Biology subjects

Kurokawa, K.

Publications and source records attributed to Kurokawa, K..

At least 19 recordsLinked to original sources

bioRxiv2026

An iPSC-based experimental framework for investigating phenotypic variation associated with Jomon ancestry in the present-day Japanese population

Ancestry-related genomic variation may contribute to phenotypic diversity. However, its cellular consequences remain difficult to evaluate. To address this, we developed a human induced pluripotent stem cell (hiPSC)-based framework for investigating such phenotypes. We used the Japanese population as a model of Jomon-related and continental East Asian ancestry admixture. Jomon ancestry, estimated using the Jomon allele score (JAS), was associated with clinical measures, including renal-related traits and serum triglycerides in 34,152 Tohoku Medical Megabank participants. Peripheral blood mononuclear cell transcriptomics of donors from the upper and lower extremes of the JAS distribution (n = 10) suggested group-level differences in immune-related gene expression. To test whether the serum triglyceride association coincided with hepatic cellular phenotypes, we differentiated hiPSCs from these donors into hepatocyte-like cells. Neither intracellular triglycerides nor lipid-related gene expression differed between groups. These findings highlight the value of a genetically characterized hiPSC-based framework for investigating ancestry-associated phenotypes across cellular contexts.

genomics↗

bioRxiv2026

Contact of mobile cis-Golgi network with ER exit sites executes COPI-mediated receptor recycling

COPI-mediated retrograde transport is essential for maintaining homeostasis between the endoplasmic reticulum (ER) and the Golgi in eukaryotic cells. However, its spatiotemporal dynamics remain unclear. In budding yeast, ER export occurs through a hug-and-kiss mechanism, wherein mobile cis-Golgi network (CGN) elements transiently approach ER exit sites (ERES) to capture cargo before departing to deliver it to the Golgi. Here, using high-resolution 3D and 4D live imaging, we show that the COPI-mediated recycling of a cargo receptor from the CGN back to the ER occurs during the hug-and-kiss event. Furthermore, this recycling is complete before the CGN detaches from the ERES, suggesting that COPI-mediated retrograde transport is spatiotemporally coupled to ER export during a single and transient CGN-ERES association. Consistent with this model, when COPI function is impaired, the receptor fails to return efficiently to the ER and instead remains in the CGN after separation from the ERES. Additionally, COPI impairment prolonged CGN-ERES association, suggesting that COPI function also facilitates CGN detachment from ERES. Thus, we propose that rapid COPI-mediated recycling drives CGN maturation directly at the ERES interface, enabling the CGN to detach and proceed along the secretory pathway.

cell biology↗

bioRxiv2026

Genome-resolved biogeography reveals multidimensional structuring of freshwater giant viruses across global deep lakes

Giant viruses (GV) are increasingly recognized as important ecosystem regulators. While metagenomics has uncovered extensive GV diversity, the global distributions of individual species and the biogeographic processes driving the pattern remain poorly understood. Here, we reconstructed GV metagenome-assembled genomes (MAGs) from 35 globally distributed deep freshwater lakes spanning five continents, aiming to identify their biogeographic patterns. The resulting 1663 non-redundant MAGs significantly expanded the known freshwater GV diversity, with [~]84% lacking a previously reported species representative. These MAGs were grouped into cosmopolitan and geographically restricted lineages. We identified 27 cosmopolitan GV species spanning multiple viral lineages, including families of Imitervirales, Pimascovirales, and mirusviruses order Styxvirales. The cosmopolitan species were characterized by their larger genomes and expanded gene repertoires of host-interaction functions, which may facilitate interactions with diverse hosts and contribute to their global distributions. The presence of geographically restricted species and the stronger distance-decay in community similarity observed in freshwater than marine ecosystems suggest that physical connectivity between ecosystems is an important factor influencing GV dispersal. We identified 312 and 177 GV MAGs almost exclusively associated with the epilimnion and hypolimnion, respectively. This water-layer preference of individual MAGs was highly consistent across lakes, suggesting conserved vertical partitioning in association with the thermal stratification of the water column. Overall, our findings reveal that GV biogeography in deep freshwater lakes is structured by the combined influence of horizontal dispersal limitation, vertical partitioning, and lineage-specific evolutionary histories.

microbiology↗

bioRxiv2026

Analytical methodology for unveiling the physical effect of detergents on the function of full-length membrane proteins using a single-molecule tracking system

G protein-coupled receptors (GPCRs) are important targets for drug discovery because they are the largest and most diverse family of membrane proteins in the human body. As exemplified by {beta}2-adrenergic receptor ({beta}2AR), which is a typical class-A GPCRs, they are prone to denaturation and inactivation after solubilization. Although diverse techniques have been developed, current structural and functional analyses are still limited to proteins with relatively stable and high expression. However, some mutant variants and misfolded proteins involved in diseases have extremely low expression levels and may be difficult to analyze. To overcome these limitations, we established a novel analytical platform for evaluating the ligand-binding ability of full-length {beta}2AR as a model at the single-molecule level without purification and addressing challenges such as membrane proteins with low expression levels and structural instability. This method enables the direct use of unpurified receptors immediately after solubilization and allows us to use only a small amount of sample ([~]10 ng) for observation and to distinguish between specific and nonspecific ligand binding by fitting. Furthermore, we unveiled the physical properties of detergents on the structural stability of solubilized receptors and found that the lateral pressure within detergent micelles affects ligand-binding ability. Detergents that provided a fluid microenvironment were able to maintain ligand-binding ability for several days even after solubilization; conversely, detergents that provided a rigid microenvironment caused the protein to lose its activity earlier. Our method could be a promising tool for the structural and functional analysis of membrane proteins untargeted until now. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/740883v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@3d274corg.highwire.dtl.DTLVardef@defd0forg.highwire.dtl.DTLVardef@1b81eb4org.highwire.dtl.DTLVardef@e7c275_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Benchmarking long-context genome language models on biosynthetic gene clusters

Recent advances in language models for natural language processing have spread to the field of genomics, driving the development of genome language models (gLMs) to decipher genomic information. Cutting-edge long-context gLMs are promising approaches for understanding and designing biological complexity, but their evaluation remains underdeveloped. In this study, we introduce BGCs-Bench, a unified benchmark focused on biosynthetic gene clusters for assessing long-range genomic modeling on three downstream tasks: biosynthetic class prediction, taxonomic classification and coding sequence annotation. Using BGCs-Bench, we perform systematic and layer-wise evaluations of the embedding representations of long-context gLMs, demonstrating that layer selection is crucial for downstream task performance. In addition to the evaluation results, the logit lens analysis of autoregressive gLMs suggests that StripedHyena-based models consist of earlier layers to encode biologically meaningful information from input DNA sequences and deeper layers to optimize embeddings for sequence generation. These findings provide insights for more effective development and application of long-context gLMs.

bioinformatics↗

bioRxiv2025

Cohesin prevents local mixing of condensed euchromatic domains in living human cells

The human genome is folded into chromatin loops by the cohesin complex, forming functional chromatin domains that underlie transcription and DNA replication/repair. However, how cohesin organizes these domains in living cells, especially in active euchromatin, remains elusive. To address this question, we combined single-nucleosome imaging/tracking and super-resolution 3D-structured illumination microscopy (3D-SIM) with euchromatin-specific labeling of histone H3.3. Using this nanoscopic approach, we revealed that euchromatin forms condensed domains that are constrained by cohesin-mediated loops. This organization refines the classical textbook view of euchromatin as largely open, in line with emerging evidence. Transcription machinery appears to be located near the condensed domain surfaces/borders. Cohesin loss increased nucleosome fluidity within these domains without altering their overall compaction, leading to local mixing of domains and compromising transcriptional insulation. These findings uncover an unexpected physical role of cohesin in maintaining the integrity of condensed euchromatic domains and ensuring proper higher-order regulation of gene expression.

cell biology↗

bioRxiv2025

Muc6-expressing gastric isthmus progenitors contribute to regeneration and metaplasia supported by myeloid-mesenchymal interactions

Gastric mucosal homeostasis is maintained by tissue-resident stem and progenitor cells residing in the isthmus region. Following mucosal injury, surviving cells contribute to regeneration, coinciding with characteristic pathological changes such as atrophic gastritis and metaplasia. To comprehensively understand the cellular dynamics involved in this process, we performed single-cell and spatial transcriptomics using newly generated transgenic mice. In human samples and mouse models, loss of gastric chief cells precedes, and even induces, loss of parietal cells during the progression of atrophy and metaplasia, validating the causal relationship underlying the decrease of these two lineages. Single-cell analysis confirmed robust stemness and metaplastic changes in the Muc6-expressing neck lineage following either chief or parietal cell ablation, and lineage-tracing experiments revealed that Muc6-expressing isthmus progenitors serve as a source of metaplasia and regeneration. Mechanistically, mucosal injury recruits IL-1-expressing myeloid cells, which stimulates NRG1 production in stromal fibroblasts, leading to mucosal proliferation and regeneration mediated by Myc activation in isthmus progenitors. These findings highlight the injury-responsible stem cell-like function of Muc6-expressing isthmal progenitors, which play a critical role in mucosal homeostasis and disease progression. Visual abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/648856v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@10fc2eaorg.highwire.dtl.DTLVardef@1c5b82corg.highwire.dtl.DTLVardef@1be747dorg.highwire.dtl.DTLVardef@d1d722_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Deuterium-reinforced polyunsaturated fatty acids protect against muscle atrophy induced by type 1 diabetes in mice

HIGHLIGHTSO_LID-PUFA diet prevents muscle atrophy in STZ-induced diabetic mice. C_LIO_LID-PUFA diet prevents muscle weakness depending on increased calcium release in STZ-induced diabetic mice. C_LIO_LID-PUFA diet may show a trend to decrease blood glucose in STZ-induced diabetic mice. C_LIO_LID-PUFA diet does not alter ferroptosis-related protein profiles including ACSL4, LPCAT3, ALOX12, and Gpx4. C_LI Oxidative stress and reactive oxygen species (ROS) have been linked to muscle atrophy and weakness. Diabetes increases the oxidative status of lipoproteins in nearly all tissues, including muscle tissues, but the role of lipid ROS on diabetes-induced muscle atrophy is not fully understood. Deuterium reinforced polyunsaturated fatty acids (D-PUFA) are more resistant to ROS-initiated chain reaction of lipid peroxidation than regular hydrogenated PUFA (H-PUFA). In this study, we tested the hypothesis that D-PUFA would protect muscle atrophy induced by diabetes driven by an accumulation of lipid hydroperoxides (LOOH). C57BL/6J mice were dosed with H-PUFA or D-PUFA for four weeks through dietary supplementation and then injected with streptozotocin (STZ) to induce insulin-deficient diabetes. After two weeks, muscles tissues were analyzed for individual muscle mass, force generating capacity and cross-sectional area. Skeletal muscle fibers from diabetic mice exhibited increased total ROS and LOOH. This was abolished by the D-PUFA supplementation regardless of accumulated iron. D-PUFA were found to be protective against muscle atrophy and weakness from STZ-induced diabetes. Prevention of muscle atrophy and weakness by D-PUFA might be independent of ACSL4/LPCAT3/15-LOX pathway. These findings provide novel insights into the role of LOOH in the mechanistic link between oxidative stress and diabetic myopathy and suggest a novel therapeutic approach to diabetes-associated muscle weakness.

pathology↗

bioRxiv2024

Replication-dependent histone (Repli-Histo) labeling dissects the physical properties of euchromatin/heterochromatin in living human cells.

A string of nucleosomes, where genomic DNA is wrapped around histones, is organized in the cell as chromatin. Chromatin in the cell varies greatly, from euchromatin to heterochromatin, in its genome functions. It is important to understand how heterochromatin is physically different from euchromatin. However, their specific labeling methods in living cells are limited. To address this, we have developed replication-dependent histone labeling (Repli-Histo labeling) to label nucleosomes in euchromatin and heterochromatin based on DNA replication timing. We investigated local nucleosome motion in the four chromatin classes from euchromatin to heterochromatin of living human and mouse cells. We found that more euchromatic regions (earlier replicated regions) show greater nucleosome motion. Notably, the motion profile in each chromatin class persists throughout interphase. Genome chromatin is essentially replicated from regions with greater nucleosome motions, even though the replication timing program is perturbed. Our findings, combined with computational modeling, suggest that earlier replicated regions have more accessibility and local chromatin motion can be a major determinant of genome-wide replication timing.

cell biology↗

bioRxiv2024

Concentration-dependent formation of intersegment interactions in viral droplets of influenza A virus infected cells

The influenza A virus genome consists of eight RNA segments, each incorporated into a virion. It has been proposed that intersegment interactions bundle these segments, and viral inclusions, which contain viral ribonucleoproteins (vRNPs) and Rab11, facilitate this process. However, the locations and mechanisms of intersegment interaction formation remain unclear. To investigate this, we identified comprehensive intersegment interactions in infected cells using customized LIGR-seq. Our results revealed that intersegment interactions in infected cells overlapped with those in the virion and were partially formed through direct RNA-RNA interactions. Additionally, we found that the formation of these interactions was delayed in cells expressing a Rab11 dominant-negative. Furthermore, artificially increasing vRNP concentrations in the nucleus, where intersegment interactions typically do not occur, triggered the formation of these interactions, which again overlapped with those in the virion. These results suggest that intersegment interactions are formed in viral inclusions where progeny vRNPs accumulate.

microbiology↗

bioRxiv2024

Enhanced tameness by Limosilactobacillus reuteri from gut microbiota of selectively bred mice

Domestication alters animal behaviour, primarily their tameness. In this study, we examine the effect of gut bacteria on mouse tameness. We previously conducted selective breeding for active tameness, defined as the motivation to approach a human hand, using genetically heterogeneous mice derived from eight wild inbred strains. We examined gut microbiota in the selectively bred mice by analysing faecal samples from 80 mice through shotgun metagenomic analysis. In the current study, we found that the selectively bred mice exhibit higher levels of active tameness as well as higher levels of blood oxytocin, which plays a key role in social behaviours. Selection for tameness did not substantially alter the taxonomic or functional diversity of the gut microbiota. However, we observed an increased abundance of Limosilactobacillus reuteri in the selected groups and higher pyruvate levels in their plasma. We isolated L. reuteri strains secreting extracellular pyruvate from mice faeces and administrated the cultured bacteria through drinking water. Mice treated with L. reuteri showed higher colonization of the bacteria in the gut, as well as higher levels of active tameness behaviour and blood oxytocin. Additionally, we generated 374 high-quality metagenome-assembled genomes (MAGs) of bacteria across 11 phyla. This collection includes 27 novel species level bacterial MAGs not previously known to exist in the mouse gut. This study elucidates the potential role of L. reuteri in the animal domestication process and explores the underlying mechanisms that may influence this process.

microbiology↗

bioRxiv2023

Presence of the ER-Golgi intermediate compartment that matures into the Golgi in yeast

Cargo traffic through the Golgi apparatus is mediated by cisternal maturation, but it remains largely unclear how the cis-cisternae, the earliest Golgi sub-compartment, is generated. Here, we use high-speed, high-resolution confocal microscopy to analyze the spatiotemporal dynamics of a diverse set of proteins that reside in and around the Golgi in budding yeast. We find many mobile punctate structures that harbor yeast counterparts of mammalian endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC) proteins, which we term "yeast ERGIC". It occasionally attaches onto the ER exit sites and gradually matures into the cis-Golgi. Upon treatment with the Golgi-disrupting agent brefeldin A, the ERGIC proteins form larger aggregates corresponding to the Golgi entry core compartment in plants, while cis- and medial-Golgi proteins are absorbed into the ER. We further analyze the dynamics of several late Golgi proteins. Together with our previous studies, we demonstrate a detailed spatiotemporal profile of the cisternal maturation process from ERGIC to Golgi and further to the trans-Golgi network. SummaryTojima et al. perform spatiotemporal mapping of a variety of proteins residing in and around the Golgi apparatus in budding yeast using super-resolution live imaging microscopy. They identified the ER-Golgi intermediate compartment that matures into the Golgi.

cell biology↗

bioRxiv2023

Remodeling of the secretory pathway is coordinated with de novo membrane formation in budding yeast gametogenesis

Gametogenesis in budding yeast involves a large-scale rearrangement of membrane traffic to allow de novo formation of a membrane, called the prospore membrane (PSM). However, the mechanism underlying this event is not fully elucidated. Here, we show that the number of endoplasmic reticulum exit sites (ERES) per cell fluctuates and switches from decreasing to increasing upon the onset of PSM formation. Reduction in ERES number, presumably accompanying a transient stall in membrane traffic, resulting in the loss of preexisting Golgi apparatus from the cell, was followed by local ERES regeneration, leading to Golgi reassembly in nascent spores. We have revealed that protein phosphatase-1 (PP-1) and its development-specific subunit, Gip1, promote ERES regeneration through Sec16 foci formation. Furthermore, sed4{Delta}, a mutant with impaired ERES formation, showed defects in PSM growth and spore formation. Thus, ERES regeneration in nascent spores facilitates the segregation of membrane traffic organelles, leading to PSM growth.

cell biology↗

bioRxiv2022

Golgi retention and oncogenic KIT signaling via PLCγ2-PKD2-PI4KIIIβ activation in GIST cells

Most gastrointestinal stromal tumors (GISTs) develop due to gain-of-function mutations in the tyrosine kinase, KIT. We recently showed that mutant KIT mislocalizes to the Golgi area and initiates uncontrolled signaling. However, the molecular mechanisms underlying its Golgi retention remain unknown. Here, we show that protein kinase D2 (PKD2) is activated by the mutant, which causes KITs Golgi retention. In PKD2-inhibited cells, KIT migrates from the Golgi region to lysosomes and subsequently undergoes degradation. Importantly, delocalized KIT is unable to trigger downstream activation. In the Golgi area, KIT activates the PKD2-phosphatidylinositol 4-kinaseIII{beta} (PKD2-PI4KIII{beta}) pathway through phospholipase {gamma}2 (PLC{gamma}2) to generate a PI4P-rich membrane domain, where the AP1-GGA1 complex is aberrantly recruited. Disruption of any factors in this cascade results in KIT release from the Golgi region, indicating that these PKD2-related pathways are responsible for the Golgi retention of KIT. Our findings unveil the molecular mechanisms underlying KIT mislocalization and provide evidence for a new strategy for inhibition of oncogenic signaling.

cancer biology↗

bioRxiv2022

Metagenomic thermometer

Various microorganisms exist in environments, and each of which has an optimal growth temperature (OGT). The relationship between genomic information and OGT of each species has long been studied, and one such study revealed that OGT of prokaryotes can be accurately predicted based on the fraction of seven amino acids (IVYWREL) among all encoded amino-acid sequences in its genome. Extending this discovery, the fraction of IVYWREL among all amino acids encoded in the metagenomic DNA in an environment may reflect the environmental temperature to which the microorganisms have adapted. In the present study, we developed a Metagenomic Thermometer as a means of predicting environmental temperature based on metagenomic sequences. Analysis of 41 metagenomic samples obtained from hot springs of varying temperature revealed that the Metagenomic Thermometer could indeed predict environmental temperature with high accuracy (R2 = 0.75). Although the taxonomic composition of microbial community was substantially affected by pH, the performance of the Metagenomic Thermometer was refractory to changes in community composition. The Metagenomic Thermometer was also applied to 616 human gut metagenomic samples, yielding a reasonably accurate value (i.e., 36.22 {+/-} 1.98{degrees}C) for human body temperature. Our results suggest that environmental temperature can be predicted based on metagenomic sequence data.

bioinformatics↗

bioRxiv2021

Building new compartments for unconventional protein secretion from the early and late Golgi membranes

CUPS, a compartment for unconventional secretion of signal sequence lacking proteins, is built during starvation. CUPS, lacking the Golgi specific glycosyltransferases, form by COPI independent extraction of membranes from the early Golgi cisterna, require PI4P for their biogenesis and PI3P for stability. We now show that a PI4P effector Drs2 of the trans-Golgi network, relocates to a new compartment monikered TCUPS because it touches CUPS. Although localized to TCUPS, Drs2 is required for CUPS formation specifically by interacting with Rcy1, and this process is essential for unconventional secretion. Visualizing cells by 4D SCLIM technology revealed that tubules emanating from TCUPS are often collared by CUPS and severed. Incidentally, while CUPS are stable, TCUPS are vesiculated at late stages of starvation. This mirrors the dynamics of the early and late Golgi during conventional protein secretion. TCUPS and CUPS thus emerge as the functional equivalent of early and late Golgi of the conventional secretory pathway, thus representing key compartments in unconventional secretion.

cell biology↗

bioRxiv2021

Liquid-liquid phase separation of florigen activation complex induces flowering

Floral transition, regulated by the systemic action of the mobile florigen protein FLOWERING LOCUS T (FT), is essential for successful plant reproduction1. How FT controls downstream gene expression remains incompletely understood, although it relies on the florigen activation complex (FAC), a core component of FT function2-4. The FAC is a nucleus-localized transcriptional activator of genes encoding MADS-box transcription factors critical to reproductive development and consists of florigen FT; a scaffold 14-3-3 protein that is a key component for complex assembly; and FD, a basic leucine-zipper protein that recruits the FAC to DNA. Here we report that the FAC exhibits phase separation. In rice shoot apical meristem cells, rice florigen Heading date 3a (Hd3a) fused to the green fluorescent protein formed speckles in the nucleus. The FAC speckle is formed in a FAC-dependent manner in tobacco cells. Recombinant Hd3a, but not OsFD1, phase-separated in vitro, and this effect was enhanced in the presence of 14-3-3 protein. Furthermore, mutations affecting functionally important residues in the pocket region or C-terminal disordered region of Hd3a affected FAC phase separation, providing a biochemical framework for the proteins effect on flowering. The ability to form condensates via phase transition represents a previously unknown mechanism for gene activation by the FAC.

plant biology↗

bioRxiv2021

Unique metabolic strategies in Hadean analogues reveal hints for primordial physiology

Primordial microorganisms are postulated to have emerged in H2-rich alkaline Hadean serpentinite-hosted environments with homoacetogenesis as a core metabolism. However, investigation of two modern serpentinization-active analogues of early Earth reveals that conventional H2-/CO2-dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, "Ca. Lithoacetigenota", that exclusively inhabits Hadean analogues and harbors genes encoding alternative modes of H2-utilizing lithotrophy. Rather than CO2, these metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein - the glycine reductase. A survey of serpentinite-hosted system microbiomes shows that glycine reductases are diverse and nearly ubiquitous in Hadean analogues. "Ca. Lithoacetigenota" glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation for gaining energy from geogenic H2 even under serpentinization-associated hyperalkaline, CO2-poor conditions. This draws remarkable parallels with ancestral archaeal H2-driven methyl-reducing methanogenesis recently proposed. Unique non-CO2-reducing metabolic strategies presented here may provide a new view into metabolisms that supported primordial life and the diversification of LUCA towards Archaea and Bacteria.

microbiology↗