Inoue Laboratory, ISSP, Univ. Tokyo

Publication

Research articles

  1. Kinetic Study on The Molecular Mechanism of Light-driven Inward Proton Transport by Schizorhodopsins
    Yuma Kawasaki, Masae Konno, Keiichi Inoue*. (2022) Biochimica et Biophysica Acta (BBA) - Biomembranes, published on the web
    doi: 10.1016/j.bbamem.2022.184016
  2. Rhodopsin-bestrophin Fusion Proteins from Unicellular Algae form Gigantic Pentameric Ion Channels
    Andrey Rozenberg†, Igor Kaczmarczyk†, Donna Matzov†, Johannes Vierock†, Takashi Nagata, Masahiro Sugiura, Kota Katayama, Yuma Kawasaki, Masae Konno, Yujiro Nagasaka, Mako Aoyama, Ishita Das, Efrat Pahima, Jonathan Church, Suliman Adam, Veniamin A. Borin, Ariel Chazan, Sandra Augustin, Jonas Wietek, Julien Dine, Yoav Peleg, Akira Kawanabe, Yuichiro Fujiwara, Ofer Yizhar, Mordechai Sheves, Igor Schapiro, Yuji Furutani, Hideki Kandori, Keiichi Inoue, Peter Hegemann, Oded Béjà*, Moran Shalev-Benami*. (2022) Nature Structural & Molecular Biology, 29, issue 6, pp 592-603
    doi: 10.1038/s41594-022-00783-x (†: Equally contributed)
  3. Saccharibacteria Harness Light Energy Using Type-1 Rhodopsins That May Rely on Retinal Sourced from Microbial Hosts
    Alexander L. Jaffe†, Masae Konno†, Yuma Kawasaki, Chihiro Kataoka, Oded Béjà, Hideki Kandori, Keiichi Inoue*, Jillian F. Banfield*. (2022) The ISME Journal, published on the web
    doi: 10.1038/s41396-022-01231-w (†: Equally contributed)
  4. Structural Characterization of Proton-pumping Rhodopsin Lacking a Cytoplasmic Proton Donor Residue by X-ray Crystallography
    Kano Suzuki†, María del Carmen Marín†, Masae Konno†, Reza Bagherzadeh, Takeshi Murata*, Keiichi Inoue*. (2022) Journal of Biological Chemistry, published on the web
    doi: 10.1016/j.jbc.2022.101722 (†: Equally contributed)
  5. Structural Basis for Channel Conduction in the Pump-like Channelrhodopsin ChRmine
    Koichiro E. Kishi†, Yoon Seok Kim†, Masahiro Fukuda†, Masatoshi Inoue†, Tsukasa Kusakizako†, Peter Y. Wang†, Charu Ramakrishnan, Eamon F.X. Byrne, Elina Thadhani, Joseph M. Paggi, Toshiki E. Matsui, Keitaro Yamashita, Takashi Nagata, Masae Konno, Sean Quirin, Maisie Lo, Tyler Benster, Tomoko Uemura, Kehong Liu, Mikihiro Shibata, Norimichi Nomura, So Iwata, Osamu Nureki, Ron O. Dror, Keiichi Inoue, Karl Deisseroth*, Hideaki E. Kato*. (2022) Cell, 185, published on the web
    doi: 10.1016/j.cell.2022.01.007 (†: Equally contributed)
  6. Diverse Heliorhodopsins Detected via Functional Metagenomics in Freshwater Actinobacteria, Chloroflexi and Archaea
    Ariel Chazan†, Andrey Rozenberg†, Kentaro Mannen, Takashi Nagata, Ran Tahan, Shir Yaish, Shirley Larom, Keiichi Inoue, Oded Béjà, Alina Pushkarev*. (2022) Environmental Microbiology, published on the web
    doi: 10.1111/1462-2920.15890 (†: Equally contributed)
  7. Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms
    Paul-Adrian Bulzu, Vinicius Silva Kavagutti, Maria-Cecilia Chiriac, Charlotte D. Vavourakis, Keiichi Inoue, Hideki Kandori, Adrian-Stefan Andrei, Rohit Ghai*. (2021) mSphere, 6, Article number: e00661-21
    doi: 10.1128/mSphere.00661-21
  8. Pro219 is an Electrostatic Color Determinant in the Light-driven Sodium Pump KR2
    Yuta Nakajima†, Laura Pedraza-González†, Leonardo Barneschi, Keiichi Inoue, Massimo Olivucci*, Hideki Kandori*. (2021) Communications Biology, 4, Article number: 1185
    doi: 10.1038/s42003-021-02684-z (†: Equally contributed)
  9. Thermostable Light-Driven Inward Proton Pump Rhodopsins
    Yuma Kawasaki, Masae Konno, Keiichi Inoue*. (2021) Chemical Physics Letters,
    779, Article number: 138868
    doi: 10.1016/j.cplett.2021.138868
  10. Crystal Structure of Schizorhodopsin Reveals Mechanism of Inward Proton Pumping
    Akimitsu Higuchi, Wataru Shihoya, Masae Konno, Tatsuya Ikuta, Hideki Kandori, Keiichi Inoue*, Osamu Nureki*. (2021) Proceedings of the National Academy of Sciences of the United States of America, 118, issue 14, Article number: e2016328118
    doi: 10.1073/pnas.2016328118
  11. Exploration of Natural Red-shifted Rhodopsins Using a Machine Learning-based Bayesian Experimental Design
    Keiichi Inoue*, Masayuki Karasuyama, Ryoko Nakamura, Masae Konno, Daichi Yamada, Kentaro Mannen, Takashi Nagata, Yu Inatsu, Hiromu Yawo, Kei Yura, Oded Béjà, Hideki Kandori, Ichiro Takeuchi*. (2021) Communications Biology, 4, Article number: 362
    doi: 10.1038/s42003-021-01878-9
  12. TAT Rhodopsin is an Ultraviolet-Dependent Environmental pH Sensor
    Chihiro Kataoka, Teppei Sugimoto, Shunta Shigemura, Kota Katayama, Satoshi P. Tsunoda, Keiichi Inoue, Oded Béjà, Hideki Kandori*. (2021) Biochemistry, in press
    doi: 10.1021/acs.biochem.0c00951
  13. Active Learning for Level Set Estimation under Input Uncertainty and Its Extensions
    Yu Inatsu, Masayuki Karasuyama, Keiichi Inoue, Ichiro Takeuchi*. (2020) Neural Computation, 32, issue 12, pp 2486-2531
    doi: 10.1162/neco_a_01332
  14. Active Learning of Bayesian Linear Models with High-Dimensional Binary Features by Parameter Confidence-Region Estimation
    Yu Inatsu, Masayuki Karasuyama, Keiichi Inoue, Hideki Kandori, Ichiro Takeuchi*. (2020) Neural Computation, 32, issue 10, pp 1998-2031
    doi: 10.1162/neco_a_01310
  15. Excitonic Coupling Effect on the Circular Dichroism Spectrum of Sodium-pumping Rhodopsin KR2
    Kazuhiro J. Fujimoto*, Keiichi Inoue. (2020) Journal of Chemical Physics, 153, Article number: 045101
    doi: 10.1063/5.0013642
  16. Gate-keeper of Ion Transport ―A Highly Conserved Helix-3 Tryptophan in A Channelrhodopsin Chimera, C1C2/ChRWR
    Yujiro Nagasaka†, Shoko Hososhima†, Naoko Kubo, Takashi Nagata, Hideki Kandori, Keiichi Inoue and Hiromu Yawo*. (2020) Biophysics and physicobiology (BPPB), 17, pp 59-70
    doi: 10.2142/biophysico.BSJ-2020007 (†: Equally contributed)
  17. Schizorhodopsins: A family of Rhodopsins from Asgard Archaea that Function as Light-driven Inward H+ Pumps
    Keiichi Inoue*, Satoshi P. Tsunoda, Manish Singh, Sahoko Tomida, Shoko Hososhima, Masae Konno, Ryoko Nakamura, Hiroki Watanabe, Paul-Adrian Bulzu, Horia L. Banciu, Adrian-Ştefan Andrei, Takayuki Uchihashi, Rohit Ghai, Oded Béjà, Hideki Kandori*. (2020) Science Advances, 6, No. 15, Article number: eaaz2441
    doi: 10.1126/sciadv.aaz2441
  18. Infrared Spectroscopic Analysis on Structural Changes around the Protonated Schiff Base upon Retinal Isomerization in Light-driven Sodium Pump KR2
    Sahoko Tomida, Shota Ito, Tomoya Mato, Yuji Furutani, Keiichi Inoue, Hideki Kandori*. (2020) Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1861, issue 7, Article number: 148190
    doi: 10.1016/j.bbabio.2020.148190
  19. Physical Disuse Contributes to Widespread Chronic Mechanical Hyperalgesia, Tactile Allodynia, and Cold Allodynia through Neurogenic Inflammation and Spino-Parabrachio-Amygdaloid Pathway Activation
    Yusuke Ohmichi†,*, Mika Ohmichi†, Ryoichi Tashima, Koji Osuka, Kaori, Fukushige, Dominika Kanikowska, Yugo Fukazawa, Hiromu Yawo, Makoto Tsuda, Munekazu Naito, Takashi Nakano. (2020) Pain, 161, issue 8, pp 1808-1823
    doi: 10.1097/j.pain.0000000000001867. (†: Equally contributed)
  20. Allosteric Communication to the Retinal Chromophore upon Ion Binding in a Light-driven Sodium Ion Pumping Rhodopsin
    Akihiro Otomo, Misao Mizuno, Keiichi Inoue, Hideki Kandori, Yasuhisa Mizutani*. (2020) Biochemistry, 59, issue 4, pp 520-529
    doi: 10.1021/acs.biochem.9b01062
  21. Optogenetic Analysis of Respiratory Neuronal Networks in The Ventral Medulla of Neonatal Rats Producing Channelrhodopsin in Phox2b-Positive Cells
    Keiko Ikeda, Hiroyuki Igarashi, Hiromu Yawo, Kazuto Kobayashi, Satoru Arata, Kiyoshi Kawakami, Masahiko Izumizaki, Hiroshi Onimaru. (2019) Pflügers Arch, 471, issue 11-12, pp 1419-1439
    doi: 10.1007/s00424-019-02317-9
  22. Crystal Structure of Heliorhodopsin
    Wataru Shihoya, Keiichi Inoue, Manish Singh, Masae Konno, Shoko Hososhima, Keitaro Yamashita, Kento Ikeda, Akimitsu Higuchi, Tamaki Izume, Sae Okazaki, Masanori Hashimoto, Ritsu Mizutori, Sahoko Tomida, Yumeka Yamauchi, Rei Abe-Yoshizumi, Kota Katayama, Satoshi P. Tsunoda, Mikihiro Shibata, Yuji Furutani, Alina Pushkarev, Oded Béjà, Takayuki Uchihashi, Hideki Kandori*, Osamu Nureki*. (2019) Nature, 574, issue 7776, pp 132-136
    doi: 10.1038/s41586-019-1604-6
  23. Unique Photochemistry Observed in a New Microbial Rhodopsin
    Chihiro Kataoka, Keiichi Inoue, Kota Katayama, Oded Béjà, Hideki Kandori*. (2019) The Journal of Physical Chemistry Letters, 10, pp 5117-5121
    doi: 10.1021/acs.jpclett.9b01957
  24. X-ray Crystallographic Structure and Oligomerization of Gloeobacter Rhodopsin
    Takefumi Morizumi†, Wei-Lin Ou†, Ned Van Eps, Keiichi Inoue, Hideki Kandori, Leonid S. Brown, Oliver P. Ernst*. (2019) Scientific Reports, 9, Article number: 11283
    doi: 10.1038/s41598-019-47445-5 (†: Equally contributed)
  25. Engineered Functional Recovery of Microbial Rhodopsin without Retinal-Binding Lysine
    Yumeka Yamauchi, Masae Konno, Daichi Yamada, Kei Yura, Keiichi Inoue, Oded Béjà, Hideki Kandori*. (2019) Photochemistry and Photobiology, 95, pp 1116-1121
    doi: 10.1111/php.13114
  26. Red-shifting Mutation of Light-driven Sodium Pump Rhodopsin
    Keiichi Inoue, María del Carmen Marín, Sahoko Tomida, Ryoko Nakamura, Yuta Nakajima, Massimo Olivucci, Hideki Kandori*. (2019) Nature Communications, 10, Article number: 1993
    doi: 10.1038/s41467-019-10000-x
  27. Casting Light on Asgardarchaeota Metabolism in a Sunlit Microoxic Niche
    Paul-Adrian Bulzu†, Adrian-Ştefan Andrei†, Michaela M. Salcher, Maliheh Mehrshad, Keiichi Inoue, Hideki Kandori, Oded Béjà, Rohit Ghai*, Horia L. Banciu. (2019) Nature Microbiology, 4, issue 7, pp 1129-1137
    doi: 10.1038/s41564-019-0404-y (†: Equally contributed)
  28. Ultrafast Dynamics of Heliorhodopsins
    Shinya Tahara, Manish Singh, Hikaru Kuramochi, Wataru Shihoya, Keiichi Inoue, Osamu Nureki, Oded Béjà, Yasuhisa Mizutani, Hideki Kandori, Tahei Tahara*. (2019) The Journal of Physical Chemistry B, 123, issue 11, pp 2507-2512
    doi: 10.1021/acs.jpcb.9b00887
  29. Heliorhodopsins are Absent in Diderm (Gram-negative) Bacteria: Some Thoughts and Possible Implications for Activity
    José Flores-Uribe†, Gur Hevroni†, Rohit Ghai, Alina Pushkarev, Keiichi Inoue, Hideki Kandori, Oded Béjà*. (2019) Environmental Microbiology Reports, 11, issue 3, pp 419-424
    doi: 10.1111/1758-2229.12730 (†: Equally contributed)
  30. Resonance Raman Investigation of the Chromophore Structure of Heliorhodopsins
    Akihiro Otomo, Misao Mizuno, Manish Singh, Wataru Shihoya, Keiichi Inoue, Osamu Nureki, Oded Béjà, Hideki Kandori, Yasuhisa Mizutani*. (2018) The Journal of Physical Chemistry Letters, 9, issue 22, pp 6431-6436
    doi: 10.1021/acs.jpclett.8b02741
  31. Understanding Colour Tuning Rules and Predicting Absorption Wavelengths of Microbial Rhodopsins by Data-Driven Machine-Learning Approach
    Masayuki Karasuyama†, Keiichi Inoue†, Ryoko Nakamura, Hideki Kandori*, Ichiro Takeuchi*. (2018) Scientific Reports, 8, Article number:15580
    doi: 10.1038/s41598-018-33984-w (†: Equally contributed)

Review articles

  1. Rhodopsins at a Glance
    Takashi Nagata*, Keiichi Inoue*. (2021) Journal of Cell Science, 134, Article number: jcs258989
    doi: 10.1242/jcs.258989
  2. Microbial Rhodopsins: The Last Two Decades
    Andrey Rozenberg†, Keiichi Inoue†, Hideki Kandori, Oded Béjà. (2021) Annual Review of Microbiology, 75, Published on the web
    doi: 10.1146/annurev-micro-031721-020452 (†: Equally contributed)

Books

  1. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins
    Keiichi Inoue* (2021) in Optogenetics − Light-Sensing Proteins and Their Applications in Neuroscience and Beyond (eds. Hiromu Yawo, Hideki Kandori, Amane Koizumi, Ryoichiro Kageyama) pp 89-126 (Springer Nature, 2021)
    doi: 10.1007/978-981-15-8763-4_6
  2. Application of Optogenetics for Muscle Cells and Stem Cells
    Toshifumi Asano, Daniel Boon Loong Teh, Hiromu Yawo* (2021) in Optogenetics − Light-Sensing Proteins and Their Applications in Neuroscience and Beyond (eds. Hiromu Yawo, Hideki Kandori, Amane Koizumi, Ryoichiro Kageyama) pp 359-375 (Springer Nature, 2021)
    doi: 10.1007/978-981-15-8763-4_23

Protocols

  1. Ion Transport Assay of SzRs in E. coli cells
    Masae Konno, Keiichi Inoue*, Hideki Kandori*. (2021) Bio-protocol, bio-protocol.org/prep800

Commentaries

  1. The Third Class of Rhodopsin: Heliorhodopsin
    Keiichi Inoue* (2021) CSJ, Chemistry & Chemical Industry "Division Topics", 74, issue 4, pp 307
  2. Shining Light on Rhodopsin Selectivity: How Do Proteins Decide Whether to Transport H+ or Cl?
    Keiichi Inoue* (2020) The Journal of Biological Chemistry, 295, issue 44, pp 14805-14806
    doi: 10.1074/jbc.H120.016032
  3. A Series of Commentaries for A Symposium Entitled “Session 3SDA - Optogenetics: Applying Photoreceptor for Understanding Biological Phenomena”
    Satoshi P. Tsunoda*, Keiichi Inoue (2020) Biophysical Reviews, 12, issue 2, pp 295-296
    doi: 10.1007/s12551-020-00674-9

Awards

  1. 2019 Sir Martin Wood Prize
    Keiichi Inoue, November 23, 2019