Biology subjects

Shimobayashi, S. F.

Publications and source records attributed to Shimobayashi, S. F..

5 recordsLinked to original sources

bioRxiv2025

Synaptic active zones are ordered nanostructures designed by supramolecular block copolymers

Neurotransmitters are released at presynaptic active zones, where a conserved cytomatrix exhibits nanoscale order first visualized by electron microscopy over half a century ago. However, the physical principles underlying this architecture have remained unclear. Here we show that active zone scaffolds act as protein block copolymers, whose nanoscale microphase separation produces hexagonally packed nanodot arrays. Super-resolution imaging combined with block-copolymer theory identifies ELKS and RIM as the minimal pair sufficient to reproduce this ordered lattice, mediated by orthogonal interactions between ELKS coiled-coil domains and RIM intrinsically disordered regions. Additional active zone proteins, including RIMBP and Liprin-, modulate lattice spacing and morphology in a stoichiometry-dependent manner, coupling nanoscale order to neurotransmission. More broadly, block-copolymer microphase separation emerges as a design principle for constructing functional nanostructures in living systems.

biophysics↗

bioRxiv2023

Critical capillary waves of biomolecular condensates

Biomolecular condensates formed by phase separation are key players in cellular organization, yet their interfacial mechanics remain poorly understood. Here, we show that both synthetic and endogenous nuclear condensates exhibit critical-like interfacial behaviors near the phase boundary, including enhanced capillary fluctuations, critical slowing down, and reduced surface tension. By combining optogenetic control with sub-micron-resolution fluctuation spectroscopy, we quantitatively estimate surface tension, bending rigidity, and effective viscosity. Surface tension diminishes as the system approaches the critical composition, consistent with classical theories of phase separation. Notably, bending elasticity emerges as an unexpected feature of these nuclear liquid-like structures, suggesting the formation of structured interfacial layers that progressively weaken near criticality. Among these condensates, the nucleolus displayed exceptionally high viscosity, which may arise in part from viscoelastic coupling to the surrounding perinucleolar heterochromatin, effectively increasing the apparent viscosity in the long-time fluctuation regime. This non-invasive approach enables probing condensate mechanics in living cells and may provide a basis for diagnosing or modulating condensates in biomedical contexts.

biophysics↗

bioRxiv2020

Regulation of gene expression by repression condensates during development

There is emerging evidence for transcription condensates in the activation of gene expression1-3. However, there is considerably less information regarding transcriptional repression, despite its pervasive importance in regulating gene expression in development and disease. Here, we explore the role of liquid-liquid phase separation (LLPS) in the organization of the Groucho/TLE (Gro) family of transcriptional corepressors, which interact with a variety of sequence-specific repressors such as Hes/Hairy4. Gro-dependent repressors have been implicated in a variety of developmental processes, including segmentation of the Drosophila embryo and somitogenesis in vertebrates. These repressors bind to specific recognition sequences, but instead of interacting with coactivators (e.g., Mediator) they recruit Gro corepressors5. Gro contains a series of WD40 repeats that are thought to mediate oligomerization6. How putative Hes/Gro oligomers repress transcription has been the subject of numerous studies5, 6. Here we show that Hes/Gro complexes form discrete puncta within nuclei of living Ciona embryos. These puncta rapidly dissolve during the onset of mitosis and reappear in the ensuing cell cycle. Modified Hes/Gro complexes that are unable to bind DNA exhibit the properties of viscous liquid droplets, similar to those underlying the biogenesis of P-granules in C. elegans7 and nucleoli in Xenopus oocytes8. These observations provide vivid evidence for LLPS in the control of gene expression and suggest a simple physical exclusion mechanism for transcriptional repression. WD40 repeats have been implicated in a wide variety of cellular processes in addition to transcriptional repression9. We suggest that protein interactions using WD40 motifs might be a common feature of processes reliant on LLPS.

developmental biology↗

bioRxiv2019

Universal phase behaviors of intracellular lipid droplets

Lipid droplets are cytoplasmic micro-scale organelles involved in energy homeostasis and handling of cellular lipids and proteins. The core structure is mainly composed of two kinds of neutral lipids, triglycerides and cholesteryl esters, which are coated by a phospholipid monolayer and proteins. Despite the liquid crystalline nature of cholesteryl esters, the connection between the lipid composition and physical states is poorly understood. Here, we present the first universal intracellular phase diagram of lipid droplets, semi-quantitatively consistent with the in vitro phase diagram, and reveal that cholesterol esters cause the liquid-liquid crystal phase transition under near-physiological conditions. The internal molecules of the liquid crystallized lipid droplets are aligned radially. We moreover combine in vivo and in vitro studies, together with the theory of confined liquid crystals, to suggest that the radial molecular alignments in intracellular lipid droplets are caused by an anchoring force at the droplet surface. Our findings on the phase transition of lipid droplets and resulting molecular organization contribute to a better understanding of their biological functions and diseases.

biophysics↗

bioRxiv2019

Nucleated transcriptional condensates amplify gene expression

Liquid-liquid phase separation is thought to underly gene transcription, through the condensation of the large-scale nucleolus, or in smaller assemblies known as transcriptional hubs or condensates. However, phase separation has not yet been directly linked with transcriptional output, and our biophysical understanding of transcription dynamics is poor. Here, we utilize an optogenetic approach to control condensation of key FET-family transcriptional regulators, particularly TAF15. We show that amino acid sequence-dependent phase separation of TAF15 is enhanced significantly due to strong nuclear interactions with the C-terminal domain (CTD) of RNA Pol II. Nascent CTD clusters at primed genomic loci lower the energetic barrier for nucleation of TAF15 condensates, which in turn further recruit RNA Pol II to drive transcriptional output. These results suggest a model in which positive feedback between key transcriptional components drives intermittent dynamics of localized phase separation, to amplify gene expression.

biophysics↗