Biology subjects

Sakata, K.

Publications and source records attributed to Sakata, K..

8 recordsLinked to original sources

bioRxiv2025

IDR-dependent MORC1 bodies limit chromatin accessibility to tune transposon repression

Germline-specific MORC1-mediated transposon repression intersects with the MIWI2-piRNA pathway and involves H3K9me3 deposition, yet the underlying mechanism remains unclear. Here, we show that MORC1 assembles nuclear bodies in gonocytes. Using a doxycycline-inducible MORC1 expression system in NIH3T3 cells, we find that condensate formation is confined to the nucleus via an IDR containing a bipartite NLS, and that TRIM28, a corepressor that recruits the H3K9 methyltransferase SETDB1, is enriched in these bodies through protein-protein interactions. An IDR-deficient MORC1 mutant fails to form nuclear condensates but retains TRIM28 binding. ChIP-seq analysis reveals that this mutant exhibits higher occupancy at heterochromatin-embedded transposons than wild-type MORC1, with a pronounced preference for evolutionarily young transposon subfamilies that strongly overlap endogenous MORC1 targets in gonocytes. Wild-type MORC1 shows weaker enrichment at these elements and instead exhibits a greater tendency to occupy open chromatin. Condensates formed by exogenous MORC1 expression in NIH3T3 cells are substantially larger than those observed in gonocytes. These findings support a model in which MORC1-dependent transposon repression is governed by physical engagement with TRIM28 and by IDR-dependent, yet quantitatively restrained, nuclear body formation, which limits MORC1 chromatin accessibility, curtails off-target binding, and concentrates repression on bona fide transposon targets.

molecular biology↗

bioRxiv2025

Proposed mechanism for Rft1-mediated scrambling of a dolichol-linked oligosaccharide

The membrane protein Rft1 is proposed to play an essential role in yeast and human cells by scrambling the glycolipid Man5GlcNAc2-PP-dolichol (M5-DLO) across the endoplasmic reticulum (ER) for protein N-glycosylation. While this activity has been demonstrated in liposomes reconstituted with purified Rft1, biochemical evidence of additional M5-DLO scramblases and the viability of Rft1-null Trypanosoma brucei suggest that scrambling may be a moonlighting function of Rft1 rather than its essential cellular role. To investigate this paradox, we used AlphaFold3 and Chai-1 to model the conformational dynamics of yeast Rft1-M5-DLO complexes. The models suggest an alternating access mechanism, typical of Multidrug/Oligosaccharidyl-lipid/Polysaccharide (MOP) superfamily transporters, in which a cationic central cavity coordinates the anionic headgroup of M5-DLO, while the dolichol tail of the lipid is accommodated through a lateral portal formed by two transmembrane helices. We used the models to design mutations to disrupt the interaction between Rft1 and the M5-DLO headgroup, and to engineer a salt bridge to block the portal and stall transport. Using a Tet-off yeast reporter strain, we tested 26 central cavity mutants and identified two that supported cell growth poorly despite being well-expressed. Strikingly, the portal-blocking mutant which lacks scramblase activity supported robust growth. These data suggest that while M5-DLO binding is important for Rft1s essential function, scrambling activity is dispensable. We propose that Rft1s essential role may be as an M5-DLO chaperone, capturing and routing M5-DLO propitiously on the cytoplasmic side of the ER to coordinate DLO biosynthesis. ImportanceCell surface and secreted proteins are decorated with sugar chains. These chains are first assembled on a lipid carrier. Initial stages of assembly occur on the cytoplasmic side of a subcellular structure called the endoplasmic reticulum (ER). To complete assembly, the partially assembled lipid-linked sugar chain must be flipped across the ER. Here we use computationally guided cell-based assays to examine the role of the Rft1 protein in this process.

biochemistry↗

bioRxiv2025

Astringent flavanol fires the locus-noradrenergic system, regulating neurobehavior and autonomic nerves

Astringent flavanols (FLs) have shown enhanced cognitive function in a large intervention trial, but their mechanism remains unclear due to poor bioavailability. An oral dose of FLs increased spontaneous locomotion and memory, with activation of the sympathetic-adrenergic-medullary (SAM) and hypothalamic-pituitary-adrenal (HPA) axis, as shown by increased urinary catecholamine concentrations and corticotropin-releasing hormone (CRH) mRNA expression in the paraventricular nucleus (PVN) of mice. MS imaging showed high intensity of noradrenaline (NA) in the locus coeruleus (LC), which plays a key role in learning and memory, the hypothalamus lateral preoptic area, which affects sleep and arousal, and the brainstem as the origin of the sympathetic nervous system, immediately after FLs administration. Subsequent in situ hybridization (ISH) analysis showed that these NAs originated from LC. Astringent compounds like FLs influence brain function and physiological changes. Furthermore, the present series of results presents novel mechanisms by which food sensory properties maintain homeostasis. Highlights- A oral dose of astringent flavanols (FLs) immediately fires locus coeruleus-noradrenaline axis - FLs enhance spontaneous locomotion and short-term memory in mice - SAM and HPA axis are also activated by an oral dose of FLs - FLs astringency affects the brain and body, contributing to homeostasis.

synthetic biology↗

bioRxiv2025

Data-Driven Feed Optimization for Sustainable Aquaculture through Integrated Omics Analysis and Two-stage Bayesian optimization

In aquaculture and livestock farming, developing feed that promotes efficient growth while minimizing environmental impact is crucial for sustainability. We developed a data-driven feed optimization system (DFOS) that integrates omics analysis with machine learning-based optimization technologies. First, DFOS employed Bayesian optimization (BO) to identify the optimal proportions of proteins and lipids, which are crucial feed components. Simultaneously, omics analysis was conducted to assess the physiological response of the targets to a given feed and identify key dietary components essential for growth. Next, BO was used to efficiently modify the combination and proportion of the specific additives identified in the first stage. We demonstrated the efficacy of DFOS by applying it to develop a new feed for the high-demand leopard coral grouper (Plectropomus leopardus) in Southeast Asia. This system provides an efficient data-driven framework for feed optimization across aquaculture and livestock, contributing significantly to more sustainable and productive farming practices.

ecology↗

bioRxiv2024

Evolution of invertebrate Cdk4/6-Cdkn2 system

The cell cycle is driven by cyclin-dependent kinases (Cdks). The decision whether the cell cycle proceeds is made during G1 phase, when Cdk4/6 functions. Cyclin-dependent kinase inhibitor 2 (Cdkn2) is a specific inhibitor of Cdk4/6, and their interaction depends on D84 in Cdkn2 and R24/31 in Cdk4/6. This knowledge is based mainly on studies in mammalian cells. Here, we comprehensively analyzed Cdk4/6 and Cdkn2 in invertebrates and found that Cdk4/6 was present in most of the investigated phyla, but the distribution of Cdkn2 was rather uneven among and within the phyla. The positive charge of R24/R31 in Cdk4/6 was conserved in all analyzed species in phyla with Cdkn2. The presence of Cdkn2 and the conservation of the positive charge were statistically correlated. We also found that Cdkn2 has been tightly linked to Fas associated factor 1 (Faf1) during evolution. We discuss potential interactions between Cdkn2 and Cdk4/6 in evolution and the possible cause of the strong conservation of the microsynteny.

evolutionary biology↗

bioRxiv2024

A comprehensive stroke risk assessment by combining atrial computational fluid dynamics simulations and functional patient data

Stroke, a major global health concern often rooted in cardiac dynamics, demands precise risk evaluation for targeted intervention. Current risk models, like the CHA2DS2-VASc score, often lack the granularity required for personalized predictions. In this study, we present a nuanced and thorough stroke risk assessment by integrating functional insights from cardiac magnetic resonance (CMR) with patient-specific computational fluid dynamics (CFD) simulations. Our cohort, evenly split between control and stroke groups, comprises eight patients. Utilizing CINE CMR, we compute kinematic features, revealing smaller left atrial volumes for stroke patients. The incorporation of patient-specific atrial displacement into our hemodynamic simulations unveils the influence of atrial compliance on the flow fields, emphasizing the importance of LA motion in CFD simulations and challenging the conventional rigid wall assumption in hemodynamics models. Standardizing hemodynamic features with functional metrics enhances the differentiation between stroke and control cases. While standalone assessments provide limited clarity, the synergistic fusion of CMR-derived functional data and patient-informed CFD simulations offers a personalized and mechanistic understanding, distinctly segregating stroke from control cases. Specifically, our investigation reveals a crucial clinical insight: normalizing hemodynamic features based on ejection fraction fails to differentiate between stroke and control patients. Differently, when normalized with stroke volume, a clear and clinically significant distinction emerges and this holds true for both the left atrium and its appendage, providing valuable implications for precise stroke risk assessment in clinical settings. This work introduces a novel framework for seamlessly integrating hemodynamic and functional metrics, laying the groundwork for improved predictive models, and highlighting the significance of motion-informed, personalized risk assessments.

bioengineering↗

bioRxiv2020

Inositol synthesis gene is required for circadian rhythm of Drosophila melanogaster mating behavior.

Accumulating evidence indicates that the molecular circadian clock underlies the mating behavior of Drosophila melanogaster. However, information about which gene affects circadian mating behavior is poorly understood in animals. The present study found that feeding Myo-inositol enhanced the close-proximity (CP) rhythm of D. melanogaster mating behavior and lengthened the period of the CP rhythm. Then, to understand a role for inositol synthesis to fly mating behavior, we established the Inos (Myo-inositol 1-phosphate synthase) gene knock down fly strains with RNAi. Interestingly, the CP behavior of this three-different driver knock down strains was arrhythmic, but the locomotor rhythm was rhythmic. The data of three-different Inos knock down strains suggests that Inos gene expression of upper LNd, l-LNV, 5ths-LNv in brain is necessary for proper CP rhythm generation in D. melanogaster. The data indicated that the Inos gene is involved in the role for the circadian rhythm of D. melanogaster mating behavior.

animal behavior and cognition↗

bioRxiv2017

Disproportional distribution of radioactive elements in the marine ecosystems surrounding the accident site of the Fukushima Daiichi Nuclear Power Plant

After the Fukushima Daiichi Nuclear Power Plant accident, various surveys have been performed to measure the extent of radioactive contamination in marine sediments, surface waters, plankton, and fish. However, the radioactive contamination of one of the most important ecological niches, biofilms, has not been investigated. Therefore, in this study, we sampled biofilms from sea floor stones around Hisanohama Port, which is less than 30 km south of the accident site, and then analyzed the microbial community structure and element profiles, including those of radioactive elements, of these biofilms in order to determine the accumulation and retention of radioactive elements in them. Our results showed that the biofilm samples contained relatively high levels of radioactive cesium even when the sampling was performed 8-11 months after the accident. Our results also suggested that the structure of the biofilm organismal community is related to the element profile of radioactive cesium. Thus, our study suggests that biofilms are a possible radioactive compound accumulator in the natural environment and that they can retain radioactive material for at least 8-11 months.

ecology↗