Research Results - Associated research group

*Corresponding author, #These authors contributed equally to this work.
Underlines denote the study representative, and dotted underlines denote research team members

 
Arimura group Ashikari group Buzas Group Fujii group
Kanaoka group Kawasaki group Kiba group Kimura group
Matsushita group Miura group Nagano group Notaguchi group
Saijo group Seki group Suzaki group Takahashi group
Takezawa group Uchida group Yamaguchi group

Arimura group

  • -2017-
    Original papers
    Nemoto, K., Ramadan, A., Arimura, G., Imai, K., Tomii, K., Shinozaki, K., and Sawasaki, T. (2017) Tyrosine phosphorylation of the GARU E3 ubiquitin ligase promotes gibberellin signalling by preventing GID1 degradation. Nat. Commun., 8, 1004. (15 pages)
    https://www.nature.com/articles/s41467-017-01005-5
    Ozawa, R., Endo, H., Iijima, M., Sugimoto, K., Takabayashi, T., Gotoh, T. and Arimura, G. (2017) Intraspecific variation among Tetranychid mites for ability to detoxify and to induce plant defenses. Sci. Rep., 7, 43200.
    https://www.nature.com/articles/srep43200
    Review papers
    Yazaki, K., Arimura, G., Ohnishi, T. (2017) 'Hidden' terpenoids in plants: their biosynthesis, localisation and ecological roles. Plant Cell Physiol., 58, 1615-1621.
    https://academic.oup.com/pcp/article/58/10/1615/4096626
    Books
    Arimura, G. and Pearse, I. (2017) From the lab bench to the forest: ecology and defence mechanisms of volatile-mediated "talking trees." In "Advances in Botanical Research vol. 82. Communication between Plants, and between Plants and Other Organisms" edited by Becard, G. Elsevier, in press.
  • -2016-
    Books
    Arimura, G. and Maffei, M. E. (2016) Plant specialized metabolism: genomics, biochemistry, and biological functions. CRC Press, Boca Raton, FL, USA, 376.
    Arimura, G. and Maffei, M. E. (2016) Introduction to plant specialized metabolism. In "Plant Specialized Metabolism: Genomics, Biochemistry, and Biological Functions" edited by Arimrua, G. and Maffei, M.E. CRC Press, 1-7.
    Arimura, G., Matsui, K., Koeduka, T., Holopainen, J.K. (2016) Biosynthesis and regulation of plant volatiles, and their functional roles in ecosystem interactions and global environmental changes. In "Plant Specialized Metabolism: Genomics, Biochemistry, and Biological Functions" edited by Arimrua, G. and Maffei, M.E. CRC Press, 185-237.

Ashikari group

  • -2017-
    Original papers
    Bessho-Uehara, K., Furuta, T., Masuda, K., Yamada, S., Angeles-Shim, R., Ashikari, M., *Takashi, T. (2017) Construction of rice chromosome segment substitution lines harboring Oryza barthii genome and evaluation of yield-related traits. Breeding Science, in press.
    Gamuyao, R., Nagai, K., Ayano, M., Mori, Y., Minami, A., Kojima, M., Suzuki, T., Sakakibara, H., Higashiyama, T., Ashikari, M., *Reuscher, S. (2017) Hormone distribution and transcriptome profiles in bamboo shoots provide insights on bamboo stem emergence and growth. Plant Cell Physiol., 58, 702-716.
    https://www.ncbi.nlm.nih.gov/pubmed/28204696
  • -2016-
    Original papers
    Furuta, T., Bessho-Uehara, K., Angeles-Shim, R., Shim, J., Nagai, K., Ashikari, M.,*Takashi, T. (2016) Development of chromosome segment substitution lines harboring Oryza nivara genomic segments in Koshihikari and evaluation of yield-related traits. Breeding Science, 66, 845-850.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282765/
    *Kanako Bessho- Uehara, *Diane R. Wang, Tomoyuki Furuta, Anzu Minami, Keisuke Nagai, Rico Gamuyao, Kenji Asano, Rosalyn B. Angeles-Shim, Yoshihiro Shimizu, Madoka Ayano, Norio Komeda, Kazuyuki Doi, Kotaro Miura, Yosuke Toda, Toshinori Kinoshita, Satohiro Okuda, Tetsuya Higashiyama, Mika Nomoto, Yasuomi Tada, Hidefumi Shinohara, Yoshikatsu Matsubayashi, Anthony Greenberg, Jianzhong Wu, Hideshi Yasui, Atsushi Yoshimura, Hitoshi Mori, Susan R. McCouch & Motoyuki Ashikari (2016) Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice, PNAS, 113, 8969-8974.
    http://www.pnas.org/content/early/2016/07/26/1604849113

Buzas Group

Fujii group

Kawasaki group

  • -2016-
    Original papers
    Yamada, K., Yamaguchi, K., Shirakawa, T., Nakagami, H., Mine, A., Ishikawa, K., Fujiwara, M., Narusaka, M., Narusaka, Y., Ichimura, K., Kobayashi, Y., Matsui, H., Nomura, Y., Nomoto, M., Tada, Y., Fukao, Y., Fukamizo, T., Tsuda, K., Shirasu, K., Shibuya, N., and *Kawasaki, T. (2016) The Arabidopsis CERK1-associated kinase PBL27 connects chitin perception to MAPK activation. EMBO J., 35, 2468-2483.
    http://emboj.embopress.org/content/early/2016/09/26/embj.201694248

Kiba group

  • -2017-
    Original papers
    Pudasaini, A., Shim, J. S., Song, Y. H., Shi, H., Kiba, T., Somers, D. E., Imaizumi, T., and *Zoltowski, D. E. (2017) Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis. eLIFE, 6, e21646 (27 pages).
    https://elifesciences.org/articles/21646#abstract
    Osugi, O., Kojima, M., Takebayashi, Y., Ueda, N., Kiba, T., and *Sakakibara, H. (2017) Systemic transport of trans-zeatin and its precursor have differing roles in Arabidopsis shoots. Nature Plants, 3 , 17112.
    https://www.nature.com/articles/nplants2017112
    #Spallek, T., #Melnyk, C., W., Wakatake, T., Zhang, J., Sakamoto, Y., Kiba, T., Yoshida, S., Matsunaga, S., Sakakibara, H. and *Shirasu, K. (2017) Inter-species hormonal control of host root morphology by parasitic plants. Proc. Natl. Acad. Sci. USA, 114, 5283-5288.
    http://www.pnas.org/content/114/20/5283
  • -2016-
    Original papers
    *Takatoshi Kiba and Rossana Henriques (2016) Assessing protein stability under different light and circadian conditions. Methods Mol. Biol., 398, 141-152.
    https://www.ncbi.nlm.nih.gov/pubmed/26867622
    *Norihito Nakamichi, Saori Takao, Toru Kudo, Takatoshi Kiba, Yin Wang, Toshinori Kinoshita, and Hitoshi Sakakibara (2016) Improvement of Arabidopsis biomass and cold-, drought-, and salinity-stress tolerance by modified circadian clock-associated PSEUDO-RESPONSE REGULATORs. Plant Cell Physiol., 57, 1085-1097.
    http://pcp.oxfordjournals.org/content/57/5/1085.long
    Review papers
    *Takatoshi Kiba and *Anne Krapp (2016) Plant nitrogen acquisition under low availability: regulation of uptake and root architecture. Plant Cell Physiol., 57, 707-714.
    http://pcp.oxfordjournals.org/content/57/4/707.full?sid=2e7034da-c8fb-496b-b1ef-fa15bf698b86

Kimura group

  • -2018-
    Original papers
    #Uchida, N., #Takahashi, K., Iwasaki, R., Yamada, R., Yoshimura, M., Endo, T. A., Kimura, S., Zhang, H., Nomoto, M., Tada, Y., Kinoshita, T., Itami, K., *Hagihara, S., and *Torii, K. U. (2018). Chemical hijacking of auxin signaling with an engineered auxin-TIR1 pair. Nat. Chem. Biol., in press.
    https://www.nature.com/articles/nchembio.2555
  • -2017-
    Original papers
    Yoshiyama, K. O., Kaminoyama, K., Sakamoto, T., and *Kimura, S. (2017) Increased phosphorylation of Ser-Gln sites on SUPPRESSOR OF GAMMA RESPONSE 1 strengthens the DNA damage response in Arabidopsis thaliana. Plant Cell, in press.
    http://www.plantcell.org/content/early/2017/12/05/tpc.17.00267
    *Nakamasu, A., Suematsu, N. J., and Kimura, S. (2017) Asymmetries in leaf branch are associated with differential speeds along growth axes: A theoretical prediction. Developmental Dynamics, in press.
    http://onlinelibrary.wiley.com/doi/10.1002/dvdy.24587/full
    Kawakatsu, Y., Nakayama, H., Kaminoyama, K., Igarashi, K., Yasugi, M., Kudoh, H., Nagano A. J., Yano K, Kubo N, and Kimura, S. (2017) A GLABRA1 ortholog on LG A9 controls trichome number in the Japanese leafy vegetables Mizuna and Mibuna (Brassica rapa subsp. Nipposinicai L. H. Bailey): evidence from QTL analysis. Journal of Plant Research, 130, 539-550.
    https://www.ncbi.nlm.nih.gov/pubmed/28258381
    Review papers
    Nakayama, H., Sinha, N., and *Kimura, S. (2017) How do plants and phytohormones accomplish heterophylly, leaf phenotypic plasticity, in response to environmental cues. Front. Plant Sci., 8, 1717 (7 pages).
    https://www.frontiersin.org/articles/10.3389/fpls.2017.01717/full

Matsushita group

  • -2017-
    Original papers
    #Ushijima, T., #Hanada, K., Gotoh, E., Yamori, W., Kodama, Y., Tanaka, H., Kusano, M., Fukushima, A., Tokizawa, M., Yamamoto, Y. Y., Tada, Y., Suzuki, Y., and *Matsushita, T. (2017) Light controls protein localization through phytochrome-mediated alternative promoter selection. Cell, 171, 1316-1325.
    http://www.sciencedirect.com/science/article/pii/S0092867417312400

Miura group

  • -2017-
    Original papers
    Shimatani, Z., Kashojiya, S., Takayama, M., Terada, R., Arazoe, T., Ishii, H., Teramura, H., Yamamoto, T., Komatsu, H., Miura, K., Ezura, H., Nishida, K., Ariizumi, T., and Kondo, A. (2017) Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nat. Biotechnol., 35, 441-443.
    http://www.nature.com/nbt/journal/v35/n5/abs/nbt.3833.html?lang=en
  • -2016-
    Original papers
    Lin XL, Niu D, Hu ZL, Kim DH, Jin YH, Cai B, Liu P, Miura K, Yun DJ, Kim WY, Lin R, and *Jin JB (2016) An Arabidopsis SUMO E3 ligase, SIZ1 negatively regulates photomorphogenesis by promoting COP1 activity. PLoS Genet. 12, e1006016.
    http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006016
    *Kitajima, S., *Miura, K., Aoki, W., Yamato, K. T., Taira, T., Murakami, R., and Aburaya, S. (2016) Transcriptome and proteome analyses provide insight into laticifer's defense of Euphorbia tirucalli against pests. Plant Physiol. Biochem., 108, 434-446.
    https://www.ncbi.nlm.nih.gov/pubmed/27566924

Nagano group

  • -2017-
    Original papers
    Iwayama, K., Aisaka, Y., Kutsuna, N., *Nagano, A. J. (2017) FIT: Statistical modeling tool for transcriptome dynamics under fluctuating field conditions. Bioinformatics, 33, 1672-1680.
    https://www.ncbi.nlm.nih.gov/pubmed/28158396
  • -2016-
    Original papers
    #*Hoshino, A., #Jayakumar, V., Nitasaka, E., Toyoda, A., Noguchi, H., Itoh, T., Shin-I, T., Minakuchi, Y., Koda, Y., Nagano, A. J., Yasugi, M., Honjo, M., Kudoh, H., Seki, M., Kamiya, A., Shiraki, T., Carninci, P., Asamizu, E., Nishide, H., Tanaka, S., Park, K.I., Morita, Y., Yokoyama, K., Uchiyama, I., Tanaka, Y., Tabata, S., Shinozaki, K., Hayashizaki, Y., Kohara, Y., Suzuki, Y., Sugano, S., Fujiyama, A., Iida, S. and *Sakakibara, Y. (2016) Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nat. Commun., 7, 13295. (10 pages)
    http://www.nature.com/articles/ncomms13295

Notaguchi group

  • -2016-
    Original papers
    #*Kasahara, R. D., #Notaguchi, M., Nagahara, S., Suzuki, T., Susaki, D., Honma, Y., Maruyama, D., Higashiyama, T. (2016) Pollen tube contents initiate ovule enlargement and enhance seed coat development without fertilization. Sci. Adv., 2, e1600554 (7 pages).
    http://advances.sciencemag.org/content/2/10/e1600554.full

Saijo group

  • -2018-
    Review papers
    *Saijo, Y., Loo, E. P., and Yasuda, S. (2018) Pattern recognition receptors and signaling in plant-microbe interactions. Plant J., in press.
  • -2017-
    Original papers
    Ariga, H., Katori, T., Tsuchimatsu, T., Hirase, T., Tajima, Y., Parker, J. E., Alcázar R, Koornneef, M., Hoekenga, O., Lipka, A. E., Gore, M. A., Sakakibara, H., Kojima, M., Kobayashi, Y., Iuchi, S., Kobayashi, M., Shinozaki, K., Sakata, Y., Hayashi, T., Saijo, Y., and *Taji, T. (2017) NLR locus-mediated trade-off between abiotic and biotic stress adaptation in Arabidopsis. Nature Plants, 3, 17072 (8 pages).
    https://www.nature.com/articles/nplants201772
    Review papers
    #Yasuda, S., #Okada, K., and *Saijo, Y. (2017) A look at plant immunity through the window of the multitasking coreceptor BAK1. Curr. Opin. Plant Biol., 38, 10-18.
    http://www.sciencedirect.com/science/article/pii/S1369526617300110?via%3Dihub

Seki group

  • -2018-
    Books
    *Nakaminami, K. and Seki, M. (2018) RNA regulation in plant cold stress response. In "Survival Strategies in Extreme Cold and Desiccation: Adaptation Mechanisms and their Application" edited by Drs. Iwaya-Inoue, M., Uemura, M. and Sakurai, M. Springer Japan, in press.
    Matsui, A. and *Seki, M. (2018) Analysis of lncRNAs in plant abiotic stress responses. In "Methods in Molecular Biology - Plant lncRNAs -" edited by Drs. Chekanova, J. and Wang, H. L. Springer, in press.
  • -2017-
    Original papers
    Ueda, M., Matsui, A., Tanaka, M., Nakamura, T., Abe, T., Sako, K., Sasaki, T., Kim, J.M., Ito, A., Nishino, N., Shimada, H., Yoshida, M. and *Seki, M. (2017) The distinct roles of class I and II RPD3-like histone deacetylases in salinity stress response. Plant Physiol., in press.
    http://www.plantphysiol.org/content/early/2017/10/10/pp.17.01332.long
    Li, W., Nguyen, K., Chu, D.H., Ha, C.V., Watanabe, Y., Osakabe, Y., Leyva-Gonzalez, M., Sato, M., Toyooka, K., Voges, L., Tanaka, M., Seki, M., Seo, M., Yamaguchi, S., Nelson, D., Herrera-Estrella, L. and *Tran, L.S. (2017) The karrikin receptor KAI2 promotes drought resistance in Arabidopsis thaliana. PLoS Genet., 13:e1007076 (23 pages).
    http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007076
    Shirai, K., Matsuda, F., Nakabayashi, R., Okamoto, M., Tanaka, M., Fujimoto, A., Shimizu, M., Shinozaki, K., Seki, M., Saito, K. and *Hanada, K. (2017) A highly specific genome-wide association study integrated with transcriptome data reveals the contribution of copy number variations to specialized metabolites in Arabidopsis thaliana accessions. Mol. Biol. Evol., 34, 3111-3122.
    https://academic.oup.com/mbe/article-abstract/34/12/3111/4110007?redirectedFrom=fulltext
    Matsui, A., Iida, K., Tanaka, M., Yamaguchi, K., Mizunashi, K., Kim, J. M., Takahashi, S., Kobayashi, N., Shigenobu, S., Shinozaki, K. and *Seki, M. (2017) Novel stress-inducible antisense RNAs of protein-coding loci are synthesized by RNA-dependent RNA polymerase. Plant Physiol., 175, 457-472.
    http://www.plantphysiol.org/content/175/1/457.long
    Nguyen, C. C., Nakaminami, K., Matsui, A., Watanabe, S., Kanno, Y., Seo, M. and *Seki, M. (2017) Overexpression of oligouridylate binding protein 1b results in ABA hypersensitivity. Plant Signal. Behav., 12, e1282591.
    https://www.ncbi.nlm.nih.gov/pubmed/28112571
    Patanun, O., Ueda, M., Itouga, M., Kato, Y., Utsumi, Y., Matsui, A., Tanaka, M., Utsumi, C., Sakakibara, H., Yoshida, M., Narangajavana, J., and *Seki, M. (2017) The histone deacetylase inhibitor suberoylanilide hydroxamic acid alleviates salinity stress in cassava. Front. Plant Sci, 7, 2039.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5220070/
    #Kurita,K., #Sakamoto,T., Yagi, N., Sakamoto, Y., Ito, A., Nishino, N., Sako,K., Yoshida, M., Kimura, H., Seki, M. and *Matsunaga, S. (2017) Live imaging of H3K9 acetylation in plant cells. Sci. Rep., 7, 45894 (9 pages).
    https://www.nature.com/articles/srep45894
    Books
    Nakaminami, K. and Seki, M. (2017) RNA regulation in plant cold stress response. In "Survival Strategies in Extreme Cold and Desiccation: Adaptation Mechanisms and their Application" edited by Drs. Mari Iwaya-Inoue, Matsuo Uemura and Minoru Sakurai. Springer Japan, in press.
    Bashir, K., Rasheed, S., Matsui, A., Iida, K., Tanaka, M. and *Seki, M. (2017) Monitoring transcriptomic changes in soil-grown roots and shoots of Arabidopsis thaliana subjected to a progressive drought stress. In "Methods in Molecular Biology - Root Development" edited by Drs. Elke Barbez and Daniela Ristova, in press.

Suzaki group

  • -2018年-
    Original papers
    Nishida, H., Tanaka, S., Handa, Y., Ito, M., Sakamoto, Y., Matsunaga, S., Betsuyaku, S., Miura, K., Soyano, T., Kawaguchi, M., and *Suzaki, T. (2018) A NIN-LIKE PROTEIN mediates nitrate-induced control of root nodule symbiosis in Lotus japonicus. Nat. Commun., 9, 499. (14 pages)
    https://www.nature.com/articles/s41467-018-02831-x
  • -2016-
    Original papers
    Nishida, H., Handa, Y., Tanaka, S., *Suzaki, T. and *Kawaguchi, M. (2016) Expression of the CLE-RS3 gene suppresses root nodulation in Lotus japonicus. J. Plant Res., 129, 909-919.
    http://link.springer.com/article/10.1007%2Fs10265-016-0842-z
    Pfeiffer, A., Janocha, D., Dong, Y., Medzihradszky, A., Schöne, S., Daum, G.,Suzaki, T., Forner, J., Langenecker, T., Rempel, E., Schmid, M., Wirtz, M., Hell, R., and *Lohmann, J.U. (2016) Integration of light and metabolic signals for stem cell activation at the shoot apical meristem. eLife, 5, e17023 (21 pages).
    https://elifesciences.org/content/5/e17023

Takahashi group

  • -2018-
    Books
    Takahashi, F., Kuromori, T., Sato, H., and *Shinozaki, K. (2018) Regulatory gene networks in drought stress responses and resistance in plants. In "Survival strategies in extreme cold and desiccation: Adaptation mechanisms and their application" edited by Iwaya-Inoue, M., Sakurai, M., and Uemura, M. Springer, Chapter 12, in press.
  • -2017-
    Original papers
    #Morimoto, K., #Ohama. N., Kidokoro, S., Mizoi, J., Takahashi, F., Todaka, D., Mogami, J., Sato, H., Qin, F., Kim, J. S., Fukao, Y., Fujiwara, M., Shinozaki, K., and *Shinozaki, K. Y. (2017) BPM-CUL3 E3 ligase modulates thermotolerance by facilitating negative regulatory domain-mediated degradation of DREB2A in Arabidopsis. Proc. Natl. Acad. Sci. USA, 114, E8528-E8536.
    http://www.pnas.org/content/114/40/E8528.full
    Kidokoro, S., Yoneda, K., Takasaki, H., Takahashi, F., Shinozaki, K., and *Shinozaki, K. Y. (2017) Different cold-signaling pathways function in the responses to rapid and gradual decreases in temperature. Plant Cell, in press.
    http://www.plantcell.org/content/early/2017/03/28/tpc.16.00669
    #Soma, F., #Mogami, J., Yoshida, T., Abekura, M., Takahashi, F., Kidokoro, S., Mizoi, J., Shinozaki, K., and *Shinozaki, K. Y. (2017) ABA-unresponsive SnRK2 protein kinases regulate mRNA decay under osmotic stress in plants. Nat. Plants, 3, 16204.
    https://www.nature.com/articles/nplants2016204
  • -2016-
    Original papers
    Ohama, N., Kusakabe, K., Mizoi, J., Zhao, H., Kidokoro, S., Koizumi, S., Takahashi, F., Ishida, T., Yanagisawa, S., Shinozaki, K., and *Shinozaki, K. Y. (2016) The transcriptional cascade in the heat stress response of Arabidopsis is strictly regulated at the level of transcription factor expression. Plant Cell, 28, 181-201.
    https://www.ncbi.nlm.nih.gov/pubmed/26715648

Takezawa group

  • -2016-
    Original papers
    Ghosh, T. K., Kaneko, M., Akter, K., Murai, S., Komatsu, K., Ishizaki, K., Yamato, T. K., Kohchi, T. and *Takezawa, D. (2016) Abscisic acid-induced gene expression in the liverwort Marchantia polymorpha is mediated by evolutionarily conserved promoter elements. Physiol. Plant., 156, 407-420.
    http://onlinelibrary.wiley.com/doi/10.1111/ppl.12385/pdf

Uchida group

  • -2018-
    Original papers
    #Uchida, N., #Takahashi, K., Iwasaki, R., Yamada, R., Yoshimura, M., Endo, T. A., Kimura, S., Zhang, H., Nomoto, M., Tada, Y., Kinoshita, T., Itami, K., *Hagihara, S., and *Torii, K. U. (2018) Chemical hijacking of auxin signaling with an engineered auxin-TIR1 pair. Nat. Chem. Biol., in press.
    https://www.nature.com/articles/nchembio.2555
    Kimura, Y., Tasaka, M., *Torii, K. U. and *Uchida, N. (2018) ERECTA-family genes coordinate stem cell functions between the epidermal and internal layers of the shoot apical meristem. Development, 145, dev156380 (9 pages).
    http://dev.biologists.org/content/145/1/dev156380.long

Yamaguchi group

  • -2018-
    Original papers
    Nishizawa-Yokoi, A. and *Yamaguchi, N. (2018) Gene expression and transcription factor binding tests using mutated-promoter reporter lines. Methods Mol. Biol., in press.
    Uemura, A., Yamaguchi, N., Xu, Y., Wee, W. Y., Ichihashi, Y., Suzuki, T., Shibata, A., Shirasu, K., and *Ito, T. (2018) Regulation of floral meristem activity through the interaction of AGAMOUS, SUPERMAN, and CLAVATA3 in Arabidopsis. Plant Reproduction, in press.
  • -2017-
    Original papers
    #Yamaguchi, N., #Huang, J., Xu, Y., Tanoi, K., and *Ito, T. (2017) Fine-tuning of auxin homeostasis governs the transition from floral stem cell maintenance to gynoecium formation. Nat. Commun., 8, 1125 (15 pages).
    https://www.nature.com/articles/s41467-017-01252-6