Bioresource Research Collaborative Group Shinozaki ... Shinozaki Research Collaborative Group RIKEN

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Transcript of Bioresource Research Collaborative Group Shinozaki ... Shinozaki Research Collaborative Group RIKEN

  • ― 170 ―

    Laboratory Head

    Shinozaki Research Collaborative Group



    Plants differ from animals in various ways and have inherent

    capabilities that animals lack, such as plant-hormone-mediated

    regulation, responses to various environmental stresses, light

    regulation, and high-efficiency totipotency. Our research group

    is studying the functions of plant genes using various mutants

    (T-DNA/transposon insertional mutants and enhancer-tagged

    mutants) of Arabidopsis thaliana. The group is interested in

    plant genes involved in environmental stress response and

    Analysis of plant genes using insertional mutants,

    enhance-tagged mutants or FOX lines

    Collection of plant full-length cDNAs

    Members Chief Scientist, Director of Gene Discovery Research Group

    Kazuo SHINOZAKI, Ph.D. (2005. 4~) (1989. 4~2005.3 Director of Plant Molecular Biology Laboratory)

    Research Scientist

    Taishi UMEZAWA, Ph.D. (2005. 4~)

    Miki FUJITA, Ph.D. (2006. 4~) (2003.4~2006.3 CREST Research Scientist)

    Takashi KUROMORI, Ph.D. (2005.4~) Fumiyoshi MYOUGA, Ph.D. (2005.4~)

    Postdoctoral Researcher

    Kaoru URANO, Ph. D. (2005. 4~)

    Fuminori TAKAHASHI, Ph.D. (2007. 5~) (2004.4~2007.3 Junior Research Associate)

    Special Postdoctral Researcher

    Rie NISHIYAMA, Ph. D. (2006. 4~)

    JSPS Research Fellow

    Behnam Babak, Ph.D. (2007.10~)

    Special Fixed Term Contract Employee

    Saho MIZUKADO (2008.4~) (2006.4~2008.3 PSC Technical Staff)

    Junior Research Associate

    Masahide MIZOGUCHI (2007.4~)

    Student Trainee

    Masaki NAKAMURA (2005.4~2007.3)



    tolerance, plant hormone response, seed development and

    germination. The group aims to understand complex systems

    involved in the regulation of gene expression cellular signal

    transduction in response to environmental stimuli in higher

    plants. The group also wants to contribute to the collection of

    useful resources for basic biology and biotechnology through

    their research and development.

    Analysis of plant genes involved in environmental stress

    response and tolerance, plant hormone response, seed

    development and germination

    Comprehensive analysis of plant stress response by the

    “-omics” approach



    Bioresource Research Collaborative Group

    Kazuo SHINOZAKI, Ph.D.

  • Shinozaki Research Collaborative Group RIKEN BRC Annual Report 2005 ~ 2007

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    Umezawa, Nishiyama, Ito, Babak, Mizukado, Kobayashi, Matsuo, Eto, Urano Takahashi, Fujita, Mizoguchi, Shinozaki, Shodai, Ozawa

    Specific Aims

    1. Phenome analysis of Arabidopsis genes using Ds transposon mutant collection

    Using Ds-tagged Arabidopsis mutants with homozygous

    knockout genes , we are analyzing gene funct ions

    comprehensively. We have observed phenotypic changes of

    the mutants and analyzed the function of disrupted genes.

    In the course of the project, we have isolated a male sterile

    mutant, male sterility1 (ms1) (Fig. 1). The MS1 gene encodes

    a PHD-type transcriptional activator and regulates pleiotropic

    steps such as pollen grain and tapetum development.

    2. Soybean full-length cDNA project RIKEN PSC is planning to collect large sets of full-length

    cDNAs from various crops or trees. Our group constructed

    a full-length enriched cDNA library from soybean, which

    is the most important legume crop, as part of the project.

    Approximately 40,000 cDNA clones were collected, and

    Agency Staff

    Hatsuyo SHODAI (2000.1~) Hiroko KOBAYASHI (2003.4~)

    Kumiko OZAWA (2003.4~)

    [Antibiotic Laboratory]

    Senior Research Scientist

    Takuya ITO, Ph.D. (2007. 4~)(2000.4~2007.3 Plant Molecular Biology Laboratory)

    [Plant Molecular Biology Laboratory]

    Research Scientist

    Takeshi KATAGIRI, Ph.D. (2001.10~2007.3)

  • Shinozaki Research Collaborative Group RIKEN BRC Annual Report 2005 ~ 2007

    ― 172 ―

    some of the cDNAs were sequenced and analyzed. We are

    now preparing a database system for browsing our database of

    soybean full-length cDNAs (Fig.2).

    3. Miniscale FOX hunting system Recently, we developed a novel system known as full-length

    cDNA over-expressor (FOX) gene hunting, which involves

    the random overexpression of a normalized. Arabidopsis full-

    length cDNA library. Using a miniscale version of the system,

    which focused on 41 stress-inducible transcription factors, we

    identified AtbZIP60, a bZIP-type transcription factor, as a salt-

    tolerant gene.

    4. Functional analysis of plant genes involved in environmental stress response

    Plants have a complex network of signal transduction and

    gene expression through plant hormones in response to

    various environmental stresses, such as dehydration, high

    Figure 1. Transmission electron microscopic analysis of the ms1 mutant. MI: Microspore, TA: Tapetum. (A and C) Wild type. (B and D) ms1 mutant. (Compare A and B) In the ms1 mutant, microspores (arrows) and tapetum (arrow heads) became vacuolated, and finally, no mature pollen grains were formed. (Compare C and D) In the ms1 mutant, characteristic pollen wall structure, exine, was not formed.

    Figure 2. Schematic diagram of Soybean cDNA Project

    Soybean RNA mixture

    Full-length cDNA library


    Sequencing for 5’/3’-ends

    Clustering analysis






    markers etc.

    salinity and low temperature. To increase plant productivity,

    our research group is conducting gene hunting and functional

    analysis in relation to environmental stress response.

    5. Transgenic wheat project: Toward the practical use of stress tolerant crops (Fig. 3)

    To generate stress-tolerant transgenic wheat, we constructed

    transformation vectors containing useful Arabidopsis drought-

    tolerant genes such as AtGolS2, NCED3, and SnRK2C. In

    addition, we collected 38 wheat full-length genes orthologous

    to Arabidopsis genes that have been reported to function in

    drought stress. Based on the information from wheat EST

    pools, full-length cDNA clones, and microarray analysis,

    we are identifying the wheat constitutive or drought-stress-

    inducible promoters.

    6. Comprehensive analysis of ABA-regulated dehydration response utilizing metabolomics and transcriptomics in Arabidopsis

    In plants, adaptation to stress is a complex biological process

    involving global changes in gene expression and metabolite

    composition. We carried out an integrated analysis of the

    metabolome and transcriptome to reveal new molecular

    mechanisms of dynamic metabolic networks in response to

    dehydration using a knockout mutant of the NCED3 gene

    involved in the dehydration-inducible biosynthesis of ABA.

  • Shinozaki Research Collaborative Group RIKEN BRC Annual Report 2005 ~ 2007

    ― 173 ―

    Figure 3. Engineering environmental stress tolerant wheat We search and select the stress-inducible promoters and functional genes for molecular breeding about drought tolerance. Based on these knowledge, we produce the stress tolerant wheat in the field.

    Publications 【Original Papers】 (*Peer reviewed journals)

    Sakurai T., Satou M., Akiyama K., Iida K., Seki M.,

    Kuromori T., Ito T., Konagaya A., Toyoda T., Shinozaki

    K.: “RARGE: a large-scale database of RIKEN

    Arabidopsis resources ranging from transcriptome to

    phenome.” Nuc. Acid. Res. 33, D647-D650 (2005).*

    Osakabe Y., Maruyama K., Seki M., Satou M., Shinozaki

    K., Yamaguchi-Shinozaki K.: “An LRR receptor kinase,

    RPK1, is a key membrane-bound regulator of abscisic

    acid early signaling in Arabidopsis.” Plant Cell 17,

    1105-1119 (2005).*

    Urano K., Hobo T., Shinzoaki K.: “Arabidopsis ADC

    genes involved in polyamine biosynthesis are essential

    for seed development.” FEBS Lett. 579, 1557-1564


    Katagiri T., Ishiyama K., Kato T., Tabata S., Kobayashi

    M., Shinozaki K.: “An important role of phosphatidic

    acid in ABA signaling during germination in Arabidopsis

    thaliana.” Plant J. 43, 107-117 (2005).*

    Yamada M., Morishita H., Urano K., Shinozaki N.,






    Yamaguchi-Shinozaki K., Shinozaki K., Yoshiba Y.:

    “Effects of free proline accumulation in petunias under

    drought stress.” J. Exp. Bot. 56. 1975-1981 (2005).*

    Noutoshi Y., Ito T., Seki M., Nakashita H., Yoshida S.,

    Marco Y., Shirasu K., Shinozaki K.: “A single amino acid

    insetion in the WRKY domain of the Arabidopsis TIR-

    NBS-LRR-WRKY type disease resistance protein SLH

    (SENSITIVE TO LOW HUMIDITY1) causes activation

    of defense responses and hypersensitive cell death.” Plant

    J. 43, 873-888 (2005).*

    Ito T., Motohashi R., Kuromori T., Noutoshi Y., Seki M.,

    Kamiya A., Mizukado S., Sakurai T., Shinozaki K.: “A

    resource of 5,814 dissociation transposon-tagged and

    sequence-indexed lines of Arabidopsis tran