Natsumi Ageta-Ishihara

Stimulus-dependent changes in the localization of cytoskeleton/organelle complexes for physiological functions

Researcher

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Natsumi Ageta-Ishihara

Outline

Although localization changes of organelles have been observed for a long time, the physiological significance of stimulus-dependent localization changes is unknown. By elucidating the functional correlations and causal relationships between stimulus-dependent organelle movement via the cytoskeleton-motor protein complex to spines that mediate neuronal information processing and memory consolidation, we aim to propose a conceptual advance that organelle localization changes in response to stimuli are the basis of physiological functions.

Takayuki Ariga

Analysis of the influence of nonthermal fluctuations by intracellular single molecule manipulations

Researcher

Takayuki Ariga

Outline

Biomolecular motors have been considered to work efficiently by utilizing the thermal fluctuations of the environment. Still, their efficiency has not been able to measure in their actual working environment, living cells. On the other hand, it was revealed that not only thermal fluctuations but also nonthermal fluctuations are spontaneously generated inside living cells. In this research, I will develop a novel measurement system to manipulate a single molecule in a living cell to unveil the effect of the intracellular nonthermal fluctuations on the efficiency of individual molecules by measuring their mechanical responses and fluctuations.

Yukiko Imai

Initiation of meiotic recombination: approach to nuclear dynamics in zebrafish

Researcher

Yukiko Imai

Outline

Meiotic recombination is at the basis of inheritance and genetic diversity of sexually reproducing organisms. The objective of this project is to understand how meiotic recombination is initiated in the context of dynamic changes in nuclear structures. I address this question using zebrafish, which shares key meiotic features in common with human spermatogenesis. In order to capture nuclear dynamics during meiosis, a live imaging method will be developed by adopting an in vitro culture system of zebrafish germ cells. By combining this method with genetic and biochemical approaches, I aim to figure out initial steps of meiotic recombination from a dynamic point of view.

Keita Kamino

Interrogating noise and response in cellular signal transduction using Bayesian single-cell FRET analyses

Researcher

Keita Kamino

Outline

Cells process environmental information using chemical reaction networks called signaling systems. The systems have been characterized mostly through population averages; however, recent single-cell studies suggest that cell-to-cell variation and temporal fluctuations in cell signaling are functional and selectable traits. Here, using the E. coli chemotaxis signaling pathway as a model system, I will combine single-cell FRET measurements and Bayesian inference to analyze the dynamics and function of the system at the single-cell level.

Akihiro Kawamoto

High resolution structural analysis of the intracellular functional structure of the type III secretion system

Researcher

Akihiro Kawamoto

Outline

Protein-protein interactions and transient complex formation in the cell are difficult to analyze, and structure-function relationship studies have been lagging behind. In this study, I will develop a high-resolution analysis technique of intracellular functional structures by combining minicell technology and cryo-EM. In order to elucidate the mechanism of protein secretion by the type III secretion system that enables efficient protein transport, I will analyze structural changes of the type III needle complex and protein export apparatus during protein transport.

Misuzu Kurihara

Analysis of the novel dynamic domains based on tandem cluster sequences

Researcher

Misuzu Kurihara

Outline

The nuclear space is compartmentalized by nuclear domains, allowing multiple biological reactions to proceed without confusion. However, the contribution of genomic DNA to nuclear domains is largely unknown. In this study, I focus on submegabase clusters of tandem repeat sequences, and identify the associating molecules comprehensively by the proximal biotin labeling method. I will clarify the role of the tandem clusters in the organization of the nuclear space.

Hirokazu Sakamoto

Reconstitution of supramolecular assemblies governing the neurotransmitter release

Researcher

Hirokazu Sakamoto

Outline

The probability of neurotransmitter release varies largely among neuron types and synapse types. This functional diversity should be fundamental to complex neural circuits. In this project, I reconstitute a supramolecular assembly consisting of Munc13, RIM, RIM-BP, and CAST as a possible higher-order structure that regulates the probability of neurotransmitter release. Furthermore, I reveal the working principle of the supramolecular assembly by developing novel nanoscopic imaging techniques.

Shunsuke Shimobayashi

Physical principles behind the nucleation process of biomolecular condensates

Researcher

Shunsuke Shimobayashi

Outline

Where and when do biomolecular condensates form in the cellular environment and exert their biological functions? To tackle the questions, I combine optogenetics and soft matter physics with cell engineering to quantitatively reveal molecular factors of the nucleation process. Through the findings, I develop a tool to rigorously control the process in a spatio-temporal way for asking the fundamental functions.

Kotaro Tsuboyama

Flexible disassembly and decomposition of higher-order structures using artificial proteins

Researcher

Kotaro Tsuboyama

Outline

Intracellular non-membrane organelles have been shown to have functions such as regulation of transcription and translation. However, it is still difficult to dismantle and degrade specicifc endogenous non-membrane organelles and elucidate their functions. Therefore, we aim to create artificial proteins that can manipulate the interactions of biomolecules and understand their characteristics. Based on such an understanding, we will establish a technology to disassemble and degrade a variety of non-membrane organelles and clarify the biological significance of non-membrane organelles.

Naohiro Terasaka

Directed evolution of membraneless organelles

Researcher

Naohiro Terasaka

Outline

Although artificial membraneless organelle research using phase-separating proteins and RNAs has been reported in recent years, it is still difficult to create functions that exceed those of natural ones. In this study, a molecular evolutionary system of phase-separated proteins and non-membrane organelles will be developed using a highly diverse library of 100 million species, and aim to develop compact de novo phase-separated protein tags and artificial organelles that enable highly efficient cascade reactions.

Hideki Nakamura

Spatio-temporal manipulation of glycolytic enzyme complex inside living cells to reveal a novel glucose metabolism regulation

Researcher

Hideki Nakamura

Outline

Novel synthetic biology tools will be developed in order to manipulate assembly/disassembly of a membrane-less organelle composed of glycolytic enzymes in situ, with high spatio-temporal resolution. In combination with fluorescence live-cell imaging and advanced proteomic analyses using proximity labeling techniques, these tools will reveal physiological roles of dynamic assembly/disassembly of the glycolytic complex. The results would be insightful in understanding balance regulation between glycolysis and oxygen-consuming oxidative phosphorylation pathway, which has been related to various diseases including cancer and neurodegenerative diseases in a variety of contexts. This study would thus propose a novel experimental framework for elucidating physiological roles of arbitrary membrane-less organelles that assemble and disassemble in dynamic manners.

Shoji Hata

Elucidation of the mechanisms for the construction and deconstruction of intercellular structures via reversible liquid-solid phase transition

Researcher

Shoji Hata

Outline

Intracellular structures have been thought to be build up via stochastic association of their various components, similar to the assembly of Lego blocks. However, this simple theory can not explain the construction and deconstruction mechanisms of large intracellular structures that are rapidly assembled and disassembled. This project aims to develop an innovative theory based on “liquid-liquid phase separation” and “reversible liquid-solid phase transition” for the mechanisms of rapid construction and deconstruction of large intracellular structures.

Kayo Hibino

Single molecule and super-resolution imaging of human chromosome condensation

Researcher

Kayo Hibino

Outline

The chromosome condensation during cell division is a dramatic self-reorganization of the long thin genome chromatin polymers (several centimeters) into compact short chromosomes (several micrometers). While this process requires a DNA motor, condensin, the underlying mechanism remains unclear. Here, by using single molecule imaging and super resolution techniques in living human cells, I will quantify dynamics of nucleosomes and condensins during the condensation to reveal the principles of chromosome assembly.

Yoshitaka Matsuo

The visualization of ribosome traffic jam disassembly with single-molecule resolution

Researcher

Yoshitaka Matsuo

Outline

The speed of translation elongation is tightly regulated to control gene expression. The ribosome pausing caused by translational stress leads to the formation of a ribosome traffic jam, which is sensed as an abnormal translation event and induces several cellular responses such as apoptosis and innate immune response. In this project, I will reconstitute the ribosome traffic jam using a cell-free translation system and attempt to visualize the disassembly of a ribosome traffic jam with single-molecule resolution.

Yongchan Lee

Elucidating structural dynamics and disruption mechanism of the brush border membrane

Researcher

Yongchan Lee

Outline

This research focuses on the brush border membrane (BBM), the membrane structure responsible for efficient nutrient uptake, and plans to establish a cell culture system that enables formation of the BBM on electron microscopy grids. By using electron cryo-tomography, I aim to elucidate structures and spatial distribution of molecular assemblies within the BBM, and try to resolve major structures at sub-nanometer resolution by sub-tomogram averaging.