Publications

2020

Nobori T, Wang Y, Wu J, Stolze SC, Tsuda Y, Finkemeier I, Nakagami H, Tsuda K, “Multidimensional gene regulatory landscape of a bacterial pathogen in plants”, Nature Plants, https://doi.org/10.1038/s41477-020-0690-7 (2020)

Stolze SC, Nakagami H#, Targeted quantification of phosphopeptides by parallel reaction monitoring (PRM), Methods in Molecular Biology, 2139:213-224 (2020) (#corresponding author)

Nakano RT#, Ishihama N, Wang Y, Takagi J, Uemura T, Schulze-Lefert P, Nakagami H#, “Apoplastic fluid preparation from Arabidopsis thaliana leaves upon interaction with a non-adapted powdery mildew pathogen”, Methods in Molecular Biology, 2139:79-88 (2020) (#joint corresponding authors)

Li X, Sanagi M, Lu Y, Nomura Y, Stolze SC, Yasuda S, Saijo Y, Schulze WX, Feil R, Stitt M, Lunn JE, Nakagami H#, Sato T#, Yamaguchi J, “Protein phosphorylation dynamics under identification of a cell death-related receptor-like kinase in Arabidopsis”, Frontiers in Plant Science, Apr 3;11:377 (2020) (#joint corresponding authors)

Sang Q, Pajoro A, Sun H, Song B, Yang X, Stolze SC, Andrés F, Schneeberger K, Nakagami H, Coupland G, “Mutagenesis of a quintuple mutant impaired in environmental responses reveals roles for CHROMATIN REMODELING 4 in Arabidopsis floral transition”, The Plant Cell, 32(5):1479-1500 (2020)

Kimura S, Hunter K, Vaahtera L, Tran HC, Citterico M, Vaattovaara A, Rokka A, Stolze SC, Harzen A, Meißner L, Tabea Wilkens MMT, Hamann T, Toyota M, Nakagami H, Wrzaczek M, “CRK2 and C-terminal phosphorylation of NADPH oxidase RBOHD regulate ROS production in Arabidopsis”, The Plant Cell 32(4):1063-1080 (2020)

2019

Kato S, Okamura E, Matsunaga TM, Nakayama M, Kawanishi Y, Ichinose T, Iwane AH, Sakamoto T, Imoto Y, Ohnuma M, Nomura Y, Nakagami H, Kuroiwa H, Kuroiwa T, Matsunaga S, “Cyanidioschyzon merolae aurora kinase phosphorylates evolutionarily conserved sites on its target to regulate mitochondrial division”, Communications Biology, 2:477 (2019)

Koide E, Suetsugu N, Iwano M, Gotoh E, Nomura Y, Stolze SC, Nakagami H, Kohchi T, Nishihama R, “Regulation of photosynthetic carbohydrate metabolism by a Raf-like kinase in the liverwort Marchantia polymorpha”, Plant Cell & Physiology, 2019 Dec 18. pii: pcz232 (2019)

Matsui H, Iwakawa H, Hyon GS, Yotsui I, Katou S, Monte I, Nishihama R, Franzen R, Solano R, Nakagami H#, “Isolation of natural fungal pathogens from Marchantia polymorpha reveals antagonism between salicylic acid and jasmonate during liverwort-fungus interactions”, Plant Cell & Physiology, 2019 Sep 27. pii: pcz187 (2019) (#corresponding author)

Yang C, Sofroni K, Wijnker E, Hamamura Y, Carstens L, Harashima H, Stolze SC, Vezon D, Chelysheva L, Orban-Nemeth Z, Pochon G, Nakagami H, Schlögelhofer P, Grelon M, Schnittger A, “The Arabidopsis Cdk1/Cdk2 homolog CDKA;1 controls chromosome axis assembly during plant meiosis”, The EMBO Journal, e101625 (2019)

Ishikawa S, Barrero JM, Takahashi F, Nakagami H, Peck SC, Gubler F, Shinozaki K, Umezawa T, “Comparative phosphoproteomic analysis reveals a decay of ABA signaling in barley embryos during after-ripening”, Plant Cell & Physiology, 60(12):2758-2768 (2019)

Sano N, Takebayashi Y, To A, Mhiri C, Rajjou L, Nakagami H#, Kanekatsu M#, “Shotgun proteomic analysis highlights roles of long-lived mRNAs and de novo transcribed mRNAs upon imbibition in rice embryos”, Plant Cell & Physiology, 60(11):2584-2596 (2019) (#joint corresponding authors)

Carella P, Gogleva A, Hoey DJ, Bridgen AJ, Stolze SC, Nakagami H, Schornack S, “Conserved biochemical defenses underpin host responses to oomycete infection in an early-divergent land plant lineage”, Current Biology, 29(14):2282-2294.e5 (2019)

Hu Z, Ghosh A, Stolze SC, Horváth M, Bai B, Schaefer S, Zündorf S, Liu S, Harzen A, Hajheidari M, Sarnowski TJ, Nakagami H, Koncz Z, Koncz C, “Gene modification by fast-track recombineering for cellular localization and isolation of components of plant protein complexes”, The Plant Journal, Oct;100(2):411-429 (2019)

Zhao L, Phuong LT, Luan MT, Fitrianti AN, Matsui H, Nakagami H, Noutoshi Y, Yamamoto M, Ichinose Y, Shiraishi T, Toyoda K, “A class III peroxidase PRX34 is a component of disease resistance in Arabidopsis”, Journal of General Plant Pathology, 85, 405–412 (2019)

Yang C, Hamamura Y, Sofroni K, Böwer F, Stolze SC, Nakagami H, Schnittger A, “SWITCH 1/DYAD is a WINGS APART-LIKE antagonist that maintains sister chromatid cohesion in meiosis”, Nature Communications, 10(1):1755 (2019)

Shinkawa H, Kajikawa M, Nomura Y, Ogura M, Sawaragi Y, Yamano T, Nakagami H, Sugiyama N, Ishihama Y, Kanesaki Y, Yoshikawa H, Fukuzawa H, “Algal protein kinase, triacylglycerol accumulation regulator 1, modulates cell viability and gametogenesis in carbon/nitrogen-imbalanced conditions”, Plant Cell & Physiology, 60(4):916-930 (2019)

Uemura T, Nakano RT, Takagi J, Wang Y, Kramer K, Finkemeier I, Nakagami H, Tsuda K, Ueda T, Schulze-Lefert P, Nakano A, “A Golgi-Released Subpopulation of the Trans-Golgi Network Mediates Protein Secretion in Arabidopsis”, Plant Physiology, 179(2):519-532 (2019)

2018

Fichman Y, Koncz Z, Reznik N, Miller G, Szabados L, Kramer K, Nakagami H, Fromm H, Koncz C, Zilberstein A, “SELENOPROTEIN O is a chloroplast protein involved in ROS scavenging and its absence increases dehydration tolerance in Arabidopsis thaliana”, Plant Science, 270:278-291 (2018)

Myouga F, Takahashi K, Tanaka R, Nagata N, Kiss AZ, Funk C, Nomura Y, Nakagami H, Jansson S, Shinozaki K, “Stable Accumulation of Photosystem II Requires ONE-HELIX PROTEIN1 (OHP1) of the Light Harvesting-Like Family”, Plant Physiology, 176(3):2277-2291 (2018)

Yokoo S, Inoue S, Suzuki N, Amakawa N, Matsui H, Nakagami H, Takahashi A, Arai R, Katou S, “Comparative analysis of plant isochorismate synthases reveals structural mechanisms underlying their distinct biochemical properties”, Bioscience Reports, 8(2) (2018)

Oide M, Okajima K, Nakagami H, Kato T, Sekiguchi Y, Oroguchi T, Hikima T, Yamamoto M, Nakasako M, “Blue light-excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from Arabidopsis”, The Journal of Biological Chemistry, 293(3):963-972 (2018)

2017

Matsui H, Nomura Y, Egusa M, Hamada T, Hyon GS, Kaminaka H, Watanabe Y, Ueda T, Trujillo M, Shirasu K, Nakagami H, “The GYF domain protein PSIG1 dampens the induction of cell death during plant-pathogen interactions”, PLoS Genetics, 13(10):e1007037 (2017)

Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rövekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J, “Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome”, Cell, 171(2):287-304.e15 (2017)

Furlan G, Nakagami H, Eschen-Lippold L, Jiang X, Majovsky P, Kowarschik K, Hoehenwarter W, Lee J, Trujillo M, “Changes in PUB22 Ubiquitination Modes Triggered by MITOGEN-ACTIVATED PROTEIN KINASE3 Dampen the Immune Response”, Plant Cell, 29(4):726-745 (2017)

2016

Yamada K, Saijo Y, Nakagami H, Takano Y, “Regulation of sugar transporter activity for antibacterial defense in Arabidopsis”, Science, 354(6318):1427-1430 (2016)

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, Kawasaki T, “The Arabidopsis CERK1-associated kinase PBL27 connects chitin perception to MAPK activation”, The EMBO Journal, 35(22):2468-2483 (2016)

Harashima H, Dissmeyer N, Hammann P, Nomura Y, Kramer K, Nakagami H, Schnittger A, “Modulation of plant growth in vivo and identification of kinase substrates using an analog-sensitive variant of CYCLIN-DEPENDENT KINASE A;1”, BMC Plant Biology, 16(1):209 (2016)

Choudhary MK, Nomura Y, Shi H, Nakagami H, Somers DE, “Circadian profiling of the Arabidopsis proteome using 2D-DIGE”, Frontiers in Plant Science, 7:1007 (2016)

Cifuentes M, Jolivet S, Cromer L, Harashima H, Bulankova P, Renne C, Crismani W, Nomura Y, Nakagami H, Sugimoto K, Schnittger A, Riha K, Mercier R, “TDM1 regulation determines the number of meiotic divisions”, PLoS Genetics, 12(2):e1005856 (2016)

Bowman JL, Araki T, Arteaga-Vazquez MA, Berger F, Dolan L, Haseloff J, Ishizaki K, Kyozuka J, Lin SS, Nagasaki H, Nakagami H, Nakajima K, Nakamura Y, Ohashi-Ito K, Sawa S, Shimamura M, Solano R, Tsukaya H, Ueda T, Watanabe Y, Yamato KT, Zachgo S, Kohchi T, “The Naming of Names: Guidelines for Gene Nomenclature in Marchantia”, Plant Cell & Physiology, 57(2):257-61 (2016)

1996 - 2015

Egusa M, Matsui H, Urakami T, Okuda S, Ifuku S, Nakagami H, Kaminaka H, “Chitin nanofiber elucidates the elicitor activity of polymeric chitin in plants”, Frontiers in Plant Science, 6:1098 (2015)

Choudhary MK, Nomura Y, Wang L, Nakagami H, Somers DE, “Quantitative circadian phosphoproteomic analysis of Arabidopsis reveals extensive clock control of key components in physiological, metabolic and signaling pathways”, Molecular & Cellular Proteomics, 14(8):2243-60 (2015)

Mogami J, Fujita Y, Yoshida T, Tsukiori Y, Nakagami H, Nomura Y, Fujiwara T, Nishida S, Yanagisawa S, Ishida T, Takahashi F, Morimoto K, Kidokoro S, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K, “Two distinct families of protein kinases are required for plant growth under high external Mg2+ concentrations in Arabidopsis”, Plant Physiology, 167(3):1039-57 (2015)

Nakaminami K, Matsui A, Nakagami H, Minami A, Nomura Y, Tanaka M, Morosawa T, Ishida J, Takahashi S, Uemura M, Shirasu K, Seki M, “Analysis of differential expression patterns of mRNA and protein during cold-acclimation and de-acclimation in Arabidopsis”, Molecular & Cellular Proteomics, 13(12):3602-11 (2014)

Matsui H, Fujiwara M, Hamada S, Shimamoto K, Nomura Y, Nakagami H, Takahashi A, Hirochika H, “Plasma membrane localization is essential for Oryza sativa Pto-interacting protein 1a-mediated negative regulation of immune signaling in rice”, Plant Physiology, 166(1):327-36 (2014)

Kondo Y, Ito T, Nakagami H, Hirakawa Y, Saito M, Tamaki T, Shirasu K, Fukuda H, “Plant GSK3 proteins regulate xylem cell differentiation downstream of TDIF-TDR signalling”, Nature Communications, 5:3504 (2014)

Nakagami H, “StageTip-based HAMMOC, an efficient and inexpensive phosphopeptide enrichment method for plant shotgun phosphoproteomics”, Methods in Molecular Biology "Methods in Plant Proteomics", 1072:595-607 (2014)

Fujita S, Pytela J, Hotta T, Kato T, Hamada T, Akamatsu R, Ishida Y, Kutsuna N, Hasezawa S, Nomura Y, Nakagami H, Hashimoto T, “An atypical tubulin kinase mediates stress-induced microtubule depolymerization in Arabidopsis”, Current Biology, 23(20):1969-78 (2013)

Nakagami H, Sugiyama N, Ishihama Y, Shirasu K, “Shotguns in the Front Line: Phosphoproteomics in Plants”, Plant Cell & Physiology, 53(1):118-24 (2012)

Kosetsu K, Matsunaga S, Nakagami H, Colcombet J, Sasabe M, Soyano T, Takahashi Y, Hirt H, Machida Y, “The MAP kinase MPK4 is required for cytokinesis in Arabidopsis thaliana”, The Plant Cell, 22(11):3778-90 (2010)

Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Schulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL, “MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data”, Plant Physiology, 155(1):259-70 (2011)

Nakagami H#, Sugiyama N#, Mochida K, Daudi A, Yoshida Y, Toyoda T, Tomita M, Ishihama Y, Shirasu K (#joint first authors), “Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants”, Plant Physiology, 153(3):1161-74 (2010)

Sugiyama N#, Nakagami H#, Mochida K, Daudi A, Tomita M, Shirasu K, Ishihama Y (#joint first authors), “Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis”, Molecular Systems Biology, 4:193 (2008)

Djamei A#, Pitzschke A#, Nakagami H#, Rajh I, Hirt H (#joint first authors), “Trojan horse strategy in Agrobacterium transformation: abusing MAPK defense signaling”, Science, 318(5849):453–6 (2007)

Nakagami H, Soukupová H, Schikora A, Žárský V, Hirt H, “A mitogen-activated protein kinase kinase kinase mediates reactive oxygen species homeostasis in Arabidopsis”, The Journal of Biological Chemistry, 281(50):38697–704 (2006)

Veronese P, Nakagami H, Bluhm B, Abuqamar S, Chen X, Salmeron J, Dietrich RA, Hirt H, Mengiste T, “The membrane-anchored BOTRYTIS-INDUCED KINASE1 plays distinct roles in Arabidopsis resistance to necrotrophic and biotrophic pathogens”, The Plant Cell, 18(1):257-73 (2006)

Nakagami H, Pitzschke A, Hirt H, “Emerging MAP Kinase Pathways in Plant Stress Signalling”, Trends in Plant Science, 10(7):339-46 (2005)

Jonak C, Nakagami H, Hirt H, “Heavy metal stress. Activation of distinct mitogen-activated protein kinase pathways by copper and cadmium”, Plant Physiology, 136(2):3276-83 (2004)

Nakagami H, Kiegerl S, Hirt H, “OMTK1, a novel MAPKKK, channels oxidative stress signaling through direct MAPK interaction”, The Journal of Biological Chemistry, 279(26):26959-66 (2004)

Nakagami H, Kawamura K, Sugisaka K, Sekine M, Shinmyo A, “Phosphorylation of retinoblastoma-related protein by the cyclin D/cyclin-dependent kinase complex is activated at the G1/S-phase transition in tobacco”, The Plant Cell, 14(8):1847-57 (2002)

Sorrell DA, Menges M, Healy JM, Deveaux Y, Amano C, Su Y, Nakagami H, Shinmyo A, Doonan JH, Sekine M, Murray JA, “Cell cycle regulation of cyclin-dependent kinases in tobacco Bright Yellow-2(BY-2) cells”, Plant Physiology, 126(3):1214-1223 (2001)

Sekine M, Ito M, Uemukai K, Maeda Y, Nakagami H, Shinmyo A, “Isolation and characterization of the E2F-like gene in plants”, FEBS Letter, 460(1):117-122 (1999)

Nakagami H*, Sekine M*, Murakami H, Shinmyo A (*joint first authors), “Tobacco retinoblastoma-related protein phosphorylated by a distinct cyclin dependent kinase complex with Cdc2/cyclin D in vitro”, The Plant Journal, 18(3):243-252 (1999)

Hirata K, Nakagami H, Takashina J, Mahmud T, Kobayashi M, In Y, Ishida T, Miyamoto K, “Novel violet pigment, Nostocine A, an extracellular metabolite from cyanobacterium Nostoc spongiaeforme”, Heterocycles, 43(7):1513-1519 (1996)

Hirata K, Takashina J, Nakagami H, Ueyama S, Murakami K, Kanamori T, Miyamoto K, “Growth inhibition of various organisms by a violet pigment, Nostocine A, produced by Nostoc spongiaeforme”, Bioscience, Biotechnology, and Biochemistry, 60(11):1905–6 (1996)

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