Publications of Hiro's Lab

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Since 2010

TDM1 regulation determines the number of meiotic divisions.
Cifuentes M, Jolivet S, Cromer L, Harashima H, Bulankova P, Renne C, Crismani W,Nomura YNakagami H, Sugimoto K, Schnittger A, Riha K, Mercier R.
PLOS Genetics. 2016 Feb 12;12(2):e1005856. doi: 10.1371/journal.pgen.1005856.
The naming of names: guidelines for gene nomenclature in Marchantia.
Bowman J L, Araki T, Arteaga-Vazquez M A, Berger F, Dolan L, Haseloff J, Ishizaki K, Kyozuka J, Lin S, Nagasaki H,Nakagami H, Nakajima K, Nakamura Y, Ohashi-Ito K, Sawa S, Shimamura M, Solano R, Tsukaya H, Ueda T, Watanabe Y, Yamato K T, Zachgo S, Kohchi T.
Plant Cell Physiol. 2015 Dec 7. pii: pcv193. Review.
Chitin nanofiber elucidates the elicitor activity of polymeric chitin in plants.
Egusa M,Matsui H, Urakami T, Okuda S, Ifuku S,Nakagami H, Kaminaka H.
Front Plant Sci. 2015 Nov 22;6:1098. doi: 10.3389/fpls.2015.01098.
Quantitative circadian phosphoproteomic analysis of Arabidopsis reveals extensive clock control of key components in physiological, metabolic and signaling pathways.
Choudhary M,Nomura Y, Wang L,Nakagami H, Somers D.
Mol Cell Proteomics. 2015 Aug;14(8):2243-60.
Two distinct families of protein kinases are required for plant growth under high external Mg2+ concentrations in Arabidopsis.
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.
Plant Physiol. 2015 Mar;167(3):1039-57.
Analysis of differential expression patterns of mRNA and protein during cold- and de-acclimation in Arabidopsis.
Nakaminami K, Matsui A,Nakagami H, Minami A,Nomura Y, Tanaka M, Morosawa T, Ishida J, Takahashi S, Uemura M, Shirasu K, Seki M.
Mol Cell Proteomics. 2014 Dec;13(12):3602-11.
Plasma membrane localization is essential for OsPti1a-mediated negative regulation of immune signaling in rice.
Matsui H, Fujiwara M, Hamada S, Shimamoto K,Nomura Y,Nakagami H, Takahashi A, Hirochika H.
Plant Physiol. 2014 Sep;166(1):327-36.
Plant GSK3 proteins regulate xylem cell differentiation downstream of TDIF-TDR signalling.
Kondo Y, Ito T,Nakagami H, Hirakawa Y, Saito M, Tamaki T, Shirasu K, Fukuda H.
Nat Commun. 2014 Mar 24;5:3504.
StageTip-Based HAMMOC, an Efficient and Inexpensive Phosphopeptide Enrichment Method for Plant Shotgun Phosphoproteomics.
Nakagami H.
Methods Mol Biol. 2014;1072:595-607.
An Atypical Tubulin Kinase Mediates Stress-Induced Microtubule Depolymerization in Arabidopsis.
Fujita S, Pytela J, Hotta T, Kato T, Hamada T, Akamatsu R, Ishida Y, Kutsuna N, Hasezawa S,Nomura Y,Nakagami H, Hashimoto T.
Curr Biol. 2013 Oct 21;23(20):1969-78.
Shotguns in the front line: phosphoproteomics in plants.
Nakagami H, Sugiyama N, Ishihama Y, Shirasu K.
Plant Cell Physiol. 2012 Jan;53(1):118-24. Review.
Phosphoproteomics in plant science.
Nakagami H.
Bioscience & Industry. 2011 69(6):462-6. Review. Japanese.
MASCP Gator: An Aggregation Portal for the Visualization of Arabidopsis Proteomics Data.
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.
Plant Physiol. 2011 Jan;155(1):259-70.
The MAP Kinase MPK4 Is Required for Cytokinesis in Arabidopsis thaliana.
Kosetsu K, Matsunaga S,Nakagami H, Colcombet J, Sasabe M, Soyano T, Takahashi Y, Hirt H, Machida Y.
Plant Cell. 2010 Nov;22(11):3778-90.
Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants.
Nakagami H*, Sugiyama N*, Mochida K, Daudi A, Yoshida Y, Toyoda T, Tomita M, Ishihama Y, Shirasu K. (* joint first authors)
Plant Physiol. 2010 Jul;153(3):1161-74.
Front line of plant phosphoproteome analysis.
Nakagami H, Sugiyama N, Ishihama Y.
Plant signaling: molecules and response, Kyoritsu Shuppan Co., Ltd. 30 May 2010:228-36. Review. Japanese.

Before 2009

Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis.
Sugiyama N*,Nakagami H*, Mochida K, Daudi A, Tomita M, Shirasu K, Ishihama Y. (* joint first authors)
Mol Syst Biol. 2008;4:193.
Purification method of ubiquitinated protein using ubiquitin-binding domain.
Nakagami H, Shirasu K.
Biotechnology Journal. 2007 7(5):594-8. Review. Japanese.
Trojan horse strategy in Agrobacterium transformation: abusing MAPK defense signaling.
Djamei A*, Pitzschke A*,Nakagami H*, Rajh I, Hirt H. (* joint first authors)
Science. 2007 Oct 19;318(5849):453-6.
A Mitogen-activated protein kinase kinase kinase mediates reactive oxygen species homeostasis in Arabidopsis.
Nakagami H, Soukupová H, Schikora A, Zárský V, Hirt H.
J Biol Chem. 2006 Dec 15;281(50):38697-704.
The membrane-anchored BOTRYTIS-INDUCED KINASE1 plays distinct roles in Arabidopsis resistance to necrotrophic and biotrophic pathogens.
Veronese P,Nakagami H, Bluhm B, Abuqamar S, Chen X, Salmeron J, Dietrich RA, Hirt H, Mengiste T.
Plant Cell. 2006 Jan;18(1):257-73.
Emerging MAP kinase pathways in plant stress signalling.
Nakagami H, Pitzschke A, Hirt H.
Trends Plant Sci. 2005 Jul;10(7):339-46. Review.
Heavy metal stress. Activation of distinct mitogen-activated protein kinase pathways by copper and cadmium.
Jonak C,Nakagami H, Hirt H.
Plant Physiol. 2004 Oct;136(2):3276-83.
OMTK1, a novel MAPKKK, channels oxidative stress signaling through direct MAPK interaction.
Nakagami H, Kiegerl S, Hirt H.
J Biol Chem. 2004 Jun 25;279(26):26959-66.
Phosphorylation of retinoblastoma-related protein by the cyclin D/cyclin-dependent kinase complex is activated at the G1/S-phase transition in tobacco.
Nakagami H, Kawamura K, Sugisaka K, Sekine M, Shinmyo A.
Plant Cell. 2002 Aug;14(8):1847-57.
Cell cycle regulation of cyclin-dependent kinases in tobacco cultivar Bright Yellow-2 cells.
Sorrell DA, Menges M, Healy JM, Deveaux Y, Amano C, Su Y,Nakagami H, Shinmyo A, Doonan JH, Sekine M, Murray JA.
Plant Physiol. 2001 Jul;126(3):1214-23.
Isolation and characterization of the E2F-like gene in plants.
Sekine M, Ito M, Uemukai K, Maeda Y,Nakagami H, Shinmyo A.
FEBS Lett. 1999 Oct 22;460(1):117-22.
Tobacco retinoblastoma-related protein phosphorylated by a distinct cyclin-dependent kinase complex with Cdc2/cyclin D in vitro.
Nakagami H*, Sekine M*, Murakami H, Shinmyo A. (* joint first authors)
Plant J. 1999 May;18(3):243-52.
Growth inhibition of various organisms by a violet pigment, nostocine A, produced by Nostoc spongiaeforme.
Hirata K, Takashina J,Nakagami H, Ueyama S, Murakami K, Kanamori T, Miyamoto K.
Bioscience, Biotechnology, and Biochemistry. 1996 Nov;60(11):1905-6.
Novel violet pigment, nostocine A, an extracellular metabolite from cyanobacterium Nostoc spongiaeforme.
Hirata K,Nakagami H, Takashina J, Mahmud T, Kobayashi M, In Y, Ishida T, Miyamoto K.
Heterocycles. 1996 Jul;43(7):1513-9.

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