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Biology subjects

Ohsawa, S.

Publications and source records attributed to Ohsawa, S..

9 recordsLinked to original sources

Protein-driven colloid-osmotic pressure controls nuclear size, organization, and function

The size of the cell nucleus is tightly controlled and changes in nuclear size correlate with altered nuclear function during development, cell differentiation and senescence. How nuclear size is regulated and whether changes thereof are functionally relevant remains unclear. Here, we demonstrate that nuclear size is determined by the osmotic pressure exerted by proteins in yeast, human cells and frog egg extracts. The biophysical model we establish solves the long-standing question of how the nuclear-to-cytoplasmic ratio is regulated and maintained. Furthermore, altering protein-driven osmotic balance modulates the physical properties of the nucleus, with a direct effect on chromatin organization and gene expression: Nuclear enlargement causes the dissolution of heterochromatic structures and derepression of subtelomeres and transposons, while simultaneously down-regulating highly expressed housekeeping genes. Importantly, these global transcriptional patterns closely mimic the gene expression changes that occur as yeast, human, and drosophila cells enlarge. Importantly, artificially forcing nuclear compression is sufficient to reverse these size-associated expression changes. Together, our findings provide a quantitative, mechanistic explanation for the coupling between the size of the nucleus and the cell, and they establish nuclear size as a modulator of chromatin organization and gene expression.

cell biology↗

Non-coding DNA dictates cell size and impairs fitness by sequestering RNA polymerase

Genome size varies greatly between organisms, largely because of varying amounts of non-coding DNA. In multicellular organisms, non-coding DNA can make up 99% of the genome, while unicellular organisms have little non-coding information. How non-coding DNA affects cell physiology remains a key question in understanding genome evolution. Here, we developed a system to conditionally accumulate large amounts of non-coding DNA in budding yeast cells. We show that cells adjust their size to DNA content, regardless of its coding capacity. The direct coupling of cell size to DNA content occurs independently of the known cell size control and DNA damage checkpoints and explains the long-observed correlation between cell size, genome size, and ploidy. Furthermore, we find that excess non-functional DNA compromises cell fitness and renders them hypersensitive to transcription inhibitors. Providing a potential explanation for this observation, we uncover that the transcription machinery binds non-coding DNA and is titrated away from coding genes, resulting in a reduced overall concentration of yeast transcripts. We propose that the inability of yeast to repress non-coding DNA increases the fitness cost associated with non-functional DNA and prevents its expansion in the yeast genome on evolutionary timescales.

cell biology↗

The HMD domain of the PAF complex primes Rad6-Bre1 E3 ligase complexes for H2B ubiquitination

Mono-ubiquitination of histone H2B (H2Bub) is deposited by Bre1-type E3 ubiquitin ligase complexes during transcription elongation and is critical for chromatin organization, DNA repair, and transcription regulation. In S. pombe, this activity is carried out by HULC, a complex of the Bre1 homologs Brl1 and Brl2 with Rhp6 and Shf1. While H2Bub deposition depends on recruitment of HULC to RNA Pol II by the Paf1 complex (PAF1C), the molecular basis for how PAF1C activates HULC has remained unclear. Using AlphaFold modelling, biochemical reconstitution, and functional assays, we define the architecture of HULC as a flexible 1:1:1:1 assembly in which Shf1 stabilizes an elongated coiled-coil hairpin that brings the RING and Rad6-binding domains into proximity. However, for full stimulation of HULC activity, we find that the HMD domain of the PAF1C subunit Prf1 stimulates ubiquitin transfer through a RING-binding region (RBR) that repositions the RING domains adjacent to Rhp6 in a catalytically competent configuration. These findings reveal an activation mechanism in which transcription-associated Prf1 primes HULC for ubiquitin transfer through the Prf1RBR, revealing a critical regulatory interface for H2B ubiquitination.

molecular biology↗

Extrinsic MMPs drive epithelial shape change via basal ECM disassembly in the Drosophila wing disc

Epithelial morphogenesis generates complex tissue architectures with remarkable reproducibility, yet how such self-organized shape transformations are triggered in vivo remains poorly understood. Here, we show that epithelial morphogenesis during early pupal development of the Drosophila wing disc is regulated non-autonomously through remodeling of the basal extracellular matrix (ECM) by neighboring tissues. Live imaging analyses reveal a previously unrecognized epithelial shape transition at the larval-to-pupal stage, in which the wing disc epithelium transforms from a concave to a convex configuration. Rather than being driven autonomously by the epithelium, this morphogenetic transition depends on adjacent non-epithelial cell populations, including myoblasts and tracheal cells. Mechanistically, systemic ecdysone signaling activates Mmp1 and Mmp2 in these neighboring tissues, leading to spatially restricted basal ECM disassembly that permits collective epithelial shape reorganization. Together, our findings establish ECM remodeling at tissue interfaces as a non-autonomous regulatory layer that enables epithelial self-organization during development.

developmental biology↗

EC-isHCR: a rapid method for in situ hybridization chain reaction in diverse animal samples

The in situ hybridization chain reaction (isHCR) visualizes RNA across multiple spatial scales, from organs to subcellular structures, in diverse samples. We previously proposed a rapid protocol, EC-isHCR, for Drosophila embryos and ovaries. Whether EC-isHCR retains the features of conventional isHCR, including wide-spatial-scale analyses in various samples, however, has remained unclear. Here, we show that EC-isHCR enables robust RNA detection in a broad range of samples, such as whole-mount fruit fly, parasitoid wasp, and aphid preparations; paraffin sections of trout; frozen mouse sections; and human cultured cells. Moreover, EC-isHCR enabled detection of subcellular RNA localization. EC-isHCR also visualized co-localization of RNA with phase-separated condensates in fruit fly embryos and detected the protrusion-enriched mRNA in HeLa cells. To broaden the applicability of EC-isHCR, we developed an automated probe design tool (https://github.com/ShuntaYorimoto/hcrkit). By combining this tool with EC-isHCR, we provide a fast and versatile framework to visualize mRNAs. This framework will help reduce the barrier to using fast isHCR and thereby facilitate research across diverse areas of the life sciences. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/696653v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1852584org.highwire.dtl.DTLVardef@621682org.highwire.dtl.DTLVardef@1b3bf5corg.highwire.dtl.DTLVardef@1d86841_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- EC-isHCR enables rapid acquisition of high-contrast images. - EC-isHCR preserves features of conventional isHCR, including versatile sample compatibility and high-resolution imaging. - An automated probe design tool was developed for EC-isHCR. - EC-isHCR/probe tool framework will help reduce the barrier to using fast isHCR.

bioengineering↗

Refined CRISPR/Cas9 genome editing in pea aphids uncovers the essential roles of Laccase2 in overwintering egg adaptation

The production of overwintering eggs is a critical adaptation for winter survival among many insects. Melanization contributes to eggshell pigmentation and hardening, consequently enhancing resistance to environmental stress. The complex life cycle of the pea aphid (Acyrthosiphon pisum), a model hemipteran insect with remarkable reproductive capacity, involves cyclical parthenogenesis. It enables the production of black overwintering eggs that undergo obligate diapause to survive under unfavorable conditions. Laccase2 (Lac2) is essential for cuticle sclerotization and pigmentation in other insects. We hypothesized that Lac2 plays a critical role in aphid eggshell pigmentation and survival during diapause. To test the hypothesis, we used CRISPR/Cas9 ribonucleoprotein microinjections and a novel Direct Parental CRISPR (DIPA-CRISPR) method to knockout Lac2. In Lac2 knockout (KO) crispants (G0), pigment-less eggs correlated with induced indel rates. Additionally, eggshell pigmentation was completely lost in homozygous Lac2 knockouts, leading to embryonic lethality. Observation of late-stage embryos in KO diapause eggs suggested that lethality occurred during late embryogenesis or hatching. Furthermore, eggshell stiffness was significantly reduced in Lac2 KOs, highlighting the role of this gene in eggshell hardening. Moreover, fungal growth was observed in KO eggs. These findings reveal the essential roles of Lac2 in eggshell pigmentation, hardening, late embryonic development, hatching, and fungal protection, which are critical for pea aphid survival during overwintering diapause. This study also advances CRISPR/Cas9-mediated genome editing in pea aphids by addressing the challenges associated with their unique biology, including complex life cycles, obligatory diapause, bacterial endosymbiosis, inbreeding depression, and high nuclease activity. Our optimized protocol achieved efficient targeted mutagenesis and germline transmission, thereby generating stable KO lines. Additionally, we successfully applied DIPA-CRISPR to aphids by inducing mutations via adult oviparous female injections in fertilized eggs. These robust genome-editing protocols will facilitate functional studies in aphids, a key model for research on evolution, ecology, development, and agriculture. Author SummarySurviving harsh winters is a challenge for many insects, and the production of specialized overwintering eggs is a common adaptation strategy. These eggs are protected from cold, desiccation, and fungal infections by their hardened, pigmented shells. The pea aphid, a hemipteran insect with a complex life cycle, relies on these eggs to survive winter. Aphids alternate between asexual reproduction in the warmer months and sexual reproduction in the fall, producing overwintering eggs that remain dormant until spring. In this study, we explored the role of Laccase2 (Lac2), a key gene that contributes to the strengthening and darkening of insect exoskeletons. We disrupted Lac2 in pea aphids using advanced genome-editing techniques, including a new approach called DIPA-CRISPR. This resulted in pigment-free eggs with weakened shells that were more prone to fungal infections and failed to hatch. This demonstrates that Lac2 is essential for the survival of overwintering eggs. In addition, we refined the CRISPR/Cas9 genome editing methods for pea aphids, enabling efficient and precise genetic studies. These findings and the tools we developed can facilitate research on ecology, evolution, and pest control, while shedding light on how insects adapt to challenging environments.

genetics↗

Exocytosis coordinates epithelial cell-turnover in Drosophila ribosomal protein mutants

Robust tissue growth is orchestrated by the precise coordination of cell death and cell proliferation. Our previous study found that in the developing wing pouches of Drosophila Minute/+ animals, both cell death and compensatory cell proliferation are dramatically increased, which contributes to robust growth of mutant tissue. The induction of this cell-turnover depends on activation of JNK signaling, although the mechanism by which JNK activation induces cell-turnover remained unclear. Here, we show that JNK-mediated elevation of exocytosis in dying cells is crucial for triggering cell-turnover in M/+ wing morphogenesis. Mechanistically, elevated JNK signaling in dying cells upregulates exocytosis-related genes and Wingless (Wg), leading to enhanced Wg secretion. Furthermore, this exocytosis-mediated Wg secretion generally occurs downstream of JNK signaling, regardless of the genetic background. Overall, our findings provide mechanistic insights into robust tissue growth through the orchestration of cell-turnover, which is primarily governed by JNK-mediated exocytosis during Drosophila Minute/+ wing morphogenesis.

developmental biology↗

Nitrogen signaling factor triggers a respiration-like gene expression program

Microbes have evolved intricate communication systems that enable individual cells of a population to send and receive signals in response to changes in their immediate environment. In the fission yeast Schizosaccharomyces pombe, the oxylipin Nitrogen Signaling Factor (NSF) is part of such communication system, which functions to regulate the usage of different nitrogen sources. Yet, the pathways and mechanisms by which NSF acts are poorly understood. Here, we show that NSF physically interacts with the mitochondrial sulfide:quinone oxidoreductase Hmt2 and that it prompts a change from a fermentation- to a respiration-like gene expression program independently of the carbon source. Our results suggest that NSF activity is not restricted to nitrogen metabolism alone and that it could function as a rheostat to prepare a population of S. pombe cells for an imminent shortage of their preferred nutrients.

microbiology↗

Coronin-1 controls directional cell rearrangement in Drosophila wing epithelium

Directional cell rearrangement is a critical process underlying correct tissue deformation during morphogenesis. Although the involvement of F-actin regulation in cell rearrangement has been established, the role and regulation of actin binding proteins (ABPs) in this process are not well understood. In this study, we investigated the function of Coronin-1, a WD-repeat actin-binding protein, in controlling directional cell rearrangement in the Drosophila pupal wing. Transgenic flies expressing Coronin-1-EGFP were generated using CRISPR-Cas9. We observed that Coronin-1 localizes at the reconnecting junction during cell rearrangement, which is dependent on actin interacting protein 1 (AIP1), an actin disassembler and a known regulator of wing cell rearrangement. Loss of Coronin-1 function reduces cell rearrangement directionality and hexagonal cell fraction. These results suggest that Coronin-1 promotes directional cell rearrangement via its interaction with AIP1, highlighting the role of ABPs in the complex process of morphogenesis.

cell biology↗