2025年度

• Ueda, M.*, Matsumoto, K., Nomura, T., Takaoka, Y., Okumura, T., Kozaki, W., Hoshikawa, H., Nishizato, Y., Chini, A., Solano, R., Maenaka, K. (2025) A Reactive Antagonist Strategy: Cysteine-directed Covalent Molecular Glue in Plant Hormone Receptor Regulation, Advanced Science, in press. 
  https://doi.org/10.1002/advs.202517463 

•  Nishida, M., Pecorilla, C., Masuya, T.*, Hirano, K., Abe, M, Zdorevskyi, O., Sharma V., Miyoshi, H., and Murai, M.* (2025) Dynamic binding of acetogenin-type inhibitors to mitochondrial complex I revealed by photoaffinity labeling, Biochim. Biophys. Acta (Bioenergetics), 1866, 149566.
  https://doi.org/10.1016/j.bbabio.2025.149566

• Ishikawa-Fukuda, M., Kishikawa, J., Masuya, T., Ito, T., Butler, N. L., McFee, D., Kato, T., Barquera, B., Miyoshi, H., and Murai, M.* (2025) Structural elucidation of the mechanism for inhibitor resistance in the Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae, Biochemistry 64, 1963-1972.
  https://doi.org/10.1021/acs.biochem.5c00069 

• 高岡洋輔

「天然変性領域リデザインによる植物転写因子の選択的制御」

化学と生物, 63, 438-440 (2025) 

 2025年以前の論文 ー植物ホルモンのケミカルバイオロジー関係ー

•  Takaoka, Y.*, Liu, R., Ueda, M. A structure-redesigned intrinsically disordered peptide that selectively inhibits a plant transcription factor in jasmonate signaling (2024), PNAS Nexus 3, pgae312
  https://doi.org/10.1093/pnasnexus/pgae312 

• Hayashi, K., Kato, N., Bashir, K., Nomoto, H., Nakayama, M., Chini, A., Takahashi, S., Saito, H., Watanabe, R., Takaoka, Y., Tanaka, M., Nagano, A.J., Seki, M., Solano, R., Ueda, M.*, (2023) Subtype-selective agonists of plant hormone co-receptor COI1-JAZs identified from the stereoisomers of coronatines, Commun. Biol. 6, 320.

https://doi.org/10.1038/s42003-023-04709-1

• Liu, R., Niimi, H., Ueda, M., Takaoka, Y.* (2022) Coordinately regulated transcription factors EIN3/EIL1 and MYCs in ethylene and jasmonate signaling interact with the same domain of MED25, Biosci. Biotechnol. Biochem. 86, 1405-1412.

https://doi.org/10.1093/bbb/zbac119

• Takaoka, Y.*, Suzuki, K., Nozawa, A., Takahashi, H., Sawasaki, T., Ueda, M.* (2022) Protein-protein interactions between jasmonate-related master regulator MYC and transcriptional mediator MED25 depend on a short binding domain, J. Biol. Chem. 298, 101504 (open access).

https://doi.org/10.1016/j.jbc.2021.101504 

• Suzuki, K., Takaoka, Y.*, Ueda, M.* (2021) Rational design of a stapled JAZ9 peptide inhibiting protein-protein interaction of a plant transcription factor, RSC Chem. Biol. 2, 499-502.

https://doi.org/10.1039/D0CB00204F

• Saito, R., Hayashi, K., Nomoto, H., Nakayama, M., Takaoka, Y., Saito, H., Yamagami, S., Muto, M., Ueda, M.* (2021) Extended JAZ degron sequence for plant hormone binding in jasmonate co-receptor of tomato SlCOI1-SlJAZ, Sci. Rep. 11, 13612 (open access).

https://doi.org/10.1038/s41598-021-93067-1 

•  Y. Takaoka, S. Miyagawa, A. Nakamura, S. Egoshi, S. Tsukiji, M. Ueda* (2020) Hoechst-tagged Fluorescein Diacetate for Fluorescence Imaging-based Assessment of Stomatal Dynamics in Arabidopsis thaliana, Sci. Rep. 10, 5333 (open access).

https://doi.org/10.1038/s41598-020-62239-w 

•  Takaoka, Y.,* Nagumo, K., Azizah, I. N., Oura, S., Iwahashi, M., Kato, N., Ueda, M.* (2019) A comprehensive in vitro fluorescence anisotropy assay system for screening ligands of the jasmonate COI1-JAZ co-receptor in plants, J. Biol. Chem., 294, 5074-5081.
  https://doi.org/10.1074/jbc.RA118.006639 

• Takaoka, Y., Iwahashi, M., Chini, A., Saito, H., Ishimaru, Y., Egoshi, S., Kato, N., Tanaka, M., Bashir, K., Seki, M., Solano, R., Ueda, M.* (2018) A rationally designed JAZ subtype-selective agonist of jasmonate perception, Nat. Commun., 9, 3654.
  https://doi.org/10.1038/s41467-018-06135-y 

• Takaoka, Y., Shigenaga, M., Nukadzuka, Y., Imai, M., Ishimaru, Y., Saito, K., Yokoyama, R., Nishitani, K., Ueda, M.* (2016) Protein Ligand-tethered Synthetic Calcium Indicator for Localization Control and Spatiotemporal Calcium Imaging in Plant Cells, Bioorg. Med. Chem. Lett., 26, 9-14.
  https://doi.org/10.1016/j.bmcl.2015.11.055 

その他、過去の主要論文

• Takaoka, Y., Uchinomiya, S., Kobayashi, D., Engo, M., Hayashi, T., Fukuyama, Y., Hayasaka, H., Miyasaka, M., Ueda, T., Shimada, I., Hamachi, I.* (2018) Endogenous Membrane Receptor Labeling by Reactive Cytokines and Growth Factors to Chase Their Dynamics in Live Cells, Chem (Cell press), 4, 1451-1464.

• Takaoka, Y., Nishikawa, Y., Hashimoto, Y., Sasaki, K., Hamachi, I.* (2015) Ligand-directed Dibromophenyl Benzoate Chemistry for Rapid and Selective Acylation of Intracellular Natural Proteins, Chem. Sci., 6, 3217-3224.

• Yoshii, T., Mizusawa, K., Takaoka, Y.,* Hamachi, I.* (2014) Intracellular Protein-responsive Supramolecules; Protein Sensing and In-cell Construction of Inhibitor Assay System, J. Am. Chem. Soc., 136, 16635-16642 (2014).

•  Asanuma, D.** Takaoka, Y.,** Namiki, S., Takikawa, K., Nagano, T., Urano, Y., Hirose, K.* (2014) Acidic-pH-Activatable Fluorescence Probes for Visualizing Exocytosis Dynamics, Angew. Chem. Int. Ed., 53, 6085-6089.  (** Co-first author)

• Takaoka, Y., Kioi, Y., Morito, A., Otani, J., Arita, K., Ashihara, E., Ariyoshi, M., Tochio, H., Shirakawa, M., Hamachi, I.* (2013) Quantitative comparison of protein dynamics in live cells and in vitro by in-cell 19F-NMR, Chem. Commun., 49, 2801-2803.

• Mizusawa, K., Takaoka, Y., Hamachi, I.* (2012) Specific Cell Surface Protein Imaging by Extended Self-Assembling Fluorescent Turn-on Nanoprobes, J. Am. Chem. Soc., 134, 13386-13395.

• Takaoka, Y., Kiminami, K., Mizusawa, K., Matsuo, K., Narazaki, M., Matsuda, T., Hamachi, I.* (2011) Systematic Study of Protein Detection Mechanism of Self-assembling 19F NMR/MRI Nanoprobes toward Rational Design and Improved Sensitivity, J. Am. Chem. Soc., 133, 11725-11731.

• Takaoka, Y., Sakamoto, T., Tsukiji, S., Narazaki, M., Matsuda, T., Tochio, H., Shirakawa, M., Hamachi, I.* (2009) Self-assembling nano-probes displaying off/on 19F NMR signals for protein detection and imaging, Nat. Chem., 1, 557-561.

• Tsukiji, S., Miyagawa, M., Takaoka, Y., Tamura, T., Hamachi, I.* (2009) Ligand-directed tosyl chemistry for protein labeling in vivo, Nat. Chem. Biol., 5, 341-343.

• Takaoka, Y., Tsutsumi, H., Kasagi, N., Nakata, E., Hamachi, I.* (2006) One-pot and sequential organic chemistry on an enzymatic surface to tether a fluorescent probe at the proximity of the active site with restoring enzyme activity, J. Am. Chem. Soc. 128, 3273-3280.

 2025年以前の論文　ー呼吸鎖電子伝達酵素のケミカルバイオロジー関連ー

•  Miyachi, S., Tanaka, H., Ishikawa, M., Mcfee, D., Aoki, W., Murai, M., Barquera, B., Miyoshi, H., and Masuya, T.* (2025) Pinpoint introduction of functional molecular probe into the NqrB subunit of Na+-translocating NADH-ubiquinone oxidoreductase from Vibrio cholerae, Biochim. Biophys. Acta (Bioenergetics) 1866, 149551.

• Mizutani, M., Kuroda, S., Oku, M., Aoki, W., Masuya, T., Miyoshi, H., and Murai, M.* (2024) Identification of proteins involved in intracellular ubiquinone trafficking in Saccharomyces cerevisiae using artificial ubiquinone probe, Biochim. Biophys. Acta (Bioenergetics) 1865, 149147 (open access).

• Otani, R., Masuya, T., Miyoshi H., and Murai M.* (2024) Mitochondrial respiratory complex I can be inhibited via bypassing the ubiquinone-accessing tunnel, FEBS Lett. 598, 1989-1995 (open access).

• Ikunishi, R., Otani, R., Masuya, T., Shinzawa-Itoh, K., Shiba, T., Murai, M., and Miyoshi, H.* (2023) Respiratory complex I in mitochondrial membrane catalyzes oversized ubiquinones, J. Biol. Chem. 299, 105001 (open access).

• Uno, S., Masuya, T., Zdorevskyi, O., Ikunishi, R., Shinzawa-Itoh, K., Lasham, J., Sharma, V., Murai, M., and Miyoshi, M.* (2022) Diverse reaction behaviors of artificial ubiquinones in mitochondrial respiratory complex I, J. Biol. Chem. 298, 102075 (open access).

• Kishikawa, J., Ishikawa, M., Masuya, T., Murai, M., Kitazumi, Y., Butler, N. L., Kato, T., Barquera, B., and Miyoshi, H.* (2022) Cryo-EM structures of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae, Nat. Commun. 13, 4082 (open access).

• Unten, Y., Murai, M.*, Sakai, K., Asami, Y., Yamamoto, T., Masuya, T., and Miyoshi, H. (2021) Natural tetramic acids elicit multiple inhibitory actions against mitochondrial machineries presiding over oxidative phosphorylation, Biosci. Biotechnol. Biochem. 85, 2368-2377.

• Masuya, T., Uno, S., Murai, M., and Miyoshi, H.* (2021) Pinpoint dual chemical cross-linking explores structural dynamics of the ubiquinone reaction site in mitochondrial complex I, Biochemistry 60, 813-824.

• Masuya, T., Sano, Y., Tanaka, H., Butler, N. L., Ito, T., Tosaki, T., Morgan, J. E., Murai, M., Barquera, B., and Miyoshi, H.* (2020) Inhibitors of a Na+-pumping NADH-ubiquinone oxidoreductase play multiple roles to block enzyme function, J. Biol. Chem. 295, 12739-12754 (open access).