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Discovery of Light-Powered Organic Ion Transport by a Natural Protein

Simiao Shen, Shoichiro Akita, Joji Wada, Mako Eguchi, Takashi Tsukamoto, Kwang-Hwan Jung, Yuki Sudo, Takashi Kikukawa

2025年7月

Ultrafast Protein Dynamics Prior to Retinal Photoisomerization in Microbial Rhodopsins 査読

Shinya Tahara, Rika Kurihara, Keiichi Kojima, Hikaru Kuramochi, Satoshi Takeuchi, Yuki Sudo, Tahei Tahara

The Journal of Physical Chemistry Letters 16 ( 23 ) 5732 - 5738 2025年6月

A repertoire of visible light-sensitive opsins in the deep-sea hydrothermal vent shrimp Rimicaris hybisae 査読

Yuya Nagata, Norio Miyamoto, Keita Sato, Yosuke Nishimura, Yuki Tanioka, Yuji Yamanaka, Susumu Yoshizawa, Kuto Takahashi, Kohei Obayashi, Hisao Tsukamoto, Ken Takai, Hideyo Ohuchi, Takahiro Yamashita, Yuki Sudo, Keiichi Kojima

Journal of Biological Chemistry 110291 - 110291 2025年5月

Roles of basic amino acid residues in substrate binding and transport of the light-driven anion pump Synechocystis halorhodopsin (SyHR) 査読

Masaki Nakama, Tomoyasu Noji, Keiichi Kojima, Susumu Yoshizawa, Hiroshi Ishikita, Yuki Sudo

Journal of Biological Chemistry 2025年4月

The use of microbial rhodopsin proteins in differential photodetection 査読

Louisa Reissig, Kirstin Buchanan, Thea Lindner, Marie Kurihara, Po-Chuan Chan, Falk Kibowski, Keiichi Kojima, Simon Dalgleish, Kunio Awaga, Yuki Sudo

Frontiers in Physics 12 1481341 2024年12月

Cyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria 査読

Masumi Hasegawa-Takano, Toshiaki Hosaka, Keiichi Kojima, Yosuke Nishimura, Marie Kurihara, Yu Nakajima, Yoshiko Ishizuka-Katsura, Tomomi Kimura-Someya, Mikako Shirouzu, Yuki Sudo, Susumu Yoshizawa

The ISME Journal 18 ( 1 ) wrae175 2024年11月

掲載種別：研究論文（学術雑誌）出版者・発行元：Oxford University Press (OUP)

Abstract

Microbial rhodopsins are prevalent in many cyanobacterial groups as a light-energy-harvesting system in addition to the photosynthetic system. It has been suggested that this dual system allows efficient capture of sunlight energy using complementary ranges of absorption wavelengths. However, the diversity of cyanobacterial rhodopsins, particularly in accumulated metagenomic data, remains underexplored. Here, we used a metagenomic mining approach, which led to the identification of a novel rhodopsin clade unique to cyanobacteria, cyanorhodopsin-II (CyR-II). CyR-IIs function as light-driven outward H+ pumps. CyR-IIs, together with previously identified cyanorhodopsins (CyRs) and cyanobacterial halorhodopsins (CyHRs), constitute cyanobacterial ion-pumping rhodopsins (CyipRs), a phylogenetically distinct family of rhodopsins. The CyR-II clade is further divided into two subclades, YCyR-II and GCyR-II, based on their specific absorption wavelength. YCyR-II absorbed yellow light (λmax = 570 nm), whereas GCyR-II absorbed green light (λmax = 550 nm). X-ray crystallography and mutational analysis revealed that the difference in absorption wavelengths is attributable to slight changes in the side chain structure near the retinal chromophore. The evolutionary trajectory of cyanobacterial rhodopsins suggests that the function and light-absorbing range of these rhodopsins have been adapted to a wide range of habitats with variable light and environmental conditions. Collectively, these findings shed light on the importance of rhodopsins in the evolution and environmental adaptation of cyanobacteria.

DOI： 10.1093/ismejo/wrae175

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Unusual Vibrational Coupling of the Schiff Base in the Retinal Chromophore of Sodium Ion-Pumping Rhodopsins 査読

Taiki Nakamura, Yuka Shinozaki, Akihiro Otomo, Taito Urui, Misao Mizuno, Rei Abe-Yoshizumi, Manami Hashimoto, Keiichi Kojima, Yuki Sudo, Hideki Kandori, Yasuhisa Mizutani

The Journal of Physical Chemistry B 128 ( 32 ) 7813 - 7821 2024年8月

Bidirectional Optical Control of Proton Motive Force in Escherichia coli Using Microbial Rhodopsins 査読

Kotaro Nakanishi, Keiichi Kojima, Yoshiyuki Sowa, Yuki Sudo

The Journal of Physical Chemistry B 128 ( 27 ) 6509 - 6517 2024年7月

Large-volume focus control at 10 MHz refresh rate via fast line-scanning amplitude-encoded scattering-assisted holography 査読

Atsushi Shibukawa, Ryota Higuchi, Gookho Song, Hideharu Mikami, Yuki Sudo, Mooseok Jang

Nature Communications 15 2926 2024年4月

Demonstration of iodide-dependent UVA-triggered growth inhibition in Saccharomyces cerevisiae cells and identification of its suppressive molecules 査読

Ryota Ono, Nozomu Saeki, Keiichi Kojima, Hisao Moriya, Yuki Sudo

Biochemical and Biophysical Research Communications 677 1 - 5 2023年10月

Nuclear Magnetic Resonance Detection of Hydrogen Bond Network in a Proton Pump Rhodopsin RxR and Its Alteration during the Cyclic Photoreaction 査読

Rika Suzuki, Toshio Nagashima, Keiichi Kojima, Reika Hironishi, Masafumi Hirohata, Tetsuya Ueta, Takeshi Murata, Toshio Yamazaki, Yuki Sudo, Hideo Takahashi

Journal of the American Chemical Society 145 ( 28 ) 15295 - 15302 2023年7月

Development of light-induced disruptive liposomes (LiDL) as a photoswitchable carrier for intracellular substance delivery. 査読国際誌

Taichi Tsuneishi, Keiichi Kojima, Fumika Kubota, Hideyoshi Harashima, Yuma Yamada, Yuki Sudo

Chemical Communications (Cambridge, England) 59 ( 49 ) 7591 - 7594 2023年6月

担当区分：最終著者,　責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

Light-driven inward proton pump rhodopsin RmXeR was embedded in pH-sensitive liposomes. Substance release from the proteoliposomes was observed following light illumination both in vitro and in cells, indicating the successful production of light-induced disruptive liposomes (LiDL). Thus, LiDL is a photoswitchable carrier utilized for intracellular substance delivery.

DOI： 10.1039/d3cc02056h

PubMed

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A blue-shifted anion channelrhodopsin from the Colpodellida alga Vitrella brassicaformis 査読国際誌

Keiichi Kojima, Shiho Kawanishi, Yosuke Nishimura, Masumi Hasegawa, Shin Nakao, Yuya Nagata, Susumu Yoshizawa, Yuki Sudo

Scientific Reports 13 ( 1 ) 6974 - 6974 2023年4月

担当区分：最終著者,　責任著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Springer Science and Business Media LLC

Abstract

Microbial rhodopsins, a family of photoreceptive membrane proteins containing the chromophore retinal, show a variety of light-dependent molecular functions. Channelrhodopsins work as light-gated ion channels and are widely utilized for optogenetics, which is a method for controlling neural activities by light. Since two cation channelrhodopsins were identified from the chlorophyte alga Chlamydomonas reinhardtii, recent advances in genomic research have revealed a wide variety of channelrhodopsins including anion channelrhodopsins (ACRs), describing their highly diversified molecular properties (e.g., spectral sensitivity, kinetics and ion selectivity). Here, we report two channelrhodopsin-like rhodopsins from the Colpodellida alga Vitrella brassicaformis, which are phylogenetically distinct from the known channelrhodopsins. Spectroscopic and electrophysiological analyses indicated that these rhodopsins are green- and blue-sensitive pigments (λ_max = ~ 550 and ~ 440 nm) that exhibit light-dependent ion channeling activities. Detailed electrophysiological analysis revealed that one of them works as a monovalent anion (Cl⁻, Br⁻ and NO₃⁻) channel and we named it V. brassicaformis anion channelrhodopsin-2, VbACR2. Importantly, the absorption maximum of VbACR2 (~ 440 nm) is blue-shifted among the known ACRs. Thus, we identified the new blue-shifted ACR, which leads to the expansion of the molecular diversity of ACRs.

DOI： 10.1038/s41598-023-34125-8

PubMed

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その他リンク： https://www.nature.com/articles/s41598-023-34125-8

Concerted primary proton transfer reactions in a thermophilic rhodopsin studied by time-resolved infrared spectroscopy at high temperature. 査読国際誌

Kunisato Kuroi, Takashi Tsukamoto, Naoya Honda, Yuki Sudo, Yuji Furutani

Biochimica et Biophysica Acta. Bioenergetics 1864 ( 3 ) 148980 - 148980 2023年4月

担当区分：責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

The primary proton transfer reactions of thermophilic rhodopsin, which was first discovered in an extreme thermophile, Thermus thermophilus JL-18, were investigated using time-resolved Fourier transform infrared spectroscopy at various temperatures ranging from 298 to 343 K (25 to 70 °C) and proton transport activity analysis. The analyses were performed using counterion (D95E, D95N, D229E, and D229N) and proton donor mutants (E106D and E106Q) as well. First, the initial proton transfer from the protonated retinal Schiff base (PRSB) to D95 was identified. The temperature dependency showed that the proton transfer reaction in the intermediate states dramatically changed above 318 K (45 °C). In addition, the proton transfer reaction correlated well with the structural change from turn to β-strand in the protein moiety, suggesting that this step may be regulated by the rigidity of the loop region. We also elucidated that the proton transfer reaction from proton donor E106 to the retinal Schiff base occurred synchronously with the primary proton transfer from the PRSB to D95. Surprisingly, we discovered that the direction of proton transfer was regulated by the secondary counterion, D229. Comparative analysis of Gloeobacter rhodopsin from the mesophile, Gloeobacter violaceus, highlighted that the primary proton transfer reactions in thermophilic rhodopsin were optimized at high temperatures partly due to the specific turn to β-strand structural change. This was not observed in Gloeobacter rhodopsin and other related proteins such as bacteriorhodopsin.

DOI： 10.1016/j.bbabio.2023.148980

PubMed

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Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota 査読

Titouan Jaunet-Lahary, Tatsuro Shimamura, Masahiro Hayashi, Norimichi Nomura, Kouta Hirasawa, Tetsuya Shimizu, Masao Yamashita, Naotaka Tsutsumi, Yuta Suehiro, Keiichi Kojima, Yuki Sudo, Takashi Tamura, Hiroko Iwanari, Takao Hamakubo, So Iwata, Kei-ichi Okazaki, Teruhisa Hirai, Atsuko Yamashita

Nature Communications 14 ( 1 ) 2023年4月

掲載種別：研究論文（学術雑誌）出版者・発行元：Springer Science and Business Media LLC

Abstract

An oxalate-degrading bacterium in the gut microbiota absorbs food-derived oxalate to use this as a carbon and energy source, thereby reducing the risk of kidney stone formation in host animals. The bacterial oxalate transporter OxlT selectively uptakes oxalate from the gut to bacterial cells with a strict discrimination from other nutrient carboxylates. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two distinct conformations, occluded and outward-facing states. The ligand-binding pocket contains basic residues that form salt bridges with oxalate while preventing the conformational switch to the occluded state without an acidic substrate. The occluded pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the pocket are completely blocked by extensive interdomain interactions, which can be opened solely by a flip of a single side chain neighbouring the substrate. This study shows the structural basis underlying metabolic interactions enabling favourable symbiosis.

DOI： 10.1038/s41467-023-36883-5

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その他リンク： https://www.nature.com/articles/s41467-023-36883-5

Identification of a Functionally Efficient and Thermally Stable Outward Sodium-Pumping Rhodopsin BeNaR from a Thermophilic Bacterium 査読

Marie Kurihara, Vera Thiel, Hirona Takahashi, Keiichi Kojima, David M. Ward, Donald A. Bryant, Makoto Sakai, Susumu Yoshizawa, Yuki Sudo

Chemical and Pharmaceutical Bulletin 71 ( 2 ) 154 - 164 2023年2月

Detection of Membrane Potential-Dependent Rhodopsin Fluorescence Using Low-Intensity Light Emitting Diode for Long-Term Imaging 査読

Shiho Kawanishi, Keiichi Kojima, Atsushi Shibukawa, Masayuki Sakamoto, Yuki Sudo

ACS Omega 8 4826 - 4834 2023年1月

Light-driven Proton Pumps as a Potential Regulator for Carbon Fixation in Marine Diatoms 査読

Susumu Yoshizawa, Tomonori Azuma, Keiichi Kojima, Keisuke Inomura, Masumi Hasegawa, Yosuke Nishimura, Masuzu Kikuchi, Gabrielle Armin, Yuya Tsukamoto, Hideaki Miyashita, Kentaro Ifuku, Takashi Yamano, Adrian Marchetti, Hideya Fukuzawa, Yuki Sudo, Ryoma Kamikawa

Microbes and Environments 38 ( 2 ) ME23015 2023年

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Japanese Society of Microbial Ecology

Diatoms are a major phytoplankton group responsible for approximately 20% of carbon fixation on Earth. They perform photosynthesis using light-harvesting chlo-rophylls located in plastids, an organelle obtained through eukaryote-eukaryote endosymbiosis. Microbial rhodopsin, a photoreceptor distinct from chlo-rophyll-based photosystems, was recently identified in some diatoms. However, the physiological function of diatom rhodopsin remains unclear. Heterologous expression techniques were herein used to investigate the protein function and subcellular localization of diatom rhodopsin. We demonstrated that diatom rhodopsin acts as a light-driven proton pump and localizes primarily to the outermost membrane of four membrane-bound complex plastids. Using model simulations, we also examined the effects of pH changes inside the plastid due to rhodopsin-mediated proton transport on photosynthesis. The results obtained suggested the involvement of rhodopsin-mediated local pH changes in a photosynthetic CO2-concentrating mechanism in rhodopsin-possessing diatoms.

DOI： 10.1264/jsme2.me23015

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Mutations conferring SO42- pumping ability on the cyanobacterial anion pump rhodopsin and the resultant unique features of the mutant. 査読国際誌

Yuhei Doi, Jo Watanabe, Ryota Nii, Takashi Tsukamoto, Makoto Demura, Yuki Sudo, Takashi Kikukawa

Scientific reports 12 ( 1 ) 16422 - 16422 2022年9月

記述言語：英語掲載種別：研究論文（学術雑誌）

Membrane transport proteins can be divided into two types: those that bind substrates in a resting state and those that do not. In this study, we demonstrate that these types can be converted by mutations through a study of two cyanobacterial anion-pumping rhodopsins, Mastigocladopsis repens halorhodopsin (MrHR) and Synechocystis halorhodopsin (SyHR). Anion pump rhodopsins, including MrHR and SyHR, initially bind substrate anions to the protein center and transport them upon illumination. MrHR transports only smaller halide ions, Cl- and Br-, but SyHR also transports SO42-, despite the close sequence similarity to MrHR. We sought a determinant that could confer SO42- pumping ability on MrHR and found that the removal of a negative charge at the anion entrance is a prerequisite for SO42- transport by MrHR. Consistently, the reverse mutation in SyHR significantly weakened SO42- pump activity. Notably, the MrHR and SyHR mutants did not show SO42- induced absorption spectral shifts or changes in the photoreactions, suggesting no bindings of SO42- in their initial states or the bindings to the sites far from the protein centers. In other words, unlike wild-type SyHR, these mutants take up SO42- into their centers after illumination and release it before the ends of the photoreactions.

DOI： 10.1038/s41598-022-20784-6

PubMed

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Phototriggered Apoptotic Cell Death (PTA) Using the Light-Driven Outward Proton Pump Rhodopsin Archaerhodopsin-3 査読

Shin Nakao, Keiichi Kojima, Yuki Sudo

Journal of the American Chemical Society 144 ( 9 ) 3771 - 3775 2022年2月

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