Division of Disease Proteomics

Main Research AreasResearch ProjectsMemberPublications


Main Research Areas

  • Development of Proteomic Technologies and its Application to Disease Proteomics
  • Global Analysis of Protein Phosphorylation by Signaling Proteomics
  • Structure-function relationship Studied by X-ray Crystallography


Research Projects

1.Developing mass spectrometry-based proteomics technologies and their application to the basic and clinical researches.

Using cutting edge proteomics technologies we analyze 1) the bacteria-host cell interactions in the infectious disease such as E. coli O157, 2) the secretome of human adipocytes, 3) the osteoblast differentiation, and other disease-related phenomena. We have already identified more than 30 effector proteins secreted from E.coli O157 (Tobe et al., Proc. Natl. Acad. Sci., 2006). We also study the proteome of organelles such as peroxisome (Kikuchi et al., J. Biol. Chem., 2004) and lipid droplets (Ozeki et al., J. Cell Sci., 2005). Our recent research on the mechanism of self-sterility in a hermaphroditic chordate, C. Intestinalis, identified proteins involved in the self-sterility (Harada et al., Science, 2008).

Developing mass spectrometry-based proteomics technologies and their application to the basic and clinical researches.

2.Global Analysis of Protein Phosphorylation by Signaling Proteomics.

Protein functions are regulated not only by its expression, but also by post-translational modifications such as protein phosphorylation. Our aim is to analyze various protein modifications including protein phosphorylation and acylation in a large-scale proteomics manner. The signaling pathways downstream of the EGF receptor and those of ERK map kinases are analyzed. We have identified several novel effector proteins in the EGF receptor signaling (Tashiro et al., J. Biol. Chem., 2006; Konishi et al., J. Biol. Chem., 2006). The phosphorylation and regulation of the nuclear pore complex by the ERK pathways have been elucidated (Kosako et al., Nature Struc. Mol. Biol., 2009).

Global Analysis of Protein Phosphorylation by Signaling Proteomics.

Two novel proteins identified by the signaling proteomics of EGF receptor signaling. Ymer binds to the EGFR in phosphorylation- and ubiquitination-dependent manner.


3.Structure-function relationship Studied by X-ray Crystallography.

The structure and function relationships of various proteins are studied by analyzing 3D structure by X-ray crystallography. The target proteins include the PKC major substrate protein, MARCKS, proteins involved in the glycine-cleavage system, and other signaling proteins.

Structure-function relationship Studied by X-ray Crystallography.

The 3D structure of T-protein in glycine cleavage system. Disease-related mutations found in human NKH patients are mapped on the structure.



Professor Hisaaki TaniguchiProfessor
Hisaaki Taniguchi
TEL : 088-633-7426
E-mail : hisatan@ier.tokushima-u.ac.jp
Associate professor Hidetaka KosakoAssociate professor
Hidetaka Kosako
TEL : 088-633-9414
E-mail : kosako@ier.tokushima-u.ac.jp
Assistant professor Kazuko IkedaAssistant professor
Kazuko Ikeda
TEL : 088-633-9254
E-mail : ikeda@ier.tokushima-u.ac.jp



  1. Tashiro, K., Tsunematsu, T., Okubo, H., Ohta, T., Sano, E., Yamauchi, E., Taniguchi, H. and Konishi, H. (2009) GAREM, a novel adaptor protein for growth factor receptor-bound protein 2, contributes to cellular transformation through the activation of extracellular signal-regulated kinase signaling. J. Biol. Chem., 284, 20206-20214.
  2. Yamada, L., Saito, T., Taniguchi, H., Sawada, H. and Harada, Y. (2009) Comprehensive egg-coat proteome of an ascidian Ciona intestinalis reveals gamete recognition molecules involved in self-sterility. J. Biol. Chem., 284, 9402-9410.
  3. Kosako, H., Yamaguchi, N., Aranami, C., Ushiyama, M., Kose, S., Imamoto, N., Taniguchi, H., Nishida, E. and Hattori, S. (2009) Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport. Nature Struct. Mol. Biol., 16, 1026-1035.
  4. Harada, Y., Takagaki, Y., Sunagawa, M., Saito, T., Yamada, L., Taniguchi, H., Shoguchi, E. and Sawada, H. (2008) Mechanism of self-sterility in a hermaphroditic chordate. Science, 320, 548-550.
  5. Omi, S., Nakata, R., Okamura-Ikeda, K., Konishi, H., and Taniguchi, H. (2008) Contribution of peroxisome-specific isoform of Lon protease in sorting PTS1 protein to peroxisomes J. Biochem.143 (5) 649-660
  6. Ishino, Y., Okada, H., Ikeuchi, M. and Taniguchi, H. (2007) Mass spectrometry-based prokaryote gene annotation. Proteomics, 22, 4053-4065.
  7. Fujiwara, K., Hosaka, H., Matsuda, M., Okamura-Ikeda, K., Motokawa, Y., Suzuki, M., Nakagawa, A. and Taniguchi, H. (2007) Crystal structure of bovine lipoyltransferase in complex with lipoyl-AMP. J. Mol. Biol., 371, 222-234.
  8. Tashiro, K., Konishi, H., Sano, E., Nabeshi, H., Yamauchi, E. and Taniguchi, H. (2006) Suppression of the ligand-mediated downregulation of epidermal growth factor receptor by Ymer, a novel tyrosine phosphorylated and ubiquitinated protein. J. Biol. Chem., 281, 24612-24622.
  9. Konishi, H., Tashiro, K., Murata, Y., Nabeshi, H., Yamauchi, E. and Taniguchi, H. (2006) CFBP is a novel tyrosine phosphorylated protein which might function as a regulator of CIN85/CD2AP. J. Biol. Chem., 281, 28919-28931.
  10. Maezawa, K., Shigenobu, S., Taniguchi, H., Kubo, T., Aizawa, S. and Morioka, M. (2006) Hundreds of flagellar basal bodies cover the cell surface of the endosymbiotic bacterium Buchnera aphidicola sp. strain APS. J. Bacteriol., 188, 6539-6543.
  11. Tobe, T., Beatson, A.S., Taniguchi, H., Abe, H., Bailey, M.C., Fivian, A., Younis, R., Matthews, S., Marches, O., Frankel, G., Hayashi, T. and Pallen, J.M. (2006) An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. Proc. Natl. Acad. Sci. USA, 103, 14941-14946.
  12. Ozeki, S., Cheng, J., Tauchi-Sato, K., Hatano, N., Taniguchi, H. and Fujimoto, T. (2005) Rab18 localizes to lipid droplets and induces their close apposition to the endoplasmic reticulum-derived membrane. J. Cell Sci., 118, 2601-2611.
  13. Okamura-Ikeda, K., Hosaka, H., Yoshimura, M., Yamashita, E., Toma, S., Nakagawa, A., Fujiwara, K., Motokawa, Y. and Taniguchi, H. (2005) Crystal Structure of Human T-protein of Glycine Cleavage System at 2.0 A° Resolution and its Implication for Understanding Non-ketotic Hyperglycinemia. J. Mol. Biol., 351, 1146-1159.
  14. Fujiwara, K., Toma, S., Okamura-Ikeda, K., Motokawa, Y., Nakagawa, A. and Taniguchi, H. (2005) Crystal Structure of Lipoate-Protein Ligase A from Escherichia coli: DETERMINATION OF THE LIPOIC ACID-BINDING SITE. J. Biol. Chem., 280, 33645 – 33651.
  15. Kikuchi, M., Hatano, N., Yokota, S., Shimozawa, N., Imanaka, T. and Taniguchi, H. (2004) Proteomic analysis of rat liver peroxisome: presence of peroxisome-specific isozyme of Lon protease. J. Biol. Chem., 279, 421-428.
  16. Matsubara, M., Nakatsu, T., Kato, H. and Taniguchi, H. (2004): Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal domain complexed with Ca(2+)/calmodulin. EMBO J. 23, 712-718.
  17. Yamauchi, E., Nakatsu, T., Matsubara, M., Kato, H., and Taniguchi, H (2003) Crystal structure of a MARCKS peptide containing the calmodulin-binding domain in complex with Ca2+-calmodulin. Nature Struc. Biol. 10, 226-231.