Biology subjects

Shibuya, R.

Publications and source records attributed to Shibuya, R..

3 recordsLinked to original sources

bioRxiv2025

Unipolar polysaccharide-mediated attachment of the N2O-reducing bacterium Bradyrhizobium ottawaense SG09 to plant roots.

Agricultural soils are an important source of nitrous oxide (N2O), which has greenhouse and ozone-depleting effects. Bradyrhizobium ottawaense SG09 is a nitrogen-fixing rhizobium with high N2O-reducing activity. Rhizobia form symbiotic nodules in leguminous plants. The initial physical attachment of bacteria to plant roots is a critical step in the establishment of symbiotic interactions. In this study, we performed microscopic analysis using DsRed-expressing B. ottawaense SG09. We revealed that B. ottawaense SG09 attached to both the root surface and root hairs via single cellular poles. This polar attachment was observed not only to the symbiotic host soybean, but also to non-leguminous plants, such as Arabidopsis, rice, corn, and wheat. We identified and analyzed the unipolar polysaccharide (upp) gene cluster, which is proposed to be involved in polar attachment of rhizobia, in the genome of B. ottawaense SG09. We established an Arabidopsis-based interaction assay and demonstrated that uppC and uppE play a critical role in attachment to both the root surface and root hairs.

microbiology↗

bioRxiv2025

Lipids Are Involved in Heterochromatin Condensation: A Quantitative Raman and Brillouin Microscopy Study

Chromatin, a fundamental component of eukaryotic genomes, is categorized into euchromatin and heterochromatin, which play distinct roles in gene regulation. Although these two chromatin states are distinguished by their degree of condensation, quantitatively measuring the degree of chromatin condensation, as well as the physical properties of chromatin in living cells, remains challenging. In this study, label-free in situ quantitative imaging was performed using a Raman-Brillouin microscope to visualize the spatial distribution of molecular concentration and viscoelasticity within the nuclear environment of a living cell. A quantitative concentration distribution image of each intracellular biomolecule was obtained by combining Raman imaging with multivariate curve resolution analysis, using a water Raman band as an internal standard. Simultaneous Raman-Brillouin imaging enables the quantitative visualization of viscoelasticity within a cell. Using this approach, we found that, in addition to DNA, heterochromatin is enriched in lipids and that lipids play a critical role in heterochromatin formation, determining its mechanical properties. These findings provide new insights into the mechanism of heterochromatin formation and its chemical and physical properties, leading to a comprehensive understanding of gene regulation and nuclear organization.

biophysics↗

bioRxiv2023

In situ Quantification of Biomolecular Concentration of Cytoplasmic Membraneless Organelles in a Living Cell

Liquid droplets formed via intracellular Liquid-liquid phase separation (LLPS) are called membraneless organelles and provide enzymatic reaction fields for maintaining cellular homeostasis, while they can be sources of protein aggregates and fibrils, causing neurodegenerative diseases. To understand the nature of intracellular liquid droplets, it is essential to quantify liquid droplets inside a living cell. Here, we performed near-IR fluorescence and Raman imaging to quantify chemical components inside stress granules (SGs) formed via LLPS in living cells under oxidative stress. The Raman images of stressed cells indicate the concentration of nucleic acids in the SGs was 20% higher than surrounding cytoplasm, while the lipid concentration was lower. The intensity of biomolecular C-H bands relative to the water band shows the net concentration of biomolecules was almost the same inside and outside the SGs, indicating intracellular droplets are not highly condensed, but the crowding environments are similar to the surroundings. TOC GRAPHICS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/540722v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@17237ecorg.highwire.dtl.DTLVardef@1b57922org.highwire.dtl.DTLVardef@123b771org.highwire.dtl.DTLVardef@1e07e26_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗