Core Research Group

The objective of this area of study is to clarify the distributed response of cells and tissues of plants, which do not have a central nervous system, and to determine how plants control such information through the whole-organism signal transduction system. This research will lead to a complete picture of the mechanisms underlying dynamic signal transduction in response to environmental stimuli that are unique to plants.

We carefully selected eight planning groups that are essential for completing this objective. In order to achieve a comprehensive understanding of the molecular mechanisms of various environmental responses in plants, the research program cannot be structured as a collection of individual studies; rather, it must be an integrated and strategic research program. Therefore, we did not break up the research areas, and instead opted for an organic, collaborative research framework in which the eight planning group team members work together to forge a new field of study.

Moreover, we centralized common, large equipment and analysis using the latest technologies at the research support centers, so that they can provide support for the entire program, leading to efficient research progress.

Kinoshita Group: Analysis of stomatal aperture control mechanisms in response to environmental stimuli

Research plan representative	Toshinori Kinoshita Professor, Institute of Transformative Bio-Molecules (ITbM) & Graduate School of Science, Nagoya University
Research team member	Yasuomi Tada Professor, Center for Gene Research, Nagoya University
Research team member	Norihito Nakamichi Designated Associate Professor, Institute of Transformative Bio-Molecules (ITbM) & Graduate School of Science, Nagoya University
Research team member	Takamasa Suzuki Lecturer, Dept. of Biological Chemistry Bioscience and Biotechnology (graduate school)
Research Collaborator	Hiroyuki Tsuji Assistant Professor, Kihara Institute for Biological Research, Yokohama City University

Using the stomatal guard cells as model cells for environmental responses, our goal is to determine novel factors involved in the signal transductions in response to environmental stimuli in plants and their mechanisms of action. Additionally, we will analyze the environmental memory system, which involves chromatin modifications that occur in stomatal guard cells and shoot apical meristem in response to a variety of environmental stimuli. Furthermore, we will clarify the physiological significance of environmental memory on control of stomatal aperture and floral induction. Finally, by analyzing the long-distance signal transduction system that controls stomatal aperture in response to the nutritional condition of soil or environmental stresses, we will seek to elucidate the autonomous distributed environmental response control system in plants.

Matsubayashi Group: Response mechanisms to a fluctuating environment through long-distance signaling

Research plan representative	Yoshikatsu Matsubayashi Professor, Graduate School of Science, Nagoya University
Research team member	Keiko Kuwata Designated Assistant Professor, Institute of Transformative Bio-Molecules (ITbM) & Graduate School of Science, Nagoya University

Nitrogen nutrients are distributed very heterogeneously in the natural world. Therefore, plants must extend their roots in multiple directions; moreover, when a subset of roots senses nitrogen deficiency, other roots can compensate and increase nitrogen uptake. To date, we have determined the first step of long-distance signaling, in which the expression of secretory peptide CEP is induced in roots that sense nitrogen deficiency; this information travels a long distance above the surface through the xylem to be recognized by a specific receptor (CEPR) in leaves. In this study, using this system as a model, we will elucidate how local environmental stimuli in the roots can be controlled by leaves, and how this information is transmitted throughout the entire plant.

Matsunaga Group: Elucidation of mechanisms that control chromatin movement in response to environmental stimuli

Research plan representative	Sachihiro Matsunaga Professor, Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
Research Collaborator	Minako Ueda Designated Associate Professor, Institute of Transformative Bio-Molecules (ITbM) & Graduate School of Science, Nagoya University
Research Collaborator	Takuya Sakamoto Assistant Professor, Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
Research Collaborator	Satoru Fujimoto Postdoctral Fellow, Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
Research Collaborator	Daisuke Kurihara Designated Associate Professor, Division of Biological Science, Graduate School of Science, Nagoya University
Research Collaborator	Keishi Osakabe Professor, Faculty of Bioscience and Bioindustry, Tokushima University

Chromatin undergoes epigenetic changes in response to environmental stimuli. Taking advantage of the DNA damage (radiation or drugs) sensitivity of plants, we will identify factors that control the movement of chromatin associated with histone modifications or chromatin remodeling, as well as the molecular mechanisms of such epigenetic changes. Moreover, through live imaging of changes in chromatin movement and functional obstruction through optical manipulation of cells, we will identify the group of cells that remember environmental stimuli. These techniques will help elucidate the mechanism underlying the autonomously distributed environmental memory system of plants from an epigenetic standpoint.

Sugimoto Group: Control of cellular reprogramming in response to environmental stress

Research plan representative	Keiko Sugimoto Team Leader, Center for Sustainable Resource Science, RIKEN
Research Collaborator	Akira Iwase Postdoctral Fellow, Center for Sustainable Resource Science, RIKEN
Research Collaborator	Momoko Ikeuchi Postdoctral Fellow, Center for Sustainable Resource Science, RIKEN
Research Collaborator	Yosuke Tamada Associate Professor, School of Engineering, Utsunomiya University

Plant cells exhibit totipotency or pluripotency more easily than most of animal cells. It is well known that differentiated somatic cells in mature plant organs can dedifferentiate and redifferentiate in response to various environmental stimuli, however, the molecular mechanisms underlying these responses have not been established. This study aims at elucidating how plants induce cellular reprogramming after severe damages by studying how plants perceive and transduce environmental signal inputs and modify epigenetic cellular memories.

Fukuda Group: Analysis of the autonomous distributed control of signal transduction via the vascular system in plants

Research plan representative	Hiroo Fukuda Professor, Graduate School of Science, The University of Tokyo
Research Collaborator	Yuki Kondo Assistant Professor, Graduate School of Science, The University of Tokyo

In this study, we will elucidate the integration mechanism of local signals and long distance signals transported via the vascular system. For this purpose, we will use CLE peptides and the circadian clock as an index. Additionally, we will establish a phloem cell differentiation system, which will be used in combination with the already established xylem differentiation induction system to analyze long distance transport mechanism of signals.

Shinozaki Group: Spatiotemporal response and molecular mechanisms of memory in response to drought or temperature stress in plants

Research plan representative	Kazuko Yamaguchi-Shinozaki Professor, Graduate School of Agricultural and Life Sciences, The University of Tokyo
Research team member	Hidetaka Ito Assistant Professor, Graduate School of Life Science, Hokkaido University

Plants are threatened by drought or extreme changes in temperature. This study aims to determine the molecular mechanisms of plant spatiotemporal responses under drought or temperature stress conditions. Additionally, we will determine the mechanisms of the long-term stress signal transduction between plant tissues via signaling molecules such as plant hormones and peptides through the vascular bundle. We will also analyze the mechanisms of long-term memory in response to repetitive stress treatments. In this manner, we will elucidate the mechanisms underlying the autonomously distributed control system for environmental stress responses in plants.

Kakutani Group: Environmental response control mechanisms involving chromatin long-term memory

Research plan representative	Tetsuji Kakutani Professor, National Institute of Genetics, Research Organization of Information and Systems

The ON/OFF state of gene expression, which reflects the environmental and genetic background, is recorded on chromatin. This memory is manifested physically as histone modifications or DNA methylation. DNA methylation is a particularly stable modification, and contributes to control of repetitive sequences such as transposons as long-term memory. DNA methylation can be found in the coding regions of genes in many organisms, ranging from plants to humans; however, its function is incompletely understood. In this study, we focused on the interactions between histone and DNA methylation and their effects on long-term chromatin memory. By genetic and genomic approaches, we will elucidate the control mechanisms of these modifications and memory in the context of cellular proliferation and responsiveness to the environment.

Shirasu Group: Elucidation of the information hijacking mechanism of the vascular bundle of parasitic plants

Research plan representative Ken Shirasu
Group Director, Center for Sustainable Resource Science, RIKEN
Some plants parasitize other plants. We seek to comprehensively understand how both plants (parasite and host) obtain information about the other; how they differentiate this information from their own; how they control, decide, remember, and transmit this information; and the molecular mechanisms underlying these processes.