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Matsunaga, S.

Publications and source records attributed to Matsunaga, S..

12 recordsLinked to original sources
bioRxiv2026

Osmotic-stress-inducible nuclear condensates restrict gene inducibility

Plants, as sessile organisms, have developed various mechanisms to respond to environmental stress conditions. The plant hormone abscisic acid (ABA) is necessary for the plant to adapt to osmotic stress conditions. However, the molecular mechanisms preceding ABA accumulation remain largely unknown. To isolate transcriptional complexes on the promoter region of NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3) encoding a rate-limiting enzyme in the ABA biosynthetic pathway in planta, we developed the insertional chromatin immunoprecipitation (iChIP) screen method. The identified ALBA proteins formed condensates through liquid-liquid phase separation (LLPS) in response to osmotic stress conditions. ALBA4 directly binds to stress-inducible genes, including NCED3, and suppresses their stress inducibility. Our results demonstrate how plants respond to osmotic stress at early timepoints before ABA biosynthesis through condensate formation as osmo-sensors.

plant biology↗
bioRxiv2026

Ectopic overproduction of cell wall glucan through membrane perturbation by an antifungal peptide theonellamide A in fission yeast

Ergosterol has multiple functions in filamentous fungi and yeasts, although only a part of the functions seems to be understood. An antifungal peptide, theonellamide A (TNM-A) induces drastic morphological changes in fission yeast cells by targeting plasma membrane ergosterol. TNM-A induces overproduction and ectopic accumulation of cell wall glucan at both growing tips and septum through a yet unknown mechanism. Here we show that TNM-A treatment causes accumulation of 1,3-{beta}-glucan at cell-polarity sites, not by increased activity of 1,3-{beta}-glucan synthase, but by an increased, persistent localization of the glucan synthase enzymes. Screening based on subcellular localization of proteins at periphery or polarity sites suggested the involvement of the Rho family GTPase Cdc42. In agreement, TNM-A induced both activation of Cdc42 and enhancement of membrane trafficking of glucan synthase enzymes. In conclusion, our chemical genetics analyses using TNM-A suggest that membrane ergosterol regulates the activity of Cdc42, which further regulates the localization of glucan synthases and cell wall biosynthesis. Highlights (four sentences)- Thenoellamide A (TNM-A) induces an ectopic overproduction of cell wall glucan. - TNM-A treatment causes increased, persistent localization of glucan synthases at the cell tips and septum. - TNM-A activates Cdc42 and upregulates membrane trafficking of glucan synthases. - Ergosterol is involved in proper activation/inactivation of Cdc42.

cell biology↗
bioRxiv2025

A blue light receptor CRY1 regulates de novo shoot regeneration

Tissue culture enables plant transformation and gene editing, yet inefficient regeneration remains a major bottleneck, and the downstream circuitry linking light perception to tissue culture has not been investigated. Here we demonstrate that the blue-light photoreceptor CRYPTOCHROME 1 (CRY1) enhances Arabidopsis thaliana shoot regeneration in a blue light dependent manner. In a two-step root-to-shoot tissue culture system, cry1 mutant exhibits reduced shoot regeneration. Transcriptomic analyses in the cry1 mutant reveal that CRY1 suppresses the expression of AUXIN RESPONSE TRANSCRIPTION FACTOR 3 (ARF3). Consistently, arf3 mutant exhibits enhanced shoot regeneration phenotype. Additionally, genetic and protein interaction assays show that ARF3 acts downstream of CRY1 at both transcriptional and post-translational levels. Furthermore, transcriptomic analyses in the arf3 mutant show that ARF3 activates salicylic acid (SA)-responsive genes that suppress shoot formation, and exogenous SA inhibits regeneration in arf3 calli. Integrating RNA-seq with cis-motif analysis identifies stress-responsive ARF3 targets within the CRY1 network. Our results establish a novel CRY1-ARF3 regulatory module that links blue-light perception to hormonal signaling during regeneration, revealing how plants integrate environmental cues with growth-defense trade-offs. SynopsisThe blue-light photoreceptor CRY1 promotes de novo shoot regeneration in Arabidopsis thaliana by restraining ARF3-mediated SA signaling. It reveals a fundamental trade-off between defense responses and regenerative growth in plants, coordinated by CRY1-ARF3 module. O_LICRY1-mediated blue light signaling enhances de novo shoot regeneration from callus. C_LIO_LIARF3 acts downstream of CRY1 and CRY1 physically interacts with ARF3. C_LIO_LIARF3-activated SA pathway represses shoot regeneration. C_LIO_LICRY1 enhances shoot regeneration by suppressing ARF3-activated stress responsive genes. C_LI

plant biology↗
bioRxiv2024

Symbiotic Bacterial Partners for Chemical Defense are Vertically Transmitted in a Marine Sponge

Marine sponges host diverse symbiotic bacteria, some of which are essential for chemical defense. However, the mechanisms governing the inheritance of these defensive symbionts remain elusive. Here we report the first case of a transmission mechanism for symbionts producing cytotoxins in the sponge Mycale nullarosette, for which we established the full life-cycle cultivation method. The identification of Candidatus Synechomycale tutelaris as the cytotoxins producer enabled us to unveil their vertical transmission to offspring via bacteriocyte-like structures from the embryonic stage. This study demonstrates that sponges have evolved a sophisticated system to ensure the inheritance of significant bacterial partners crucial for host defense, which is likely one of the reasons that sponges have survived throughout the long history of multicellular organisms.

microbiology↗
bioRxiv2024

Experimental bleaching of photosymbiotic amoeba revealed strain-dependent differences in algal symbiosis ability.

Photosymbioses, the symbiotic relationships between photosynthetic algal symbionts and non-photosynthetic eukaryotic hosts, are sporadically found in a lot of eukaryotic lineages, but only a few taxa, such as cnidarians and ciliates hosting algal endosymbionts, have been actively studied for a long time. That has hindered understanding the universal mechanisms of the photosymbiosis establishment. Especially in Amoebozoa, only two species, Mayorella viridis and Parachaos zoochlorella, are reported as photosymbiotic in nature, and their mechanisms of establishing symbiotic relationships are still unclear. To investigate the extent to which and how photosymbiotic amoebae depend on the symbiotic relationships, M. viridis were treated with reagents that are known to induce the collapsing of photosymbiotic relationships, or bleaching, in other photosymbiotic species. As a result, we succeeded in artificially removing algal symbionts from host M. viridis cells with an herbicide, 2-amino-3-chloro-1,4-naphthoquinone. The apo-symbiotic state amoeba cells were able to survive and grow to the same extent as the symbiotic state cells when they fed microbial prey, indicating that the algal symbionts are not essential for the host growth under certain conditions. Furthermore, to see whether the photosymbiotic state is reversible, we fed two strains of algal symbionts to the apo-symbiotic amoeba host. The result showed that the apo-symbiotic hosts were able to ingest symbiont cells and re-establish the symbiotic state. The efficiencies of ingesting algal cells were significantly different depending on algal symbiont strains, indicating that different algal strains possess discrete symbiotic abilities to M. viridis. To our knowledge, we provide first insights on the establishment and collapse of photosymbiosis in Amoebozoa, which pave the way to understand the universal mechanism of photosymbiosis utilizing M. viridis as a model system.

evolutionary biology↗
bioRxiv2024

Metagenomic Insights Reveal Unrecognized Diversity of Entotheonella in Japanese Theonella Sponges

Numerous biologically active natural products have been discovered from marine sponges, particularly from Theonella swinhoei, which is known to be a prolific source of natural products such as polyketides and peptides. Recent studies have revealed that many of these natural products are biosynthesized by Candidatus Entotheonella phylotypes, which are uncultivated symbionts within T. swinhoei. Consequently, Entotheonella is considered an untapped biochemical resource. In this study, we conducted metagenomic analyses to assess the diversity of Entotheonella in four T. swinhoei individuals (two each of chemotypes Y and W), after separating filamentous bacteria using density gradient centrifugation. We obtained five Entotheonella genomes from filamentous bacteria-enriched fractions. Notably, one of these genomes is significantly different from previously reported Entotheonella variants. Additionally, we identified closely related Entotheonella members present across different chemotypes of T. swinhoei. Thus, our metagenomic insights reveal that the diversity of Entotheonella within Theonella sponges is greater than previously recognized.

microbiology↗
bioRxiv2022

The plant nuclear lamina disassembles to regulate genome folding in stress conditions

The nuclear lamina (NL) is a complex network of nuclear lamins and lamin-associated nuclear membrane proteins, which scaffold the nucleus to maintain structural integrity. In Arabidopsis thaliana, Nuclear Matrix Constituent Proteins (NMCPs) are essential components of the NL and are required to maintain the structural integrity of the nucleus and specific perinuclear chromatin anchoring. At the nuclear periphery, suppressed chromatin overlapping with repetitive sequences and inactive protein coding genes are enriched. At a chromosomal level, plant chromatin organization in interphase nuclei displays flexibilities in response to various developmental cues and environmental stimuli. Based on these observations in Arabidopsis, and given the role of AtNMCP genes (CRWN1 and CRWN4) in organizing chromatin positioning at the nuclear periphery, one can expect considerable changes in chromatin-NL interactions when the global chromatin organization patterns are being altered in plants. Here, we report the highly flexible nature of plant nuclear lamina, which disassembles substantially under various stress conditions. Particularly, under heat stress, we reveal that chromatin domains, initially tethered to the nuclear envelope, remain largely associated with CRWN1 and become scattered in the inner nuclear space. Via investigating the three-dimensional chromatin contact network, we further reveal that CRWN1 proteins play a structural role in shaping the changes in genome folding under heat stress. Also, CRWN1 acts as a negative transcriptional co-regulator to modulate the shift of the plant transcriptome profile in response to heat stress.

genomics↗
bioRxiv2022

Chromosome-level genome assembly of Rorippa aquatica revealed its allotetraploid origin and mechanisms of heterophylly upon submergence

The ability to respond to environmental variability is essential for living systems, especially to sessile organisms such as plants. The amphibious plant Rorippa aquatica exhibits a drastic type of phenotypic plasticity known as heterophylly, a phenomenon where leaf form is altered in response to the surrounding environment. Although heterophylly has been studied in various plant species, its molecular mechanism has not been fully elucidated. To establish the genetic basis and analyze the evolutionary processes responsible for heterophylly, we assembled the chromosome-level genome of R. aquatica by combining data from Illumina short-read sequencing, PacBio long-read sequencing, and High-throughput Chromosome Conformation Capture (Hi-C) sequencing technologies. Fine-scale comparative chromosome painting and chromosomal genomics revealed that allopolyploidization and subsequent post-polyploid descending dysploidy occurred during R. aquatica speciation. The genomic information above was the basis for the transcriptome analyses to examine the mechanisms involved in heterophylly, especially in response to the submerged condition, which uncovered that the ethylene and blue light signaling pathways participate in regulating heterophylly under submerged conditions. The assembled R. aquatica reference genome provides novel insights into the molecular mechanisms and evolution of heterophylly.

plant biology↗
bioRxiv2021

Single-cell metabolite detection and genomics reveals uncultivated talented producer

The production of bioactive metabolites is increasingly recognized as an important function of host-associated bacteria. An example is defensive symbiosis that might account for much of the chemical richness of marine invertebrates including sponges (Porifera), one of the oldest metazoans. However, as most complex microbiomes remain largely uncultivated and lack reference genomes, unequivocally linking metabolic functions to a cellular source is a challenge. Here we report an analysis pipeline of microfluidic encapsulation, Raman microscopy, and integrated digital genomics (MERMAID) for an efficient identification of uncultivated producers. We applied this method to the chemically rich bacteriosponge Theonella swinhoei, previously shown to contain Entotheonella symbionts providing most of its bioactive substances except for the antifungal aurantosides that lacked biosynthetic gene candidates in the metagenome. Raman-guided single-bacterial analysis and sequencing revealed a cryptic, distinct multiproducer, Candidatus Poriflexus aureus from a new Chloroflexi lineage. Its exceptionally large genome contains numerous biosynthetic loci and suggested an even higher chemical richness of this sponge than previously appreciated. This study highlights the importance of complementary technologies to uncover microbiome functions, reveals remarkable parallels between distantly related symbionts of the same host, and adds functional support for diverse chemically prolific lineages being present in microbial dark matter. Significance StatementThe production of bioactive metabolites is increasingly recognized as an important function of host-associated bacteria. However, the acquisition of integrated genomic and metabolic data from uncultivated environmental bacteria is still challenging. In this work, we explored the combination of Raman microscopy and single-cell sequencing to localize chemical features to a specific bacterium in an uncultivated microbiome, and we specified the bacteria in the uncultured lineage as a producer of aurantoside, an antifungal natural product, from a chemically and microbially complex sponge. This study offers a new methodology as well as insights into chemical functions of uncultivated life.

microbiology↗
bioRxiv2020

Production of a tributyltin-binding protein 2 knockout mutant strain of Japanese medaka, Oryzias latipes

Tributyltin-binding proteins (TBT-bps), members of the lipocalin family, bind TBT in fish blood and are presumed to contribute to detoxification of TBT. Recent studies have shown that many fish species have TBT-bp genes, and that these genes are induced by stresses such as exposure to chemicals or fish pathogenic bacteria. However, the function of TBT-bps, and the mechanisms of their induction and detoxification activity are still unclear. Here, towards elucidating the functions of TBT-bp2, we produced a TBT-bp2 knockout (TBT-bp2-/-) strain of Japanese medaka, Oryzias latipes, by using the CRISPR/Cas9 system. Gene expression of the mutated TBT-bp2 was reduced, and the cDNA sequencing and predicted protein structure suggested possible loss of function. However, the fish could be grown under normal conditions. Exposure of the TBT-bp2-/- strain of medaka to various stresses in future experiments is expected to contribute to our understanding of this novel detoxification system in aquatic organisms.

pharmacology and toxicology↗
bioRxiv2019

Micro- and nanostructural characteristics of rat masseter muscle entheses -Characteristics of masseter muscle entheses-

The entheses of the masticatory muscles differ slightly from those of the trunk and limb muscles. However, the bones of the skull are subject to various functional pressures, including masticatory force, resulting in a complex relationship between bone structure and muscle function that remains to be fully elucidated. The present study aimed to clarify aspects of masseter muscle-tendon-bone morphological characteristics and local load environment through quantitative analysis of biological apatite (BAp) crystallite alignment and collagen fiber orientation together with histological examination of the entheses.\n\nResult of histological observation, the present findings show that, in the entheses of the masseter muscle in the first molar region, tendon attaches to bone via unmineralized fibrocartilage, while some tendon collagen fibers insert directly into the bone, running parallel to the muscle fibers. Furthermore, BAp crystallites in the same region show uniaxial preferential alignment at an angle that matches the insertion angle of the tendon fibers. Conversely, in the entheses of the masseter muscle in the third molar region, the tendon attaches to the bone via a layer of thickened periosteum and chondrocytes. As in the first molar region, the results of bone quality analysis in the third molar region showed BAp crystallite alignment parallel to the orientation of the tendon fibers. This indicates that the local mechanical environment generates differences in enthesis morphology.\n\nThe present study showed a greater degree of uniaxial BAp crystallite alignment in entheses with direct insertion rather than indirect tendon-bone attachment and the direction of alignment was parallel to the orientation of tendon fibers. These findings suggest that functional pressure from the masseter muscle greatly affects bone quality as well as the morphological characteristics of the enthesis, specifically causing micro- and nanostructural anisotropy in the direction of resistance to the applied pressure.

biophysics↗