Biology subjects

Matsui, T.

Publications and source records attributed to Matsui, T..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

Zinc controls histone acetyltransferase KAT7 activity to maintain cellular zinc homeostasis

Zinc is an indispensable micronutrient for optimal physiological functions, and zinc deficiency has been implicated in the pathogenesis of various human diseases. One potential mechanism underlying such pathogenic effects is the alteration of gene expression caused by zinc deficiency; however, the details of this process remain largely unexplored. Here, we show that during zinc deficiency, the histone acetyltransferase KAT7 loses its enzymatic activity, leading to the attenuated acetylation of histone H3 at Lys14 (H3K14ac) at enhancer regions. Physiologically, the decrease in H3K14ac leads to the upregulation of the expression of ZIP10, a plasma membrane-localized zinc transporter, thereby facilitating the import of extracellular zinc to maintain cellular zinc homeostasis. Moreover, prolonged zinc deficiency in mice induced by a zinc-deficient diet or high-fat diet, accompanied by decreased H3K14ac levels in the liver, upregulated the expression of genes associated with intracellular lipid droplet formation, leading to the accumulation of lipids within liver tissue. Our findings demonstrate that cells respond to zinc deficiency by converting it into an epigenetic signal that drives physiological or pathophysiological biological processes.

cell biology↗

bioRxiv2023

Growth inhibitory factor/metallothionein-3 is a sulfane sulfur-binding protein

Cysteine-bound sulfane sulfur atoms in proteins have received much attention as key factors in cellular redox homeostasis. However, the role of sulfane sulfur in zinc regulation has been underinvestigated. We report here that cysteine-bound sulfane sulfur atoms serve as ligands to hold and release zinc ions in growth inhibitory factor (GIF)/metallothionein-3 (MT-3) with an unexpected C-S-S-Zn structure. Oxidation of such a zinc/persulfide cluster in Zn7GIF/MT-3 results in the release of zinc ions, and intramolecular tetrasulfide bridges in apo-GIF/MT-3 efficiently undergo S-S bond cleavage by thioredoxin to regenerate Zn7GIF/MT-3. Three-dimensional molecular modeling confirmed the critical role of the persulfide group in the thermostability and Zn-binding affinity of GIF/MT-3. The present discovery raises the fascinating possibility that the function of other Zn-binding proteins is controlled by sulfane sulfur.

biochemistry↗

bioRxiv2023

Syntaxin 17 recruitment to mature autophagosomes is temporally regulated by PI4P accumulation

During macroautophagy, cytoplasmic constituents are engulfed by autophagosomes. Lysosomes fuse with closed autophagosomes but not with unclosed intermediate structures. This is achieved in part by the late recruitment of the autophagosomal SNARE syntaxin 17 (STX17) to mature autophagosomes. However, how STX17 recognizes autophagosome maturation is not known. Here, we show that this temporally regulated recruitment of STX17 depends on the positively charged C-terminal region of STX17. Consistent with this finding, mature autophagosomes are more negatively charged compared with unclosed intermediate structures. This electrostatic maturation of autophagosomes is likely driven by the accumulation of phosphatidylinositol 4-phosphate (PI4P) in the autophagosomal membrane. Accordingly, dephosphorylation of autophagosomal PI4P prevents the association of STX17 to autophagosomes. Furthermore, molecular dynamics simulations support PI4P-dependent membrane insertion of the transmembrane helices of STX17. Based on these findings, we propose a model in which STX17 recruitment to mature autophagosomes is temporally regulated by a PI4P-driven change in the surface charge of autophagosomes.

cell biology↗

bioRxiv2023

TAX1BP1 recruits ATG9 vesicles through SCAMP3 binding

Macroautophagy is a cellular process that delivers cytoplasmic material to lysosomes for degradation via autophagosomes. It often involves the selective degradation of ubiquitinated proteins. During selective macroautophagy, five ubiquitin-binding adaptors, p62, NBR1, OPTN, NDP52, and TAX1BP1, form biomolecular condensates with ubiquitinated proteins and recruit ATG9 vesicles, which serve as the initial membrane source required for autophagosome formation. However, the molecular details underlying the cargo/adaptor-dependent recruitment of ATG9 vesicles remain unclear. Here, we show that ATG9 vesicles are recruited by three cargo adaptors: TAX1BP1, NBR1, and OPTN. We also find that ATG9A itself is not the determinant for recruitment by these cargo adaptors, and that TAX1BP1-dependent ATG9 vesicle recruitment is mediated by SCAMP3, a transmembrane protein on the ATG9 vesicles, through binding to the coiled-coil 1 domain of TAX1BP1. These findings provide mechanistic insights into the cargo/adaptor-dependent assembly of ATG9 vesicles in mammals.

molecular biology↗

bioRxiv2023

Genome-scale analysis of interactions between genetic perturbations and natural variation

Interactions between genetic perturbations and segregating loci can cause perturbations to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing to measure the fitness effects of 7,700 CRISPRi perturbations targeting 1,712 distinct genes in 169 yeast cross progeny (or segregants). We identified 460 genes whose perturbation has different effects across segregants. Several factors caused perturbations to show variable effects, including baseline segregant fitness, the mean effect of a perturbation across segregants, and interacting loci. We mapped 234 interacting loci and found four hub loci that interact with many different perturbations. Perturbations that interact with a given hub exhibit similar epistatic relationships with the hub and show enrichment for cellular processes that may mediate these interactions. These results suggest that an individuals response to perturbations is shaped by a network of perturbation-locus interactions that cannot be measured by approaches that examine perturbations or natural variation alone.

genetics↗

bioRxiv2022

Zero-shot reconstruction of mutant spatial transcriptomes

Mutant analysis is the core of biological/pathological research, and measuring spatial gene expression can facilitate the understanding of the disorganised tissue phenotype1-5. The large numbers of mutants are worth investigating; however, the high cost and technically challenging nature of experiments to measure spatial transcriptomes may act as bottlenecks6. Spatial transcriptomes have been computationally predicted from single-cell RNA sequencing data based on teaching data of spatial gene expression of certain genes7; nonetheless, this process remains challenging because teaching data for most mutants are unavailable. In various machine-learning tasks, zero-shot learning offers the potential to tackle general prediction problems without using teaching data8. Here, we provide the first zero-shot framework for predicting mutant spatial transcriptomes from mutant single-cell RNA sequencing data without using teaching data, such as a mutant spatial reference atlas. We validated the zero-shot framework by accurately predicting the spatial transcriptomes of Alzheimers model mice3 and mutant zebrafish embryos with lost Nodal signaling9. We propose a spatially informed screening approach based on zero-shot framework prediction that identified novel Nodal-downregulated genes in zebrafish. We expect that the zero-shot framework will provide novel phenotypic insights by leveraging the enormous mutant/disease single-cell RNA sequencing data collected.

bioinformatics↗

bioRxiv2022

Prediction of elimination of intrahepatic cccDNA in hepatitis B virus-infected patients by a combination of noninvasive viral markers

Evaluation of intrahepatic covalently closed circular DNA (cccDNA) is a key for searching an elimination of hepatitis B virus (HBV) infection. HBV RNA and HBV core-related antigen have been proposed as surrogate markers for evaluating cccDNA activity, although they do not necessarily estimate the amount of cccDNA. Here, we developed a novel multiscale mathematical model describing intra- and inter-cellular viral propagation, based on the experimental quantification data in both HBV-infected cell culture and humanized mouse models. We applied it to HBV-infected patients under treatment and developed a model which can predict intracellular HBV dynamics only by use of noninvasive extracellular surrogate biomarkers. Importantly, the model prediction of the amount of cccDNA in patients over time was confirmed to be well-correlated with the liver biopsy data. Thus, our noninvasive method enables to predict the amount of cccDNA in patients and contributes to determining the treatment endpoint required for elimination of intrahepatic cccDNA.

microbiology↗

bioRxiv2022

Complex genetics cause and constrain fungal persistence in different parts of the mammalian body

Determining how genetic polymorphisms enable certain fungi to persist in mammalian hosts can improve understanding of opportunistic fungal pathogenesis, a source of substantial human morbidity and mortality. We examined the genetic basis of fungal persistence in mice using a cross between a clinical isolate and the lab reference strain of the budding yeast Saccharomyces cerevisiae. Employing chromosomally-encoded barcodes, we tracked the relative abundances of 822 genotyped, haploid segregants in multiple organs over time and performed linkage mapping of their persistence in hosts. Detected loci showed a mix of general and antagonistically pleiotropic effects across organs. General loci showed similar effects across all organs, while antagonistically pleiotropic loci showed contrasting effects in the brain and the kidneys, liver, and spleen. Persistence in an organ required both generally beneficial alleles and organ-appropriate pleiotropic alleles. This genetic architecture resulted in many segregants persisting in the brain or in non-brain organs, but few segregants persisting in all organs. These results show complex combinations of genetic polymorphisms collectively cause and constrain fungal persistence in different parts of the mammalian body.

genetics↗

bioRxiv2021

TBC1D18, a novel Rab5-GAP, coordinates endosome maturation together with Mon1

Endosome maturation is essential for efficient degradation of internalized extracellular molecules and plasma membrane proteins. Two Rab GTPases, Rab5 and Rab7, are known to regulate endosome maturation, and a Rab5-to-Rab7 conversion mediated by a Rab7 activator, Mon1-Ccz1, is essential for progression of the maturation process. However, the importance and mechanism of Rab5 inactivation during endosome maturation is poorly understood. Here we report a novel Rab5 inactivator (Rab5-GTPase activating protein [Rab5-GAP]), TBC1D18, which is associated with Mon1 and mediates endosome maturation. We found that Rab5 hyperactivation in addition to Rab7 inactivation occurs in the absence of Mon1. We present evidence showing that the severe defects in endosome maturation observed in Mon1-KO cells are attributable to Rab5 hyperactivation rather than to Rab7 inactivation. We then identified TBC1D18 as a Rab5-GAP by comprehensive screening of TBC-domain-containing Rab-GAPs. Expression of TBC1D18 in Mon1-KO cells rescued the defects in endosome maturation, whereas its depletion attenuated endosome formation and degradation of endocytosed cargos. Moreover, TBC1D18 was found to be able to interact with Mon1, and it localized in close proximity to lysosomes in a Mon1-dependent manner. Thus, TBC1D18 is a crucial regulator of endosome maturation that functions together with Mon1.

cell biology↗

bioRxiv2021

Executive control by fronto-parietal activity explains counterintuitive decision behavior in complex value-based decision-making

In real life, humans make decisions by taking into account multiple independent factors, such as delay and probability. Cognitive psychology suggests that cognitive control mechanisms play a key role when facing such complex task conditions. However, in value-based decision-making, it still remains unclear to what extent cognitive control mechanisms become essential when the task condition is complex. In this study, we investigated decision-making behaviors and underlying neural mechanisms using a multifactor gambling task where participants simultaneously considered probability and delay. Decision-making behavior in the multifactor task was modulated by both probability and delay. The behavioral effect of probability was stronger than delay, consistent with previous studies. Furthermore, in a subset of conditions that recruited fronto-parietal activations, reaction times were paradoxically elongated despite lower probabilistic uncertainty. Notably, such a reaction time elongation did not occur in control tasks involving single factors. Meta-analysis of brain activations suggested an association between the paradoxical increase of reaction time and strategy switching. Together, these results suggest a novel aspect of complex value-based decision-makings that is strongly influenced by fronto-parietal cognitive control. Highlights* A value-based decision task with concurrent delay and probabilistic uncertainty * Stronger behavioral effect of probability than delay * Paradoxically long reaction time despite low probabilistic uncertainty * The task activated fronto-parietal cognitive control network * Reaction time elongation coincided with activation similar to strategy switching

neuroscience↗

bioRxiv2021

Hidden pathway for cytokine receptor activation: Structural insights into a marine sponge-derived lectin that activates the thrombopoietin receptor via recognition of the fucose moiety

N-glycan-mediated activation of the thrombopoietin receptor (MPL) under pathological conditions has been implicated in myeloproliferative neoplasms induced by mutant calreticulin, which forms an endogenous receptor-agonist complex that constitutively activates the receptor. However, the molecular basis for this mechanism has not been studied because no external agonists existed. We describe the structure and function of a marine sponge-derived MPL agonist, thrombocorticin (ThC), a homodimerized lectin with calcium-dependent fucose-binding properties. ThC-induced activation persists due to limited receptor internalization. The strong synergy between ThC and thrombopoietin suggests that ThC catalyzes the formation of receptor dimers on the cell surface. MPL is subject to sugar-mediated activation, where the kinetics differ from those of cytokines. This result suggests the presence of diverse receptor activation pathways in human thrombopoiesis. One-sentence summaryA marine sponge lectin catalyzes thrombopoietin receptor dimerization and activation, exhibiting strong synergy with thrombopoietin, and modulates internalization of the receptor.

cell biology↗

bioRxiv2021

On co-activation pattern analysis and non- stationarity of resting brain activity

The non-stationarity of resting-state brain activity has received increasing attention in recent years. Functional connectivity (FC) analysis with short sliding windows and coactivation pattern (CAP) analysis are two widely used methods for assessing the dynamic characteristics of brain activity observed with functional magnetic resonance imaging (fMRI). However, the statistical nature of the dynamics captured by these techniques needs to be verified. In this study, we found that the results of CAP analysis were similar for real fMRI data and simulated stationary data with matching covariance structures and spectral contents. We also found that, for both the real and simulated data, CAPs were clustered into spatially heterogeneous modules. Moreover, for each of the modules in the real data, a spatially similar module was found in the simulated data. The present results suggest that care needs to be taken when interpreting observations drawn from CAP analysis as it does not necessarily reflect non-stationarity or a mixture of states in resting brain activity. HighlightsO_LICAP was conducted for real fMRI data and a stationary null model. C_LIO_LIThe results of CAP analysis were similar for the real and simulated data. C_LIO_LISimilar results for real and simulated data in both ROI- and voxel-based analyses. C_LIO_LIResults of CAP analysis may not reflect non-stationarity of resting brain activity. C_LI

neuroscience↗

bioRxiv2021

Crocosphaera as a major consumer of fixed nitrogen despite its capability of nitrogen fixation

Crocosphaera watsonii (hereafter Crocosphaera) is a key nitrogen (N) fixer in the ocean, but its ability to consume combined N sources is still unclear. Using in situ microcosm incubations with an ecological model, we show that Crocosphaera has high competitive capability both under low and moderately high combined N concentrations. In field incubations, Crocosphaera accounted for the highest consumption of ammonium and nitrate, followed by pico-eukaryotes. The model analysis shows that cells have a high ammonium uptake rate ([~]7 mol N (mol N)-1 d-1 at the maximum), which allows them to compete against pico-eukaryotes and non-diazotrophic cyanobacteria when combined N is sufficiently available. Even when combined N is depleted, their capability of nitrogen fixation allows higher growth rates compared to potential competitors. These results suggest the high fitness of Crocosphaera in combined N limiting, oligotrophic oceans, and thus heightens its potential significance in its ecosystem and in biogeochemical cycling.

microbiology↗

bioRxiv2021

The interplay of additivity, dominance, and epistasis in a diploid yeast cross

We used a double barcoding system to generate and phenotype a panel of ~200,000 diploid yeast segregants that can be partitioned into hundreds of interrelated families. This experimental design enabled the detection of thousands of genetic interactions and many loci whose effects vary across families. Traits were largely specified by a small number of hub loci with major additive and dominance effects, and pervasive epistasis. Genetic background commonly influenced both the additive and dominance effects of loci, with multiple modifiers typically involved. The most prominent dominance modifier was the mating locus, which had no effect on its own. Our findings show that the interplay between additivity, dominance, and epistasis underlies a complex genotype-to-phenotype map in diploids. One sentence summaryIn diploids, epistasis frequently modifies both additivity and dominance.

genetics↗

bioRxiv2021

A Ca2+ wave generates a force during cell extrusion in zebrafish

When oncogenic transformed or damaged cells appear within an epithelial sheet, they are apically extruded by surrounding cells. Recently, using cultured mammalian epithelial cells and zebrafish embryonic epithelial cells, we found that a calcium (Ca2+) wave propagates from RasV12-transformed cells and laser-irradiated damaged cells to surrounding cells and promotes apical extrusion by inducing polarized movements of the surrounding cells. In mammalian cell cultures, we reported that the inositol trisphosphate (IP3) receptor, gap junctions, and the mechanosensitive Ca2+ channel TRPC1 are involved in Ca2+ wave-mediated polarized movements. However, which molecules regulate Ca2+ wave-mediated polarized movements in zebrafish and whether the Ca2+ wave can generate a force remain unknown. In this study, we aimed to answer these questions. By performing pharmacological and gene knockout experiments, we showed that a Ca2+ wave induced by the IP3 receptor and trpc1 led to formation of cryptic-lamellipodia and polarized movements of surrounding cells toward extruding cells in zebrafish. By using an in vivo force measurement method, we found that the Ca2+ wave generated approximately 1 kPa of force toward extruding cells. Our results reveal a previously unidentified molecular mechanism underlying the Ca2+ wave in zebrafish and demonstrate that the Ca2+ wave generates a force during cell extrusion.

cell biology↗

bioRxiv2021

Vision-to-value transformations in artificial network and human brains

Humans and now computers can derive subjective valuations from sensory events although such transformation process is essentially unknown. In this study, we elucidated unknown neural mechanisms by comparing convolutional neural networks (CNNs) to their corresponding representations in humans. Specifically, we optimized CNNs to predict aesthetic valuations of paintings and examined the relationship between the CNN representations and brain activity via multivoxel pattern analysis. Primary visual cortex and higher association cortex activities were similar to computations in shallow CNN layers and deeper layers, respectively. The vision-to-value transformation is hence proved to be a hierarchical process which is consistent with the principal gradient that connects unimodal to transmodal brain regions (i.e. default mode network). The activity of the frontal and parietal cortices was approximated by goal-driven CNN. Consequently, representations of the hidden layers of CNNs can be understood and visualized by their correspondence with brain activity-facilitating parallels between artificial intelligence and neuroscience.

neuroscience↗

bioRxiv2021

RBD11, a bioengineered Rab11-binding module for visualizing and analyzing endogenous Rab11

The small GTPase Rab11 plays pivotal roles in diverse physiological phenomena, including the recycling of membrane proteins, cytokinesis, neurite outgrowth, and epithelial morphogenesis. One effective method of analyzing the function of endogenous Rab11 is to overexpress a Rab11-binding domain of one of its effectors, e.g., the C-terminal domain of Rab11-FIP2 (Rab11-FIP2-C), as a dominant-negative construct. However, the drawback of this method is the broader Rab binding specificity of the effector domain, because Rab11-FIP2-C binds to Rabs other than Rab11, e.g., to Rab14 and Rab25. In this study, we bioengineered an artificial Rab11-specific binding domain, named RBD11. Expression of RBD11 visualized endogenous Rab11 without affecting its localization or function, whereas expression of a tandem RBD11, named 2xRBD11, inhibited epithelial morphogenesis and induced a multi-lumen phenotype characteristic of Rab11-deficient cysts. We also developed two tools for temporally and reversibly analyzing Rab11-dependent membrane trafficking: tetracycline-inducible 2xRBD11 and an artificially oligomerized domain (FM)-tagged RBD11.

cell biology↗

bioRxiv2021

An early-morning flowering trait in rice helps retain grain yield under heat stress field conditions at flowering stage

Early-morning flowering (EMF) trait is supposed to be effective in retaining grain yield due to mitigation of heat-induced spikelet sterility at flowering in rice. This study evaluated (i) phenotypic differences between a near-isogenic line carrying a QTL for EMF trait, designated as IR64+qEMF3, and a recurrent parent, IR64, under wide variation in climates and (ii) whether an EMF trait can retain grain yield under heat stress at flowering. IR64+qEMF3 had significant earlier flower opening time (FOT) in diverse environmental conditions including temperate, subtropical, and tropical regions. Under normal temperatures at flowering, IR64+qEMF3 had similar grain yield to IR64 with some significant changes in agronomic traits and yield components. Field trials in heat-vulnerable regions of central Myanmar for seven crop seasons showed that higher percentage of filled grains contributed to the significantly higher grain yield in IR64+qEMF3 among yield components when plants were exposed to daily maximum air temperatures around 36.5 {degrees}C or higher. Lower spikelet sterility in IR64+qEMF3 was attributed to the earlier FOT during cooler early morning hours. This is the first field study that clearly demonstrates the advantage of the EMF trait for retaining grain yield by stabilizing percentage of fertile grains under heat stress at flowering.

developmental biology↗