The cloned gene was expressed in Escherichia coli, and the recombinant protein was purified, subjected to protease-treatments. The cleavage sites of the 33 kDa protein by chymotrypsin or V8 protease were determined and compared among a cyanobacterium (Synechococcus elongatus), a euglena (Euglena gracilis), a green alga (Chlamydomonas reinhardtii) and two higher plants (Spinacia oleracea and Oryza sativa). The cleavage sites by chymotrypsin were at 156F and 190F for the cyanobacterium, 159M, 160F and 192L for red alga, 11Y and 151F for euglena, 10Yand 150F for green alga, and 16Y for spinach, respectively. The cleavage sites by V8 protease were at 181E (cyanobacterium), 182E and 195E (red alga), 13E, 67E, 69E, 153D and 181E (euglena), 176E and 180E (green alga), and 18E or 19E (higher plants). Since most of the residues at these cleavage sites were conserved among the six organisms, the results indicate that the structure of the 33 kDa protein, at least the structure based on the accessibility by proteases, is different among these organisms. In terms of the cleavage sites, the structure of the 33 kDa protein can be divided into three major groups: cyanobacterial and red algal-type has cleavage sites at residues around 156-195, higher plant-type at residues 16-19, and euglena and green algal-type at residues of both cyanobacterial and higher plant-types.

3H1330 X-ray crystallographic study of the icosahedral assembly of light-harvesting chlorophyll a/b protein complex

Hino T., Shen J-R., Kouyama T.

Seibutsu Butsuri 42 ( 2 ) S170 2002

EPR Studies of spin Centers in the even-number oxidation states of Water Oxidizing Center in Photosystem II

Arao S., Yamada S., Kawamori A., Shen J-R., Ionnidis Nikolaos, Petrouleas Vasili

Seibutsu Butsuri 41 S72 2001

Formation mechanism of icosahedral structure of light-harvesting chlorophyll a/b protein complex

Hino T., Kanamori E., Okumura H., Matsui Y., Shen JR., Inoue Y., Kouyama T.

Seibutsu Butsuri 40 S158 2000

Crystallizaion of oxygen-evolving photosystem II complex.

Shen J.-R., Kamiya N.

Seibutsu Butsuri 39 S106 1999

X-ray crystallographic study of spherical assembly of light-harvesting cholorophyll a/b protein complex

Kanamori E., Hino T., Okumura H., Matsui Y., Shen J-R., Inoue Y., Kouyama T.

Seibutsu Butsuri 39 S106 1999

Cloning and expression of genes encoding a 12 kDa protein and cytochrome c(550), two extrinsic proteins of PSII, from a red alga Cyanidium caldarium Reviewed

H Ohta, A Okumura, T Katoh, Shen, JR, M Kamo, Enami, I

PHOTOSYNTHESIS: MECHANISMS AND EFFECTS, VOLS I-V 2979 - 2982 1998

Possible functional differences between dimer and monomer of photosystem II complex Reviewed

Shen, JR

PHOTOSYNTHESIS: MECHANISMS AND EFFECTS, VOLS I-V 941 - 944 1998

Topological analysis of PS II reaction center using monoclonal antibodies Reviewed

Tatsuya Tomo, Kenji Ogawa, Yorinao Inoue, Jian-Ren Shen

Photosynthesis: Mechanisms and Effects 2 993 - 996 1998

Functional characterization of Synechocystis sp. PCC 6803 delta psbU and delta psbV mutants reveals important roles of cytochrome c-550 in cyanobacterial oxygen evolution Reviewed

SHEN J. -R.

Biochemistry 37 1551 - 1558 1998

Identification of domains on the 43KDa chlorophyll-carring protein(CP43)that are shielded from tryptic attack by binding of the extrinsic 33KDa protein with photosystem II complex Reviewed

Enami, I, Tohri, A, Kamo, M, Ohta, H, Shen, J. R

Biochim Biophys Acta 1320 17 - 26 1997.5

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

The structural association of the spinach 33 kDa extrinsic protein with the 43 kDa chlorophyll-carrying protein (CP43) in oxygen-evolving photosystem II (PS II) complexes was investigated by comparing the peptide mappings and N-terminal sequences of the trypsin-digested products of NaCl-washed PS II membranes, which bind the 33 kDa protein, with those of CaCl2-washed PS II membranes, which lack the 33 kDa protein. (1) Peptide from N-terminus to Arg26 of CP43, which is exposed to stromal side, was digested in both PS II membranes, independent of binding of the 33 kDa protein. (2) Peptide bond of Arg357-Phe358 located in the large extrinsic loop E of CP43, which is exposed to lumenal side, was cleaved by trypsin in CaCl2-washed PS II membranes but not in NaCl-washed PS II membranes. This indicates that the region around Arg357-Phe358 in loop E of CP43 is shielded from tryptic attack by binding of the 33 kDa protein to PS II. (3) Trypsin treatment of CaCl2-washed PS II membranes also cleaved peptide bond between Lys457 and Gly458 in C-terminal region of CP43, while no cleavage of this region was detected by trypsin treatment of NaCl-washed PS II membranes. This implies that a conformational change of the C-terminal region of CP43 which is exposed to stromal side occurred upon removal of the 33 kDa protein, which makes the C-terminal region accessible to trypsin. (4) Release of peptide from Gln60 to C-terminus of the alpha-subunit of cytochrome b-559 was detected only in trypsin treatment of CaCl2-washed PS II membranes, indicating that the C-terminal region of this subunit is shielded from tryptic attack by binding of the 33 kDa protein. (5) The PS II membranes, in which Arg357-Phe358, Lys457-Gly458 of CP43 and the C-terminal part of the cytochrome b-559 alpha-subunit had been cleaved by trypsin, was no longer able to bind the 33 kDa protein. This strongly suggests that a domain in loop E of CP43 and/or the C-terminal region of the cytochrome b-559 alpha-subunit are necessary for binding of the extrinsic 33 kDa protein to PS II.

DOI： 10.1016/S0005-2728(97)00005-4

Identification of domains on the extrinsic 33KDa protein possibly involved in electrostatic interaction with photosystem II complex by means of chemical modification Reviewed

Miura, T, Shen, J. R, Takahashi, S, Kamo, M, Nakamura, E, Ohta, H, Kamei, A, Inoue, Y, Domae, N, Takio, K, Nakazato, K, Enami, I

J Biol Chem 272 ( 6 ) 3788 - 3798 1997.2

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

The extrinsic 33-kDa protein of photosystem II (PSII) was modified with various reagents, and the resulting proteins were checked for the ability to rebind to PSII and to reactivate oxygen evolution. While modification of more than eight carboxyl groups of aspartyl and glutamyl residues with glycine methyl ester did not affect the rebinding and reactivating capabilities, modification of amino groups of lysyl residues with either N-succinimidyl propionate or 2, 4,6-trinitrobenzene sulfonic acid or modification of guanidino groups of arginyl residues with 2,3-butanedione resulted in a loss of rebinding and reactivating capabilities of the 33-kDa protein. Moreover, the number of lysyl and arginyl residues susceptible to modification was significantly decreased when the protein was bound to PSII as compared with when it was free in solution, whereas the number of carboxyl groups modified was little affected. These results suggested that positive charges are important for the electrostatic interaction between the extrinsic 33-kDa protein and PSII intrinsic proteins, whereas negative charges on the protein do not contribute to such interaction. By a combination of protease digestion and mass spectroscopic analysis, the domains of lysyl residues accessible to N-succinimidyl propionate or 2,4, 6-trinitrobenzene sulfonic acid modification only when the 33-kDa protein is free in solution were determined to be Lys4, Lys20, Lys66-Lys76, Lys101, Lys105, Lys130, Lys159, Lys186, and Lys230-Lys236. These domains include those previously reported accessible to N-hydroxysuccinimidobiotin only in solution (Frankel and Bricker (1995) Biochemistry 34, 7492-7497), and may be important for the interaction of the 33-kDa protein with PSII intrinsic proteins.

DOI： 10.1074/jbc.272.6.3788

Isolation and characterization of photosystem II core complex from the red alga Cyanidium caldarium : association of cytochrome c-550 and 12kDa protein with the complex Reviewed

Enami, I, Murayama, H, Ohta, H, Kamo, M, Nakazato, K, Shen, J. R

Biochim Biophys Acta 1232 208 - 216 1995.12

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

A Photosystem II (PS II) complex was purified from an acidophilic as well as a thermophilic red alga, Cyanidium caldarium. The purified PS II complex was essentially devoid of phycobiliproteins and other contaminating components, and showed a high oxygen-evolving activity of 2375 mumol O2/mg Chl per h using phenyl-p-benzoquinone as the electron acceptor. The expression of this high activity did not require addition of exogenous Ca2+, although EDTA reduced the activity by 40%. This effect of EDTA can be reversed not only by Ca2+ but also by Mg2+; a similar Mg2+ effect has been observed in purified cyanobacterial PS II but not in higher plant PS II. Immunoblotting analysis indicated the presence of major intrinsic polypeptides commonly found in PS II from cyanobacteria and higher plants as well as the extrinsic 33 kDa protein. Antibodies against the extrinsic 23 and 17 kDa proteins of higher plant PS II, however, did not crossreact with any polypeptides in the purified PS II, indicating the absence of these proteins in the red alga. In contrast, two other extrinsic proteins of 17 and 12 kDa were present in the red algal PS II; they were released by 1 M Tris or Urea/NaCl treatment but not by 1 M NaCl. The 17 kDa polypeptide was identified to be cytochrome c-550 from heme-staining, immunoblot analysis and N-terminal amino acid sequencing, and the 12 kDa protein was found to be homologous to the 12 kDa extrinsic protein of cyanobacterial PS II from its N-terminal sequence. These results indicate that PS II from the red alga is closely related to PS II from cyanobacteria rather than to that from higher plants, and that the replacement of PS II extrinsic cytochrome c-550 and the 12 kDa protein by the extrinsic 23 and 17 kDa proteins occurred during evolution from red algae to green algae and higher plants.

DOI： 10.1016/0005-2728(95)00122-0

An independent role of cytochrome c-550 in cyanobacterial photosystem II as revealed by double-deletion mutagenesis of the psbO and psbV genes in Synechocystis sp. PCC 6803 Reviewed

SHEN J.-R.

Biochemistry 34 12661 - 12668 1995

CAUSE FOR DARK, CHILLING-INDUCED INACTIVATION OF PHOTOSYNTHETIC OXYGEN-EVOLVING SYSTEM IN CUCUMBER LEAVES Reviewed

SHEN, JR, TERASHIMA, I, S KATOH

PLANT PHYSIOLOGY 93 ( 4 ) 1354 - 1357 1990.8

ISOLATION AND CHARACTERIZATION OF PHOTOSYSTEM-II COMPLEXES WHICH LACK LIGHT-HARVESTING CHLOROPHYLL-A/B PROTEINS BUT RETAIN 3 EXTRINSIC PROTEINS RELATED TO OXYGEN EVOLUTION FROM SPINACH Reviewed

ENAMI, I, K KAMINO, SHEN, JR, K SATOH, S KATOH

BIOCHIMICA ET BIOPHYSICA ACTA 977 ( 1 ) 33 - 39 1989.10

NEAREST NEIGHBOR RELATIONSHIPS AMONG CONSTITUENT PROTEINS OF OXYGEN-EVOLVING PHOTOSYSTEM-II MEMBRANES - BINDING AND FUNCTION OF THE EXTRINSIC 33 KDA PROTEIN Reviewed

ENAMI, I, T MIYAOKA, Y MOCHIZUKI, SHEN, JR, K SATOH, S KATOH

BIOCHIMICA ET BIOPHYSICA ACTA 973 ( 1 ) 35 - 40 1989.1

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