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Biology subjects

Kato, N.

Publications and source records attributed to Kato, N..

At least 19 recordsLinked to original sources

Oxidized phosphatidylinositol impairs lysosomal membrane repair to promote ferroptosis

Ferroptosis is a regulated form of cell death driven by iron-dependent and unrestrained lipid peroxidation, which generates phospholipid hydroperoxides that cause membrane rupture. Oxidized phospholipid species, including oxidized arachidonic acid-containing phosphatidylethanolamines (PE), are abundant during ferroptosis. However, previous studies have examined only a limited number of lipid species, and it remains unclear which oxidized phospholipids consistently arise across distinct cell types and ferroptosis-inducing conditions. Here, we comprehensively profiled oxidized phospholipids generated during ferroptosis across multiple cell lines and animal models. We identified PE 18:0_20:4;O3 and phosphatidylinositol (PI) 18:0_20:4;O3 as oxidized phospholipid species that are consistently detectable across all tested ferroptosis-inducing conditions. Furthermore, oxidized phosphatidylinositol impairs the phosphoinositide-initiated membrane tethering and lipid transport (PITT) pathway, a key mechanism for lysosomal membrane repair. These results indicate that the oxidized phospholipids identified here may serve as markers of ferroptosis while also acting as bioactive mediators that compromise lysosomal membrane homeostasis and repair.

cell biology↗

Epithelial Glutamate Retention Protects against Colitis

Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract that encompasses ulcerative colitis and Crohns disease. Here we identify the cystine/glutamate antiporter xCT as being markedly upregulated in the inflamed intestinal epithelium of patients with IBD. To clarify its functional contribution to disease pathogenesis, we performed genetic loss-of-function study and found that inhibition of xCT confers robust protection against dextran sulfate sodium (DSS)-induced colitis in mice. Intestinal epithelial cell (IEC)-specific deletion of xCT markedly attenuated colitis severity, demonstrating that epithelial xCT upregulation acts as a disease-exacerbating factor in IBD. Mechanistically, xCT deficiency preserved intracellular glutamate levels and protein polyglutamylation, thereby maintaining epithelial barrier integrity and protecting IECs from inflammatory injury. Consistently, pharmacological inhibition of glutamine synthetase, which increases intracellular glutamate, exerted a potent anti-inflammatory effect on the DSS-induced colitis. These findings identify intracellular glutamate retention in IECs as a previously unrecognized mechanism of epithelial protection and highlight both inhibition of xCT-dependent glutamate efflux and suppression of glutamine synthetase as potential therapeutic strategies for IBD.

molecular biology↗

Oligo DNA-based quantum dot (QD) single-particle tracking for multicolor single-molecule imaging

Quantum dot single-particle tracking (QD-SPT), a powerful tool for analyzing membrane domains that are critical to various cellular processes, is widely used in membrane molecular dynamics research. QDs, which possess both a broad excitation range and a narrow emission bandwidth, are inherently suited for multicolor imaging at various wavelengths. However, applying multicolor QD-SPT with multiple biomolecular targets has been challenging due to the limited methods for specifically conjugating QDs to biomolecules. Here, we propose a DNA hybridization-based QD labeling method that generates several specific interactions based on sequence. QD fused with 20-mer oligo DNA specifically labeled membrane lipid 1,2-dipalmitoyl-sn-glycero-3-phosphatidylethanolamine (DPPE) covalently bound to complementary oligo DNA, forming a stable label that is suitable for SPT. The combination of polyA-polyT sequence as the linker oligo caused more QDs to fuse to DPPE compared with a random sequence linker. Oligo DNA-based QD-SPT accurately reflected the diffusion dynamics of DPPE measured using the single-fluorescence tracking technique and was compatible with conventional QD-SPT utilizing secondary antibody Fab. Using different pairs of oligo DNA sequences, we successfully achieved multicolor QD-SPT that distinguishes the lateral diffusion of DPPE and a membrane protein, GABAA receptor (GABAAR), within the same cell. The oligo DNA-based QD labeling method developed in this study is anticipated to substantially advance simultaneous multicolor QD-SPT of different living cell membrane molecules specific to DNA sequences.

biophysics↗

The Role of SIAMESE in G2 Checkpoint Regulation in Arabidopsis thaliana

In Arabidopsis, SIAMESE (SIM) is a cyclin-dependent kinase inhibitor that restricts progression through mitosis. SIM is well known as a regulator of endoreplication in trichomes and roots. Mathematical modeling of the cell cycle has indicated that SIM may also modulate the length of G2 during mitotic cycles, potentially replacing the WEE1/CDC25 circuit that regulates G2 timing in animals and fungi, which is absent in plants. The predictions of this model were tested in several ways. First, the root meristem is longer in sim mutant roots than in wild-type (WT) roots. Second, two independent methods of measuring cell cycle phases, long-term live-cell imaging using fluorescent protein cell cycle markers and 5-ethynyl-2-deoxyuridine (EdU) pulse-chase imaging, showed that the length of G2 in root meristem cortex cells is shorter in sim mutant plants compared to WT, consistent with the view that these changes in G2 length are due to greater G2 CDK activity in sim mutants. Additionally, the fluorescence of a CYCB:GFP fusion both rose and declined more sharply in the mutant than in wild-type. Because both transcription and degradation of this fusion are directly affected by G2 CDK activity, this result is consistent with sim mutants having greater G2 CDK activity. Taken together, these results suggest that, in addition to its known role in inducing endoreplication, SIM may play a role in regulating the length of G2 during mitotic cycles, at least partially replacing the absence of WEE1/CDC25 regulation of the mitotic cell cycle.

plant biology↗

Membrane-bound Guanylyl Cyclase COP5/HKR1 changes ciliary beat pattern and biases cell steering during chemotaxis in Chlamydomonas reinhardtii

This study investigates the control of ciliary beat patterns during ammonium chemotaxis in the model ciliate microalgae Chlamydomonas reinhardtii. Screening the chemotaxis response of mutant strains with ciliary defects revealed that a strain lacking CAV2, the alpha subunit of the voltage-gated Ca2+ channel, is deficient in ammonium chemotaxis. CAV2 regulates the switching of the ciliary beat pattern from the asymmetric to the symmetric waveform. Strains lacking COP5/HKR1 (chlamyopsin 5/histidine kinase rhodopsin 1), a membrane-bound guanylyl cyclase, are also deficient in ammonium chemotaxis. Conversely, strains defective in phototaxis perform ammonium chemotaxis normally. Cell motility analysis revealed wild-type cells reduce the incidences of switching the ciliary beat pattern from the asymmetric to symmetric waveform when swimming up the ammonium gradient. In contrast, the COP5/HKR1 disrupted strain does not bias ciliary beat pattern switching in the gradient. This finding reveals that a membrane-bound guanylyl cyclase plays a critical role in Chlamydomonas chemotaxis signaling transduction, similarly to animal chemotaxis. On the other hand, ciliary beat pattern switching induces randomized directional changes, analogous to run-and-tumble chemotaxis of bacteria and archaea. This study reveals that Chlamydomonas signaling transduction is similar to the eukaryotic mechanism, yet the cellular locomotion follows the bacteria and archaea mechanism.

microbiology↗

Induction of the aggresome and insoluble tau aggregation using an optogenetic tool

Tauopathy is a spectrum of diseases characterized by fibrillary tau aggregate formation in neurons and glial cells in the brain. Tau aggregation originates in the brainstem and entorhinal cortex and then spreads throughout the brain in Alzheimers disease (AD), which is the most prevalent type of tauopathy. Understanding the mechanism by which locally developed tau pathology propagates throughout the brain is crucial for comprehending AD pathogenesis. Therefore, a novel model of tau pathology that artificially induces tau aggregation in targeted cells at specific times is essential. This study describes a novel optogenetic module, OptoTau, which is a human tau with the P301L mutation fused with a photosensitive protein CRY2olig, inducing various forms of tau according to the temporal pattern of blue light illumination pattern. Continuous blue light illumination for 12 h to Neuro2a cells that stably express OptoTau (OptoTauKI cells) formed clusters along microtubules, many of which eventually accumulated in aggresomes. Conversely, methanol-resistant tau aggregation was formed when alternating light exposure and darkness in 30-min cycles for 8 sets per day were repeated over 8 days. Methanol-resistant tau was induced more rapidly by repeating 5-min illumination followed by 25-min darkness over 24 h. These results indicate that OptoTau induced various tau aggregation stages based on the temporal pattern of blue light exposure. Thus, this technique exhibits potential as a novel approach to developing specific tau aggregation in targeted cells at desired time points. SignificanceThis study developed an approach to manipulate tau aggregation in a blue light-dependent manner using cells that stably express OptoTau, which is an optogenetic tool based on the CRY2olig module. Tau accumulation in aggresomes or stable tau aggregation were selectively induced by blue light illumination conditions. These results are crucial as they provide a new technological basis for establishing a singular point of tau aggregation in specific targeted cells at a particular time.

biophysics↗

Downstream metabolites of (+)-cis-12-oxo-phytodienoic acid function as noncanonical bioactive jasmonates in Arabidopsis thaliana.

(+)-cis-12-oxo-phytodienoic acid (cis-OPDA) is a biosynthetic precursor of the plant hormone (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile). It functions as an endogenous chemical signal independent of the JA-Ile receptor COI1-JAZ in Arabidopsis thaliana. The bioactive form of cis-OPDA that induces COI1-JAZ-independent gene expression remains unknown. In this study, we hypothesized that the genuine bioactive forms of cis-OPDA are the downstream metabolites, which upregulate the expression of the OPDA marker genes such as ZAT10/ERF5 in a JA-Ile-independent manner. These downstream metabolites function independently of the JA-Ile-COI1-JAZ-MYCs canonical jasmonate signaling module, and its electrophilic nature is essential for its bioactivity.

plant biology↗

Ploidy inference from single-cell data: application to human and mouse cell atlases

Ploidy is relevant to numerous biological phenomena, including development, metabolism, and tissue regeneration. Single-cell RNA-seq and other omics studies are revolutionizing our understanding of biology, yet they have largely overlooked ploidy. This is likely due to the additional assay step required for ploidy measurement. Here, we developed a statistical method to infer ploidy from single-cell ATAC-seq data. When applied to the data from human and mouse cell atlases, our method enabled systematic detection of polyploidy across a range of cell types. This method allows for the integration of ploidy analysis into single-cell studies. Article summaryPloidy plays a crucial role in many biological processes. Though modern studies offer deep insights into biology, they often neglect ploidy because its challenging to measure. In this research, we have created a new method to detect ploidy using single-cell data. This technique helps identify polyploid cells across various cell types, bridging a gap in our understanding.

bioinformatics↗

Genetic reprogramming by brief inhibition of the renin-angiotensin system in spontaneously hypertensive rats leads to persistently reduced kidney renin and low blood pressure.

BACKGROUNDPrevention of human hypertension is an important challenge and has been achieved in experimental models. Brief treatment with renin-angiotensin system (RAS) inhibitors permanently reduces the genetic hypertension of the spontaneously hypertensive rat (SHR). The kidney is involved in this reprogramming, but relevant genetic changes are unknown. METHODSIn SHR, we studied the effect of treatment between 10 and 14 weeks of age with the angiotensin receptor blocker, losartan, or the angiotensin-converting enzyme (ACE) inhibitor, perindopril (with controls for non-specific effects of lowering BP) on differential RNA expression, DNA methylation and renin immunolabelling in the kidney at 20 weeks of age. RESULTSRNA sequencing revealed a 6-fold increase in renin gene (Ren) expression during losartan treatment (P < 0.0001). At 20 weeks, six weeks after treatment cessation, mean arterial pressure remained lower in the treated SHR (P = 0.006), kidney Ren expression was reduced by 23% (P = 0.03) and DNA methylation within the Ren promoter region was increased (P = 0.04). Experiments with the ACE inhibitor perindopril confirmed a long-term reduction in kidney Ren expression of 43% (P = 1.4 x 10-6). Renin immunolabelling was also lower after losartan or perindopril treatment (P = 0.002). RNA sequencing identified differential expression of 13 candidate genes (Grhl1, Ammecr1l, Hs6st1, Nfil3, Fam221a, Lmo4, Adamts1, Cish, Hif3a, Bcl6, Rad54l2, Adap1, Dok4) and the miRNA miR-145-3p. We found correlations between expression of mRNAs, miRNAs and lncRNAs that we believe represent genetic networks underpinning the decreased Ren expression and lower BP. Gene ontogeny analyses revealed that these networks were enriched with genes relevant to BP, RAS and the kidneys. CONCLUSIONSEarly RAS inhibition in SHR reprograms genetic pathways and networks resulting in a legacy of reduced Ren expression and the persistent reduction in BP.

genetics↗

Wnt4a is indispensable for genital duct elongation but not for gonadal sex differentiation in the medaka Oryzias latipes

In most vertebrates, oviducts are derived from Mullerian ducts and sperm ducts from Wolffian ducts. In teleosts, however, Mullerian ducts are absent. Wolffian ducts function as nephric ducts in both sexes, and genital ducts are formed by posterior extension of either ovaries or testes. Whether genital ducts of teleosts are newly evolved organs or are a variant of the Mullerian ducts is an important question for evolutionary mechanisms of morphogenesis. One of the genes essential for Mullerian duct formation in mice, wnt4, is expressed in the mesenchyme and induces invagination of the coelomic epithelium and its posterior elongation. Here, we approached to the above question by examining genital duct development in mutants of two Wnt4 genes in medaka (wnt4a is orthologous to mouse wnt4 and wnt4b paralogous). The wnt4b mutants had short body but were fertile with normal genital ducts. In contrast, both male and female wnt4a mutants had posterior elongation of the gonads stopped within or just outside the coelom, depending on the mutated alleles. Genetic females of the scl mutants (unable to synthesize testosterone or estrogens) have gonads containing both previtellogenic oocytes and spermatogenic cysts. Their gonads do not have ovarian cavities or sperm duct primordia and are lacking genital ducts completely. The results suggest Wnt4a target organs are posterior parts of the ovarian cavities or the sperm duct primordia. Medaka wnt4a was expressed in the mesenchyme ventral to the genital ducts in both sexes. Thus, the aborted elongation of genital ducts in the wnt4a mutants, the ortholog of mouse wnt4, suggests strongly that mouse Mullerian ducts and teleost genital ducts share homologous developmental processes. To further demonstrate this possible homology, mechanisms of genital duct formation and possible roles of Wnt4 should be compared before and after the appearance of Mullerian ducts in vertebrate phylogeny, namely jawless fish and cartilaginous fish. Additionally, wnt4a and wnt4b single mutants or double mutants did not show sex-reversal, suggesting both genes are dispensable for gonadal sex differentiation in medaka. This is in contrast to indispensable function of Wnt4 in mammalian ovarian differentiation.

developmental biology↗

Generalizable neuromarker for autism spectrum disorder across imaging sites and developmental stages: A multi-site study

Autism spectrum disorder (ASD) is a lifelong condition, and its underlying biological mechanisms remain elusive. The complexity of various factors, including inter-site and development-related differences, makes it challenging to develop generalizable neuroimaging-based biomarkers for ASD. This study used a large-scale, multi-site dataset of 730 Japanese adults to develop a generalizable neuromarker for ASD across independent sites (U.S., Belgium, and Japan) and different developmental stages (children and adolescents). Our adult ASD neuromarker achieved successful generalization for the US and Belgium adults (area under the curve [AUC] = 0.70) and Japanese adults (AUC = 0.81). The neuromarker demonstrated significant generalization for children (AUC = 0.66) and adolescents (AUC = 0.71; all P<0.05, family-wise-error corrected). We identified 141 functional connections (FCs) important for discriminating individuals with ASD from TDCs. These FCs largely centered on social brain regions such as the amygdala, hippocampus, dorsomedial and ventromedial prefrontal cortices, and temporal cortices. Finally, we mapped schizophrenia (SCZ) and major depressive disorder (MDD) onto the biological axis defined by the neuromarker and explored the biological continuity of ASD with SCZ and MDD. We observed that SCZ, but not MDD, was located proximate to ASD on the biological dimension defined by the ASD neuromarker. The successful generalization in multifarious datasets and the observed relations of ASD with SCZ on the biological dimensions provide new insights for a deeper understanding of ASD.

neuroscience↗

PNPO-PLP Axis Senses Prolonged Hypoxia by Regulating Lysosomal Activity

Oxygen is critical for all metazoan organisms on the earth and impacts various biological processes in physiological and pathological conditions. While oxygen sensing systems inducing acute hypoxic response, including HIF pathway, have been identified, those operating in prolonged hypoxia remain to be elucidated. Here, we show that pyridoxine 5-phosphate oxidase (PNPO) that catalyzes bioactivation of vitamin B6 serves as an oxygen sensor and regulates lysosomal activity in macrophages. Decline of PNPO activity under prolonged hypoxia reduced an active form of vitamin B6, pyridoxal 5-phosphate (PLP), and inhibited lysosomal activity, leading to the augmentation of inflammatory response of macrophages. The PNPO-PLP axis creates a distinct layer of oxygen sensing, which gradually turns down and up the PLP-dependent metabolism according to prolonged changes in oxygen availability.

biochemistry↗

Single-nucleus ATAC-seq elucidates major modules of gene regulation in the development of non-alcoholic fatty liver disease

We investigated the progression of non-alcoholic fatty liver disease (NAFLD) from fatty liver to steatohepatitis using single-nucleus and bulk ATAC-seq on the livers of rats fed a high-fat diet (HFD). Rats fed HFD for 4 weeks developed fatty liver, and those fed HFD for 8 weeks further progressed to steatohepatitis. We observed an increase in the proportion of inflammatory macrophages, consistent with the pathological progression. Utilizing machine learning, we divided global gene regulation into modules, wherein transcription factors within a module could regulate genes within the same module, reaffirming known regulatory relationships between transcription factors and biological processes. We identified core genes--central to co-expression and protein-protein interaction--for the biological processes discovered. Notably, a large part of the core genes overlapped with genes previously implicated in NAFLD. Single-nucleus ATAC-seq, combined with data-driven statistical analysis, offers insight into in vivo global gene regulation as a combination of modules and assists in identifying core genes of relevant biological processes. Summary blurbThis study uncovers cell type-specific global gene regulation in NAFLD progression, identifying core genes and shedding light on the diseases molecular mechanisms.

genomics↗

The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5

UHRF1-dependent ubiquitin signaling plays an integral role in the regulation of maintenance DNA methylation. UHRF1 catalyzes transient dual mono-ubiquitylation of PAF15 (PAF15Ub2), which regulates the localization and activation of DNMT1 at DNA methylation sites during DNA replication. Although the initiation of UHRF1-mediated PAF15 ubiquitin signaling has been relatively well characterized, mechanisms underlying its termination and how they are coordinated with the completion of maintenance DNA methylation have not yet been clarified. This study shows that deubiquitylation by USP7 and unloading by ATAD5 (ELG1 in yeast) are pivotal processes for the removal of PAF15 from chromatin. On replicating chromatin, USP7 specifically interacts with PAF15Ub2 in a complex with DNMT1. USP7 depletion or inhibition of the interaction between USP7 and PAF15 results in abnormal accumulation of PAF15Ub2 on chromatin. Furthermore, we also find that the non-ubiquitylated form of PAF15 (PAF15Ub0) is removed from chromatin in an ATAD5-dependent manner. PAF15Ub2 was retained at high levels on chromatin when the catalytic activity of DNMT1 was inhibited, suggesting that the completion of maintenance DNA methylation is essential for termination of UHRF1-mediated ubiquitin signaling. This finding provides a molecular understanding of how the maintenance DNA methylation machinery is disassembled at the end of the S phase.

molecular biology↗

A dynamic model of the ABA Signaling pathway with its core components: translation rate of PP2C determines the kinetics of ABA-induced gene expression

The abscisic acid (ABA) signaling pathway is the key defense mechanism against drought stress in plants, yet the connectivity of cellular molecules related to gene expression in response to ABA is little understood. A dynamic model of the core components of the ABA signaling pathway was built using ordinary differential equations to understand the connectivity. Parameter values of protein-protein interactions and enzymatic reactions in the model were implemented from the data obtained by previously conducted experiments. On the other hand, parameter values of gene expression and translation were determined by comparing the kinetics of gene expression in the model to those of ABA-induced RD29A (response to desiccation 29A) in actual plants. Based on the analyses of the optimized model, we hypothesized that the translation rate of PP2C (protein phosphatase type 2C) is downregulated by ABA to increase the ABRE (ABA-responsive element) promoter activity. The hypotheses were preliminarily supported by newly conducted experiments using transgenic Arabidopsis plants that carry a luciferase expression cassette driven by the RD29A promoter (RD29A::LUC). The model suggests that identifying a mechanism that alters PP2C translation rate would be one of the next research frontiers in the ABA signaling pathway.

systems biology↗

Isolation of gametes and zygotes from Setaria viridis

Setaria viridis, the wild ancestor of foxtail millet (Setaria italica), is an effective model plant for larger C4 crops because it has several desirable traits, such as short generation time, prolific seed production and a small genome size. These advantages are well suited for investigating molecular mechanisms in angiosperms, especially C4 crop species. Here, we report a procedure for isolating gametes and zygotes from S. viridis flowers. To isolate egg cells, ovaries were harvested from unpollinated mature flowers and cut transversely, which allowed direct access to the embryo sac. Thereafter, an egg cell was released from the cut end of the basal portion of the dissected ovary. To isolate sperm cells, pollen grains released from anthers were immersed in a mannitol solution, resulting in pollen-grain bursting, which released sperm cells. Additionally, S. viridis zygotes were successfully isolated from freshly pollinated flowers. Isolated zygotes cultured in a liquid medium developed into globular-like embryos and cell masses. Thus, isolated S. viridis gametes, zygotes and embryos are attainable for detailed observations and investigations of fertilization and developmental events in angiosperms.

plant biology↗

Effects of upgrading acquisition-techniques and harmonization methods: A multi-modal MRI study with implications for longitudinal designs

A downside of upgrading MRI acquisition sequences is the discontinuity of technological homogeneity of the MRI data. It hampers combining new and old datasets, especially in a longitudinal design. Characterizing upgrading effects on multiple brain parameters and examining the efficacy of harmonization methods are essential. This study investigated the upgrading effects on three structural parameters, including cortical thickness (CT), surface area (SA), cortical volume (CV), and resting-state functional connectivity (rs-FC) collected from 64 healthy volunteers. We used two evaluation metrics, Cohens d and classification accuracy, to quantify the effects. In classification analyses, we built classifiers for differentiating the protocols from brain parameters. We investigated the efficacy of three harmonization methods, including traveling subject (TS), TS-ComBat, and ComBat methods, and the sufficient number of participants for eliminating the effects on the evaluation metrics. Finally, we performed age prediction as an example to confirm that harmonization methods retained biological information. The results without harmonization methods revealed small to large mean Cohens d values on brain parameters (CT:0.85, SA:0.66, CV:0.68, and rs-FC:0.24) with better classification accuracy (>92% accuracy). With harmonization methods, Cohens d values approached zero. Classification performance reached the chance level with TS-based techniques when data from less than 26 participants were used for estimating the effects, while the Combat method required more participants. Furthermore, harmonization methods improved age prediction performance, except for the ComBat method. These results suggest that acquiring TS data is essential to preserve the continuity of MRI data.

neuroscience↗

The Conserved Colletotrichum spp. Effector CEC3 Induces Nuclear Expansion and Cell Death in Plants

Plant pathogens secrete small proteins, known as effectors, that promote infection by manipulating host cells. Members of the phytopathogenic fungal genus Colletotrichum collectively have a broad host range and generally adopt a hemibiotrophic lifestyle that includes an initial biotrophic phase and a later necrotrophic phase. We hypothesized that Colletotrichum fungi use a set of conserved effectors during infection to support the two phases of their hemibiotrophic lifestyle. This study aimed to examine this hypothesis by identifying and characterizing conserved effectors among Colletotrichum fungi. Comparative genomic analyses using genomes of ascomycete fungi with different lifestyles identified seven effector candidates that are conserved across the genus Colletotrichum. Transient expression assays showed that one of these conserved effectors, CEC3, induces nuclear expansion and cell death in Nicotiana benthamiana, suggesting that CEC3 is involved in promoting host cell death during infection. Nuclear expansion and cell death induction were commonly observed in CEC3 homologs from four different Colletotrichum species that vary in host specificity. Thus, CEC3 proteins could represent a novel class of core effectors with functional conservation in the genus Colletotrichum.

microbiology↗