Biochemical analysis of low thermal isomerization mechanism of rod visual pigment.

• Project/Area Number: 26650119
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Animal physiology/Animal behavior
• Research Institution: Kyoto University
• Principal Investigator: Shichida Yoshinori 京都大学, 理学(系)研究科(研究院), 教授 (60127090)
• Project Period (FY): 2014-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2014: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: 視物質 / 視細胞 / 暗ノイズ / 生化学的方法 / 分子進化 / 生化学的手法

Outline of Final Research Achievements

Low dark noise is a prerequisite for rod cells, which mediate our dim-light vision. The low dark noise is achieved by the extremely stable character of the rod visual pigment, rhodopsin, which evolved from less stable cone visual pigments. We have developed a biochemical method to quickly evaluate the thermal isomerization rate of the chromophore in visual pigments. Using an isomerization locked chromophore, we confirmed that thermal isomerization rate of the chromophore in rhodopsin is about 1/1000 of that of cone visual pigment and identified two critical residues (E122 and I189) in the chromophore binding pocket which account for the extremely low thermal activation rate of rhodopsin. Furthermore, we found that anura blue-sensitive cone visual pigment expressed in green rods acquired the low thermal isomerization rate of the chromophore by the specific mutation during the molecular evolution, which led to optimization for scotopic vision.

Research Products

• [Journal Article] Origin of the low thermal isomerization rate of rhodopsin chromophore (2015)
  • Author(s): Yanagawa, M.; Kojima, K.; Yamashita, T.; Iwamoto, Y.; Matsuyama, T.; Nakanishi, K.; Yamano, Y.; Wada, A.; Sako, Y.; Shichida, Y.
  • Journal Title: Sci. Rep. Volume: 5 Issue: 1 Pages: 11081-11081
  • DOI: 10.1038/srep11081
  • NAID: 120005690204
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Helical rearrangement of photoactivated rhodopsin in monomeric and dimeric forms probed by high-angle X-ray scattering. (2015)
  • Author(s): Imamoto Y, Kojima K, Oka T, Maeda R, Shichida Y
  • Journal Title: Photochem. Photobiol. Sci. Volume: 14(11) Issue: 11 Pages: 1965-1973
  • DOI: 10.1039/c5pp00175g
  • NAID: 120005741088
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Diversification of non-visual photopigment parapinopsin in spectral sensitivity for diverse pineal functions (2015)
  • Author(s): M. Koyanagi, S. Wada, E. Kawano-Yamashita, Y. Hara, S. Kuraku, S. Kosaka, K. Kawakami, S. Tamotsu, H. Tsukamoto, Y. Shichida, A. Terakita
  • Journal Title: BMC Biology Volume: 13 Issue: 1 Pages: 73-73
  • DOI: 10.1186/s12915-015-0174-9
  • NAID: 120005758203
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Diversity of active states in TMT opsins (2015)
  • Author(s): K. Sakai
  • Journal Title: PLoS One Volume: 10 Issue: 10 Pages: 1-12
  • DOI: 10.1371/journal.pone.0141238
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Intramolecular interactions that induce helical rearrangement upon rhodopsin activation: Light-induced structural changes in metarhodopsin IIa probed by cysteine S-H stretching vibrations (2014)
  • Author(s): Y. Yamazaki, T. Nagata, A. Terakita, H. Kandori, Y. Shichida, Y. Imamoto*
  • Journal Title: J. Biol. Chem Volume: 289 Issue: 20 Pages: 13792-13800
  • DOI: 10.1074/jbc.m113.527606
  • NAID: 120005741087
  • Peer Reviewed
• [Journal Article] Contribution of glutamic acid in the conserved E/DRY triad to the functional properties of rhodopsin. (2014)
  • Author(s): Sato, K., Yamashita, T., and Shichida, Y.
  • Journal Title: Biochemistry Volume: 53 Issue: 27 Pages: 4420-4425
  • DOI: 10.1021/bi5003772
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] Thermal isomerization of chromophore in rod and cone visual pigments (2015)
  • Author(s): Y. Shichida
  • Organizer: Pacifichem 2015
  • Place of Presentation: Honolulu, USA
  • Year and Date: 2015-12-19
  • Int'l Joint Research / Invited
• [Presentation] Molecular evolution of the low thermal isomerization rate of rhodopsin chromophore (2015)
  • Author(s): Y. Shichida
  • Organizer: 7th AOCP
  • Place of Presentation: Taipei, Taiwan
  • Year and Date: 2015-11-18
  • Int'l Joint Research / Invited
• [Presentation] 両生類の緑桿体に含まれる青色錐体視物質の熱活性化頻度 (2015)
  • Author(s): 松谷優樹、小島慧一、柳川正隆、山下高廣、今元泰、山野由美子、和田昭盛、七田芳則
  • Organizer: 日本動物学会大86回大会
  • Place of Presentation: 新潟
  • Year and Date: 2015-09-17
• [Presentation] 視物質の低い熱活性化頻度をもたらす分子メカニズム (2015)
  • Author(s): 小島慧一、柳川正隆、山下高廣、松谷優樹、今元泰、松山オジョス武、中西香爾、山野由美子、和田昭盛、佐甲靖志、七田芳則
  • Organizer: 日本生物物理学会第53回年会
  • Place of Presentation: 金沢
  • Year and Date: 2015-09-13
• [Presentation] ロドプシンの低い熱活性化頻度の分子メカニズム (2014)
  • Author(s): 小島慧一、柳川正隆、山下高廣、今元泰、松山武、中西香爾、山野由美子、和田昭盛、佐甲靖志、七田芳則
  • Organizer: 日本生物物理学会
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 2014-09-25 – 2014-09-27
• [Presentation] ロドプシン発色団の低い熱異性化速度の生化学的測定 (2014)
  • Author(s): 柳川正隆、小島慧一、山下高廣、今元泰、松山武、中西香爾、山野由美子、和田昭盛、佐甲靖志、七田芳則
  • Organizer: 日本動物学会
  • Place of Presentation: 東北大学
  • Year and Date: 2014-09-11 – 2014-09-13
• [Book] 光と生命の辞典 (2016)
  • Author(s): 七田芳則
  • Total Pages: 422
  • Publisher: 朝倉書店
• [Book] Vertebrate Photoreceptors (2014)
  • Author(s): Sato, K. and Shichida, Y.
  • Total Pages: 349
  • Publisher: Springer
• [Remarks] 七田研ホームページ
  • URL: http://photo1.biophys.kyoto-u.ac.jp/shichida/home_jp.html