Biology subjects

Shiraishi, K.

Publications and source records attributed to Shiraishi, K..

11 recordsLinked to original sources

bioRxiv2026

Cytoskeletal-nuclear control of alveolar fibroblast identity directs lung regeneration

Respiratory mechanics direct cell fate in the lung, but the mechanisms by which these mechanical signals are sensed and transmitted to the nucleus to control cell state remain unclear. We paired in vivo perturbations of respiratory mechanics with single-cell genomics and found that alveolar fibroblasts are highly sensitive to physical changes in their microenvironment, exhibiting persistent shifts in their transcriptional identity after injury. Surprisingly, transmission of these signals through the nuclear envelope was not essential for maintaining transcriptional or epigenetic stability during homeostasis. However, severing mechanical-nuclear signaling promoted the normalization of alveolar fibroblast identity after acute injury, resulting in improved epithelial regeneration and reduced dysplastic remodeling. These studies reveal the importance of mechanical-nuclear signaling in the regulation of alveolar cell identity and function and reveal that targeting this complex can enhance tissue regeneration.

cell biology↗

bioRxiv2026

High-resolution spatial profiling identifies disease-specific molecular architecture in palmoplantar pustulosis

Palmoplantar pustulosis (PPP) and dyshidrotic eczema (DE) are chronic vesiculopustular dermatoses with overlapping clinical presentations but distinct underlying biology. Although comparative transcriptomic and proteomic analyses between PPP and DE have been reported, they remain limited in number and scope, with no comprehensive understanding of their distinct molecular signatures. Moreover, their molecular mechanisms remain unclear, and currently available therapeutic options are limited. To clarify disease-specific epidermal programs underlying vesicle formation, we conducted Visium HD spatial transcriptomic analysis of FFPE lesional skin samples obtained from patients with PPP and DE, followed by immunohistochemical validation against normal palmoplantar skin controls. Spatial clustering identified a keratinocyte subpopulation adjacent to vesicles that exhibited distinct transcriptional programs in the two diseases. In PPP, vesicle-associated keratinocytes demonstrated marked downregulation of aquaporin-3 (AQP3) and E-cadherin, together with strong, spatially localized activation of JAK-STAT3 signaling. Conversely, DE exhibited diffuse AQP3 expression and more homogeneous activation of JAK-STAT3 signaling throughout the epidermis. These results indicate that, although PPP and DE share inflammatory pathways, they differ substantially in their spatial molecular architecture. Reduced AQP3 expression and localized STAT3 activation may contribute to vesicle formation in PPP, supporting our previous hypothesis that implicates intraepidermal sweat leakage as a pathogenic mechanism in PPP. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/723901v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@72a341org.highwire.dtl.DTLVardef@3c0beaorg.highwire.dtl.DTLVardef@325098org.highwire.dtl.DTLVardef@1493ebf_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2026

High extracellular osmolarity promotes yeast thermotolerance through osmotic modulation and glycerol-dependent adaptation.

High-temperature stress is a major constraint on yeast growth and fermentation, and has traditionally been interpreted primarily in terms of intracellular molecular damage such as protein denaturation and aggregation. Despite this extensive focus on intracellular mechanisms, how physical factors within the extracellular environment influence yeast thermotolerance remains poorly understood. Here we demonstrate that increases in extracellular osmolarity markedly attenuate growth inhibition under high-temperature conditions in yeast. This protective effect was consistently observed in multiple laboratory and industrial strains of Saccharomyces cerevisiae, as well as in ascomycetous and basidiomycetous yeasts, indicating that osmotic pressure-dependent thermotolerance is a broadly conserved phenomenon. We also found that extracellular osmolarity dynamically increases during growth and then decreases in a diauxic shift-like pattern after growth arrest. At high temperature, the secretion of glucose-derived metabolites decreased, but that of other solutes increased, suggesting that heat stress alters the composition of extracellular solutes contributing to osmolarity. In addition, intracellular glycerol levels increased at high temperature, and this increase was further enhanced under high-osmolarity conditions. Notably, expression of a constitutively active Hog1 mutant exhibited raised intracellular glycerol levels, enhanced nuclear localization of Hog1, and improved growth under high-temperature conditions. Collectively, these findings support a model in which extracellular osmolarity is modulated to avoid excessive intracellular osmolarity under high-temperature conditions, while the intracellular accumulation of glycerol contributes to yeast adaptation at high-temperature. Our results highlight extracellular-intracellular osmotic coordination as an additional physiological layer of high-temperature stress adaptation in yeast.

microbiology↗

bioRxiv2026

Phenotypic diversity of yeasts curated in the 5th edition of The Yeasts: A data-driven visualization approach

Yeasts have long served as key experimental systems in genetics, cell biology, and fermentation research; however, these studies have largely focused on a limited number of model species. In contrast, yeasts are a fungal group with remarkable physiological and ecological diversity. To provide a global overview of yeast diversity, we compiled and visualized phenotypic information for approximately 1,300 yeast species documented in The Yeasts (5th edition), including carbon utilization profiles, fermentation capacity, growth temperature ranges, and reported isolation sources. Taxonomic reconciliation revealed extensive reannotation, with approximately 44% of the species undergoing name changes and recognized genera increasing from 143 to 233. Integrative analyses revealed pronounced phylogenetic structuring of metabolic breadth. Many basidiomycetous yeasts, particularly Agaricomycotina, exhibited broader, generalist-like carbon utilization, whereas ascomycetous yeasts, especially Saccharomycotina, more frequently displayed sugar-centered, specialist-like narrower profiles; model yeasts such as Saccharomyces cerevisiae and Schizosaccharomyces pombe fell at the narrow end of this spectrum. Fewer than half of all species fermented glucose, a trait largely confined to Saccharomycotina. In addition, nearly one-fifth of species failed to grow at 30 {degrees}C, the standard laboratory temperature. By reconstructing and visualizing decades of dispersed taxonomic knowledge accumulated in The Yeasts, this study reframes yeasts not merely as laboratory model organisms but as metabolically diverse fungi whose phenotypic diversity reflects diverse ecological contexts. The analytical framework presented here provides a foundation for integrating standardized quantitative phenotypes and newly described species and offers a starting point for exploring the latent ecological and metabolic potential of yeast diversity.

microbiology↗

bioRxiv2025

P-body formation is required for yeast proliferation in the phyllosphere

Processing bodies (P-bodies) are major cytosolic ribonucleoprotein granules involved in post-transcriptional regulation. Yeast has been an invaluable model for elucidating the functions of P-bodies under laboratory conditions. However, the physiological significance of P-bodies in natural environments remains unclear. Here, we demonstrate that P-body formation is required for yeast proliferation in the phyllosphere, the aerial parts of plants. Deletion of EDC3, a gene critical for P-body formation, impaired proliferation of the methanol-utilizing yeast Candida boidinii on Arabidopsis thaliana leaves where the yeast assimilates methanol as the carbon source while adapting to changes in environmental conditions. In vitro experiments showed that P-bodies contribute to the spatiotemporal regulation of methanol-induced mRNAs (mimRNAs). These mimRNAs form cytosolic dot structures (termed mimRNA granules) that harbor multiple kinds of mimRNAs. In the edc3{Delta} strain, the formation of mimRNA granules was reduced along with a decrease in mimRNA abundance. Under oxidative stress, colocalization of P-bodies with mimRNA granules markedly increased and growth of the edc3{Delta} strain on methanol was suppressed, suggesting active sequestration of mimRNAs within P-bodies as a stress tolerance response. Time-lapse microscopy revealed dynamic interactions between P-bodies and mimRNAs granules with transient colocalization. Together, our findings indicate that P-bodies function as temporal storage sites where mimRNAs are protected from degradation in the phyllosphere. Impact statementP-bodies support yeast survival on plant leaves by sequestering and protecting methanol-induced mRNAs from degradation

microbiology↗

bioRxiv2025

Trehalose promotes wound healing in vitro by enhancing the migration of human keratinocytes via the VEGF/JNK/PI3K pathway

BackgroundTrehalose is a naturally occurring disaccharide found in invertebrates but cannot be synthesized by vertebrates. We previously reported that high-concentration trehalose induces a transient senescent-like state in fibroblasts, leading to cell cycle arrest and growth factor secretion via CDKN1A/p21, and this process promoted keratinocyte proliferation, enhancing capillary formation and wound closure in vivo. ObjectiveThis study aimed to investigate the effect of trehalose on human keratinocytes. MethodsPreviously published RNA-seq data of cytokine-untreated samples from our group of trehalose-treated human keratinocytes were re-analyzed, and an in vitro scratch assay was performed using cells treated with mitomycin C. ResultsThe trehalose-treated group exhibited increased wound closure. A significantly increased secretion of vascular endothelial growth factor (VEGF) was observed in keratinocytes treated with high-concentration trehalose, which is one of the most crucial molecules inducing angiogenesis in the skin. Significant upregulation of mRNA level and protein secretion of VEGF was confirmed using qPCR and ELISA, respectively. Furthermore, treatment with axitinib, a VEGF receptor inhibitor, significantly suppressed trehalose-induced activation of keratinocyte migration. Additionally, the increase in trehalose-induced migration activity was significantly inhibited by the Jun N-terminal kinase (JNK) inhibitor SP600125 and the PI3K inhibitor LY294002. ConclusionTrehalose promotes wound healing via VEGF secretion from keratinocytes and the PI3K and JNK pathways. The findings of this study may lead to the development of novel therapeutic agents that can alter the wound healing process. IMPORTANTO_LIManuscripts submitted to Review Commons are peer reviewed in a journal-agnostic way. C_LIO_LIUpon transfer of the peer reviewed preprint to a journal, the referee reports will be available in full to the handling editor. C_LIO_LIThe identity of the referees will NOT be communicated to the authors unless the reviewers choose to sign their report. C_LIO_LIThe identity of the referee will be confidentially disclosed to any affiliate journals to which the manuscript is transferred. C_LI GUIDELINESO_LIFor reviewers: https://www.reviewcommons.org/reviewers C_LIO_LIFor authors: https://www.reviewcommons.org/authors C_LI CONTACTThe Review Commons office can be contacted directly at: office@reviewcommons.org

cell biology↗

bioRxiv2025

Methylotrophic yeast Candida boidinii enhances the colonization of plant growth-promoting yeast Papiliotrema laurentii in the phyllosphere

Methanol-utilizing microbes are ubiquitous in the phyllosphere, where they assimilate methanol released from pectin, the major component of the plant cell wall. While methylotrophic bacteria Methylobacterium spp. are well studied for their symbiotic relationships with the host plants, the ecology and functional roles of methylotrophic yeasts on plants remain poorly understood. In the effort to isolate yeasts from 26 phyllosphere samples, we identified Candida boidinii as the only methylotrophic yeast, while the remaining isolates, categorized into 17 species in 12 genera, lacked this metabolic trait. To obtain insight into the role of methylotrophic yeasts in the phyllosphere, we investigated the interaction of C. boidinii with a plant growth-promoting yeast (PGPY), Papiliotrema laurentii, one of the identified yeast species during isolation. We found that the colonization of P. laurentii was enhanced by the presence of C. boidinii on Arabidopsis thaliana leaves. Co-cultivation assays revealed that the cell yield of P. laurentii was enhanced by C. boidinii during cultivation on pectin and that the methanol-utilizing ability and pectin methylesterase (PME) activity of C. boidinii contributed to this enhancement. Stable carbon isotope labeling of pectin methylester groups unambiguously confirmed their assimilation by C. boidinii, but not by P. laurentii. These findings suggest that C. boidinii not only survives in the phyllosphere by utilizing pectin-derived methanol but also contributes to the fitness of other yeast species through metabolic cooperation. This study provides new insights into the niche construction and survival strategies of phyllosphere methylotrophic yeasts, highlighting their potential role in shaping microbial community dynamics and promoting beneficial plant-microbe interactions.

microbiology↗

bioRxiv2025

Hypomorphic Lig4 gene mutation in mice predisposes to Th1-skewing intestinal inflammation

Dysregulation of DNA double-strand break (DSB) repair leads to adaptive immunodeficiency, whereas the remaining lymphocytes are aberrantly activated and provoke inflammations. However, no model mice were available to consistently manifest inflammation under defective DSB repair. We generated mutant mice carrying a missense mutation p.W447C in the gene encoding DNA ligase IV (LIG4), critical for DSB repair. Lig4W447C/W447C mice showed growth retardation and severe intestinal inflammations under adaptive immunodeficiency. The inflammations were featured by marked infiltration of T helper type 1 (Th1) cells and macrophages and was dependent on lymphocytes. When Ifng was deleted, Th2 and Th17 instead of Th1 cells drove the inflammations. Lig4W447C/W447C mice showed expansion of oligoclonal T cells with T cell receptor repertoire skewed towards more proximal 3 V and 5 J gene segments. Thus, our novel hypomorphic Lig4 mutant mice show that defective DSB repair leads to Th1-dependent intestinal inflammations under severe adaptive immunodeficiency.

immunology↗

bioRxiv2024

Methanol chemoreceptor MtpA- and flagellin protein FliC-dependent methylotaxis determines the spaciotemporal colonization of PPFM in the phyllosphere

Pink-pigmented facultative methylotrophs (PPFMs) capable of growth on methanol are dominant and versatile phyllosphere bacteria that provide positive effects on plant growth through symbiosis. However, the spatiotemporal behavior of PPFMs on plant surfaces and its molecular basis are unknown. Here we show that Methylobacterium sp. strain OR01 inoculated onto red perilla seeds colonized across the entire plant surface in the phyllosphere concomitant with the plant growth. FliC flagellin proteins required for motility were necessary for distributed colonization on plant leaves, but not for colonization at the leaf periphery. Methanol-sensing chemoreceptor MtpA-dependent chemotaxis (methylotaxis; chemotaxis toward methanol) facilitated the bacterial movement from the peripheral to the inner part of leaves and further entry into the stomatal cavity, indicating that methanol functions as a volatile messenger attracting PPFMs to particular leaf locations possibly to support with photosynthesis and to afford protection from pathogenic invasion.

microbiology↗

bioRxiv2021

Highly concentrated trehalose induces transient senescence-associated secretory phenotype in fibroblasts via CDKN1A/p21

Trehalose is the nonreducing disaccharide of glucose, evolutionarily conserved in invertebrates, but does not exist in vertebrates. The living skin equivalent (LSE) is an organotypic coculture containing keratinocytes cultivated on fibroblast-populated dermal substitutes. We demonstrated that human primary fibroblasts treated with highly concentrated trehalose promote significantly extensive spread of the epidermal layer of LSE without any deleterious effects. The RNA-seq analysis data and Ingenuity pathway analysis of the differentially expressed genes of trehalose-treated 2D and 3D fibroblasts at early time points revealed the involvement of the CDKN1A pathway, which is necessary for the marked upregulation of growth factors including DPT. By contrast, the mRNA-seq data of LSEs 2-weeks after air exposure indicated that gene expression profiles are similar for untreated and trehalose-treated cells in both keratinocytes and fibroblasts. The trehalose-treated fibroblasts were positive for senescence-associated {beta}-galactosidase with the significantly downregulated expressions of LMNB1. Finally, we demonstrated that transplantation of the dermal substitute with trehalose-treated fibroblasts accelerated wound closure and increased capillary formation significantly in the experimental mouse wounds in vivo. These data indicate that high-concentration trehalose can induce the beneficial senescence-associated secretory phenotype in fibroblasts via CDKN1A/p21, which may be therapeutically useful for optimal wound repair.

cell biology↗

bioRxiv2021

Microstructured hydrogels to guide self-assembly and function of lung alveolospheres

Epithelial cell organoids have increased opportunities to probe questions on tissue development and disease in vitro and for therapeutic cell transplantation. Despite their potential, current protocols to grow these organoids almost exclusively depend on culture within three-dimensional (3D) Matrigel, which limits defined culture conditions, introduces animal components, and results in heterogenous organoids (i.e., shape, size, composition). Here, we describe a method that relies on polymeric hydrogel substrates for the generation and expansion of lung alveolar organoids (alveolospheres). Using synthetic hydrogels with defined chemical and physical properties, human induced pluripotent stem cell (iPSC)-derived alveolar type 2 cells (iAT2s) self-assemble into alveolospheres and propagate in Matrigel-free conditions. By engineering pre-defined microcavities within these hydrogels, the heterogeneity of alveolosphere size and structure was reduced when compared to 3D culture while maintaining alveolar type 2 cell fate of human iAT2 and primary mouse tissue-derived progenitor cells. This hydrogel system is a facile and accessible culture system for the culture of primary and iPSC-derived lung progenitors and the method could be expanded to the culture of other epithelial progenitor and stem cell aggregates.

bioengineering↗