Scientific Research on Innovative Areas, a MEXT Grant-in Aid Project FY2015-2019
Integrative system of autonomous environmental signal recognition and memorization for plant plasticity

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

• Research plan representative	Gen-ichiro Arimura Associate Professor, Department of Biological Science & Technology, Faculty of Industrial Science & Technology, Tokyo University of Science
  Research Collaborator	Sachihiro Matsunaga Professor, Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
  Research Collaborator	Takuya Sakamoto Assistant Professor, Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
  	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

  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

  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
  Research Collaborator	Takashi Tsuchimatsu Associate Professor, Department of Biology, Faculty of Science, Chiba University
  Research Collaborator	Seiji Takayama Professor, Graduate School of Agricultural and Life Sciences, The University of Tokyo
  	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
  Research Collaborator	Koji Yamaguchi Associate Professor, Graduate School of Agriculture, Kindai University
  	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
  Research Collaborator	Hitoshi Sakakibara Professor, Graduate School of Bioagricultural Sciences, Nagoya University
  	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
  Research Collaborator	Keiko Torii Visiting Professor, ITBM, Nagoya University
  Research Collaborator	Tomoaki Sakamoto Research Associate, Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University
  Research Collaborator	Shuka Ikematsu Postdoctoral Researcher, Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University
  	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

  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
  	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
  Research Collaborator	Yuri Tajima Designated Assistant Professor, Graduate School of Biological Sciences, Nara Institute of Science and Technology
  	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
  Research Collaborator	Akihiro Matsui Postdoctoral Fellow, RIKEN CSRS, Plant Genomic Network Research Team
  	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
  Research Collaborator	Hiroshi Kudoh Professor, Center for Ecological Research, Kyoto University
  Research Collaborator	Toshiaki Tameshige Research Assistant Professor, Kihara Institute for Biological Research, Yokohama City University
  	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
  Research Collaborator	Masayoshi Kawaguchi Professor, National Institute for Basic Biology
  	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
  Research Collaborator	Kazuo Shinozaki Director, RIKEN Center for Sustainable Resource Science
  	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

  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
  Research Collaborator	Yoichi Sakata Professor, Faculty of Applied Biosciences, Tokyo University of Agriculture
  	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 Associate Professor, School of Engineering, Utsunomiya University
  Research Collaborator	Mitsuyasu Hasebe Professor, Division of Evolutionary Biology, National Institute for Basic Biology
  	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

  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,

  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

  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.