Functional proteomics team

1 Protein Expression　　2 Protein Network Analysis

Mission ： 1 Protein Expression

Leader Naoki Goshima

Tne complete ORF regions of full-length human cDNAs are going to be cloned using gateway entry vectors.
Gateway entry vectors are an efficient and versatile method for transferring DNA segments to various vectors rapidly.
It is hoped that development of new expression vectors will expand the usage of the Gateway system in protein expression studies.

Accomplishments

The creation of 49,000 Gateway entry clones derived from 22,000 full-length human cDNA clones.
Obtaining the protein expression information for more than 20,000 clones.
Success in the production of 20,000 Human Protein Microarrays.

Research result

2014

Detection of tumor-associated antigens in culture supernatants using autoantibodies in sera from patients with bladder cancer. Biomedical Research (Tokyo) 35 (1) 25-35, (2014) Sho MINAMI, Ryo NAGASHIO, Junpei UEDA, Kazumasa MATSUMO, Naoki GOSHIMA, Manabu HATTORI,Kazuo HACHIMURA, Masatsugu IWAMURA, and Yuichi SATO

Genome-wide co-localization screening of nuclear body components using a fluorescently tagged FLJ cDNA clone library. Methods in Molecular Biology (in press)(2014) Tetsuro Hirose and Naoki Goshima

2013

Integrated View of the Human Chromosome X-centric Proteome Project. J. Proteome Res., 12, 58−61, (2013) Tadashi Yamamoto, Keiichi Nakayama, Hisashi Hirano, Takeshi Tomonaga, Yasushi Ishihama, Tetsushi Yamada, Tadashi Kondo, Yoshio Kodera, Yuichi Sato, Norie Araki, Hiroshi Mamitsuka, and Naoki Goshima.

An active C-terminally truncated form of Ca2+/calmodulin-dependent protein kinase phosphatase-N (CaMKP-N/PPM1E) BioMed Research International（in press） vol. 2013, Article ID 134813, 10 pages, 2013. doi:10.1155/2013/134813. (2013) Atsuhiko Ishida, Kumiko Tsumura, Megu Oue, Yasuhiro Takenaka, Yasushi Shigeri, Naoki Goshima, Yasuhiro Ishihara, Tetsuo Hirano, Hiromi Baba, Noriyuki Sueyoshi,Isamu Kameshita and Takeshi Yamazaki.

An Efficient Non-viral Method to Generate Integration-Free Human iPS Cells from Cord Blood and Peripheral Blood Cells. Stem Cells, 31(3), 458-66 (2013) Keisuke Okita, Tatsuya Yamakawa, Yasuko Matsumura, Yoshiko Sato, Naoki Amano, Akira Watanabe, Naoki Goshima, and Shinya Yamanaka

Non-canonical NOTCH signaling limits self-renewal of human epithelial and iPS cells through ROCK activation. Mol Cell Biol.33（22）, 4434 – 4447（2013） Takashi Yugawa, Koichiro Nishino, Shin-ichi Ohno, Tomomi Nakahara, Masatoshi Fujita, Naoki Goshima, Akihiro Umezawa and Tohru Kiyono

2012

Specificity of botulinum protease for human VAMP family proteins. Microbiol Immunol. 56, 245-253. Yamamoto, H., Ida, T., Tsutsuki, H., Mori, M., Matsumoto, T., Kohda, T., Mukamoto, M., Goshima, N., Kozaki, S. and Ihara, H.

Anti-HuC and -HuD autoantibodies are differential sero-diagnostic markers for small cell carcinoma from large cell neuroendocrine carcinoma of the lung. Int J Oncol. 40, 1957-62. Matsumoto, T., Ryuge, S., Kobayashi, M., Kageyama, T., Hattori, M., Goshima, N., Jiang, S. X., Saegusa, M., Iyoda, A., Satoh, Y., Masuda, N. and Sato, Y.

HGPD: Human Gene and Protein Database, 2012 update. Nucleic Acids Res. 40, D924-9. Maruyama, Y., Kawamura, Y., Nishikawa, T., Isogai, T., Nomura, N. and Goshima, N.

CAXII Is a Sero-Diagnostic Marker for Lung Cancer. PLoS One. 7, e33952. Kobayashi, M., Matsumoto, T., Ryuge, S., Yanagita, K., Nagashio, R., Kawakami, Y., Goshima, N., Jiang, S. X., Saegusa, M., Iyoda, A., Satoh, Y., Masuda, N. and Sato, Y.

2011

Efficient protein transduction method using cationic peptides and lipids. J Biomed Biotechnol. 2011, 872065. Yamaguchi, K., Inoue, M. and Goshima, N.

Cathepsin L is highly expressed in gastrointestinal stromal tumors. Int J Oncol. 39, 1109-15. Miyamoto, K., Iwadate, M., Yanagisawa, Y., Ito, E., Imai, J., Yamamoto, M., Sawada, N., Saito, M., Suzuki, S., Nakamura, I., Ohki, S., Saze, Z., Kogure, M., Gotoh, M., Omicronbara, K., Ohira, H., Tasaki, K., Abe, M., Goshima, N., Watanabe, S., Waguri, S. and Takenoshita, S.

Nuclear Chk1 prevents premature mitotic entry. J Cell Sci. 124, 2113-9. Matsuyama, M., Goto, H., Kasahara, K., Kawakami, Y., Nakanishi, M., Kiyono, T., Goshima, N. and Inagaki, M.

Direct reprogramming of somatic cells is promoted by maternal transcription factor Glis1. Nature. 474, 225-9. Maekawa, M., Yamaguchi, K., Nakamura, T., Shibukawa, R., Kodanaka, I., Ichisaka, T., Kawamura, Y., Mochizuki, H., Goshima, N. and Yamanaka, S.

Statistical analysis of features associated with protein expression/solubility in an in vivo Escherichia coli expression system and a wheat germ cell-free expression system. J Biochem. 150, 73-81. Hirose, S., Kawamura, Y., Yokota, K., Kuroita, T., Natsume, T., Komiya, K., Tsutsumi, T., Suwa, Y., Isogai, T., Goshima, N. and Noguchi, T.

Development and evaluation of data-driven designed tags (DDTs) for controlling protein solubility. N Biotechnol. 28, 225-31. Hirose, S., Kawamura, Y., Mori, M., Yokota, K., Noguchi, T. and Goshima, N.

2010

A novel yeast cell-based screen identifies flavone as a tankyrase inhibitor. Biochem Biophys Res Commun. 394, 569-73. Yashiroda, Y., Okamoto, R., Hatsugai, K., Takemoto, Y., Goshima, N., Saito, T., Hamamoto, M., Sugimoto, Y., Osada, H., Seimiya, H. and Yoshida, M.

Comparative analysis of human SRC-family kinase substrate specificity in vitro. J Proteome Res. 9, 5982-93. Takeda, H., Kawamura, Y., Miura, A., Mori, M., Wakamatsu, A., Yamamoto, J., Isogai, T., Matsumoto, M., Nakayama, K. I., Natsume, T., Nomura, N. and Goshima, N.

High-throughput kinase assay based on surface plasmon resonance. Methods Mol Biol. 627, 131-45. Takeda, H., Goshima, N. and Nomura, N.

Introduction of amino acid residues at the N-terminus of the zeocin-resistance protein increases its expression in Saccharomyces cerevisiae. Biotechnol Lett. 32, 1515-21. Sugano, Y., Kawamura, Y., Goshima, N., Morita, N. and Ohgiya, S.

Comprehensive screening of human genes with inhibitory effects on yeast growth and validation of a yeast cell-based system for screening chemicals. J Biomol Screen. 15, 368-78. Sekigawa, M., Kunoh, T., Wada, S., Mukai, Y., Ohshima, K., Ohta, S., Goshima, N., Sasaki, R. and Mizukami, T.

Expression of RACK1 is a novel biomarker in pulmonary adenocarcinomas. Lung Cancer. 69, 54-9. Nagashio, R., Sato, Y., Matsumoto, T., Kageyama, T., Satoh, Y., Shinichiro, R., Masuda, N., Goshima, N., Jiang, S. X. and Okayasu, I.

A novel human dynactin-associated protein, dynAP, promotes activation of Akt, and ergosterol-related compounds induce dynAP-dependent apoptosis of human cancer cells. Mol Cancer Ther. 9, 2934-42. Kunoh, T., Noda, T., Koseki, K., Sekigawa, M., Takagi, M., Shin-ya, K., Goshima, N., Iemura, S., Natsume, T., Wada, S., Mukai, Y., Ohta, S., Sasaki, R. and Mizukami, T.

2009

Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics. Nucleic Acids Res. 37(Database issue), D762-6. Yukio Maruyama, Ai Wakamatsu, Yoshifumi Kawamura, Kouichi Kimura, Jun-ichi Yamamoto, Tetsuo Nishikawa, Yasutomo Kisu, Sumio Sugano, Naoki Goshima, Takao Isogai, Nobuo Nomura.

Novel In Vitro Protein Fragment Complementation Assay Applicable to High-Throughput Screening in 1536-Well Format. Journal of Biomolecular Screening. 14(8), 970-979. Junko Hashimoto, Taku Watanabe, Tatsuya Seki, Satoshi Karasawa, Miho　Izumikawa, Tomoe Seki, Shun-ichiro Iemura, Tohru Natsume, Nobuo Nomura, Naoki Goshima, Atsushi Miyawaki, Motoki Takagi1 and Kazuo Shin-ya.

Expression of RACK1 is a novel biomarker in pulmonary adenocarcinomas. Lung Cancer　In press. Ryo Nagashio, Yuichi Sato, Toshihide Matsumoto, Taihei Kageyama, Yukitoshi Satoh, Ryuge Shinichiro, Noriyuki Masuda, Naoki Goshima, Shi-Xu Jiang, Isao Okayasu.

2008

Human protein factory for converting the transcriptome into an in vitro-expressed proteome. Nature Methods. 5(12), 1011-7. Naoki Goshima, Yoshifumi Kawamura, Akiko Fukumoto, Aya Miura, Reiko Honma, Ryohei Satoh, Ai Wakamatsu, Jun-ichi Yamamoto, Kouichi Kimura, Tetsuo Nishikawa, Taichi Andoh, Yuki Iida, Kumiko Ishikawa, Emi Ito, Naoko Kagawa, Chie Kaminaga, Kei-ichi Kanehori, Bunsei Kawakami, Kiyokazu Kenmochi, Rie Kimura, Miki Kobayashi, Toshihiro Kuroita, Hisashi Kuwayama, Yukio Maruyama, Kiyoshi Matsuo, Kazuyoshi Minami, Mariko Mitsubori, Masatoshi Mori, Riyo Morishita, Atsushi Murase, Akira Nishikawa, Shigemichi Nishikawa, Toshihiko Okamoto, Noriko Sakagami, Yutaka Sakamoto, Yukari Sasaki, Tomoe Seki, Saki Sono, Akio Sugiyama, Tsuyoshi Sumiya, Tomoko Takayama, Yukiko Takayama, Hiroyuki Takeda, Takushi Togashi, Kazuhide Yahata, Hiroko Yamada, Yuka Yanagisawa, Yaeta Endo, Fumio Imamoto, Yasutomo Kisu, Shigeo Tanaka, Takao Isogai, Jun-ichi Imai, Shinya Watanabe, Nobuo Nomura.

2007

A Novel Nuclear Export Inhibitor JBIR-02, a New Piericidin Discovered from Streptomyces sp. ML55. J Antibiot (Tokyo). 60(7), 459-62. Jun-Ya Ueda, Takushi Togashi, Susumu Matukura, Aya Nagai, Takuji Nakashima, Hisayuki Komaki, Kozue Anzai, Shigeaki Harayama, Takayuki Doi, Takashi Takahashi, Tohru Natsume, Yasutomo Kisu, Naoki Goshima, Nobuo Nomura, Motoki Takagi, Kazuo Shin-Ya.

Structural basis of the collagen-binding mode of discoidin domain receptor 2. EMBO J. 16, 17703188. Osamu Ichikawa, Masanori Osawa, Noritaka Nishida, Naoki Goshima, Nobuo Nomura, Ichio Shimada.

2006

Immobilization of diverse foreign proteins in viral polyhedra and potential application for protein microarrays. PROTEOMICS. vol.6, 54-66. Keiko Ikeda, Hiroshi Nakazawa, Ai Shimo-Oka, Kaoru Ishio,Seiji Miyata, Yoichiroh Hosokawa, Satoshi Matsumura, Hiroshi Masuhara,Serge Belloncik, Robert Alain, Naoki Goshima, Nobuo Nomura, Kenichi Morigaki, Atsushi Kawai, Toshihiro Kuroita, Bunsei Kawakami,Yaeta Endo and Hajime Mori.

Comprehensive analysis of the ICEN (Interphase Centromere Complex) components enriched in the CENP-A chromatin of human cells. Genes to Cells. 11, 673-684. Izuta H, Ikeno M, Suzuki N, Tomonaga T, Nozaki N, Obuse C, Kisu Y, Goshima N, Nomura F, Nomura N, Yoda K.

High-throughput kinase assay based on surface plasmon resonance suitable for nayive protein substrates. Anal. Biochem. 357(2), 262-271. Hiroyuki Takeda, Akiko Fukumoto, Aya Miura, Naoki Goshima, Nobuo Nomura.

Differential responses of normal human coronary artery endothelial cells against multiple cytokines comparatively assessed by gene expression profiles. FEBS Letters. 580(30), 6871-9. Aya Miura, Reiko Honma, Takushi Togashi, Yuka Yanagisawa, Emi Ito, Jun-ichi Imai, Takao Isogai, Naoki Goshima, Shinya Watanabe, Nobuo Nomura.

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