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Analysis of Assembly Intermediates of Photosynthetic Pigment Proteins by RNA-Probe-Based Exhaustive Single-Molecule Spectroscopy

Research Project

Project/Area Number 21K19200
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
Research InstitutionTohoku University

Principal Investigator

Shibata Yutaka  東北大学, 理学研究科, 准教授 (20300832)

Project Period (FY) 2021-07-09 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2022: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2021: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000)
Keywords単一分子分光 / RNAプローブ / 光化学系修復 / 励起スペクトル / 過渡的中間体 / 蛍光寿命
Outline of Research at the Start

分子量数10万を超える光合成タンパク質が新規合成される際に、100を超える色素分子がどのように所定の部位に挿入されるのか、その機構は謎に包まれてきた。合成直後の光合成タンパク質複合体は過渡的に存在する不安定な分子種であることが、その解析を極めて困難にしてきた。本研究では、光合成タンパク質のmRNAの相補鎖に蛍光色素を結合したRNAプローブを用いて、リボソームを介してmRNAとの結合を維持している合成途上複合体を検出し、そのクロロフィル蛍光寿命や励起スペクトル測定により色素の機能解析を行い、これまで手付かずであった光合成タンパク質の合成途上複合体の解明を飛躍的に推進し、新たな学術を切り拓く。

Outline of Final Research Achievements

Photosystem II (PSII) has been known to be repeatedly damaged and repaired in photosynthesis organisms. Here I proposed and tried a method to detect the assembly intermediates of PSII using designed RNA probes. A model organism Chlamydomonas was used. Since D1 subunit at the center of the PSII complex is the target of the repair process, I designed an RNA probe which is complementary to the mRNA sequence of D1 subunit and contains Alexa555 at its both ends as the fluorophore. Chlamydomonas cells were incubated under high light and then under mild light to activate the repair process. Thylakoid membranes were isolated from the cells treated as above and the RNA probe was hybridized with the thylakoids. I detected the fluorescence signal of Alexa555 from the hybridized thylakoid membranes, confirming the validity of the method proposed in the present project.

Academic Significance and Societal Importance of the Research Achievements

光合成タンパク質のAssembly過程の解明は、光合成研究において未だ解明されていない難問の一つである。水から電子を引き抜く過程は、分子に大きな酸化力の実現を要求し、同時に大量の酸素分子を発生させる。高い酸化力が内在することや、反応性の高い酸素分子が大量発生することは、どちらもタンパク質の損傷の原因となる。こうした困難な状況をやり繰りするため、生物は壊れないタンパク質を進化させるのではなく、壊れても迅速に修復が可能となるシステムを進化させた。人工の新規タンパク質を設計し合成することが可能となりつつある現代において、光合成系の修復機構解明は人工光合成を実現させる上でも示唆に富むものとなる。

Report

(3 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • Research Products

    (24 results)

All 2023 2022 2021 Other

All Journal Article (8 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 8 results,  Open Access: 3 results) Presentation (15 results) (of which Int'l Joint Research: 5 results) Remarks (1 results)

  • [Journal Article] Uphill energy transfer mechanism for photosynthesis in an Antarctic alga2023

    • Author(s)
      Kosugi Makiko、Kawasaki Masato、Shibata Yutaka、Hara Kojiro、Takaichi Shinichi、Moriya Toshio、Adachi Naruhiko、Kamei Yasuhiro、Kashino Yasuhiro、Kudoh Sakae、Koike Hiroyuki、Senda Toshiya
    • Journal Title

      Nature Communications

      Volume: 14 Issue: 1 Pages: 730-730

    • DOI

      10.1038/s41467-023-36245-1

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of Line-Detected UV?Vis Absorption Microscope and Its Application to Quantitative Evaluation of Lithium Surface Reactivity2023

    • Author(s)
      Inoue Ken-ichi、Mao Jianxin、Okamoto Rika、Shibata Yutaka、Song Wenbo、Ye Shen
    • Journal Title

      Analytical Chemistry

      Volume: 95 Issue: 9 Pages: 4550-4555

    • DOI

      10.1021/acs.analchem.2c05759

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Exciton quenching by oxidized chlorophyll Z across the two adjacent monomers in a photosystem II core dimer.2022

    • Author(s)
      Ahmed Mohamed, Shunsuke Nishi, Keisuke Kawakami, Jian-Ren Shen, Shigeru Itoh, Hiroshi Fukumura, Yutaka Shibata
    • Journal Title

      Photosynthesis Research

      Volume: 154 Issue: 3 Pages: 277-289

    • DOI

      10.1007/s11120-022-00948-1

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] State transition is quiet around pyrenoid and LHCII phosphorylation is not essential for thylakoid deformation in Chlamydomonas 137c2022

    • Author(s)
      Zhang XJ, FujitaY, Kaneda N, Tokutsu R, Ye S, Minagawa J, Shibata Y
    • Journal Title

      Proceedings of the National Academy of Sciences of the United States of America

      Volume: 119 Issue: 37

    • DOI

      10.1073/pnas.2122032119

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Accumulation of quenched LHCII around PSI in Chlamydomonas cells in state2 revealed by cryo-fluorescence lifetime imaging2022

    • Author(s)
      Fujita Yuki、Zhang XianJun、Mohamed Ahmed、Ye Shen、Shibata Yutaka
    • Journal Title

      Journal of Photochemistry and Photobiology B: Biology

      Volume: 236 Pages: 112584-112584

    • DOI

      10.1016/j.jphotobiol.2022.112584

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Recent advances in single-molecule spectroscopy studies on light-harvesting processes in oxygenic photosynthesis2022

    • Author(s)
      Kondo Toru、Shibata Yutaka
    • Journal Title

      Biophysics and Physicobiology

      Volume: 19 Issue: 0 Pages: n/a

    • DOI

      10.2142/biophysico.bppb-v19.0013

    • ISSN
      2189-4779
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High-speed excitation-spectral microscopy uncovers in-situ rearrangement of light-harvesting apparatus in Chlamydomonas during state transitions at submicron precision2021

    • Author(s)
      Zhang XianJun、Fujita Yuki、Tokutsu Ryutaro、Minagawa Jun、Ye Shen、Shibata Yutaka
    • Journal Title

      Plant and Cell Physiology

      Volume: 未定 Issue: 5 Pages: 872-882

    • DOI

      10.1093/pcp/pcab047

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Fluctuating Energy-Transfer Pathway of Photosynthetic Antenna Systems Observed by Single-Molecule Fluorescence Spectroscopy2021

    • Author(s)
      SHIBATA Yutaka
    • Journal Title

      Seibutsu Butsuri

      Volume: 61 Issue: 1 Pages: 023-026

    • DOI

      10.2142/biophys.61.023

    • NAID

      130007976661

    • ISSN
      0582-4052, 1347-4219
    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Quenched LHCII Accumulation around PSI in Chlamydomonas Cells in State2 Revealed by Cryo-Fluorescence Lifetime and Spectral Microscopy2022

    • Author(s)
      Yuki Fujita, XianJun Zhang, Ahmed Mohamed Ali, Shen Ye, Yutaka Shibata
    • Organizer
      18th International Congress on Photosynthesis Research
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Site-Dependent State Transition and Ultrastructural Changes of Thylakoid in Chlamydomonas2022

    • Author(s)
      XianJun Zhang, Yuki Fujita, Naoya Kaneda, Ryutaro Tokutsu, Jun Minagawa, Shen Ye, Yutaka Shibata
    • Organizer
      18th International Congress on Photosynthesis Research
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Assignment of fluorescence bands of chlorophyll-f containing photosystem I by single-molecule spectroscopy2022

    • Author(s)
      Rin Taniguchi, Toshiyuki Shinoda, Tatsuya Tomo, Shen Ye, Yutaka Shibata
    • Organizer
      18th International Congress on Photosynthesis Research
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Site-Dependent State Transition and Ultrastructural Changes of Thylakoid in Chlamydomonas2022

    • Author(s)
      XianJun Zhang, Yuki Fujita, Naoya Kaneda, Ryutaro Tokutsu, Shen Ye, Jun Minagawa, Yutaka Shibata
    • Organizer
      International Symposium On Photosynthesis And Chloroplast Regulation
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Microspectroscopic study on artificial thylakoid membranes supported by polymerized lipid bilayers2022

    • Author(s)
      酒井 颯太, 楠 祐佳, 森垣 憲一, 叶 深, 柴田 穣
    • Organizer
      2022年度 化学系学協会東北大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Study on light-harvesting regulation mechanism in algal cells by space-wavelength-time-resolved analysis by cryogenic microscope2022

    • Author(s)
      Yuki Fujita, XianJun Zhang, Shen Ye, Yutaka Shibata
    • Organizer
      第60回日本生物物理学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Assignment of fluorescence bands of chlorophyll-f containing photosystem I to elucidate its reaction mechanism by near-infrared light2022

    • Author(s)
      Rin Taniguchi, Toshiyuki Shinoda, Tatsuya Tomo, Shen Ye, Yutaka Shibata
    • Organizer
      第60回日本生物物理学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Excitation-spectral microscopy uncovers in-situ rearrangement of LHCII in Chlamydomonas during state transitions2021

    • Author(s)
      張 先駿, 藤田 祐輝, 得津 隆太郎, 皆川 純, 叶 深, 柴田 穣
    • Organizer
      第11回日本光合成学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] Excitation-spectral microscopy uncovers in-situ rearrangement of LHCII in Chlamydomonas during state transition2021

    • Author(s)
      張 先駿, 藤田 祐輝, 得津 隆太郎, 皆川 純, 叶 深, 柴田 穣
    • Organizer
      第28回光合成セミナー2021: 反応中心と色素系の多様性
    • Related Report
      2021 Research-status Report
  • [Presentation] 光化学系Iassembly中間体の時間分解蛍光および単一分子分光解析2021

    • Author(s)
      金田直也, Sreedhar Nellaepalli, 高橋裕一郎, 柴田穣
    • Organizer
      第28回光合成セミナー2021: 反応中心と色素系の多様性
    • Related Report
      2021 Research-status Report
  • [Presentation] 二次元蛍光寿命相関分光による光化学系Iタンパク質の単一分子電子移動速度の測定2021

    • Author(s)
      谷口凜,篠田稔行,鞆達也,叶深,近藤徹,柴田穣
    • Organizer
      第15回分子科学討論会
    • Related Report
      2021 Research-status Report
  • [Presentation] 光化学系I assembly中間体の単粒子分光と時間分解蛍光解析2021

    • Author(s)
      金田直也, Sreedhar Nellaepalli, 高橋裕一郎, 叶深, 柴田穣
    • Organizer
      2021年度 化学系学協会東北大会
    • Related Report
      2021 Research-status Report
  • [Presentation] ストリークカメラを検出器とした細胞内局所での時間分解顕微蛍光分光2021

    • Author(s)
      藤田 祐輝,張 先駿, 金田 直也,柴田 穣
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] 励起スペクトル顕微鏡と超解像イメージングで明らかになったステート遷移におけるチラコイ ド膜の不規則な構造変化2021

    • Author(s)
      張 先駿, 藤田 祐輝, 金田 直也, 得津 隆太郎, 皆川 純, 叶 深, 柴田 穣
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] Uphill energy transfer mechanism for photosynthesis in the Antarctic alga2021

    • Author(s)
      Makiko Kosugi, Masato Kawasaki, Yutaka Shibata, Kojiro Hara, Shinichi Takaichi, Toshio Moriya, Naruhiko Adachi, Yasuhiro Kamei, Yasuhiro Kashino, Sakae Kudoh, Hiroyuki Koike, Toshiya Senda
    • Organizer
      The 12th Symposium on Polar Science
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Remarks] 光で単一分子の挙動を測る

    • URL

      http://sub.web.tohoku.ac.jp/orgphys/content/files/research_Shibata.pdf

    • Related Report
      2021 Research-status Report

URL: 

Published: 2021-07-13   Modified: 2024-01-30  

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