Biology subjects

Ohta, K.

Publications and source records attributed to Ohta, K..

16 recordsLinked to original sources

bioRxiv2026

Multi-layered control of chromosomal assembly of the meiotic DNA break machinery

Meiotic DNA double-strand breaks (DSBs) form in chromatin loops that are tethered to chromosome axes. How proteins required for DSB formation in vivo (DSB proteins) assemble on meiotic chromosomes to control non-random DSB distribution remains unsolved. Here we mapped the spatial distributions of all ten DSB proteins that form three complexes (Spo11-Ski8-Rec102-Rec104 [Spo11-core], Rec114-Mei4-Mer2 [RMM], and Mre11-Rad50-Xrs2 [MRX]) in budding yeast and elucidated their functional dependencies with axial proteins Red1 and Hop1. At local levels, our analysis suggests that their axis-associated assembly involves two distinct pathways, Hop1-RMM-MRX and Red1-Spo11 core, whereas Spo11-core alone can bind DSB sites. Red1 also binds DSB sites in a DSB-dependent manner, supporting its critical role in DSB repair. At large scale, all ten DSB proteins and both axial proteins are enriched at DSB-hot domains 20-40 kb wide that correspond to sizes of the axis-loop units. Further analysis at short and long distances suggests that their local assembly, short-range/intra-loop distributions, and long-range/inter-loop distributions are distinctly controlled. Similarly in mouse spermatocytes, MEl4 and a Hop1 homolog HORMAD1 are enriched at DSB-hot domains 1-3 Mb wide, and their long-range distributions are distinctly controlled from their local assembly. Our results elucidate multi-layered mechanisms of chromosomal assembly of the DSB machinery in shaping the DSB landscape in yeast and mouse.

Molecular Biology↗

bioRxiv2026

Circadian Timekeeping in the Tropics: Rhythmic Transcriptome and Diurnal Regulatory Networks in Rubroshorea leprosula

Circadian rhythms allow plants to regulate internal processes to align with daily rhythms in the environment. Comparing circadian clocks across environments is essential because latitude-dependent variation in light and temperature imposes distinct selection pressures that shape the evolution and function of circadian timing systems. However, circadian clock studies have largely focused on temperate and subtropical species, leaving transcriptional circadian networks in tropical plants under relatively constant environments poorly understood. We report the first comprehensive circadian transcriptome of the ecologically important dipterocarp species Rubroshorea leprosula, a dominant species in tropical rainforests in Southeast Asia. One sapling was sampled every four hours for 48 hours under constant darkness and used for transcriptomic analyses. Only 283 of 20,748 expressed genes ([~]1.3%) exhibited significant circadian oscillations, with periods strongly concentrated between 23 and 25 h. Hierarchical clustering revealed four temporal clusters with alternate phases of expression and functional specialisation; morning clusters in processes related to light and chloroplast, midday clusters in hormone and signalling mechanisms, afternoon clusters in mitochondrial and peptide biosynthesis functions, and night clusters in protein quality control and autophagy. Comparative analysis identified clear orthologs for all major Arabidopsis circadian clock components (LHY, CCA1, PRRs, TOC1, ELF4, LUX, GI, ZTL, RVEs), with conserved synteny to Parashorea chinensis, a close relative of R. leprosula. Time-lagged cross-correlation (TLCC) network reconstruction identified a characteristic circadian topological similarity with Arabidopsis, including coupled morning and evening feedback loops and paralog expansion that maintained overall structure. Peak expression timing of these core clock genes in the tropical tree was largely consistent with that observed in Arabidopsis thaliana. In contrast to this conserved phase relationship, Rubroshorea orthologs exhibited reduced amplitudes and lower coefficients of variation in their circadian oscillations, suggesting diminished robustness of rhythmic gene expression. These findings demonstrate a conserved but regulated circadian mechanism in R. leprosula, in preparation for adaptation to tropical rainforests stable light and temperature regimes. This study lays the molecular foundation for circadian regulation in dipterocarps and offers a system for integrating rhythmic gene expression to ecological function and forest productivity in tropical communities.

plant biology↗

bioRxiv2025

MAP7-driven cytoskeletal cross-talk establishes Sertoli cell polarity crucial for germ cell meiotic progression

How specialized apical membrane domains are assembled in vivo remains poorly understood. In the mouse testis, Sertoli cells build a luminal apical domain after birth that organizes the seminiferous epithelium and supports germ cell differentiation, distinct from fetal polarity established during cord formation. Here, we identify the microtubule-associated protein MAP7 as a key regulator of cytoskeletal organization during apical domain formation. MAP7 preferentially localizes to apical microtubules in Sertoli cells, showing limited overlap with stable microtubule markers. Native-tissue imaging indicates that MAP7-decorated microtubules, initially lacking obvious directionality, become increasingly aligned along the tubule axis as the apical domain matures. In Map7-deficient testes, microtubule abundance is maintained, but higher-order organization is disrupted and accompanied by persistent luminal F-actin accumulation. These defects compromise apical domain maturation and lumen formation during the first wave of spermatogenesis and are associated with altered tight-junction patterning. Proteomic analysis identifies the non-muscle myosin II heavy chains MYH9 and MYH10 among MAP7-associated proteins. MYH9 becomes enriched at luminal regions where microtubules and F-actin converge, but remains diffuse in Map7-deficient Sertoli cells despite ectopic luminal cytoskeletal assemblies, suggesting that MAP7 helps establish a cytoskeletal context that supports spatially restricted NMII enrichment. Single-cell RNA sequencing shows that Sertoli transcriptional differentiation largely proceeds without MAP7, whereas germ cells exhibit delayed meiotic progression with expansion of pachytene-stage subpopulations. Together, these findings establish MAP7-dependent microtubule remodeling as an organizing mechanism for postnatal apical domain maturation and suggest how epithelial cytoskeletal architecture shapes a niche that helps pace developmental progression of neighboring germ cells.

cell biology↗

bioRxiv2025

Mammalian cells evacuate and shelter mitochondrial DNA from destruction following hypoxia response-induced mitophagy

Cells use a specialized process called mitophagy to degrade mitochondria, and the conditions that induce mitophagy can endanger mitochondrial DNA (mtDNA). Here, we report a novel mechanism by which cells undergoing hypoxia response (HR)-induced mitophagy protect their mtDNA from destruction by segregating it into large mitochondria (Mito-L). Using time-lapse imaging, we found that Mito-L are formed when mitochondria undergo tubular-to-spherical transitions and then fuse together. Under HR-activating conditions, we found the mitophagy process itself is essential for Mito-L formation. When we fragmented mitochondria prior to inducing the HR, we observed fewer Mito-L and more mtDNA degradation. Thus, mammalian cells protect mtDNA against excessive mitophagy induced by HR, thereby preventing the loss of the genetic information. Hypoxia response-induced mitophagy triggers cells to shelter mitochondrial DNA (70 characters)

cell biology↗

bioRxiv2025

Global propagation of genetic perturbation effects through genome-wide stoichiometry conservation architecture

Understanding how specific genetic changes lead organisms to different phenotypes is the cornerstone of genetics. However, even a single gene perturbation can cause global changes in gene expression profiles. Consequently, predicting which genes will be affected by a particular genetic perturbation remains a challenge. Here, we analyze changes in genome-wide gene expression profiles caused by single-gene perturbations in bacterial, worm, and human cells and show a simple rule that genes that intrinsically maintain the ratio of expression levels (stoichiometry) with a perturbed gene are more likely to be affected when it is deleted or inactivated. Furthermore, deleting a gene that maintains their stoichiometry with more genes tend to affect the expression levels of other genes genome-wide. Stoichiometry-conserving gene clusters can be found beyond local transcriptional regulatory units and metabolic pathways. Thus, the effects of genetic perturbations are propagated to other genes through a multi-level stoichiometry-conserving architecture in cells.

systems biology↗

bioRxiv2024

Mitochondrial Dysfunction and ER Stress in CB1 Receptor Antagonist-Induced Apoptosis in Human Neuroblastoma SH-SY5Y Cells

Cannabinoid receptor type 1 (CB1R) is the key modulator of neuronal viability. In particular, CB1R antagonists provide neuroprotective effects on neurotoxicity caused by e.g. neuronal injury. However, the underlying mechanisms and potential limitations of CB1R antagonism remain unclear. Here we investigated the impact of environmental conditions on CB1R antagonist effects. Unexpectedly, we have found that cell-permeable CB1R antagonists, rimonabant and AM251, induced significant cell death in human neuroblastoma SH-SY5Y cells under serum-free conditions. Mitochondrial morphological analysis revealed mitochondrial swelling characterized by their network fragmentation and cristae reduction. Additionally, phosphoproteomics analysis showed an upregulation of phosphorylated EIF2AK3 (also known as PERK), leading to the activation of the eIF2/ATF4/CHOP pathway, indicative of endoplasmic reticulum (ER) stress. Rimonabant and AM251 treatment also triggered caspase-dependent apoptosis, evidenced by the detection of cleaved caspase 3 and cleaved PARP. These results suggest that cell-permeable CB1R antagonists promote apoptosis via mitochondrial dysfunction and ER stress under serum-free conditions in SH-SY5Y cells. Our findings indicate that while CB1R antagonists may be neuroprotective in certain conditions, they may also pose a neurotoxic risk in environments characterized by cellular stress or nutrient deprivation.

pharmacology and toxicology↗

bioRxiv2024

SLC35G1: A highly chloride-sensitive transporter responsible for the basolateral membrane transport in intestinal citrate absorption

The intestinal absorption of essential nutrients, especially those not readily biosynthesized, is a critical physiological process for maintaining homeostasis. Numerous studies have indicated that intestinal absorption is mediated by various membrane transporters. Citrate, a crucial bioactive compound produced as an intermediate in the Krebs cycle, is absorbed in the small intestine through carrier-mediated systems because of its high hydrophilicity. While the luminal absorption of citrate is mediated by Na+-dicarboxylate cotransporter 1 (NaDC1/SLC13A2), the mechanism governing the release of the transported citrate into the bloodstream remains unknown. Here, we explored the transporters responsible for intestinal citrate absorption at the basolateral membrane, focusing on highly expressed orphan transporters in the small intestine as candidates. Consequently, SLC35G1, originally identified as a partner of stromal interaction molecule 1, a cell surface transmembrane glycoprotein, was found to play a role in the intestinal absorption of citrate at the basolateral membrane. Furthermore, our results revealed that SLC35G1-mediated citrate transport was diminished by chloride ions at physiologically relevant extracellular concentrations. This suggests that SLC35G1, to our best knowledge, is the first transporter identified to be extremely sensitive to chloride ions among those functioning on the basolateral membrane of intestinal epithelial cells. This study provides valuable insights into the intestinal absorption of citrate and significantly contributes to elucidating the poorly understood molecular basis of the intestinal absorption system.

physiology↗

bioRxiv2023

Rapamycin-sensitive mechanisms confine the growth of fission yeast below the temperatures detrimental to cell physiology

Cells cease to proliferate above their growth-permissible temperatures, a ubiquitous phenomenon generally attributed to protein denaturing and heat damage to other cellular macromolecules. We here report that, in the presence of the macrolide compound rapamycin, the fission yeast Schizosaccharomyces pombe can proliferate at high temperatures that normally arrest its growth. Rapamycin is a potent inhibitor of the protein kinase complex TOR Complex 1 (TORC1), and consistently, mutations to the TORC1 subunit RAPTOR/Mip1 and the TORC1 substrate Sck1 significantly improve cellular heat resistance. These results suggest that TORC1, a well-established growth promoter, restricts the high-temperature growth of fission yeast and that compromised TORC1 signaling allows cell proliferation at higher temperatures. Aiming for a more comprehensive understanding of the negative regulation of high-temperature growth, we conducted genome-wide screens in S. pombe, which identified Sck1 and additional factors that appear to suppress cell proliferation at high temperatures. Our study has uncovered unexpected mechanisms of growth restraint even below the temperatures deleterious to cell physiology. Thus, growth arrest at high temperatures may not directly result from heat damage to cellular components essential for proliferation and viability. Significance StatementThe immunosuppressant rapamycin is a specific inhibitor of the protein kinase Target Of Rapamycin (TOR), and the drug is known to extend the lifespan of diverse eukaryotic organisms. In this study, we have found that rapamycin confers heat resistance on fission yeast, allowing its proliferation above the normal permissive temperatures. This unexpected observation suggests that TOR, which is known as a growth-promoting kinase, is inhibitory to cell proliferation at high temperatures. Our genome-wide screens have identified additional genes whose deletion leads to improved growth under heat stress. Thus, cells may have mechanisms that restrict proliferation even below the temperatures deleterious to their physiology.

cell biology↗

bioRxiv2023

Seasonal gene-expression signatures of delayed fertilization in Fagaceae

In the family Fagaceae, fertilization is delayed by several weeks to one year after pollination, leading to one- or two-year fruiting species depending on whether fruiting occurs in the same or the next year after flowering. To investigate physiological responses underlying the regulation of delayed fertilization, we monitored seasonal changes in genome-wide gene expression in tissues including leaves and buds over two years under natural conditions in one- (Quercus glauca) and two-year fruiting species (Lithocarpus edulis). Genes associated with the responses to cold stress, photosynthesis, and cell proliferation, which are essential for survival and growth, showed highly conserved seasonal expression profiles regardless of species. However, seasonal expression profiles diverged between the one- and two-year fruiting species in genes associated with pollination, an important process contributing to the origin and maintenance of the reproductive barrier between plant species. By comparing seasonal progression of ovule development and gene expression in pistillate flowers, we revealed that ovules started developing after winter in the two-year fruiting species, which could be linked to the activation of genes involved in fertilization and female gametophyte development after winter. These findings suggest that the two-year fruiting species may have evolved a requirement of winter cold to prevent fertilization before winter and facilitate fertilization and embryo development in the following spring when temperature rises. This study offers new possibilities to explore the evolution of reproductive strategies in Fagaceae.

ecology↗

bioRxiv2023

The molecular clock in long-lived tropical trees is independent of growth rate

The rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes of two tropical trees, Shorea laevis (slow-growing) and S. leprosula (fast-growing), in central Borneo, Indonesia. Using newly-constructed genomes, we identified a greater number of somatic mutations in tropical trees than in temperate trees. In both species, we observed a linear increase in the number of somatic mutations with physical distance between branches. However, we found that the rate of somatic mutation accumulation per meter of growth was 3.7-fold higher in S. laevis than in S. leprosula. This difference in the somatic mutation rate was scaled with the slower growth rate of S. laevis compared to S. leprosula, resulting in a constant somatic mutation rate per year between the two species. We also found that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. These findings suggest that somatic mutations accumulate with absolute time and older trees have a greater contribution towards generating genetic variation. Significance StatementThe significance of our study lies in the discovery of an absolute time-dependent accumulation of somatic mutations in long-lived tropical trees, independent of growth rate. Through a comparative analysis of somatic mutation landscapes in slow- and fast-growing species, we observed a clock-like accumulation of somatic mutations in both species, regardless of their growth rates. Although the majority of somatic mutations were restricted to a single branch, we also identified mutations present in multiple branches, likely transmitted during growth. Our findings suggest that older trees make a greater contribution towards generating genetic variation.

evolutionary biology↗

bioRxiv2022

Dopaminergic neurons dynamically update sensory values during navigation

Updating the value of sensory cues through experiences is a critical element of adaptive behavior. Although dopaminergic neurons (DANs) achieve this by driving associative learning, whether they contribute to assessment of sensory values outside the context of association remains largely unexplored. Here we show in Drosophila that DANs in the mushroom body encode the innate value of odors and constantly update the current value by inducing plasticity during olfactory navigation. Simulation of neuronal activity in a network based on the connectome data reproduced the characteristics of DAN responses, proposing a concrete circuit mechanism for computation. Notably, odors alone induced value- and dopamine-dependent changes in the activity of mushroom body output neurons, which store the current value of odors, as well as the behavior of flies steering in a virtual environment. Thus, the DAN circuit known for discrete, associative learning also continuously updates odor values during navigation in a non-associative manner.

neuroscience↗

bioRxiv2022

Gene mapping methodology powered by induced genome rearrangements

Phenotypic variation occurs through genome rearrangements and mutations in certain responsible genes; however, systematic gene identification methodologies based on genome rearrangements have not been fully established. Here, we explored the loci responsible for the given phenotype using the TAQing system and compared it with a conventional mutagenesis-based method. Two yeast strains with different genetic backgrounds and flocculation phenotypes were fused and genomic rearrangements were induced by transient DNA breaks. Then, selection pressure was applied and multiple mutants were generated, showing different flocculation abilities. We also raised mutants with altered cohesiveness due to spontaneous mutations during long-term recursive passages of haploid strains without TAQing treatment. Comparative genomic analysis of the TAQed mutants revealed three chromosomal regions harboring pivotal flocculation genes, whereas conventional mutagenesis generated a more diverse list of candidate loci after prolonged selection. The combined use of these approaches will accelerate the identification of genes involved in complex phenotypes.

genetics↗

bioRxiv2021

Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts

The sparseness of chromosomal contact information and the presence of homologous chromosomes with very similar nucleotide sequences make Hi-C analysis difficult. We propose a new algorithm using allele-specific single-nucleotide variations (SNVs) to reconstruct the three-dimensional (3D) chromosomal architectures from the Hi-C dataset of single diploid cells. Our algorithm has a function to discriminate SNVs specifically found between homologous chromosomes to our "recurrence plot"-based algorithm to estimate the 3D chromosome structure, which does not require imputation for ambiguous segment information. The new algorithm can efficiently reconstruct 3D chromosomal structures in single human diploid cells by employing only Hi-C segment pairs containing allele-specific SNVs. The datasets of the remaining pairs of segments without allele-specific SNVs are used to validate the estimated chromosome structure. This approach was used to reconstruct the 3D structures of human chromosomes in single diploid cells at a 1-Mb resolution. Introducing a subsequent mathematical measure further improved the resolution to 40-kb or 100-kb. The reconstruction data reveals that human chromosomes form chromosomal territories and take fractal structures where the mean dimension is a non-integer value. We also validate our approach by estimating 3D protein/polymer structures.

bioinformatics↗

bioRxiv2020

Autotoxin-mediated voluntary triage in starved yeast community

When organisms face crises, such as starvation, every individual should adapt to environmental changes (1, 2), or the community alters their behaviour (3-5). Because a stressful environment reduces the carrying capacity (6), the population size of unicellular organisms shrinks in such conditions (7, 8). However, the uniform stress response of the cell community may lead to overall extinction or severely damage their entire fitness. How microbial communities accommodate this dilemma remains poorly understood. Here, we demonstrate an elaborate strategy of the yeast community against glucose starvation, named the voluntary triage. During starvation, yeast cells release some autotoxins, such as leucic acid and L-2keto-3methylvalerate, which can even kill the cells producing them. Although it may look like mass suicide at first glance, cells use epigenetic "tags" to adapt to the autotoxin inheritably. If non-tagged latecomers, regardless of whether they are closely related, try to invade the habitat, autotoxins kill them and inhibit their growth, but the tagged cells can selectively survive. Phylogenetically distant fission and budding yeast (9) share this strategy using the same autotoxins, which implies that the universal system of voluntary triage may be relevant to the major evolutional transition from unicellular to multicellular organisms (10).

microbiology↗

bioRxiv2019

Biosynthesis of β-(1->5)-Galactofuranosyl Chains of Fungal-Type and O-Mannose-Type Galactomannans within the Invasive Pathogen Aspergillus fumigatus

The pathogenic fungus Aspergillus fumigatus contains galactomannans localized on the surface layer of its cell walls, which are involved in various biological processes. Galactomannans comprise -(1[->]2)-/-(1[->]6)-mannan and {beta}-(1[->]5)-/{beta}-(1[->]6)-galactofuranosyl chains. We previously revealed that GfsA is a {beta}-galactofuranoside {beta}-(1[->]5)-galactofuranosyltransferase involved in the biosynthesis of {beta}-(1[->]5)-galactofuranosyl chains. Here, we clarified the entire biosynthesis of {beta}-(1[->]5)-galactofuranosyl chains in A. fumigatgus. Two paralogs exist within A. fumigatus: GfsB and GfsC. We show that GfsB and GfsC, in addition to GfsA, are {beta}-galactofuranoside {beta}-(1[->]5)-galactofuranosyltransferases by biochemical and genetic analyses. GfsA, GfsB, and GfsC can synthesize {beta}-(1[->]5)-galactofuranosyl oligomers up to lengths of 7, 3, and 5 galactofuranoses within an established in vitro highly efficient assay of galactofuranosyltransferase activity. Structural analyses of galactomannans extracted from the strains {Delta}gfsB, {Delta}gfsC, {Delta}gfsAC, and {Delta}gfsABC revealed that GfsA and GfsC synthesized all {beta}-(1[->]5)-galactofuranosyl residues of fungal-type and O-mannose-type galactomannans, and GfsB exhibited limited function in A. fumigatus. The loss of {beta}-(1[->]5)-galactofuranosyl residues decreased the hyphal growth rate and conidia formation ability as well as increased the abnormal hyphal branching structure and cell surface hydrophobicity, but this loss is dispensable for sensitivity to antifungal agents and virulence toward immune-compromised mice.\n\nIMPORTANCE{beta}-(1[->]5)-galactofuranosyl residues are widely distributed in the subphylum Pezisomycotina of the phylum Ascomycota. Pezizomycotina includes many plant and animal pathogens. Although the structure of {beta}-(1[->]5)-galactofuranosyl residues of galactomannans in filamentous fungi was discovered long ago, it remains unclear which enzyme is responsible for biosynthesis of this glycan. Fungal cell wall formation processes are complicated, and information concerning glycosyltransferases is essential for their understanding. In this study, we show that GfsA and GfsC are responsible for the biosynthesis of all {beta}-(1[->]5)-galactofuranosyl residues of fungal-type and O-mannose-type galactomannans. The data presented here indicates that {beta}-(1[->]5)-galactofuranosyl residues are involved in cell growth, conidiation, polarity, and cell surface hydrophobicity. Our new understanding of {beta}-(1[->]5)-galactofuranosyl residue biosynthesis provides important novel insights into the formation of the complex cell wall structure and the virulence of the subphylum Pezisomycotina.

microbiology↗

bioRxiv2017

Transcriptomes and Raman spectra are linked linearly through a shared low-dimensional subspace

Raman spectroscopy is an imaging technique that can reflect whole-cell molecular compositions in vivo, and has been applied recently in cell biology to characterize different cell types and states. However, due to the complex molecular compositions and spectral overlaps, the interpretation of cellular Raman spectra have remained unclear. In this report, we compared cellular Raman spectra to transcriptomes of Schizosaccharomyces pombe and Escherichia coli, and provide firm evidence that they can be computationally connected and interpreted. Specifically, we find that the dimensions of high-dimensional Raman spectra and transcriptomes measured by RNA-seq can be effectively reduced and connected linearly through a shared low-dimensional subspace. Accordingly, we were able to reconstruct global gene expression profiles by applying the calculated transformation matrix to Raman spectra, and vice versa. Strikingly, highly expressed ncRNAs contributed to the Raman-transcriptome linear correspondence more significantly than mRNAs in S. pombe, which implies their major role in coordinating molecular compositions. This compatibility between whole-cell Raman spectra and transcriptomes marks an important and promising step towards establishing spectroscopic live-cell omics studies.

systems biology↗