Overview
Overview
Greetings from the Head Investigator
Tatsuo Fukagawa
Graduate School of Frontier Biosciences, Osaka University
In our research area “Cluster Cell Biology”, we focus on “supramolecular complexes” that are clustered to a higher order structure and function within cells, aiming to elucidate their characteristics, formation mechanisms, and their relationship to cellular functions.
In this area, we define “Biological Clusters” as functional “supramolecular complexes”. Research on Biological Clusters requires a multifaceted approach, and we have established an organized research group that combines molecular cell biology with high-precision imaging including cryo-electron tomography, advanced fluorescence correlation spectroscopy, super-resolution imaging, and computational science including physical quantity measurement, theory, and mathematical simulations. We hope to establish a new cell view of Biological Clusters by filling the gap between molecular complexes that can be reconstructed in vitro and the supramolecular complexes that actually function in cells.
This research area consists of Group A01, which aims to elucidate the relationship between the molecular basis of Biological Clusters and cellular functions, Group A02, which aims to visualize Biological Clusters and elucidate their structural basis, and Group A03, which aims to elucidate the formation mechanisms of Biological Clusters through physical and theoretical analyses.
We aim to propose new concepts from the close collaboration of these three groups.
What are Biological Clusters?
In the cells of living organisms, various proteins perform diverse functions to maintain life activities. Some proteins form complexes and protein complexes are clustered to a higher order structure called “supramolecular complexes”, which governs various cellular functions.
In this research area, we define such supramolecular complexes that exhibit biological significance by forming clusters as “Biological Clusters”. We conduct research to elucidate the mechanisms of their formation and the characteristics.
For example, some biological clusters secure a certain volume, acquire physical strength, and form functional systems by forming clusters within cells, functioning as controlled supramolecular complexes.
In addition to intermolecular interactions, various factors such as the spatial effects of the crowded molecular environment and platform effects may be involved in cluster formation within cells.
Considering these factors, research on “Biological Clusters”, which aims to fill the gap between the structural information of protein complexes and the supramolecular complexes in cells, would be a challenge that will bring about a transformation in biology.
Approach of This Research Area
To analyze the formation mechanisms and significance of Biological Clusters, it is necessary to combine cell biology, biochemistry, and structural biology with advanced electron microscopy, fluorescence correlation spectroscopy, super-resolution imaging methods, and soft matter physics and mathematical simulations that treat their dynamics from a physical perspective. By combined physical theories with the observation of phenomena in cells and physical quantities measured, and by complementing biology and physics with each other, we promote the integrated research.
In this area, we particularly focus on supramolecular complexes that exist within cells, such as centrosomes, centromeres, and chromosomes, and aim to elucidate their structural basis and formation mechanisms.
Research Group A01
Elucidation of the molecular basis of Biological Clusters and their relationship to cellular functions
For each supramolecular complex, we aim to identify factors involved in cluster formation, elucidate the significance of cluster formation in cells, its formation control, and the characteristics acquired by clustering, in order to understand how they relate to specific cellular functions.
Specifically, the planned research groups conduct structural and biochemical analyses of the basic units of the complexes, as well as cell biological analyses using mutant cells lacking the cluster formation or with artificially induced clusters for kinetochore complexes, SMC complexes, CPC complexes, and centrosome complexes. By combined the obtained findings of Group A01 with those of Groups A02 and A03, we elucidate the mechanisms by which these complexes form clusters within cells and the characteristics obtained as a result, to understand their relationship to cellular functions.
Planned Research 1Formation mechanism of functional kinetochores via Biological Clusters
Principal Investigator:
Tatsuo Fukagawa (Professor, Graduate School of Frontier Biosciences, Osaka University)
We aim to elucidate the higher-order structure of clusters that constitute kinetochores within cells, the characteristics obtained by clustering, the elements that promote cluster formation and their regulation mechanisms, and to understand the importance of clustering of kinetochore complexes for accurate chromosome segregation.
Planned Research 2Role of SMC complex clusters in chromosome organization
Principal Investigator:
Yasuto Murayama (Associate Professor, Department of Chromosome Science, National Institute of Genetics)
We aim to elucidate the cluster structure of the cohesin complex that controls higher-order genome organisation, the factors involved in cohesin clustering, the biological function of the cluster formation, and then extend its analogy to other essential SMC complexes to understand the mechanism of chromosome organisation from the point of view of SMC complexes as Biological Clusters.
Planned Research 3Formation and characteristics of Biological Clusters at centromeres
Principal Investigator:
Toru Hirota (Division Head, Cancer Institute, Japanese Foundation for Cancer Research)
We aim to elucidate the higher-order structure of clusters formed by the chromosome passenger complex (CPC), which ensures the fidelity of chromosome segregation, at M phase centromeres, the mechanisms promoting cluster formation, and the structural control that gives rise to functional characteristics as a reaction field for Aurora B, and to understand its relationship to chromosome segregation abnormalities in cancer cells.
Planned Research 4Formation mechanism of centrosomes via Biological Clusters
Principal Investigator:
Daiju Kitagawa (Professor, Graduate School of Pharmaceutical Sciences, The University of Tokyo)
For centrosomes, which serve as microtubule organizing centers and are responsible for various intracellular functions, we aim to elucidate the mechanisms by which their constituent factors progressively mature into supramolecular complexes, the elements that promote cluster formation including the platform effect of centrioles, the higher-order structure of clusters that give rise to functional characteristics, and to understand their relationship to intracellular functions.
Research Group A02
Visualization of Biological Clusters and their molecular dynamics
We clarify the structural characteristics of clusters and the regulatory mechanism of cluster formation within cells using state-of-the-art electron microscopy and super-resolution microscopy. In addition, we aim to elucidate the “physical characteristics” of clusters such as volume and strength, and the “biochemical characteristics” such as system formation using molecular dynamics analyses.
Specifically, we analyze the characteristics of higher-order clustering of each complex analyzed in Group A01 in cells, using advanced imaging techniques such as cryo-ET, super-resolution microscopy, and expansion microscopy. We utilize the interaction data of complexes elucidated in Group A01 research as a reference. In addition to conventional fluorescence correlation spectroscopy (FCS, FCCS), we try to establish a new ultimate spatiotemporal correlation spectroscopy to quantitatively analyze the characteristics and dynamics of Biological Clusters within cells.
Planned Research 5Structural and dynamic analysis of Biological Clusters using cryo-TEM and SEM
Principal Investigator:
Masayuki Oda (Professor, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi)
Co-Investigator:
Takayuki Kato (Professor, Institute for Protein Research, Osaka University)
Co-Investigator:
Satoshi Kusumi (Assistant Professor, Graduate School of Medical and Dental Sciences, Kagoshima University)
For each supramolecular complex, we achieve high-precision analysis of cluster structures formed within cells (including artificial cells) using cryo-TEM and SEM, and establish an ultrastructural analysis platform to observe Biological Clusters by utilizing the latest EM/ET techniques such as cryo-FIB-SEM and cryo-CLEM.
Planned Research 6Establishment of ultimate spatiotemporal correlation spectroscopy for analyzing Biological Clusters
Principal Investigator:
Akira Kitamura (Senior Lecturer, Faculty of Advanced Life Science, Hokkaido University)
Co-Investigator:
Ryusuke Nozawa (Researcher, Department of Experimental Pathology, Cancer Institute, Japanese Foundation for Cancer Research)
Research Collaborator:
Yasuhiro Hirano (Specially Appointed Researcher, Department of Experimental Pathology, Cancer Institute, Japanese Foundation for Cancer Research / Visiting Faculty, Graduate School of Frontier Biosciences, Osaka University)
Based on conventional FCS, we establish extreme ultimate spatiotemporal correlation spectroscopy and combine it with various super-resolution imaging methods to establish a technological basis for dynamic analysis of intermolecular interactions, molecular dynamics, number of molecules and their spatial arrangement related to supramolecular complexes within cells.
Research Group A03
Formation and characterization of Biological Clusters by physical and mathematical analysis
We measure various physical quantities of cluster formation phenomena using artificial cell systems and acquire their characteristics in cell-sized spaces. Evaluating them in comparison with cellular data obtained from Group A01/A02 and theoretical or computational analysis elucidate the direct and indirect effects acting on clusters.
Specifically, we introduce various designed supramolecular complexes into artificial cells and measure the physical quantities of each cluster, that clarify the indirect effects created generated from cell-sized spaces and the platform (structures surrounding the clusters). In addition, we incorporate the knowledge obtained here and the experimental results from A01/A02 to perform mathematical simulations of the cluster formation process. We provide these knowledge feedback to Group A01/A02 research for experimental verification and improve the accuracy of our understandings.
Planned Research 7Elucidation of biomolecular cluster formation and supramolecular structural transitions in cell-sized spaces
Principal Investigator:
Miho Yanagisawa (Associate Professor, Graduate School of Arts and Sciences, The University of Tokyo)
Co-Investigator:
Yutetsu Kuruma (Senior Scientist, Japan Agency for Marine-Earth Science and Technology)
We establish an experimental setup that enables to analysis of cluster formation within cell-sized spaces using the technique of artificial cells. The target supramolecules are introduced into the artificial cells under various conditions and are evaluated in their physical characteristics by cluster composition analysis, molecular diffusion measurements, and mechanical measurements. Based on these quantitative results, we construct the theoretical basis for cluster formation.
Planned Research 8Theoretical study for the states of biological clusters based on the characteristics of molecular fields
Principal Investigator:
Masashi Tachikawa (Associate Professor, School of Science, Yokohama City University)
Co-Investigator:
Yuji Sakai (Specially Appointed Associate Professor, School of Science, Yokohama City University)
Direct and indirect interactions between molecules is expected to work cooperatively in the cluster formation of supramolecular complexes. By reproducing the cluster formation process using mathematical models for the targets within the area, we will elucidate the cooperativity of those interactions and formulate them.