2024
Chen Y, Nishimura K, Tokizawa M, Yamamoto YY, Oka Y, Matsushita T, Hanada K, Shirai K, Mano M, Shimizu T, Masuda T. (2024)
Alternative localization of HEME OXYGENASE 1 in plant cells regulates cytosolic heme catabolism.
Plant Phyisiol., kiae288.
Hosokawa C, Yagi H, Segami S, Nagano AJ, Koumoto K, Tamura K, Oka Y, Matsushita T, Shimada T. (2024)
The Arabidopsis katamari2 mutant exhibits a hypersensitive seedling arrest response at the phase transition from heterotrophic to autotrophic growth.
Plant Cell Physiol., 65, 350-361. 論文リンク.
Seki M, Kuze Y, Zhang X, Kurotani K, Notaguchi M, Nishio H, Kudoh H, Suzaki T, Yoshida S, Sugano S, Matsushita T, Suzuki Y. (2024)
An improved method for the highly specific detection of transcription start sites.
Nuc. Acid. Res., 52, e7.
2023
Kozuka T, Oka Y, Kohzuma K, Kusaba M. (2023)
Cryptochromes suppress leaf senescence in response to blue light in Arabidopsis.
Plant Physiol., kiad042.
Moriya KC, Shirakawa M, Loue-Manifel J, Matsuda Y, Lu YT, Tamura K, Oka Y, Matsushita T, Hara-Nishimura I, Ingram G, Nishihama R, Goodrich J, Kohchi T, Shimada T. (2023)
Stomatal regulators are co-opted for seta development in the astomatous liverwort Marchantia polymorpha.
Nat. Plants, 9, 302–314. プレスリリース Research Briefing（解説記事）
Kobayashi H, Sugano SS, Tamura K, Oka Y, Matsushita T, Shimada T. Comprehensive analysis of peptide-coding genes and initial characterization of an LRR-only microprotein in Marchantia polymorpha.
Front. Plant Sci., 13:1051017.
2022
Takeda T, Shirai K, Kim YW, Higuchi-Takeuchi M, Shimizu M, Kondo T, Ushijima T, Matsushita T, Shinozaki K, Hanada K. (2022)
A de novo gene originating from the mitochondria controls floral transition in Arabidopsis thaliana.
Plant Mol. Biol., 111, 189-203
Hu S, Li B, Wu F, Zhu D, Zouhar J, Gao C, Shimada T, Rojo E, Hara-Nishimura I, Jiang L, Shen J. (2022)
Plant ESCRT protein ALIX coorfinates with retromer complex in regulating receptor-mediated sorting of soluble vacuolar proteins.
Proc. Natl. Acad. Sci. U.S.A., 119, e2200492119.
2021
Nomoto M, Skelly MJ, Itaya T, Mori T, Suzuki T, Matsushita T, Tokizawa M, Kuwata K, Mori H, Yamamoto YY, Higashiyama T, Tsukagoshi H, Spoel SH, Tada Y. (2021)
Suppression of MYC transcription activators by the immune cofactor NPR1 fine-tunes plant immune responses.
Cell Rep., 37, 110125.
Ikeda H, Suzuki T, Oka Y, Gustafsson ALS, Brochmann C, Mochizuki N, Nagatani A. (2021)
Divergence in red light responses associated with thermal reversion of phytochrome B between high- and low-alttitude species.
New Phytol., 231, 75-84
Yagi H, Tamura K, Matsushita T, Shimada T. (2021)
Spatiotemporal relationship between auxin dynamics and hydathode development in Arabidopsis leaf teeth.
Plant Signal. Behav., 1989216.
2020
Yagi H, Nagano AJ, Kim J, Tamura K, Mochizuki N, Nagatani A, Matsushita T, Shimada T. (2020)
Fluorescent protein-based imaging and tissue-specific RNA-seq analysis of Arabidopsis hydathodes.
J. Exp. Bot., 72, 1260-1270.
Sakoda K, Yamori W, Shimada T, Sugano SS, Hara-Nishimura I, Tanaka Y. (2020)
Higher Stomatal Density Improves Photosynthetic Induction and Biomass Production in Arabidopsis under Fluctuating Light.
Front. Plant Sci., 11, 1609.
Izuishi Y, Isaka N, Li H, Nakanishi K, Kageyama J, Ishikawa K, Shimada T, Masuta C, Yoshikawa N, Kusano H, Yazaki K. (2020)
Apple latent spherical virus (ALSV)-induced gene silencing in a medicinal plant, Lithospermum erythrorhizon.
Sci. Rep., 10, 1-9.
Takagi J, Kimori Y, Shimada T, Hara-Nishimura I. (2020)
Dynamic Capture-and-Release of Endoplasmic Reticulum Exit Sites by Golgi Stacks in Arabidopsis.
iScience, 101265.
Ishishita K, Higa T, Tanaka H, Inoue SI, Chung A, Ushijima T, Matsushita T, Kinoshita T, Nakai M, Wada M, Suetsugu N, Gotoh E. (2020)
Phototropin 2 contributes to the chloroplast avoidance response at the chloroplast-plasma membrane interface.
Plant Physiol., 183, 304-316.
Ichino T, Maeda K, Hara-Nishimura I, Shimada T. (2020)
Arabidopsis ECHIDNA protein is involved in seed coloration, protein trafficking to vacuoles, and vacuolar biogenesis.
J. Exp. Bot., 71, 3999-4009.
Ishikawa K, Tamura K, Fukao Y, Shimada T. (2020)
Structural and functional relationships between plasmodesmata and plant endoplasmic reticulum–plasma membrane contact sites consisting of three synaptotagmins.
New Phytol., 226, 798-808.
Hamasaki H, Ayano M, Nakamura A, Fujioka S, Asami T, Takatsuto S, Yoshida S, Oka Y, Matsui M, Shimada Y. (2020)
Light Activates Brassinosteroid Biosynthesis to Promote Hook Opening and Petiole Development in Arabidopsis thaliana.
Plant Cell Physiol., 61, 1239-1251.
2019
Sakaguchi J, Matsushita T, Watanabe Y. (2019)
DWARF4 accumulation in root tips is enhanced via blue light perception by cryptochromes.
Plant, Cell & Environ. , 42, 1615-1629.
Matsushita T (2019)
Regulation of Alternative Splicing by Phytochrome.
Phytochromes (pp. 143-148). Humana, New York, NY.
Shimada TL, Shimada T, Okazaki Y, Higashi Y, Saito K, Kuwata K, Oyama K, Kato M, Ueda T, Nakano A, Ueda T, Takano Y, Hara-Nishimura I. (2019)
HIGH STEROL ESTER 1 is a key factor in plant sterol homeostasis.
Nat. Plants, 5, 1154-1166.
Nakazaki A, Yamada K, Kunieda T, Tamura K, Hara-Nishimura I, Shimada T. (2019)
Biogenesis of leaf endoplasmic reticulum body is regulated by both jasmonate-dependent and independent pathways.
Plant Signal. Behav.,14, 1622982.
Maeda K, Kunieda T, Tamura K, Hatano K, Hara-Nishimura I, Shimada T. (2019)
Identification of periplasmic root-cap mucilage in developing columella cells of Arabidopsis thaliana.
Plant Cell Physiol., 60, 1296-1303.
Yoshinari A, Hosokawa T, Amano T, Beier MP, Kunieda T, Shimada T, Hara-Nishimura I, Naito S, Takano J. (2019)
Polar Localization of the Borate Exporter BOR1 Requires AP2-Dependent Endocytosis.
Plant Physiol.,179, 1569-1580.
Nakazaki A, Yamada K, Kunieda T, Sugiyama R, Hirai MY, Tamura K, Hara-Nishimura I, Shimada T. (2019)
Leaf ER bodies identified in Arabidopsis rosette leaves are involved in defense against herbivory.
Plant Physiol., 179, 1515-1524.
Yang Z, Chen L, Kohnen MV, Xiong B, Zhen X, Liao J, Oka Y, Zhu Q, Gu L, Lin C, Liu B. (2019)
Identification and Characterization of the PEBP Family Genes in Moso Bamboo (Phyllostachys heterocycla).
Sci. Rep., 9, 14998.
2018
Gotoh E, Suetsugu N, Higa T, Matsushita T, Tsukaya H, Wada M. (2018)
Palisade cell shape affects the light-induced chloroplast movements and leaf photosynthesis.
Sci. Rep., 8, 1-9.
Ishikawa K, Tamura K, Shimada T. (2018)
Subcellular localisation of an endoplasmic reticulum-plasma membrane tethering factor, SYNAPTOTAGMIN 1, is affected by fluorescent protein fusion.
Plant Signal. Behav., 13, e1547577.
Ishikawa K, Tamura K, Ueda H, Ito Y, Nakano A, Hara-Nishimura I, Shimada T. (2018)
Synaptotagmin-associated endoplasmic reticulum-plasma membrane contact sites are localized to immobile ER tubules.
Plant Physiol., 178, 641-653
Shimada T, Kunieda T, Sumi S, Koumoto Y, Tamura K, Hatano K, Ueda H, Hara-Nishimura I. (2018)
The AP-1 Complex is Required for Proper Mucilage Formation in Arabidopsis Seeds.
Plant Cell Physiol., 59, 2331-2338
Sugano SS, Nishihama R, Shirakawa M, Takagi J, Matsuda Y, Ishida S, Shimada T, Hara-Nishimura I, Osakabe K, Kohchi T. (2018)
Efficient CRISPR/Cas9-based genome editing and its application to conditional genetic analysis in Marchantia polymorpha.
PLoS ONE, 13, e0205117.
Ueda H, Ohta N, Kimori Y, Uchida T, Shimada T, Tamura K, Hara-Nishimura I. (2018)
Endoplasmic Reticulum (ER) Membrane Proteins (LUNAPARKs) Are Required for Proper Configuration of the Cortical ER Network in Plant Cells.
Plant Cell Physiol., 59, 1931-1941
Shimada T, Fuji K, Ichino T, Teh OK, Koumoto Y, Hara-Nishimura I. (2018)
GREEN FLUORESCENT SEED, to Evaluate Vacuolar Trafficking in Arabidopsis Seeds.
Plant Vacuolar Trafficking (pp. 1-7). Humana Press, New York, NY.
Shimada T, Takagi J, Ichino T, Shirakawa M, Hara-Nishimura I. (2018)
Plant Vacuoles.
Annu. Rev. Plant Biol., 29, 123-145.
Hatsugai N, Nakatsuji A, Unten O, Ogasawara K, Kondo M, Nishimura M, Shimada T, Katagiri F, Hara-Nishimura I. (2018)
Involvement of Adapter Protein Complex 4 in Hypersensitive Cell Death Induced by Avirulent Bacteria.
Plant Physiol., 176, 1824-1834.
Liu B, Zhang J, Yang Z, Matsui A, Seki M, Li S, Yan X, Kohnen MV, Gu L, Prasad K, Tuskan GA, Lu M, Oka Y. (2018)
PtWOX11 acts as master regulator conducting the expression of key transcription factors to induce de novo shoot organogenesis in poplar.
Plant Mol. Biol., 98, 389-406.
Wang Q, Zuo Z, Wang X, Liu Q, Gu L, Oka Y, Lin C. (2018)
Beyond the photocycle-how cryptochromes regulate photoresponses in plants?
Curr. Opin. Plant Biol., 45, 120-126.
Wang Q, Liu Q, Wang X, Zuo Z, Oka Y, Lin C. (2018)
New insights into the mechanisms of phytochrome-cryptochrome coaction.
New Phytol., 217, 547-551.
2017
Ushijima T, Hanada K, Gotoh E, Yamori W, Kodama Y, Tanaka H, Kusano M, Fukushima A, Tokizawa M, Yamamoto YY, Tada Y, Suzuki Y, Matsuhita T. (2017)
Light controls protein localization through phytochrome-mediated alternative promoter selection.
Cell, 171, 1316-1325. プレスリリース
Oota M, Gotoh E, Endo M, Ishida T, Matsushita T, Sawa S. (2017)
Negative phototaxis in M. incognita.
Int. J. Biol., 9.
Wang S, Yoshinari A, Shimada T, Hara-Nishimura I, Mitani-Ueno N, Ma JF, Naito S, Takano J. (2017)
Polar localization of the NIP5; 1 boric acid channel is maintained by endocytosis and facilitates boron transport in Arabidopsis roots.
The Plant Cell, 29, 824-842.
Sakai Y, Sugano SS, Kawase T, Shirakawa M, Imai Y, Kawamoto Y, Sugiyama H, Nakagawa T, Hara-Nishimura I, Shimada T. (2017)
The chemical compound bubblin induces stomatal mispatterning in Arabidopsis by disrupting the intrinsic polarity of stomatal lineage cells.
Development, 144, 499-506.
Shimada T, Hara-Nishimura I. (2017)
Isolation of Protein Storage Vacuoles and Their Membranes.
Methods Mol Biol., 1511, 163-168.
Wang X, Wang Q, Han YJ, Liu Q, Gu L, Yang Z, Su J, Liu B, Zuo Z, He W, Wang J, Liu B, Matsui M, Kim JI, Oka Y, Lin C. (2017)
A CRY-BIC negative-feedback cicuitry regulating blue light sensitivity of Arabidopsis.
Plant J., 92, 426-436.
Liu Q, Wang Q, Deng W, Wang X, Piao M, Cai D, Li Y, Barshop WD, Yu X, Zhou T, Liu B, Oka Y, Wohlschlegel J, Zuo Z, Lin C. (2017)
Molecular basis for blue light-dependent phosphorylation of Arabidopsis cryptochrome 2.
Nat. Commun., 11, 15234.
Yang Z, Liu B, Su J, Liao J, Lin C, Oka Y.
Cryptochromes Orchastrate Transcription Regulation of Diverse Blue Light Responses in Plants.
Photochem. Photobiol., 93, 112-127.
2016
Ishishita K, Suetsugu N, Hirose Y, Higa T, Doi M, Wada M, Matsushita T, Gotoh E. (2016)
Functional characterization of blue-light-induced responses and PHOTOTROPIN 1 gene in Welwitschia mirabilis.
J. Plant Res., 129, 175-187.
Shirakawa M, Ueda H, Shimada T, Hara-Nishimura I. (2016)
FAMA: A Molecular Link between Stomata and Myrosin Cells.
Trends Plant Sci., 21, 861-871.
Shirakawa M, Ueda H, Shimada T, Hara-Nishimura I. (2016)
Myrosin cells are differentiated directly from ground meristem cells and are developmentally independent of the vasculature in Arabidopsis leaves.
Plant Signal. Behav., 11, e1150403.
Ueda H, Yokota E, Kuwata K, Kutsuna N, Mano S, Shimada T, Tamura K, Stefano G, Fukao Y, Brandizzi F, Shimmen T, Nishimura M, Hara-Nishimura I. (2016)
Phosphorylation of the c terminus of rhd3 has a critical role in homotypic er membrane fusion in Arabidopsis.
Plant Physiol., 170, 867-880.
Fuji K, Shirakawa M, Shimono Y, Kunieda T, Fukao Y, Koumoto Y, Takahashi H, Hara-Nishimura I, Shimada T. (2016)
The adaptor complex AP-4 regulates vacuolar protein sorting at the trans-golgi network by interacting with VACUOLAR SORTING RECEPTOR1.
Plant Physiol., 170, 211-219.
Wang Q, Zuo Z, Wang X, Gu L, Yoshizumi T, Yang Z, Yang L, Liu Q, Liu W, Han YJ, Kim JI, Liu B, Wohlschlegel JA, Matsui M, Oka Y, Lin C. (2016)
Photoactivation and inactivation of Arabidopsis cryptochrome 2.
Science, 354, 343-347.
Liu B, Yang Z, Gomez A, Liu B, Lin C, Oka Y. (2016)
Signaling mechanisms of plant cryptochromes in Arabidopsis thaliana.
J. Plant Res., 129, 137-48.
2015
Okamoto K, Ueda H, Shimada T, Tamura K, Koumoto Y, Tasaka M, Morita MT, Hara-Nishimura I. (2016)
An ABC transporter B family protein, ABCB19, is required for cytoplasmic streaming and gravitropism of the inflorescence stems.
Plant Signal. Behav., 11, e1010947.
Okamoto K, Ueda H, Shimada T, Tamura K, Kato M, Tasaka M, Morita MT, Hara-Nishimura I. (2015)
An actin-myosin XI cytoskeleton regulates organ straightening adjust plant posture.
Nat. Plant, 15031.
Teh OK, Hatsugai N, Tamura K, Fuji K, Tabata R, Yamaguchi K, Shingenobu S, Yamada M, Hasebe M, Sawa S, Shimada T, Hara-Nishimura I. (2015)
BEACH-Domain Proteins Act Together in a Cascade to Mediate Vacuolar Protein Trafficking and Disease Resistance in Arabidopsis.
Mol. Plant, 8, 389-398.
Kawase T, Sugano SS, Shimada T, Hara-Nishimura I. (2015)
A direction-selective local-thresholding method, DSLT, in combination with a dye-based method for automated three-dimensional segmentation of cells and airspaces in developing leaves.
Plant J., 81, 357-366.
Shirakawa M, Ueda H, Shimada T, Kohchi T, Hara-Nishimura I. (2015)
Myrosin cell development is regulated by endocytosis machinery and PIN1 polarity in leaf primordia of Arabidopsis thaliana.
The Plant Cell, 26, 4448-4461.