木村 ゆり 研究室

ゲノム機能生化学研究室は、2023年9月に設立しました。植物の細胞壁成分 リグニン および関連芳香族化合物を対象に、その生合成や構造多様性に起因する進化の分子メカニズムを、生化学的手法を中心とした解析を通じて調べています。また、得られる知見をリグニンの有効利用や芳香族有用物質の高生産に役立てることを目指します。

Kimura Lab (Functional Genomics and Biochemistry)

We study the biosynthetic diversity and evolution of the plant cell wall polymer lignin and related aromatic compounds.

The structure of lignin has undergone significant evolution throughout the development of land plants, playing a crucial role in providing mechanical strength and facilitating water transportation for plant development. Our research is centered on uncovering the molecular mechanisms underlying the evolutionary diversification in lignin biosynthesis. We utilize a combination of in silico analysis and various biochemical and chemical assays, guided by genomic resources from a variety of plants. The insights gained from this research aim to provide fundamental knowledge for engineering plant metabolism, ultimately contributing to the efficient production of valuable aromatics derived from plants.

成果

論文

New!  Yuri Takeda-Kimura, Tetsuya Mori, Shiro Suzuki, Masahiro Sakamoto, Kazuki Saito, Ryo Nakabayashi, Yuki Tobimatsu, Toshiaki Umezawa. (2025) Altered development and lignin deposition in rice p-COUMAROYL ESTER 3-HYDROXYLASE loss-of-function mutants. The Plant Journal 121: e70039. doi: https://onlinelibrary.wiley.com/doi/10.1111/tpj.70039

New!  Songkui Cui, Yuri Takeda-Kimura, Takanori Wakatake, Jun Luo, Yuki Tobimatsu, Satoko Yoshida. (2025) Striga hermonthica induces lignin deposition at the root tip to facilitate prehaustorium formation and obligate parasitism. Plant Communications 101294-101294.  

2024年

New!  Yuri Takeda-Kimura, Bethany Moore, Samuel Holden, Sontosh K. Deb, Matt Barrett, David Lorence, Marcos V. V. de Oliveira, Jane Grimwood, Melissa Williams, Lori Beth Boston, Jerry Jenkins, Christopher Plott, Shengqiang Shu, Kerrie Barry, David M. Goodstein, Jeremy Schmutz, Matthew J. Moscou, Michael R. McKain, James H. Leebens-Mack, Hiroshi A. Maeda. (2024) Genomes of Poaceae sisters reveal key metabolic innovations preceding the emergence of grasses. bioRxiv. doi: https://doi.org/10.1101/2024.11.06.622220.

2023年

El-Azaz J., Moore B., Takeda-Kimura Y., Yokoyama R., Wijesingha Ahchige M., Chen X., Schneider M., Maeda H.A. (2023) Coordinated regulation of the entry and exit steps of aromatic amino acid biosynthesis supports the dual lignin pathway in grasses. Nature Commun. 14, 7242

Lam P.-Y., Tobimatsu Y., Suzuki S., Tanaka T., Yamamoto S., Takeda-Kimura Y., Osakabe Y., Osakabe K., Ralph J., Bartley L.E., Umezawa T. Disruption of p-Coumaroyl-CoA:monolignol transferases in rice drastically alters lignin composition. Plant Physiology (2024) 194: 832–848.

2022年

Martin A.F., Tobimatsu Y., Lam P.-Y., Matsumoto N., Tanaka T., Suzuki S., Kusumi R., Miyamoto T., Takeda-Kimura Y., Yamamura M., et al. Lignocellulose molecular assembly and deconstructions of lignin-altered CAldOMT- and CAD-deficient rice mutants. Plant Physiolosy (2022) 191:70-86

Yokoyama R., de Oliveira M.V.V., Takeda-Kimura Y., Ishihara H., Alseekh S., Arrivault S., Kukshal V., Jez J.M., Stitt M., Fernie A.R., Maeda H.A. Point mutations that boost aromatic amino acid production and CO2 assimilation in plants. Science Advances (2022) 8:23.

2021年

Lam P.-Y., Wang L., Lui A.C.W., Liu H., Takeda-Kimura Y., Chen M.-X., Zhu F.-Y., Zhang J., Umezawa T., Tobimatsu Y., Lo C. (2021) Altered flavonoid and lignin profiles in rice mutants deficient in CHS, CHI, and CHIL genes. Plant Physiology, 188:1993-2011.

2019年

Yuri Takeda, Yuki Tobimatsu, Masaomi Yamamura, Toshiyuki Takano, Masahiro Sakamoto, Toshiaki Umezawa. (2019) Comparative evaluations of lignocellulose reactivity and usability in transgenic rice plants with altered lignin composition. Journal of Wood Science, 65, 6.

Pui Ying Lam, Yuki Tobimatsu, Naoyuki Matsumoto, Shiro Suzuki, Wu Lan, Yuri Takeda, Masaomi Yamamura, Masahiro Sakamoto, John Ralph, Clive Lo, Toshiaki Umezawa. (2019) OsCAldOMT1 is a bifunctional O-methyltransferase involved in the biosynthesis of tricin-lignins in rice cell walls. Sci Rep., 9:11597.

Takuji Miyamoto, Rie Takada, Yuki Tobimatsu, Yuri Takeda, Shiro Suzuki, Masaomi Yamamura, Keishi Osakabe, Yuriko Osakabe, Masahiro Sakamoto, Toshiaki Umezawa. (2019) OsMYB108 loss-of-function enriches p-coumaroylated and tricin lignin units in rice cell walls. The Plant Journal, 98: 975-987.

Yuri Takeda, Shiro Suzuki, Yuki Tobimatsu, Keishi Osakabe, Yuriko Osakabe, Safendrri Komara Ragamustari, Masahiro Sakamoto, Toshiaki Umezawa. (2019) Lignin characterization of rice CONIFERALDEHYDE 5-HYDROXYLASE loss-of-function mutants generated with the CRISPR/Cas9 system. The Plant Journal, 97, 543-554.

Pui Ying Lam, Andy Lui, Masaomi Yamamura, Lanxiang Wang, Yuri Takeda, Shiro Suzuki, Hongjia Liu, Fu-Yuan Zhu, Mo-Xian Chen, Jian-Hua Zhang, Toshiaki Umezawa, Yuki Tobimatsu, Clive Lo. (2019) Recruitment of specific flavonoid B-ring hydroxylases for two independent biosynthesis pathways of flavone-derived metabolites in grasses. New Phytologist 223: 2014-219.

J. Musembi Mutuku, Songkui Cui, Chiaki Hori, Yuri Takeda, Yuki Tobimatsu, Ryo Nakabayashi, Tetsuya Mori, Kazuki Saito, Taku Demura, Toshiaki Umezawa, Satoko Yoshida, Ken Shirasu. (2019) Structural integrity of deposited lignin at the site of infection is crucial for resistance against Striga hermonthica in rice. Plant Physiology, 179: 1796-1809.

2018年

Yuri Takeda, Yuki Tobimatsu, Steven D. Karlen, Taichi Koshiba, Shiro Suzuki, Masaomi Yamamura, Shinya Murakami, Mai Mukai, Takefumi Hattori, Keishi Osakabe, John Ralph, Masahiro Sakamoto, Toshiaki Umezawa. (2018) Downregulation of p-COUMAROYL ESTER 3-HYDROXYLASE in rice leads to altered cell wall structures and improves biomass saccharification. The Plant Journal, 95, 796–811.

Songkui Cui, Syogo Wada, Yuki Tobimatsu, Yuri Takeda, Simon B. Saucet, Toshiyuki Takano, Toshiaki Umezawa, Ken Shirasu, Satoko Yoshida. (2018) Host lignin composition affects haustorium induction in the parasitic plants Phtheirospermum japonicum and Striga hermonthica. New Phytologist, 218, 710–723.

2017年

Yuri Takeda, Taichi Koshiba, Yuki Tobimatsu, Shiro Suzuki, Shinya Murakami, Masaomi Yamamura, Md. Mahabubur Rahman, Toshiyuki Takano, Takefumi Hattori, Masahiro Sakamoto, Toshiaki Umezawa. (2017) Regulation of CONIFERALDEHYDE 5-HYDROXYLASE expression to modulate cell wall lignin structure in rice. Planta, 246, 337-349.

Pui Ying Lam, Yuki Tobimatsu, Yuri Takeda, Shiro Suzuki, Masaomi Yamamura, Toshiaki Umezawa, Clive Lo. (2017) Disrupting Flavone Synthase II alters lignin and improves biomass digestibility. Plant Physiology, 174, 972–985.

総説及び著書

New!  Monica Borghi and Yuri Takeda-Kimura (2024) Synthesis and physiological function of lignin in the reproductive structures of angiosperms. Photochemistry Reviews, doi: https://doi.org/10.1007/s11101-024-10043-z.

木村　ゆり, 堤　祐司　（2024年） 芳香族アミノ酸の生合成, 福島和彦, 船田良, 杉山淳司, 高部圭司, 梅澤俊明, 山本浩之 編：木質の形成 第３版, 海青社, 第4章 第4節 395-400 ISBN：978-4-86099-374-0

Toshiaki Umezawa, Kenji Umemura, Masaru Kobayashi, Takuji Miyamoto, Rie Takada, Yuri Takeda-Kimura, Masaomi Yamamura. (2023) Sustainable production and utilization of grass biomass in deteriorated glasslands in Indonesia. In: Akihisa Mori, Alin Halimatussadiah (Eds.) The clinate-energy-land nexus in Indonesia. Routledge, pp 133-143.

Toshiaki Umezawa, Yuki Tobimatsu, Masaomi Yamamura, Takuji Miyamoto, Yuri Takeda, Taichi Koshiba, Rie Takada, Pui Ying Lam, Shiro Suzuki, Masahiro Sakamoto. (2020) Lignin metabolic engineering in grasses for primary lignin valorization. Lignin, 1:30-41.