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Structural analyses of reaction states of ion-pumping rhodopsins

Research Project

Project/Area Number 16K07267
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Structural biochemistry
Research InstitutionNagoya University

Principal Investigator

Kouyama Tsutomu  名古屋大学, 理学研究科, 名誉教授 (30170210)

Co-Investigator(Kenkyū-buntansha) 井原 邦夫  名古屋大学, 遺伝子実験施設, 准教授 (90223297)
Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywordsイオン能動輸送 / 光駆動塩素イオンポンプ / 光駆動プロトンポンプ / レチナールタンパク質 / レチナール異性体 / X線結晶構造解析 / ハロロドプシン / 光駆動陰イオンポンプ / レチナール光異性化 / アーキロドプシン / プロトン輸送性ロドプシン / 光駆動イオンポンプ / バクテリオロドプシン / 陰イオン輸送性ロドプシン / レチナール異性化 / 光誘起吸収変化 / 低温原子間力顕微鏡 / レチナール・タンパク質 / 陰イオン輸送 / プロトン輸送
Outline of Final Research Achievements

The anion pumping cycle of halorhodopsin is initiated when the all-trans/15-anti isomer of retinal is photo-isomerized into the 13-cis/15-anti configuration. A previous study suggested that a reaction state with 13-cis/15-syn retinal occurred during the anion release process, i.e., after the N state with the 13-cis/15-anti retinal and before the O state with all-trans/15-anti retinal. In this study, we found that the 13-cis isomer (HR'), in which the absorption spectrum was blue-shifted by 8 nm as compared with that of the trans isomer (HR), accumulated significantly when pHR-rich claret membranes in 4 M NaBr was illuminated with continuous light. It was suggested that the branching of the trans photocycle into the 13-cis isomer (HR’) occurs during the decay of an O-like state (O’) with 13-cis/15-syn retinal. At a high bromide ion concentration, the anion pumping cycle is described by the scheme: HR -(hν)-> K -> L1 -> N -> N’ -> O’ -> HR’-> HR.

Academic Significance and Societal Importance of the Research Achievements

ハロロドプシンの陰イオン輸送サイクル中に3段階のレチナール異性化反応(13-trans/15-anti―→13-cis/15-anti―→13-cis/15-syn―→13-trans/15-anti)が起こることを明らかにした。タンパク質部分も反応サイクルの間に3種類の構造変化を起こすことが示されており、これらの結果を基に、レチナールの異性化→タンパク質の構造変化→イオン移動→レチナールの異性化、…、という具合に反応が進行することで、イオンの一方向の輸送が保証される、という作業仮説を提唱した。これは、ロドプシン群タンパク質の光反応機構に関する従来の基本的な考えを大きく変えることになる。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (38 results)

All 2020 2019 2018 2017 2016

All Journal Article (26 results) (of which Int'l Joint Research: 12 results,  Peer Reviewed: 26 results,  Open Access: 21 results,  Acknowledgement Compliant: 5 results) Presentation (12 results) (of which Int'l Joint Research: 3 results,  Invited: 3 results)

  • [Journal Article] Presynaptic MAST kinase controls opposing postsynaptic responses to convey stimulus valence in Caenorhabditis elegans2020

    • Author(s)
      Nakano Shunji、Ikeda Muneki、Tsukada Yuki、Fei Xianfeng、Suzuki Takamasa、Niino Yusuke、Ahluwalia Rhea、Sano Ayana、Kondo Rumi、Ihara Kunio、Miyawaki Atsushi、Hashimoto Koichi、Higashiyama Tetsuya、Mori Ikue
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 117 Issue: 3 Pages: 1638-1647

    • DOI

      10.1073/pnas.1909240117

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] gas1 mutation extends chronological lifespan via Pmk1 and Sty1 MAPKs in Schizosaccharomyces pombe2019

    • Author(s)
      Imai Yuki、Shimasaki Takafumi、Enokimura Chihiro、Ohtsuka Hokuto、Tsubouchi Satoshi、Ihara Kunio、Aiba Hirofumi
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry

      Volume: 84 Issue: 2 Pages: 330-337

    • DOI

      10.1080/09168451.2019.1676695

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The mechanosensitive channel YbdG from Escherichia coli has a role in adaptation to osmotic up-shock.2019

    • Author(s)
      Shun Amemiya, Hayato Toyoda, Mami Kimura, Hiromi Saito, Hiroshi Kobayashi, Kunio Ihara 3 , Kiyoto Kamagata 4 , Ryuji Kawabata 5 , Setsu Kato, Yutaka Nakashimada, Tadaomi Furuta, Shin Hamamoto, Nobuyuki Uozumi
    • Journal Title

      Journal of Biological Chemistry

      Volume: 294 (33) Issue: 33 Pages: 12281-12292

    • DOI

      10.1074/jbc.ra118.007340

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comprehensive investigation of the gene expression system regulated by an Aspergillus oryzae transcription factor XlnR using integrated mining of gSELEX-Seq and microarray data.2019

    • Author(s)
      Oka H, Kojima T, Ihara K, Kobayashi T, Nakano H.
    • Journal Title

      BMC Genomics

      Volume: 20 Issue: 1 Pages: 16-16

    • DOI

      10.1186/s12864-018-5375-5

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cholecystokinin induces crowing in chickens2019

    • Author(s)
      Shimmura T, Tamura M, Ohashi S, Sasaki A, Yamanaka T, Nakao N, Ihara K, Okamura S, Yoshimura T.
    • Journal Title

      Sci Rep.

      Volume: 9 Issue: 1 Pages: 3978-3978

    • DOI

      10.1038/s41598-019-40746-9

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Three-Step Isomerization of the Retinal Chromophore during the Anion Pumping Cycle of Halorhodopsin.2018

    • Author(s)
      Kouyama T, Ihara K, Maki K, Chan SK.
    • Journal Title

      Biochemistry

      Volume: 57 Issue: 41 Pages: 6013-6026

    • DOI

      10.1021/acs.biochem.8b00631

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Obesity and mental health improvement following nutritional education focusing on gut microbiota composition in Japanese women: a randomised controlled trial2018

    • Author(s)
      Uemura Mayu、Hayashi Fumikazu、Ishioka Ken、Ihara Kunio、Yasuda Kazushi、Okazaki Kanako、Omata Junichi、Suzutani Tatsuo、Hirakawa Yoshihisa、Chiang Chifa、Aoyama Atsuko、Ohira Tetsuya
    • Journal Title

      European Journal of Nutrition

      Volume: 2018 Issue: 8 Pages: 1-12

    • DOI

      10.1007/s00394-018-1873-0

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Draft Genome Sequence of Burkholderia vietnamiensis Strain RS1, a Nitrogen-Fixing Endophyte Isolated from Sweet Potato2018

    • Author(s)
      Shinjo R, Uesaka K, Ihara K, Sakazaki S, Yano K, Kondo M, Tanaka A
    • Journal Title

      eCollection

      Volume: 7 Issue: 3

    • DOI

      10.1128/mra.00820-18

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] SLO potassium channels antagonize premature decision making in C. elegans2018

    • Author(s)
      Aoki I, Tateyama M, Shimomura T, Ihara K, Kubo Y, Nakano S, Mori I.
    • Journal Title

      Commun Biol.

      Volume: 1 Issue: 1 Pages: 123-123

    • DOI

      10.1038/s42003-018-0124-5

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] In vivo transposon tagging in the nonheterocystous nitrogen-fixing cyanobacterium Leptolyngbya boryana2018

    • Author(s)
      Tomatsu C, Uesaka K, Yamakawa H, Tsuchiya T, Ihara K, Fujita Y.
    • Journal Title

      FEBS Lett.

      Volume: 592 Issue: 10 Pages: 1634-1642

    • DOI

      10.1002/1873-3468.13079

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Co‐expression of the calcitonin receptor gene in the hypothalamic kisspeptin neurons in female rats.2018

    • Author(s)
      Assadullah, Nahoko Ieda, Narumi Kawai, Hirotaka Ishii, Kunio Ihara, Naoko Inoue, Yoshihisa Uenoyam, Hiroko Tsukamura
    • Journal Title

      Reprod Med Biol.

      Volume: 17 Issue: 2 Pages: 164-172

    • DOI

      10.1002/rmb2.12085

    • Related Report
      2018 Research-status Report 2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Formation of a Mimetic Biomembrane from the Hydrophobic Protein Zein and Phospholipids: Structure and Application2017

    • Author(s)
      Liping Wang, Toshiaaki Gotoh, Yuzhu Wang, Tsutomu Kouyama, Jin-Ye Wang
    • Journal Title

      J. Phys. Chem. C

      Volume: 121 Issue: 36 Pages: 19999-20006

    • DOI

      10.1021/acs.jpcc.7b04573

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Salinarchaeum chitinilyticum sp. nov., a chitin-degrading haloarchaeon isolated from commercial salt2017

    • Author(s)
      Minegishi H, Enomoto S, Echigo A, Shimane Y, Kondo Y, Inoma A, Kamekura M, Takai K, Itoh T, Ohkuma M, Ihara K, Takahashi-Ando N, Fukushima Y, Ishii S, Yoshida Y, Usami R
    • Journal Title

      Int J Syst Evol Microbiol.

      Volume: 67 Issue: 7 Pages: 2274-2278

    • DOI

      10.1099/ijsem.0.001941

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Complete Chloroplast Genome Sequence of the Early-Divergent Green Alga Palmophyllum crassum2017

    • Author(s)
      Furukawa R, Kunugi M, Ihara K, Takabayashi A, Tanaka A
    • Journal Title

      Genome Announcements

      Volume: 5 Issue: 10

    • DOI

      10.1128/genomea.01745-16

    • Related Report
      2017 Research-status Report 2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] A light-responsive self-assembly formed by a cationic azobenzene derivative and SDS as a drug delivery system.2017

    • Author(s)
      S. Geng, Y. Wang, L. Wang, T. Kouyama, T. Gotoh, S. Wada, J. -Y. Wang,
    • Journal Title

      Sci. Rep.

      Volume: 7 Issue: 1 Pages: 39202-39202

    • DOI

      10.1038/srep39202

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A simple method for isolation and construction of markerless cyanobacterial mutants defective in acyl-acyl carrier protein synthetase2017

    • Author(s)
      Kojima K, Keta S, Uesaka K, Kato A, Takatani N, Ihara K, Omata T, Aichi M.
    • Journal Title

      Appl Microbiol Biotechnol

      Volume: 100 Pages: 10107-10113

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Identification of a novel protein kinase that affects the chronological lifespan in fission yeast.2016

    • Author(s)
      Kurauchi T, Hashizume A, Imai Y, Hayashi K, Tsubouchi S, Ihara K, Ohtsuka H, Aiba H
    • Journal Title

      FEMS Microbiol Lett.

      Volume: ;364(2). pii: Issue: 2 Pages: fnw257-fnw257

    • DOI

      10.1093/femsle/fnw257

    • NAID

      120006305608

    • Related Report
      2017 Research-status Report 2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Crystal structure of the 11-cis isomer of pharaonis halorhodopsin: Structural constraints on interconversions among different isomeric states,2016

    • Author(s)
      Chan SK, Kawaguchi H., Kubo H.,, Murakami M., Ihara K., Maki K., Kouyama T.
    • Journal Title

      Biochemistry

      Volume: 55 Issue: 29 Pages: 4092-4104

    • DOI

      10.1021/acs.biochem.6b00277

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Crystal structures of two isozymes of citrate synthase from Sulfolobus tokodaii Strain 72016

    • Author(s)
      Murakami M., Kouyama T,
    • Journal Title

      Biochemistry. Research International,

      Volume: 2016 Pages: 7560919-7560919

    • DOI

      10.1155/2016/7560919

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Shifting transcriptional machinery is required for long-term memory maintenance and modification in Drosophila mushroom bodies.2016

    • Author(s)
      Hirano Y, Ihara K, Masuda T, Yamamoto T, Iwata I, Takahashi A, Awata H, Nakamura N, Takakura M, Suzuki Y, Horiuchi J, Okuno H, Saitoe M.
    • Journal Title

      Nat Commun.

      Volume: 7 Issue: 1 Pages: 13471-13471

    • DOI

      10.1038/ncomms13471

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Photochemical characterization of actinorhodopsin and its functional existence in the natural host2016

    • Author(s)
      Nakamura, S., Kikukawa, T., Tamogami, J., Kamiya, M., Aizawa, T., Hahn, M., Ihara, K., Kamo, N., Demura, M.
    • Journal Title

      BBA-BIOENERGETICS

      Volume: 1857 Issue: 12 Pages: 1900-1908

    • DOI

      10.1016/j.bbabio.2016.09.006

    • NAID

      120006366475

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Haloparvum alkalitolerans sp. nov., alkali-tolerant haloarchaeon isolated from commercial salt.2016

    • Author(s)
      Kondo Y, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Tanaka A, Takahashi-Ando N, Fukushima Y, Yoshida Y, Ihara K, Usami R
    • Journal Title

      Int J Syst Evol Microbiol

      Volume: 66 Issue: 12 Pages: 5314-5319

    • DOI

      10.1099/ijsem.0.001513

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Complete genome sequence of Kosakonia sacchari strain BO-1, an endophytic diazotroph isolated from a sweet potato2016

    • Author(s)
      Shinjo R, Uesaka K, Ihara K, Loshakova K, Mizuno Y, Yano K, Tanaka A
    • Journal Title

      Genome Annoucements

      Volume: 4 Issue: 5

    • DOI

      10.1128/genomea.00868-16

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Analytical Pipeline for Genome-Wide Identification of the Genes Regulated by a Transcription Factor: Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq.2016

    • Author(s)
      Kojima T, Kunitake E, Ihara K, Kobayashi T, Nakano H. A Robust
    • Journal Title

      PLoS One.

      Volume: 11 Issue: 7 Pages: e0159011-e0159011

    • DOI

      10.1371/journal.pone.0159011

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Evolution of Green Plants Accompanied Changes in Light-Harvesting Systems2016

    • Author(s)
      Kunugi M, Satoh S, Ihara K, Shibata K, Yamagishi Y, Kogame K, Obokata J, Takabayashi A and Tanaka A
    • Journal Title

      Plant and Cell Physiology

      Volume: - Issue: 6 Pages: 1231-1243

    • DOI

      10.1093/pcp/pcw071

    • NAID

      120006024384

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] FliH and FliI ensure efficient energy coupling of flagellar type III protein export in Salmonella.2016

    • Author(s)
      Minamino T, Kinoshita M, Inoue Y, Morimoto YV, Ihara K, Koya S, Hara N, Nishioka N, Kojima S, Homma M, Namba K
    • Journal Title

      Microbiologyopen

      Volume: - Issue: 3 Pages: 340-340

    • DOI

      10.1002/mbo3.340

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 筋収縮と能動輸送2019

    • Author(s)
      神山勉
    • Organizer
      日本物理学会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] アーキロドプシン-2の光化学反応のpH依存性2019

    • Author(s)
      神山勉、井原邦夫
    • Organizer
      日本生物物理学会中部支部講演会
    • Related Report
      2018 Research-status Report
  • [Presentation] ハロロドプシンのイオン輸送におけるレチナール異性化反応2018

    • Author(s)
      神山勉
    • Organizer
      日本生物物理学会年会
    • Related Report
      2018 Research-status Report
  • [Presentation] ゲノム構造変化を感度良く検出する方法:SV-Quest2018

    • Author(s)
      井原邦夫、上坂一馬
    • Organizer
      第12回 日本ゲノム微生物学会 (2018年 3月14日、京都)
    • Related Report
      2017 Research-status Report
  • [Presentation] Crystallographic studies on proton-pumping rhodopsin and anion-pumping rhodopsin2017

    • Author(s)
      T. Kouyama
    • Organizer
      the IGER international Symposium on Physics of Life.
    • Place of Presentation
      名古屋
    • Year and Date
      2017-03-25
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 光駆動塩素イオンポンプ・ハロロドプシンの作動機構2017

    • Author(s)
      神山勉
    • Organizer
      生体運動班会議
    • Place of Presentation
      神戸
    • Year and Date
      2017-01-05
    • Related Report
      2016 Research-status Report
  • [Presentation] Can halorhodopsin pump hydroxyl ions ?2017

    • Author(s)
      神山 勉, 鈴木 健太, 成瀬 圭汰, Chan Siu Kit
    • Organizer
      第55回生物物理学会年会、(9月20日、熊本大学)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] ゲノムシーケンスにもとづく微生物分類手法;好塩性古細菌を例として2017

    • Author(s)
      井原邦夫、上坂一馬、谷村要、中邨真之、越後輝敦、峯岸宏明
    • Organizer
      第30回 日本Archaea研究会 (2017年 9月1日、仙台)
    • Related Report
      2017 Research-status Report
  • [Presentation] Isomerization of the retinal chromophore during the anion pumping cycle of halorhodopsin2016

    • Author(s)
      T. Kouyama, H. Kubo, S. K. Chan, K. Maki:
    • Organizer
      日本生物物理学会第53回年会
    • Place of Presentation
      つくば
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] Crystal Structure of the 11-cis isomer of Pharaonis halorhodopsin2016

    • Author(s)
      S. K. CHAN1, H. Kawaguchi, H. Kubo, K. Maki, K. Ihara and T. Kouyama
    • Organizer
      日本生物物理学会第53回年会
    • Place of Presentation
      つくば
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] Crystal structure of the 11-cis isomer of Pharaonis Halorhodopsin at 1.7 Å resolutions2016

    • Author(s)
      S. K. CHAN, H. KAWAGUCHI, H. KUBO, K. IHARA, K. MAKI, T. KOUYAMA
    • Organizer
      日本結晶学会平成28年度年会
    • Place of Presentation
      水戸
    • Year and Date
      2016-10-17
    • Related Report
      2016 Research-status Report
  • [Presentation] Structural constraints on retinal isomerization in microbial and animal rhodopsins2016

    • Author(s)
      T. Kouyama, S. K. Chan, M. Murakami:
    • Organizer
      26th IUPAC on Photochem, Osaka, April 5, 2016
    • Place of Presentation
      大阪
    • Year and Date
      2016-04-05
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited

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Published: 2016-04-21   Modified: 2021-02-19  

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