Faculty Profiles - SHEN Jian-Ren

Papers - SHEN Jian-Ren

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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

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