Centers & Labs

RIKEN Center for Sustainable Resource Science

Plant Proteomics Research Unit

Unit Leader: Hirofumi Nakagami (Ph.D.)
Hirofumi  Nakagami(Ph.D.)

Plants have evolved unique adaptation systems to tolerate various environmental stresses. An understanding of the fundamental mechanisms underlying adaptation processes is expected to provide novel ideas for improving plant functions. The main goal of our unit is to dissect plant specific signaling networks essential for the adaptation system by employing advanced proteomics methods.

Main Research Field

Plant & Animal Science

Related Research Fields

Biology & Biochemistry / Molecular Biology & Genetics / Agricultural Sciences

Research Subjects

  • Method development for post-translational modification analysis
  • Dissection of plant immune signaling by proteomics

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.
  1. 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- and de-acclimation in Arabidopsis"
    Mol Cell Proteomics. Dec;13(12):3602-11. (2014)
  2. Matsui, H., Fujiwara, M., Hamada, S., Shimamoto, K.,Nomura, Y., Nakagami, H., Takahashi, A., Hirochika, H.:
    "Plasma membrane localization is essential for OsPti1a-mediated negative regulation of immune signaling in rice"
    Plant Physiol. Sep;166(1):327-36. (2014)
  3. 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"
    Nat Commun. Mar 24;5:3504. (2014)
  4. Nakagami, H.:
    "StageTip-based HAMMOC, an efficient and inexpensive phosphopeptide enrichment method for plant shotgun phosphoproteomics"
    Methods Mol Biol. 1072:595-607. (2014)
  5. 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"
    Curr Biol. Oct 21;23(20):1969-78. (2013)
  6. Nakagami, H., Sugiyama, N., Mochida, K., Daudi, A., Yoshida, Y., Toyoda, T., Tomita, M., Ishihama, Y., and Shirasu, K.:
    "Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants"
    Plant Physiol. Jul;153(3):1161-74. (2010)
  7. Sugiyama, N., Nakagami, H., Mochida, K., Daudi, A., Tomita, M., Shirasu, K., and Ishihama, Y.:
    "Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis"
    Mol Syst Biol. 2008;4:193. (2008)
  8. * Djamei, A., Pitzschke, A., Nakagami, H., Rajh, I., and Hirt, H.:
    "Trojan horse strategy in Agrobacterium transformation: abusing MAPK defense signaling"
    Science. Oct19;318(5849):453-6. (2007)
  9. * Nakagami, H., Soukupová, H., Schikora, A., Zárský, V., and Hirt, H.:
    "A Mitogen-activated protein kinase kinase kinase mediates reactive oxygen species homeostasis in Arabidopsis"
    J Biol Chem. Dec15;281(50):38697-704. (2006)
  10. * Nakagami, H., Kawamura, K., Sugisaka, K., Sekine, M., and 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"
    Plant Cell. Aug;14(8):1847-57. (2002)

Lab Members

Principal Investigator

Hirofumi Nakagami
Unit Leader

Core Members

Gang-Su Hyon
Research Scientist
Izumi Yotsui
Postdoctoral Researcher
Yuko Nomura
Technical Staff II

Contact information

1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan

Email: hirofumi.nakagami [at]

Related links