Associated Research Group

From April 2018, we promote this New Area of Scientific Study with the following 19 associated research groups and core research groups.


Arimura group
Memory and transition system for defense responses via plant-plant communications
Chiba group
Control of mRNA degradation related to environmental stress recovery and memory
Endo group
Time information sharing mechanism via
vascular bundles
Fujii group
A study on the physiological reversibility during self/non-self pollen recognition in the Brassicaceae species
Kawasaki group
Pattern-triggered immunity and immune priming in rice
Kiba group
Molecular mechanisms and physiological roles of long-distance cytokinin transport
Kimura group
Studies of adaptive evolution of aquatic plants using Rorippa aquatica
Matsushita group
Light-regulated modulation of protein subcellular localization
Notaguchi group
Study on systemic RNAs that respond to specific environments
Saijo group
Transcriptional reprogramming and priming via polycomb repressor complex in systemic plant immunity
Seki group
Analysis of antisense ncRNA-mediated plant environmental stress adaptation
Shimizu group
Environmental signal recognition and memorization studied by time-course transcriptome data in aseasonal tropical rain forests
Suzaki group
Elucidation of molecular mechanisms underlying nitrate-induced control of root nodule symbiosis
Takahashi group
Elucidation of long-distance signaling via peptide-receptor module in response to water-deficit conditions
Takano group
Plant defense system that autonomously responds to local invasion by pathogenic fungi
Takezawa group
Studies of integrated signaling pathways for ABA, low temperature and osmotic responses in bryophytes
Tamada group
Role of chromatin state in the reconstruction of cellular memory in plants
Toyota group
Molecular mechanisms underlying root-to-shoot rapid calcium signaling
Uchida group
Elucidation of phloem-mediated signals for growth and environmental responses
Yamaguchi group
Elucidation of molecular mechanism for heat acclimation by histone modification

Arimura Group:
Memory and transition system for defense responses via plant-plant communications

  • Research plan representative Gen-ichiro Arimura
    Associate Professor, Department of Biological Science & Technology, Faculty of Industrial Science & Technology, Tokyo University of Science
    Collaborative researcher Sachihiro Matsunaga
    Professor, Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
    Collaborative researcher Takuya Sakamoto
    Assistant Professor, Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
    Gen-ichiro Arimura
    Gen-ichiro Arimura
    Plants are able to eavesdrop on volatile organic chemicals emitted from their neighboring plants in response to herbivore attack. To reveal the mechanisms underlying defense responses promoted via these plant-plant communications, we focus on aroma-rich mint species serving as volatile emitters. We conduct our analyses to understand the maintenance and priming system for defense responses in receiver plants exposed with mint aroma.

Chiba Group:
Control of mRNA degradation related to environmental stress recovery and memory

- Since August 2018

  • Research plan representative Yukako Chiba
    Associate Professor, Faculty of Science and Graduate School of Life Science, Hokkaido University
    Yukako Chiba
    Yukako Chiba
    Plants cannot escape from unfavorable environmental conditions, therefore, they have developed various strategies to respond and adjust to environmental stresses for their survival. Control of gene expression is one important strategy in the stress response. However, expression of stress responsive genes sometimes inhibits the plant growth as a trade-off with acquisition of the stress tolerance. Therefore, when returning to favorable environmental conditions, it is necessary to abruptly decrease the mRNA amount of the stress responsive gene by mRNA degradation. In this study, we will elucidate the molecular mechanism and physiological significance of mRNA degradation control of stress responsive genes by Arabidopsis deadenylase, AtCCR4 and RNA binding protein, APUM5.

Endo Group:
Time information sharing mechanism via vascular bundles

  • Research plan representative Motomu Endo
    Professor, Graduate School of Biological Sciences, Nara Institute of Science and Technology
    Motomu Endo
    Motomu Endo
    Plants sense variety of environmental cues at a specific tissue/organ and integrate these information at an individual level. However, how plants achieve long-distance time information sharing remains unclear. Here, we aim to show a root-shoot feedback loop as a time information sharing mechanism. In particular, we test the possibility that time information is stored in roots and transmitted to the shoot as nutrients.

Fujii Group:
A study on the physiological reversibility during self/non-self pollen recognition
in the Brassicaceae species

  • Research plan representative Sota Fujii
    Assistant Professor, Graduate School of Agricultural and Life Sciences, The University of Tokyo
    Collaborative researcher Takashi Tsuchimatsu
    Associate Professor, Department of Biology, Faculty of Science, Chiba University
    Collaborative researcher Seiji Takayama
    Professor, Graduate School of Agricultural and Life Sciences, The University of Tokyo
    Sota Fujii
    Sota Fujii
    More than half of the plants discriminates self/non-self pollen via the mechanism known as the 'self-incompatibility'; to avoid self-breeding, and to promote out-crossing. This system maintains the genetic diversity in the population, and species selection maintains this system. In this project, we aim to study the integrity of cellular information, or the duration and the decay of the signals, by using the self-incompatibility system as a model. We will investigate on how the information is processed when pistils are heterologously pollinated by self and non-self pollen grains, by the live-imaging techniques.

Kawasaki Group:
Pattern-triggered immunity and immune priming in rice

  • Research plan representative Tsutomu Kawasaki
    Professor, Graduate School of Agriculture, Kindai University
    Collaborative researcher Koji Yamaguchi
    Associate Professor, Graduate School of Agriculture, Kindai University
    Tsutomu Kawasaki
    Tsutomu Kawasaki
    Plants rapidly induce a series of immune response by recognition of pathogen-associated molecular patterns (Pattern-triggered immunity: PTI). Repetitive infection of pathogens and treatment of plant defense activator BTH induce immune priming, a type of plant immunological memory. In this study, we aim to elucidate the molecular mechanisms of PTI and immune priming in rice.

Kiba Group:
Molecular mechanisms and physiological roles of long-distance cytokinin transport

  • Research plan representative Takatoshi Kiba
    Associate Professor, Graduate School of Bioagricultural Sciences, Nagoya University
    Collaborative researcher Hitoshi Sakakibara
    Professor, Graduate School of Bioagricultural Sciences, Nagoya University
    Takatoshi Kiba
    Takatoshi Kiba
    Plants maximize fitness by coordinating growth and development of organs such as the shoot and the root in response to environmental changes. Cytokinins have been implicated in the coordination acting as a long-distance signal translocated via vasculature. We aim at understanding mechanisms and physiological roles of the translocation. The project is organized into two tasks: (i) identification of the molecular basis underlying xylem loading of cytokinins and (ii) elucidation of the physiological role of root-to-shoot translocated cytokinins.

Kimura Group:
Studies of adaptive evolution of aquatic plants using Rorippa aquatica

  • Research plan representative Seisuke Kimura
    Professor, Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University
    Collaborative researcher Keiko Torii
    Visiting Professor, ITBM, Nagoya University
    Collaborative researcher Tomoaki Sakamoto
    Research Associate, Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University
    Collaborative researcher Shuka Ikematsu
    Postdoctoral Researcher, Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University
    Seisuke Kimura
    Seisuke Kimura
    Phenotypic plasticity is the ability of an organism to change its development and physiology depending on environmental conditions. Some plants demonstrate alterations in leaf form in response to changes in the environment, which is called heterophylly. Rorippa aquatica is a perennial herbaceous semiaquatic plant whose habitat is riparian area in North America. This plant shows heteropylly and develops pinnately dissected leaves under submerged conditions, while it forms simple leaves with serrated margins under terrestrial conditions. Interestingly, R. aquatica lost sexual reproduction ability and propagates asexually by regeneration in nature, which is also thought to be adaptive trait to aquatic environment. We will investigate the molecular basis of the heterophylly and the suppression of flowering to understand the process of adaptive evolution to aquatic environment.

Matsushita Group:
Light-regulated modulation of protein subcellular localization

  • Research plan representative Tomonao Matsushita
    Associate Professor, Faculty of Agriculture, Kyushu University
    Tomonao Matsushita
    Tomonao Matsushita
    It is widely believed that phytochrome regulates the transcription of light-responsive genes by modulating the activity of several transcription factors. However, we recently found that phytochrome controls not only transcription, but also other aspects of gene expression, to mediate light responses in Arabidopsis. The goal of this study is to reveal this novel mechanism of light-regulated gene exparession at a molecular level. Moreover, we try to investigate the possibility that, through this mechanism, plants may memorize protein subcellular localization patterns depending on the environmental light information.

Notaguchi Group:
Study on systemic RNAs that respond to specific environments

  • Research plan representative Michitaka Notaguchi
    Assistant Professor, Graduate School of Bioagricultural Sciences, Nagoya University
    Michitaka Notaguchi
    Michitaka Notaguchi
    Plants evolved organ-to-organ, long-distance signaling systems to control development and growth in response to surrounding environments. One of crucial mechanisms is the molecular transport via phloem. This study aims at elucidating the roles of phloem-mobile RNAs that respond to specific environments, such as the level of available macronutrients, N, P and K under the soil conditions.

Saijo Group:
Transcriptional reprogramming and priming via polycomb repressor complex
in systemic plant immunity

  • Research plan representative Yusuke Saijo
    Associate Professor, Graduate School of Biological Sciences, Nara Institute of Science and Technology
    Collaborative researcher Yuri Tajima
    Designated Assistant Professor, Graduate School of Biological Sciences, Nara Institute of Science and Technology
    Yusuke Saijo
    Yusuke Saijo
    In plants, pathogen recognition leads to immune activation through extensive transcriptional reprogramming in both challenged and distal unchallenged sites. Following this, defense-related genes become poised for a greater and/or faster activation in response to second stimulation. Our findings indicate that transcription-permissive and transcription-repressive histone modifications on defense-related genes both contribute to defense priming in Arabidopsis. We pursue in particular the mechanisms by which the polycomb repressor complex (PRC2), an evolutionarily conserved mediator of transcription-repressive histone modificaiton, positively influences defense-related transcriptional reprogramming and priming during systemic immune activation. We expect that these studies will deepen our understanding of how PRC2 modulates immune response and memory in plants.

Seki Group:
Analysis of antisense ncRNA-mediated plant environmental stress adaptation

  • Research plan representative Motoaki Seki
    Team Leader, RIKEN CSRS, Plant Genomic Network Research Team
    Collaborative researcher Akihiro Matsui
    Postdoctoral Fellow, RIKEN CSRS, Plant Genomic Network Research Team
    Motoaki Seki
    Motoaki Seki
    Recently, we demonstrated that abiotic stress-responsive antisense non-coding RNAs (ncRNAs) are synthesized from sense transcripts of protein-coding genes without the involvement of siRNA biosynthesis by RNA-dependent RNA polymerases (RDRs) and function in drought stress adaptation. In this study, we will identify novel genes involved in the biogenesis of the stress-responsive antisense ncRNAs, and elucidate the molecular mechanisms of the antisense ncRNAs-mediated plant environmental stress adaptation and memory.

Shimizu Group:
Environmental signal recognition and memorization studied by time-course transcriptome data in aseasonal tropical rain forests

  • Research plan representative Kentaro Shimizu
    Guest Professor, Kihara Institute for Biological Research, Yokohama City University
    Collaborative researcher Hiroshi Kudoh
    Professor, Center for Ecological Research, Kyoto University
    Collaborative researcher Toshiaki Tameshige
    Research Assistant Professor, Kihara Institute for Biological Research, Yokohama City University
    Kentaro Shimizu
    Kentaro Shimizu
    Plant gene network has adapted to natural complex environments, thus the laboratory regulated environments may not be enough to understand how plants sense and remember environmental stimuli. We have developed methods to analyze genome-wide expression patterns and meteorological data in naturally fluctuating environments, or in natura. We will focus on environmental responses in aseasonal tropical forests.

Suzaki Group:
Elucidation of molecular mechanisms underlying nitrate-induced control of
root nodule symbiosis

  • Research plan representative Takuya Suzaki
    Associate Professor, University of Tsukuba
    Collaborative researcher Masayoshi Kawaguchi
    Professor, National Institute for Basic Biology
    Takuya Suzaki
    Takuya Suzaki
    Root nodule symbiosis is a mutualistic interaction observed between mainly leguminous plants and nitrogen-fixing soil rhizobia, in which plants can obtain fixed atmospheric nitrogen, and provide rhizobia with photosynthate as a carbon source. In response to nitrogen amount in the soil, plants control the formation of root nodules: nodulation is significantly inhibited under nitrogen-abundant environment, whereas nitrogen-deficient condition promotes nodulation. In this research, we aim to elucidate the molecular mechanisms of the nitrogen-mediated control of nodulation, in which systemic and local regulatory mechanism are involved depending on each developmental stage of nodulation.

Takahashi Group:
Elucidation of long-distance signaling via peptide-receptor module in response to
water-deficit conditions

  • Research plan representative Fuminori Takahashi
    Researcher, RIKEN Center for Sustainable Resource Science Gene discovery research group
    Collaborative researcher Kazuo Shinozaki
    Director, RIKEN Center for Sustainable Resource Science
    Fuminori Takahashi
    Fuminori Takahashi
    Water-deficit response is an important and rapid mechanism of sensing and propagation of information about water status. It is thought that water-deficit signal is transmitted rapidly from roots to shoots and promotes abscisic acid (ABA), one of the plant hormones, accumulation in leaves. However, no long-distance signaling molecules that mediate root-to-shoot communication and trigger ABA accumulation in leaves have been identified. In this study, we focus on the receptor like kinases mediating root-to-shoot signaling, and figure out the perception mechanism that receptors recognize the peptide in response to water-deficit conditions.

Takano Group:
Plant defense system that autonomously responds to local invasion by pathogenic fungi

  • Research plan representative Yoshitaka Takano
    Professor, Graduate School of Agriculture, Kyoto University
    Yoshitaka Takano
    Yoshitaka Takano
    Each plant exhibits robust resistance against plant pathogenic fungi that are not adapted to itself. This immune system consists of multilayered defense systems that include (i) the first layered defense that control entry trials of non-adapted pathogens, and (ii) the second layered defense that is locally activated upon pathogen invasion and terminate further invasive growth. The latter is called post-invasive defense and its molecular background is largely unknown. In this study, we aim to elucidate the molecular mechanism of this local and autonomous plant immune system that is newly activated upon pathogen invasion.

Takezawa Group:
Studies of integrated signaling pathways for ABA, low temperature and
osmotic responses in bryophytes

  • Research plan representative Daisuke Takezawa
    Professor, Graduate School of Science and Engineering, Saitama University
    Collaborative researcher Yoichi Sakata
    Professor, Faculty of Applied Biosciences, Tokyo University of Agriculture
    Daisuke Takezawa
    Daisuke Takezawa
    Environmental signals such as desiccation and cold affect levels of the stress hormone abscisic acid (ABA), which plays a key role in protection of cells from stress-induced lethal damage. How different environmental signals as well as the ABA signal are integrated to control cellular processes necessary for stress tolerance has not been clarified. To elucidate mechanisms underlying autonomous responses of plant cells to various environmental stress signals, our studies focus on identification signaling factors integrating stress signals by analysis of model bryophytes. We analyze interactions between the identified factors and known signaling factors to determine critical processes necessary for integrative control of stress signals.

Tamada Group:
Role of chromatin state in the reconstruction of cellular memory in plants

  • Research plan representative Yosuke Tamada
    Assistant Professor, Division of Evolutionary Biology, National Institute for Basic Biology
    Collaborative researcher Mitsuyasu Hasebe
    Professor, Division of Evolutionary Biology, National Institute for Basic Biology
    Yosuke Tamada
    Yosuke Tamada
    Chromatin state plays a key role in the regulation of cellular memory. Roles of chromatin modifications in cellular memory become studied gradually. On the other hand, chromatin state is established by not only chromatin modifications, but also histone variants and chromatin structure. This project aims at understanding the interaction between chromatin modifications, histone variants, and chromatin structure, which is involved in the regulation of cellular memory. We use the moss Physcomitrella patens taking advantage of its clear cell identities, and one of the main focuses of the project is the role of histone variant H3.3 in chromatin state and the regulation of cellular memory.

Toyota Group:
Molecular mechanisms underlying root-to-shoot rapid calcium signaling

- Until July 2018

  • Research plan representative Masatsugu Toyota
    Associate Professor, Department of Biochemistry and Molecular Biology, Saitama University
    First_name Sirname
    Masatsugu Toyota
    Plants, unlike animals, do not have a nervous system, but they can rapidly perceive local environmental stresses, propagate this information throughout the plant body and activate systemic responses. For example, when the Arabidopsis root is mechanically wounded or attacked by insects, plants activate defense responses not only in the wounded root but also in distal organs such as shoots within a few minutes. However, the molecular machinery underlying such immediate sensory and root-to-shoot signal transduction remains largely unknown. Using genetically-encoded calcium and glutamate indicators, image splitting optics and electrophysiological techniques, we will elucidate glutamate/ionotropic glutamate receptor channels/calcium signal-based systemic defense network in plants.

Uchida Group:
Elucidation of phloem-mediated signals for growth and environmental responses

  • Research plan representative Naoyuki Uchida
    Designated Associate Professor, Institute of Transformative Bio-Molecules, Nagoya University,
    Naoyuki Uchida
    Naoyuki Uchida
    In this project, I focus on a peptide hormone secreted from the endodermis of inflorescence stems, which is perceived by its receptor at phloem companion cells. It is hypothesized that activation of the receptor triggers production of unknown secondary signal in the phloem to promote stem elongation. I aim to elucidate the nature of this phloem-derived signal and also investigate how this signal affects behaviors of its target cells/tissues in stems. As this peptide signaling seems to have another function for successful pollination at a lower temperature, I will also analyze its role in this regulation.

Yamaguchi Group:
Elucidation of molecular mechanism for heat acclimation by histone modification

  • Research plan representative Nobutoshi Yamaguchi
    Assistant Professor, Graduate School of Science and Technology, Nara Institute of Science and Technology
    Nobutoshi Yamaguchi
    Nobutoshi Yamaguchi
    As sessile organisms, plants need to adapt to surrounding environmental changes for survival. Heat experience is memorized in plants to become responsive to future thermal stimuli. Histone modification is known to mediate the changes in gene expression over long timescale. Although acclimation to relatively high temperature enables plants to tolerate subsequent lethal conditions, little is known about a molecular basis of this regulation. We have found that histone demethylases, JUMONJI30 (JMJ30) and JMJ32, play an important role in heat acclimation in Arabidopsis. Based on a molecular genetic approach, we will establish a way for 'improvement of heat memory' in plants.