2021/10/21 更新

写真a

コジマ ケイイチ
小島 慧一
KOJIMA Keiichi
所属
医歯薬学域 助教
職名
助教
外部リンク

学位

  • 博士(理学) ( 2016年3月   京都大学 )

研究キーワード

  • 光生物

  • 視覚

  • 光操作

  • 生物物理

  • ロドプシン

  • Photobiology

  • 光受容タンパク質

  • オプシン

研究分野

  • ライフサイエンス / 動物生理化学、生理学、行動学

  • ライフサイエンス / 機能生物化学

  • ライフサイエンス / 生物物理学

  • ライフサイエンス / 薬系分析、物理化学

学歴

  • 京都大学大学院   理学研究科 生物科学専攻 博士後期課程 (理学博士)  

    2013年4月 - 2016年3月

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    国名: 日本国

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  • 京都大学大学院   理学研究科 生物科学専攻 博士前期課程  

    2011年4月 - 2013年3月

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  • 京都大学   理学部  

    2007年4月 - 2011年3月

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    国名: 日本国

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経歴

  • 岡山大学学術研究院医歯薬学域 助教

    2021年4月 - 現在

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  • 岡山大学医歯薬学総合研究科 助教

    2017年12月 - 2021年3月

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  • 岡山大学医歯薬学総合研究科 助教(特任)

    2017年4月 - 2017年11月

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所属学協会

委員歴

  • 生物物理学会2021年分野別専門委員  

    2021年 - 現在   

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  • 日本生物物理学会 中国四国支部   会計  

    2019年1月 - 2020年12月   

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    団体区分:学協会

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  • 日本生物物理学会   平成31年分野別専門委員  

    2019年   

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    団体区分:学協会

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  • 日本生物物理学会   平成30年分野別専門委員  

    2018年   

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    団体区分:学協会

    日本生物物理学会

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論文

  • Evolutionary adaptation of visual pigments in geckos for their photic environment 査読

    Keiichi Kojima, Yuki Matsutani, Masataka Yanagawa, Yasushi Imamoto, Yumiko Yamano, Akimori Wada, Yoshinori Shichida, Takahiro Yamashita

    Science Advances   7 ( 40 )   2021年10月

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    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Association for the Advancement of Science (AAAS)  

    DOI: 10.1126/sciadv.abj1316

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  • Functional expression of the eukaryotic proton pump rhodopsin OmR2 in Escherichia coli and its photochemical characterization 査読

    Masuzu Kikuchi, Keiichi Kojima, Shin Nakao, Susumu Yoshizawa, Shiho Kawanishi, Atsushi Shibukawa, Takashi Kikukawa, Yuki Sudo

    Scientific Reports   11 ( 1 )   2021年7月

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    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    <title>Abstract</title>Microbial rhodopsins are photoswitchable seven-transmembrane proteins that are widely distributed in three domains of life, archaea, bacteria and eukarya. Rhodopsins allow the transport of protons outwardly across the membrane and are indispensable for light-energy conversion in microorganisms. Archaeal and bacterial proton pump rhodopsins have been characterized using an <italic>Escherichia coli</italic> expression system because that enables the rapid production of large amounts of recombinant proteins, whereas no success has been reported for eukaryotic rhodopsins. Here, we report a phylogenetically distinct eukaryotic rhodopsin from the dinoflagellate <italic>Oxyrrhis marina</italic> (<italic>O. marina</italic> rhodopsin-2, <italic>Om</italic>R2) that can be expressed in <italic>E. coli</italic> cells. <italic>E. coli</italic> cells harboring the <italic>Om</italic>R2 gene showed an outward proton-pumping activity, indicating its functional expression. Spectroscopic characterization of the purified <italic>Om</italic>R2 protein revealed several features as follows: (1) an absorption maximum at 533 nm with all-<italic>trans</italic> retinal chromophore, (2) the possession of the deprotonated counterion (p<italic>K</italic><sub>a</sub> = 3.0) of the protonated Schiff base and (3) a rapid photocycle through several distinct photointermediates. Those features are similar to those of known eukaryotic proton pump rhodopsins. Our successful characterization of <italic>Om</italic>R2 expressed in <italic>E. coli</italic> cells could build a basis for understanding and utilizing eukaryotic rhodopsins.

    DOI: 10.1038/s41598-021-94181-w

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    その他リンク: http://www.nature.com/articles/s41598-021-94181-w

  • Lokiarchaeota archaeon schizorhodopsin-2 (LaSzR2) is an inward proton pump displaying a characteristic feature of acid-induced spectral blue-shift 査読

    Keiichi Kojima, Susumu Yoshizawa, Masumi Hasegawa, Masaki Nakama, Marie Kurihara, Takashi Kikukawa, Yuki Sudo

    Scientific Reports   10 ( 1 )   2020年12月

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    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    <title>Abstract</title>The photoreactive protein rhodopsin is widespread in microorganisms and has a variety of photobiological functions. Recently, a novel phylogenetically distinctive group named ‘schizorhodopsin (SzR)’ has been identified as an inward proton pump. We performed functional and spectroscopic studies on an uncharacterised schizorhodopsin from the phylum Lokiarchaeota archaeon. The protein, LaSzR2, having an all-<italic>trans-</italic>retinal chromophore, showed inward proton pump activity with an absorption maximum at 549 nm. The pH titration experiments revealed that the protonated Schiff base of the retinal chromophore (Lys188, p<italic>K</italic><sub>a</sub> = 12.3) is stabilised by the deprotonated counterion (presumably Asp184, p<italic>K</italic><sub>a</sub> = 3.7). The flash-photolysis experiments revealed the presence of two photointermediates, K and M. A proton was released and uptaken from bulk solution upon the formation and decay of the M intermediate. During the M-decay, the Schiff base was reprotonated by the proton from a proton donating residue (presumably Asp172). These properties were compared with other inward (SzRs and xenorhodopsins, XeRs) and outward proton pumps. Notably, LaSzR2 showed acid-induced spectral ‘blue-shift’ due to the protonation of the counterion, whereas outward proton pumps showed opposite shifts (red-shifts). Thus, we can distinguish between inward and outward proton pumps by the direction of the acid-induced spectral shift.

    DOI: 10.1038/s41598-020-77936-9

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    その他リンク: http://www.nature.com/articles/s41598-020-77936-9

  • Comparative Studies of the Fluorescence Properties of Microbial Rhodopsins: Spontaneous Emission Versus Photointermediate Fluorescence 査読 国際誌

    Keiichi Kojima, Rika Kurihara, Masayuki Sakamoto, Tsukasa Takanashi, Hikaru Kuramochi, Xiao Min Zhang, Haruhiko Bito, Tahei Tahara, Yuki Sudo

    The Journal of Physical Chemistry B   124 ( 34 )   7361 - 7367   2020年8月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    Rhodopsins are seven-transmembrane photoreceptor proteins that bind to the retinal chromophore and have been utilized as a genetically encoded voltage indicator (GEVI). So far, archaerhodopsin-3 (AR3) has been successfully used as a GEVI, despite its low fluorescence intensity. We performed comparative and quantitative fluorescence analyses of 15 microbial rhodopsins to explore these highly fluorescent molecules and to clarify their fluorescence mechanism. These rhodopsins showed a wide range of fluorescence intensities in mouse hippocampal neurons. Some of them, GR, HwBR, IaNaR, MR, and NpHR, showed fluorescence intensities comparable with or higher than that of AR3, suggesting their potential for GEVIs. The fluorescence intensity in neurons correlated with that of the bright fluorescent photointermediate such as a Q-intermediate (R = 0.75), suggesting that the fluorescence in neurons originates from the fluorescence of the photointermediate. Our findings provide a crucial step for producing next-generation rhodopsin-based GEVIs.

    DOI: 10.1021/acs.jpcb.0c06560

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  • Green-Sensitive, Long-Lived, Step-Functional Anion Channelrhodopsin-2 Variant as a High-Potential Neural Silencing Tool 査読

    Keiichi Kojima, Natsuki Miyoshi, Atsushi Shibukawa, Srikanta Chowdhury, Masaki Tsujimura, Tomoyasu Noji, Hiroshi Ishikita, Akihiro Yamanaka, Yuki Sudo

    The Journal of Physical Chemistry Letters   11 ( 15 )   6214 - 6218   2020年8月

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    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpclett.0c01406

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  • Vectorial proton transport mechanism of RxR, a phylogenetically distinct and thermally stable microbial rhodopsin 査読

    Keiichi Kojima, Tetsuya Ueta, Tomoyasu Noji, Keisuke Saito, Kanae Kanehara, Susumu Yoshizawa, Hiroshi Ishikita, Yuki Sudo

    Scientific Reports   10 ( 1 )   2020年1月

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    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    <title>Abstract</title><italic>Rubrobacter xylanophilus</italic> rhodopsin (RxR) is a phylogenetically distinct and thermally stable seven-transmembrane protein that functions as a light-driven proton (H<sup>+</sup>) pump with the chromophore retinal. To characterize its vectorial proton transport mechanism, mutational and theoretical investigations were performed for carboxylates in the transmembrane region of RxR and the sequential proton transport steps were revealed as follows: (i) a proton of the retinylidene Schiff base (Lys209) is transferred to the counterion Asp74 upon formation of the blue-shifted M-intermediate in collaboration with Asp205, and simultaneously, a respective proton is released from the proton releasing group (Glu187/Glu197) to the extracellular side, (ii) a proton of Asp85 is transferred to the Schiff base during M-decay, (iii) a proton is taken up from the intracellular side to Asp85 during decay of the red-shifted O-intermediate. This ion transport mechanism of RxR provides valuable information to understand other ion transporters since carboxylates are generally essential for their functions.

    DOI: 10.1038/s41598-019-57122-2

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    その他リンク: http://www.nature.com/articles/s41598-019-57122-2

  • Mutational analysis of the conserved carboxylates of anion channelrhodopsin-2 (ACR2) expressed in <i>Escherichia coli</i> and their roles in anion transport 査読

    Keiichi Kojima, Hiroshi C. Watanabe, Satoko Doi, Natsuki Miyoshi, Misaki Kato, Hiroshi Ishikita, Yuki Sudo

    Biophysics and Physicobiology   15   179 - 188   2018年

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    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Biophysical Society of Japan  

    DOI: 10.2142/biophysico.15.0_179

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  • Evolutionary steps involving counterion displacement in a tunicate opsin 査読

    Keiichi Kojima, Takahiro Yamashita, Yasushi Imamoto, Takehiro G. Kusakabe, Motoyuki Tsuda, Yoshinori Shichida

    Proceedings of the National Academy of Sciences of the United States of America   114 ( 23 )   6028 - 6033   2017年6月

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    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Proceedings of the National Academy of Sciences  

    Ci-opsin1 is a visible light-sensitive opsin present in the larval ocellus of an ascidian, <italic>Ciona intestinalis</italic>. This invertebrate opsin belongs to the vertebrate visual and nonvisual opsin groups in the opsin phylogenetic tree. Ci-opsin1 contains candidate counterions (glutamic acid residues) at positions 113 and 181; the former is a newly acquired position in the vertebrate visual opsin lineage, whereas the latter is an ancestral position widely conserved among invertebrate opsins. Here, we show that Glu113 and Glu181 in Ci-opsin1 act synergistically as counterions, which imparts molecular properties to Ci-opsin1 intermediate between those of vertebrate- and invertebrate-type opsins. Synergy between the counterions in Ci-opsin1 was demonstrated by E113Q and E181Q mutants that exhibit a pH-dependent spectral shift, whereas only the E113Q mutation in vertebrate rhodopsin yields this spectral shift. On absorbing light, Ci-opsin1 forms an equilibrium between two intermediates with protonated and deprotonated Schiff bases, namely the MI-like and MII-like intermediates, respectively. Adding G protein caused the equilibrium to shift toward the MI-like intermediate, indicating that Ci-opsin1 has a protonated Schiff base in its active state, like invertebrate-type opsins. Ci-opsin1’s G protein activation efficiency is between the efficiencies of vertebrate- and invertebrate-type opsins. Interestingly, the E113Y and E181S mutations change the molecular properties of Ci-opsin1 into those resembling invertebrate-type or bistable opsins and vertebrate ancient/vertebrate ancient-long or monostable opsins, respectively. These results strongly suggest that acquisition of counterion Glu113 changed the molecular properties of visual opsin in a vertebrate/tunicate common ancestor as a crucial step in the evolution of vertebrate visual opsins.

    DOI: 10.1073/pnas.1701088114

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  • Adaptation of cone pigments found in green rods for scotopic vision through a single amino acid mutation 査読

    Keiichi Kojima, Yuki Matsutani, Takahiro Yamashita, Masataka Yanagawa, Yasushi Imamoto, Yumiko Yamano, Akimori Wada, Osamu Hisatomi, Kanto Nishikawa, Keisuke Sakurai, Yoshinori Shichida

    Proceedings of the National Academy of Sciences of the United States of America   114 ( 21 )   5437 - 5442   2017年5月

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    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Proceedings of the National Academy of Sciences  

    Most vertebrate retinas contain a single type of rod for scotopic vision and multiple types of cones for photopic and color vision. The retinas of certain amphibian species uniquely contain two types of rods: red rods, which express rhodopsin, and green rods, which express a blue-sensitive cone pigment (M1/SWS2 group). Spontaneous activation of rhodopsin induced by thermal isomerization of the retinal chromophore has been suggested to contribute to the rod’s background noise, which limits the visual threshold for scotopic vision. Therefore, rhodopsin must exhibit low thermal isomerization rate compared with cone visual pigments to adapt to scotopic condition. In this study, we determined whether amphibian blue-sensitive cone pigments in green rods exhibit low thermal isomerization rates to act as rhodopsin-like pigments for scotopic vision. Anura blue-sensitive cone pigments exhibit low thermal isomerization rates similar to rhodopsin, whereas Urodela pigments exhibit high rates like other vertebrate cone pigments present in cones. Furthermore, by mutational analysis, we identified a key amino acid residue, Thr47, that is responsible for the low thermal isomerization rates of Anura blue-sensitive cone pigments. These results strongly suggest that, through this mutation, anurans acquired special blue-sensitive cone pigments in their green rods, which could form the molecular basis for scotopic color vision with normal red rods containing green-sensitive rhodopsin.

    DOI: 10.1073/pnas.1620010114

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  • Origin of the low thermal isomerization rate of rhodopsin chromophore 査読

    Masataka Yanagawa, Keiichi Kojima, Takahiro Yamashita, Yasushi Imamoto, Take Matsuyama, Koji Nakanishi, Yumiko Yamano, Akimori Wada, Yasushi Sako, Yoshinori Shichida

    Scientific Reports   5 ( 1 )   2015年9月

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    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    DOI: 10.1038/srep11081

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    その他リンク: http://www.nature.com/articles/srep11081.pdf

  • Rod Visual Pigment Optimizes Active State to Achieve Efficient G Protein Activation as Compared with Cone Visual Pigments 査読

    Keiichi Kojima, Yasushi Imamoto, Ryo Maeda, Takahiro Yamashita, Yoshinori Shichida

    Journal of Biological Chemistry   289 ( 8 )   5061 - 5073   2014年2月

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    担当区分:筆頭著者   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1074/jbc.m113.508507

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  • An optogenetic assay method for electrogenic transporters using Escherichia coli co‐expressing light‐driven proton pump

    Masahiro Hayashi, Keiichi Kojima, Yuki Sudo, Atsuko Yamashita

    Protein Science   2021年7月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    DOI: 10.1002/pro.4154

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    その他リンク: https://onlinelibrary.wiley.com/doi/full-xml/10.1002/pro.4154

  • Mechanism of absorption wavelength shifts in anion channelrhodopsin-1 mutants

    Masaki Tsujimura, Tomoyasu Noji, Keisuke Saito, Keiichi Kojima, Yuki Sudo, Hiroshi Ishikita

    Biochimica et Biophysica Acta (BBA) - Bioenergetics   148349 - 148349   2020年11月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.bbabio.2020.148349

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  • A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage. 査読 国際誌

    Masumi Hasegawa, Toshiaki Hosaka, Keiichi Kojima, Yosuke Nishimura, Yu Nakajima, Tomomi Kimura-Someya, Mikako Shirouzu, Yuki Sudo, Susumu Yoshizawa

    Scientific reports   10 ( 1 )   16752 - 16752   2020年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Microbial rhodopsin is a photoreceptor protein found in various bacteria and archaea, and it is considered to be a light-utilization device unique to heterotrophs. Recent studies have shown that several cyanobacterial genomes also include genes that encode rhodopsins, indicating that these auxiliary light-utilizing proteins may have evolved within photoautotroph lineages. To explore this possibility, we performed a large-scale genomic survey to clarify the distribution of rhodopsin and its phylogeny. Our surveys revealed a novel rhodopsin clade, cyanorhodopsin (CyR), that is unique to cyanobacteria. Genomic analysis revealed that rhodopsin genes show a habitat-biased distribution in cyanobacterial taxa, and that the CyR clade is composed exclusively of non-marine cyanobacterial strains. Functional analysis using a heterologous expression system revealed that CyRs function as light-driven outward H+ pumps. Examination of the photochemical properties and crystal structure (2.65 Å resolution) of a representative CyR protein, N2098R from Calothrix sp. NIES-2098, revealed that the structure of the protein is very similar to that of other rhodopsins such as bacteriorhodopsin, but that its retinal configuration and spectroscopic characteristics (absorption maximum and photocycle) are distinct from those of bacteriorhodopsin. These results suggest that the CyR clade proteins evolved together with chlorophyll-based photosynthesis systems and may have been optimized for the cyanobacterial environment.

    DOI: 10.1038/s41598-020-73606-y

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  • Applicability of Styrene-Maleic Acid Copolymer for Two Microbial Rhodopsins, RxR and HsSRI 査読

    Tetsuya Ueta, Keiichi Kojima, Tomoya Hino, Mikihiro Shibata, Shingo Nagano, Yuki Sudo

    Biophysical Journal   2020年9月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.bpj.2020.09.026

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  • Methodology for Further Thermostabilization of an Intrinsically Thermostable Membrane Protein Using Amino Acid Mutations with Its Original Function Being Retained. 査読 国際誌

    Satoshi Yasuda, Tomoki Akiyama, Sayaka Nemoto, Tomohiko Hayashi, Tetsuya Ueta, Keiichi Kojima, Takashi Tsukamoto, Satoru Nagatoishi, Kouhei Tsumoto, Yuki Sudo, Masahiro Kinoshita, Takeshi Murata

    Journal of chemical information and modeling   60 ( 3 )   1709 - 1716   2020年3月

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    記述言語:英語  

    We develop a new methodology best suited to the identification of thermostabilizing mutations for an intrinsically stable membrane protein. The recently discovered thermophilic rhodopsin, whose apparent midpoint temperature of thermal denaturation Tm is measured to be ∼91.8 °C, is chosen as a paradigmatic target. In the methodology, we first regard the residues whose side chains are missing in the crystal structure of the wild type (WT) as the "residues with disordered side chains," which make no significant contributions to the stability, unlike the other essential residues. We then undertake mutating each of the residues with disordered side chains to another residue except Ala and Pro, and the resultant mutant structure is constructed by modifying only the local structure around the mutated residue. This construction is based on the postulation that the structure formed by the other essential residues, which is nearly optimized in such a highly stable protein, should not be modified. The stability changes arising from the mutations are then evaluated using our physics-based free-energy function (FEF). We choose the mutations for which the FEF is much lower than for the WT and test them by experiments. We successfully find three mutants that are significantly more stable than the WT. A double mutant whose Tm reaches ∼100 °C is also discovered.

    DOI: 10.1021/acs.jcim.0c00063

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  • How Does a Microbial Rhodopsin RxR Realize Its Exceptionally High Thermostability with the Proton-Pumping Function Being Retained? 査読 国際誌

    Tomohiko Hayashi, Satoshi Yasuda, Kano Suzuki, Tomoki Akiyama, Kanae Kanehara, Keiichi Kojima, Mikio Tanabe, Ryuichi Kato, Toshiya Senda, Yuki Sudo, Takeshi Murata, Masahiro Kinoshita

    The journal of physical chemistry. B   124 ( 6 )   990 - 1000   2020年2月

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    記述言語:英語  

    We often encounter a case where two proteins, whose amino-acid sequences are similar, are quite different with regard to the thermostability. As a striking example, we consider the two seven-transmembrane proteins: recently discovered Rubrobacter xylanophilus rhodopsin (RxR) and long-known bacteriorhodopsin from Halobacterium salinarum (HsBR). They commonly function as a light-driven proton pump across the membrane. Though their sequence similarity and identity are ∼71 and ∼45%, respectively, RxR is much more thermostable than HsBR. In this study, we solve the three-dimensional structure of RxR using X-ray crystallography and find that the backbone structures of RxR and HsBR are surprisingly similar to each other: The root-mean-square deviation for the two structures calculated using the backbone Cα atoms of the seven helices is only 0.86 Å, which makes the large stability difference more puzzling. We calculate the thermostability measure and its energetic and entropic components for RxR and HsBR using our recently developed statistical-mechanical theory. The same type of calculation is independently performed for the portions playing essential roles in the proton-pumping function, helices 3 and 7, and their structural properties are related to the probable roles of water molecules in the proton-transporting mechanism. We succeed in elucidating how RxR realizes its exceptionally high stability with the original function being retained. This study provides an important first step toward the establishment of a method correlating microscopic, geometric characteristics of a protein with its thermodynamic properties and enhancing the thermostability through amino-acid mutations without vitiating the original function.

    DOI: 10.1021/acs.jpcb.9b10700

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  • Bacterium Lacking a Known Gene for Retinal Biosynthesis Constructs Functional Rhodopsins 査読

    Yu Nakajima, Keiichi Kojima, Yuichiro Kashiyama, Satoko Doi, Ryosuke Nakai, Yuki Sudo, Kazuhiro Kogure, Susumu Yoshizawa

    Microbes and Environments   35 ( 4 )   n/a - n/a   2020年

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

    DOI: 10.1264/jsme2.me20085

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  • Quantitation of the neural silencing activity of anion channelrhodopsins in Caenorhabditis elegans and their applicability for long-term illumination 査読

    Taro Yamanashi, Misayo Maki, Keiichi Kojima, Atsushi Shibukawa, Takashi Tsukamoto, Srikanta Chowdhury, Akihiro Yamanaka, Shin Takagi, Yuki Sudo

    Scientific Reports   9 ( 1 )   2019年12月

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

    DOI: 10.1038/s41598-019-44308-x

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    その他リンク: http://www.nature.com/articles/s41598-019-44308-x

  • Conformational Differences among Metarhodopsin I, Metarhodopsin II, and Opsin Probed by Wide-Angle X-ray Scattering 査読

    Yasushi Imamoto, Keiichi Kojima, Toshihiko Oka, Ryo Maeda, Yoshinori Shichida

    The Journal of Physical Chemistry B   123 ( 43 )   9134 - 9142   2019年10月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpcb.9b08311

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  • A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. 査読 国際誌

    David M Needham, Susumu Yoshizawa, Toshiaki Hosaka, Camille Poirier, Chang Jae Choi, Elisabeth Hehenberger, Nicholas A T Irwin, Susanne Wilken, Cheuk-Man Yung, Charles Bachy, Rika Kurihara, Yu Nakajima, Keiichi Kojima, Tomomi Kimura-Someya, Guy Leonard, Rex R Malmstrom, Daniel R Mende, Daniel K Olson, Yuki Sudo, Sebastian Sudek, Thomas A Richards, Edward F DeLong, Patrick J Keeling, Alyson E Santoro, Mikako Shirouzu, Wataru Iwasaki, Alexandra Z Worden

    Proceedings of the National Academy of Sciences of the United States of America   116 ( 41 )   20574 - 20583   2019年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Giant viruses are remarkable for their large genomes, often rivaling those of small bacteria, and for having genes thought exclusive to cellular life. Most isolated to date infect nonmarine protists, leaving their strategies and prevalence in marine environments largely unknown. Using eukaryotic single-cell metagenomics in the Pacific, we discovered a Mimiviridae lineage of giant viruses, which infects choanoflagellates, widespread protistan predators related to metazoans. The ChoanoVirus genomes are the largest yet from pelagic ecosystems, with 442 of 862 predicted proteins lacking known homologs. They are enriched in enzymes for modifying organic compounds, including degradation of chitin, an abundant polysaccharide in oceans, and they encode 3 divergent type-1 rhodopsins (VirR) with distinct evolutionary histories from those that capture sunlight in cellular organisms. One (VirRDTS) is similar to the only other putative rhodopsin from a virus (PgV) with a known host (a marine alga). Unlike the algal virus, ChoanoViruses encode the entire pigment biosynthesis pathway and cleavage enzyme for producing the required chromophore, retinal. We demonstrate that the rhodopsin shared by ChoanoViruses and PgV binds retinal and pumps protons. Moreover, our 1.65-Å resolved VirRDTS crystal structure and mutational analyses exposed differences from previously characterized type-1 rhodopsins, all of which come from cellular organisms. Multiple VirR types are present in metagenomes from across surface oceans, where they are correlated with and nearly as abundant as a canonical marker gene from Mimiviridae Our findings indicate that light-dependent energy transfer systems are likely common components of giant viruses of photosynthetic and phagotrophic unicellular marine eukaryotes.

    DOI: 10.1073/pnas.1907517116

    PubMed

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  • Photochemical Characterization of a New Heliorhodopsin from the Gram-Negative Eubacterium Bellilinea caldifistulae (BcHeR) and Comparison with Heliorhodopsin-48C12 査読

    Shibukawa A, Kojima K, Nakajima Y, Nishimura Y, Yoshizawa S, Sudo Y

    Biochemistry   58 ( 26 )   2934 - 2943   2019年7月

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  • High Thermal Stability of Oligomeric Assemblies of Thermophilic Rhodopsin in a Lipid Environment 査読

    Tomomi Shionoya, Misao Mizuno, Takashi Tsukamoto, Kento Ikeda, Hayato Seki, Keiichi Kojima, Mikihiro Shibata, Izuru Kawamura, Yuki Sudo, Yasuhisa Mizutani

    The Journal of Physical Chemistry B   122 ( 27 )   6945 - 6953   2018年7月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society (ACS)  

    DOI: 10.1021/acs.jpcb.8b04894

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  • Production of a Light-Gated Proton Channel by Replacing the Retinal Chromophore with Its Synthetic Vinylene Derivative

    Riho Takayama, Akimasa Kaneko, Takashi Okitsu, Satoshi P. Tsunoda, Kazumi Shimono, Misao Mizuno, Keiichi Kojima, Takashi Tsukamoto, Hideki Kandori, Yasuhisa Mizutani, Akimori Wada, Yuki Sudo

    Journal of Physical Chemistry Letters   9 ( 11 )   2857 - 2862   2018年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Chemical Society  

    Rhodopsin is widely distributed in organisms as a membrane-embedded photoreceptor protein, consisting of the apoprotein opsin and vitamin-A aldehyde retinal, A1-retinal and A2-retinal being the natural chromophores. Modifications of opsin (e.g., by mutations) have provided insight into the molecular mechanism of the light-induced functions of rhodopsins as well as providing tools in chemical biology to control cellular activity by light. Instead of the apoprotein opsin, in this study, we focused on the retinal chromophore and synthesized three vinylene derivatives of A2-retinal. One of them, C(14)-vinylene A2-retinal (14V-A2), was successfully incorporated into the opsin of a light-driven proton pump archaerhodopsin-3 (AR3). Electrophysiological experiments revealed that the opsin of AR3 (archaeopsin3, AO3) with 14V-A2 functions as a light-gated proton channel. The engineered proton channel showed characteristic photochemical properties, which are significantly different from those of AR3. Thus, we successfully produced a proton channel by replacing the chromophore of AR3.

    DOI: 10.1021/acs.jpclett.8b00879

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  • Pinopsin evolved as the ancestral dim-light visual opsin in vertebrates 査読

    Sato K, Yamashita T, Kojima K, Sakai K, Matsutani Y, Yanagawa M, Yamano Y, Wada A, Iwabe N, Ohuchi H, Shichida Y

    Communications Biology   1   156   2018年

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  • Spectroscopic characteristics of Rubricoccus marinus xenorhodopsin (RmXeR) and a putative model for its inward H+ transport mechanism 査読

    Saki Inoue, Susumu Yoshizawa, Yu Nakajima, Keiichi Kojima, Takashi Tsukamoto, Takashi Kikukawa, Yuki Sudo

    Physical Chemistry Chemical Physics   20 ( 5 )   3172 - 3183   2018年

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Royal Society of Chemistry (RSC)  

    <p>On the basis of functional and spectroscopic characterization, we propose a model for the inward proton transport in<italic>Rm</italic>XeR, a newly discovered microbial rhodopsin.</p>

    DOI: 10.1039/c7cp05033j

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  • Helical rearrangement of photoactivated rhodopsin in monomeric and dimeric forms probed by high-angle X-ray scattering 査読

    Yasushi Imamoto, Keiichi Kojima, Toshihiko Oka, Ryo Maeda, Yoshinori Shichida

    Photochemical & Photobiological Sciences   14 ( 11 )   1965 - 1973   2015年

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

    <p>The light-induced conformational change of monomeric and dimeric rhodopsin in the nanodisc membrane was directly monitored by high-angle solution X-ray scattering.</p>

    DOI: 10.1039/c5pp00175g

    Web of Science

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講演・口頭発表等

  • Phosphate ion binding modulates photochemical properties of a light-driven SO42- transporter, SyHR

    第56回日本生物物理学会  2018年 

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  • Impact and mechanism of phosphate binding to a light-driven anion transporter SyHR

    18th International Conference on Retinal Proteins  2018年 

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  • Bottom-up approach for microbial rhodopsin-based optogenetic tools

    第56回日本生物物理学会  2018年 

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  • Optimization mechanism of vertebrate visual pigments for scotopic vision

    International Symposium on Biophysics of Rhodopsins  2017年 

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  • Evolutionary acquisition of low thermal noise of cone pigments for scotopic vision

    第55回日本生物物理学会  2017年 

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  • Comparative analysis of thermal activation rate in vertebrate cone visual pigments

    第87回 日本動物学会  2016年 

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  • Thermal activation rates of visual pigments expressed in rods

    第54回日本生物物理学会  2016年 

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  • Thermal isomerization rate of retinal chromophore in blue-sensitive cone pigments expressed in amphibian green rods

    17th International Conference on Retinal Proteins  2016年 

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受賞

  • 日本薬学会 中国四国支部 奨励賞

    2020年  

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  • 日本生物物理学会若手奨励賞

    2017年  

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    受賞国:日本国

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