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Inoue, T.

Publications and source records attributed to Inoue, T..

At least 19 recordsLinked to original sources

A novel metalloprotease family discovered through a tardigrade

Tardigrades possess numerous proteins with poorly understood functions, including candidates proposed to have been acquired through horizontal gene transfer. Here, we characterized RvY_14254 from Ramazzottius varieornatus, previously designated ATPM5, whose homologs are widely distributed across bacteria and eukaryotes but remain largely uncharacterized. We determined the crystal structure of the protein, hereafter termed RvPeti, at 1.35 [A] resolution. RvPeti adopts a compact, C-shaped architecture with no close structural homologs in the Protein Data Bank and contains a conserved His-Asp-Asp (HDD) metal-binding motif within a deep surface pocket. Structural comparison revealed partial similarity of the active-site architecture to that of metalloproteases, including pseudoalterin. Anomalous diffraction analyses demonstrated that the HDD site can accommodate Zn2+ and Mn2+. Biochemical assays showed that RvPeti exhibits Zn2+ dependent proteolytic activity, which was strongly reduced by a metal chelating reagent and by alanine substitutions of the metal-coordinating residues. In contrast, only weak esterase activity was detected, with the substrates tested. These results identify RvPeti as a founding member of a previously uncharacterized family of metalloproteases and provide a structural framework for investigating the physiological and evolutionary roles of this widespread protein family.

biochemistry↗

Purification-free cryo-EM reveals endogenous assemblies from minute tardigrade samples

Tardigrades are minute animals renowned for environmental stress tolerance, and their remarkable biology has motivated extensive molecular studies using biochemical and biophysical approaches. Yet the native structures of endogenous macromolecular assemblies in tardigrades remain largely inaccessible, in part because only limited biological material is available. Here we show that purification-free single-particle cryo-EM, guided by long-read cDNA sequence assignment, can recover multiple endogenous assemblies directly from crude extract of a wild-derived Macrobiotus cf. shonaicus culture. We reconstructed a dimeric vitellogenin (Vg) particle at 3.10 [A] resolution, a previously uncharacterized tardigrade ferritin at 3.09 [A] resolution, and a low-resolution ribosome map. The Vg particle is a glycosylated and metal-containing assembly with structural evidence of proteolytic processing and contains lipid-like densities occupying a broad chamber whose walls include N-linked glycans. The ferritin structure revealed a divergent C-terminal helix that lines a mineral-like density observed at a position corresponding to previously described mineralization sites in ferritin-family cages. These results establish purification-free cryo-EM as a route to structural analysis of endogenous macromolecular assemblies from minute animal samples. In tardigrades, this approach provides a foundation for future state-dependent structural studies, including desiccation, rehydration and reproduction.

biochemistry↗

Seven gut microbiome types across two Japanese cohorts defined by co-abundance-based microbial guilds and associated with host physiology

Intensive efforts have been made to capture structural features of the gut microbiome for assessing microbiota status in relation to host health. However, gut microbiome function emerges not only from individual microbial taxa but also from their organization into ecological guilds, complicating microbiome structure-function relationships. To address this challenge, we applied a co-abundance-based analytical framework to identify gut microbiome types (GMTs) across a discovery cohort (D-cohort) and an independent validation cohort (V-cohort) of Japanese adults. Using paired fecal samples collected one month apart from 116 participants in the D-cohort, we identified 27 co-abundance groups (CAGs) based on 16S rRNA amplicon sequence variants. These CAGs defined seven GMTs (MT-1 to MT-7) with characteristic short-chain fatty acid and bile acid profiles. The GMTs showed temporal stability, with more than 70% of participants remaining in the same GMT across sampling points. The 27-CAG framework classified 404 participants in the independent V-cohort into the seven GMTs, which represented reproducible microbial ecological states across cohorts. MT-4 exhibited dysbiosis-like features, including reduced microbial diversity, depletion of Faecalibacterium and butyrate, and enrichment of inflammation-associated taxa, and was associated with higher alcohol consumption and elevated {gamma}-glutamyl transferase levels. In contrast, Bifidobacterium-enriched MT-5 was associated with favorable renal function profiles. Collectively, co-abundance-defined microbial guilds capture coherent ecological and functional states of the gut microbiota, providing a transferable framework for linking gut microbiome organization to host physiology beyond conventional taxonomy-based classification.

microbiology↗

In Vivo Bioincubation Promotes Maturation of Human iPSC-Derived Cardiomyocytes in Neonatal Rat and Pig Hearts

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) hold great promise for cardiac regenerative medicine and disease modeling. However, hiPSC-CMs generated through conventional in vitro differentiation exhibit immature, fetal-like phenotypes. While in vivo bioincubation in neonatal rodent hearts promotes hiPSC-CM maturation toward adult-like phenotypes, studies in large animal models remain limited, particularly with detailed morphological characterization. In this study, we investigated bioincubation of fluorescently labeled hiPSC-CMs in both neonatal rat and pig hearts. Human iPSCs were differentiated into cardiomyocytes expressing GFP or RFP reporters and subsequently injected intramyocardially into neonatal rats (GFP-labeled) and pigs (RFP-labeled). After 4-8 weeks of bioincubation, fluorescent hiPSC-CMs were isolated using large-particle fluorescence-activated cell sorting (COPAS), which preserves cellular morphology of adult-like cardiomyocytes. Immunostaining for cardiac troponin T revealed well-organized sarcomeric structures in multinucleated hiPSC-CMs. Bioincubated hiPSC-CMs displayed rod-shaped morphology with binucleation, characteristic features of mature adult cardiomyocytes. Quantitative analysis demonstrated that bioincubated hiPSC-CMs from rat hearts exhibited sarcomere length and cell circularity comparable to native rat adult cardiomyocytes, though with higher intra-cellular variability in sarcomere organization. Histological examination confirmed successful engraftment of RFP-positive hiPSC-CMs within pig myocardium, with engrafted cells also displaying mature adult-like features. These findings provide critical proof-of-concept data for bioincubation in large animal models and support further investigation for disease modeling, drug screening, and regenerative cell therapies. SIGNIFICANCE STATEMENTHuman induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) offer tremendous potential for cardiac disease modeling and regenerative therapies, but their clinical application is limited by their immature characteristics. Here we show that in vivo bioincubation in neonatal rat hearts enables hiPSC-CMs to achieve structural maturity, exhibiting features of adult cardiomyocytes, including organized sarcomeres, rod-shaped morphology, and multinucleation. We further provided proof-of-concept evidence for engraftment in neonatal pig hearts for maturation, supporting feasibility in large animal models. The use of large-particle cell sorting enables recovery of intact, adult-sized cardiomyocytes for subsequent analysis. These findings establish a practical and scalable platform for generating structurally mature human cardiomyocytes through in vivo bioincubation.

developmental biology↗

Elastogenesis by adventitial progenitors acquiring a smooth muscle cell phenotype following aortic dissection

Following aortic dissection (AD), there is a sustained risk of vascular complications, progressive false lumen aneurysm formation, and rupture. However, no effective therapy exists to prevent these complications, highlighting the need to elucidate the pathophysiology following AD. Elastic fibers are crucial for maintaining aortic wall integrity but are thought to have limited regenerative capacity once disrupted during AD. This study defined that elastic fibers were newly generated in the false lumen wall following AD in humans and mice. In human ADs, new elastic fibers were observed in the false lumen wall 6 months after onset. In mice with descending AD induced by {beta}-aminopropionitrile (BAPN), elastin mRNA was markedly upregulated in the chronic phase following AD, accompanied by elastic fiber formation. These fibers coincided with smooth muscle cell (SMC) markers within the false lumen wall. Of note, lineage tracing studies demonstrated that these cells were not derived from resident SMCs but adventitial progenitor cells. In vitro experiments further demonstrated that adventitial progenitor cells produced elastic fibers while expressing SMC markers. Collectively, these findings suggest that adventitial progenitor cells differentiate into elastogenic SMC-like cells, contributing to false lumen remodeling through de novo elastic fiber formation following AD.

pathology↗

Cryo-EM structures of a neofunctionalized tardigrade peroxiredoxin specialized for nucleic acid binding

Some terrestrial tardigrades can endure severe oxidative stress in part through their gene-expanded repertoire of antioxidant proteins. However, among these antioxidant proteins, RvPrxL, a peroxiredoxin (Prx)-like protein from Ramazzottius varieornatus strain YOKOZUNA-1, is unusual in that the catalytic cysteine is replaced by glutamate, apparently incapacitating canonical peroxidase function. In this study, we investigated the structure and function of this atypical Prx. Biochemical assays demonstrated that RvPrxL completely lacks canonical peroxidase and chaperone activities. Cryo-EM analysis revealed a unique 20-mer structure of RvPrxL. We also observed that the tardigrade-specific N-terminal region of RvPrxL helps retain the high-order oligomeric assembly even in the presence of highly concentrated hydrogen peroxide. The N-terminal region also promotes nuclear localization of RvPrxL and mediates binding to nucleic acids including nuclear RNAs. Furthermore, combining a standard cryo-EM method and a new approach in which cell Lysates are Applied Directly on cryo-EM Grids (LApDoG), we visualized two distinct nucleic acid binding modes of RvPrxL, termed "on-ring" and "in-ring", which likely reflect distinct physiological roles or modes of action. Collectively, these findings show that RvPrxL has been neofunctionalized to interact with nucleic acids in the nucleus, highlighting unexpected functional diversification of antioxidant proteins in tardigrades.

biochemistry↗

A genetically encoded microtubule bundler for causal dissection of microtubule bundling in cells

Microtubule (MT) bundling is a conserved organizational feature of the cytoskeleton that accompanies MT stabilization, suggesting that it is involved in diverse cellular processes, including mitosis, migration, and axon morphogenesis. Although microtubule-associated proteins are known to induce MT bundling, whether bundling itself is sufficient to alter MT properties and cellular behavior has remained difficult to address due to the lack of tools that selectively manipulate MT bundling in living cells. Here, we describe the development of a genetically encoded, protein-based "MT-Bundler" by coupling an MT-binding motif to a biologically inert oligomerization scaffold, enabling direct and tunable crosslinking of intracellular MTs. The expression of MT-Bundler consisting of MAP4 and Azami-Green, drove robust MT bundling, but also conferred marked resistance to depolymerization, and elevated MT acetylation. Functionally, enforced MT bundling disrupts cell division and migration and suppresses neurite and axon outgrowth. To confirm the causal relationship behind these findings, we further engineered chemically and optically inducible MT-Bundlers that permit rapid, reversible, and spatiotemporally precise control of MT bundling. Acute induction of MT bundling triggers a rapid increase in MT acetylation, revealing bundling as an upstream organizational cue that promotes luminal access of the acetyltransferase ATAT1. Notably, MT stabilization persists even in the absence of acetylation, demonstrating that bundling itself is sufficient to mechanically stabilize MTs. Together, these results identify MT bundling as a primary determinant of MT stability and modification, establishing MT-Bundlers as a versatile tool to dissect the mechanistic basis of MT bundling in living cells.

bioengineering↗

MEIS1 is Required for Establishing Bergmann Glia-Specific Properties in the Developing Cerebellum

Compared to normal multipolar astrocytes, Bergmann glial cells (BGs), specifically differentiated astrocytes in the cerebellum, possess unique unipolar morphology and additional cellular functions. However, the molecular mechanisms that confer BG-specific properties onto normal multipolar astrocytes remain unknown. Here, we show that the transcription factor, MEIS1, is involved in BGs acquiring their unique characteristics. Targeted disruption of Meis1 in the whole cerebellum or astroglial lineage cells resulted in a marked reduction of BGs accompanied by an increase in multipolar astrocytes in mice. Postnatal deletion of Meis1 in Bergmann glia-like progenitors (BGLPs), which produce both BGs and multipolar astrocytes, suppressed their differentiation into BGs while promoting into multipolar astrocytes. Single-cell RNA sequencing, immunohistochemistry, and ChIP-Atlas analyses indicated that MEIS1 directly upregulates expression of BG-specific genes, including Vimentin and Zeb2, which are known to contribute to the correct localization and the unipolar process formation of BGs. These findings suggest that MEIS1 promotes the endowment of BG-specific properties to astrocytes by controlling the expression of BG-specific genes, thereby ensuring proper differentiation of BGLPs into BGs.

developmental biology↗

Oxytocin Modulation of Spinal Circuits Drives Therapeutic Benefits of Massage

Across social species, social touch enhances well-being and reduces pain -- two seemingly distinct benefits that enhance survival. Yet where and how the nervous system integrates these functions, and whether a single mechanism could serve both, remains unknown. Here we show that massage triggers oxytocin release, which shapes both pain and touch reward at the earliest stage of central processing -- the spinal cord -- through a single, state-dependent circuit mechanism. We report that in humans, massage enhances well-being, effects that correlate with endogenous oxytocin release. In mice, gentle touch activates hypothalamic oxytocin neurons that project directly to the spinal dorsal horn. Genetic manipulation of spinal oxytocin circuits alters behavioral responses to both gentle touch and noxious stimuli. Spinal calcium imaging and slice electrophysiology reveal that oxytocin acts on both excitatory and inhibitory spinal neurons to sculpt the relative activity of spinal ascending systems that convey both social touch and pain to the brain. Extending these findings to humans, we show that oxytocin receptors are also expressed on spinal excitatory and inhibitory neurons, and that endogenous oxytocin during massage correlates with altered spinal touch processing. Thus, spinal oxytocin signaling provides an evolutionarily conserved mechanism for the therapeutic benefits of massage.

neuroscience↗

δ2-Protocadherins organize parallel indirect basal ganglia circuits

The basal ganglia (BG) contain multiple parallel neural circuits, each of which may control different behaviors. However, how the distinct parallel BG circuits are molecularly organized is not known. Here we show that two {delta}2-protocadherins (PCDHs), PCDH17 and PCDH10, which are homophilic cell-adhesion molecules, establish and define two distinct indirect BG circuits that regulate different behaviors. PCDH17 and PCDH10 are expressed in a complementary expression pattern in the BG, anatomically defining two parallel indirect BG connections. Indirect pathway-specific Pcdh17 and Pcdh10 conditional knockout (cKO) mice show impaired establishment of the indirect BG circuits in a region-preferential manner. Finally, the Pcdh17-cKO mice show defects in task learning, while the Pcdh10-cKO mice show defects in motor/sensory habituation. These results identify PCDH17 and PCDH10 as the molecular organizers for two distinct indirect BG circuits regulating different behaviors and reveal the molecular mechanisms for organizing parallel BG circuits. TeaserDistinct protocadherins organize parallel indirect basal ganglia circuits that regulate task learning or sensorimotor habituation

neuroscience↗

Evolution of sideways locomotion in crabs

The evolutionary change in the mode of locomotion is often a major evolutionary event, triggering diversification. Sideways locomotion is a defining feature of true crabs (Brachyura) and may have contributed to their ecological success. Yet, the evolutionary origin of this unique behavior remains unknown. Here we show that the prevalence of sideways locomotion in true crabs reflects a single evolutionary origin from a forward-moving ancestor. Our behavioral analysis of 50 live crab species indicates that crab locomotion can be broadly separated into two predominant modes, sideways and forward locomotion. The phylogenetic comparative analysis revealed a single origin of sideways locomotion, with multiple independent reversions to forward locomotion in ecologically specialized groups. The species richness data show that the lineage in which sideways locomotion originated is far more diverse than its nearest outgroups. These results are consistent with the idea that sideways locomotion acted as a key innovation contributing to the evolutionary diversification of true crabs. Such a rare but innovative behavioral trait provides a framework for understanding how locomotor modes shape evolutionary diversification in animals.

evolutionary biology↗

Self-Assembling Synthetic Peptides Remodel Mitochondrial Properties via Nanopore Formation

Pore-forming peptides (PFPs) are powerful tools for engineering biological membranes in vitro and in living cells. They can be derived from natural sources or designed de novo, with synthetic peptides offering distinct advantages in rational design unconstrained by natural sequences. While native PFPs have been targeted to specific organelles to modulate their functions, the potential of synthetic PFPs for organelle engineering remains largely unexplored. Here, we show that the 28-amino acid synthetic peptides, SVG28 and its variant SVG28D2, can be selectively targeted to mitochondria for functional alteration. More specifically, molecular dynamics simulations first confirmed the structural stability of the SVG28 nanopore even when fused to the TOM20 transmembrane domain, a mitochondrial targeting sequence. In isolated lipid bilayers, TOM20-SVG28 formed pores with a 0.3-nS, conductance, or 1.0-nm pore. The expression efficiency was further enhanced by two amino acid substitutions (SVG28D2). In cells, both TOM20-SVG28 and TOM20-SVG28D2 localized to the mitochondria, induced morphological alterations, and reduced both membrane potential and ATP production. These observations in silico, in vitro and in cellulo collectively indicate that the synthetic SVG28 peptides self-assemble into pores in the outer mitochondrial membrane, likely permitting proton permeation. Importantly, the matrix protein Su9 remained confined within mitochondria, suggesting preserved inner membrane integrity, and thus specific effect on the target. This work establishes a framework for the design and application of genetically-encoded synthetic PFPs in living cells, opening new avenues for cellular engineering.

synthetic biology↗

A copper-dependent, redox-based hydrogen peroxide perception in plants

Redox-related molecules, such as quinones and reactive oxygen species (ROS), are important signaling molecules for all living organisms. A plant-specific leucine rich-repeat receptor-like kinase (LRR-RLK) CANNOT RESPOND TO DMBQ 1 (CARD1), also known as HYDROGEN-PEROXIDE-INDUCED Ca2+ INCREASES (HPCA1), perceives both quinones and ROS, but knowledge on key structural features is unknown. Here, we determine the structure of the CARD1 ectodomain and uncover its unique features. Structural studies, coupled with genetics and biochemical analysis, demonstrated that previously identified unique cysteine residues are not essential for signal perception in CARD1. Interestingly, CARD1 harbors a copper ion on the surface of the ectodomain via histidine-coordination that is crucial for hydrogen peroxide signaling. Our work reports the first copper-dependent redox receptor and highlights a unique perspective between a receptor and non-peptide stimuli during their perception.

plant biology↗

Rainbow Nucleus Charts Dynamic Interactome of Membrane-less Organelles

Membrane-less organelles (MLOs) perform diverse cellular functions, but how they interact to coordinate these processes remains poorly understood. Here we constructed a "Rainbow Nucleus" cell line to simultaneously visualize five nuclear MLOs using multi-spectral live-cell imaging. We find that MLO interactions are not random: nuclear speckles serve as hubs, and functionally related MLOs interact more frequently than unrelated MLOs. While some interactions are stable, such as those between the histone locus bodies and Cajal bodies, others are transient, such as those between PML nuclear bodies and Cajal bodies. Single particle tracking revealed that stable contacts between Cajal bodies and nuclear speckles are functional, promoting the outward trafficking of small nuclear ribonucleoproteins from Cajal bodies. Finally, RNA Polymerase II-mediated transcription is required to organize the MLO interactome. Our study reveals a structured, transcription-dependent contact network among nuclear MLOs, laying the foundation for future cellular engineering efforts to modulate the MLO interactome.

cell biology↗

Visualization of stochastic expression of clustered protocadherin β isoforms in vivo

The stochastic expression of clustered protocadherin (cPcdh) establishes a single-cell identity fundamental to cellular self/non-self-discrimination. However, it has been challenging to reveal the spatiotemporal patterning of the stochastic cPcdh expression in vivo. We developed XFP (tdTomato or GFP) knock-in mice using a new strategy to enhance XFP expression, which allows us to visualize cPcdh{beta}3 or 19-positive cells throughout the brain. These mouse lines demonstrate the cell-type selectivity, spatial biases, inter-individual differences, left-right asymmetry, developmental regulation, alteration in pathological or aging brain, and monoallelic expression of stochastic cPcdh{beta} expression in vivo. Our findings further demonstrate that the cPcdh{beta}3 expression undergoes significant changes in the mature brain over time. These results demonstrate the potential of these reporter mice to advance our understanding of cPcdh cellular barcode in vivo.\n\nOne Sentence SummaryNovel established cPcdh{beta} reporter mouse lines reveal stochastic expression of cPcdh{beta} isoforms in vivo.

neuroscience↗

A skeletal muscle-sympathetic nerve-intestine network underlies muscle inflammation and atrophy induced by immobilization

Immobility is a common cause of muscle atrophy, but the underlying mechanisms have remained unclear. Here we show that limb immobilization in mice elicits inflammation and atrophy of skeletal muscle that are preventable by neutralizing antibodies to the chemokine CXCL10. Limb immobilization also induced changes to the gut microbiota and intestinal inflammation, and either sterilization of the intestine with antibiotics or administration of 10-hydroxy-cis-12-octadecenoic acid--a linoleic acid-derived gut microbial metabolite--prevented intestinal and muscle inflammation as well as muscle atrophy induced by immobilization, implicating intestinal inflammation in muscle inflammation and atrophy. Limb immobilization activated sympathetic nerves and increased {beta}2-adrenergic receptor gene (Adrb2) expression in the intestine. Single-cell RNA-sequencing analysis revealed that, among cells expressing Adrb2 in the intestine, immobilization increased only the population of macrophages. Pharmacological inhibition or macrophage-specific ablation of Adrb2 prevented immobilization-induced intestinal and muscle inflammation. Our results thus implicate a previously unrecognized muscle-nerve-intestine network in immobilization-induced muscle atrophy.

molecular biology↗

A novel RyR2-selective stabilizer prevents and ameliorates severe arrhythmias in stress-induced ventricular tachycardia

Background and PurposeAberrant activation of the type 2 ryanodine receptor (RyR2) causes lethal arrhythmias, such as catecholaminergic polymorphic ventricular tachycardia (CPVT). Developing drugs that suppress RyR2 hyperactivation may be key to novel arrhythmia treatments. This study evaluated the antiarrhythmic potential of Ryanozole, a recently developed novel RyR2 modulator with high affinity and selectivity, using CPVT mouse models harboring mutant RyR2s. Experimental approachIn vitro effects of Ryanozole were evaluated by ER Ca2+-based assay and [3H]Ryanodine binding assay using RyR2-expressing HEK293 cells. Two lines of mice with different arrhythmia severity, RyR2-R420W and -K4750Q, were employed for in vivo assessments. Intracellular Ca2+ signals were analyzed in isolated cardiomyocytes using Cal520. Antiarrhythmic effects were evaluated by ECG under catecholaminergic challenge in anesthetized mice and during spontaneous arrhythmias in conscious mice. ECG and echocardiographic parameters were evaluated before and after drug administration. Key resultsRyanozole inhibited both wild type and mutant RyR2s with similar IC50 of 15-40 nM. The inhibition was more potent at lower cytosolic Ca2+ concentrations. It suppressed Ca2+ waves and Ca2+ sparks without affecting action potential-evoked Ca2+ transients. Ryanozole effectively prevented adrenaline-induced arrhythmias and rapidly terminated spontaneous arrhythmias during daily activity. Importantly, Ryanozole did not impair cardiac conduction or contractility, unlike conventional antiarrhythmic drugs. Conclusions and implicationsRyanozole strongly suppresses RyR2 under diastolic Ca2+ conditions, thereby preventing the arrhythmogenic trigger of aberrant Ca2+ release. This mechanism likely provides potent antiarrhythmic effects while preserving cardiac function. Ryanozole is a promising therapeutic candidate treating RyR2-mediated arrhythmias, such as CPVT.

pharmacology and toxicology↗

Optogenetically Induced Microtubule Acetylation Unveils the Molecular Dynamics of Actin-Microtubule Crosstalk in Directed Cell Migration

Microtubule acetylation is implicated in regulating cell motility, yet its physiological role in directional migration and the underlying molecular mechanisms have remained unclear. This knowledge gap has persisted primarily due to a lack of tools capable of rapidly manipulating microtubule acetylation in actively migrating cells. To overcome this limitation and elucidate the causal relationship between microtubule acetylation and cell migration, we developed a novel optogenetic actuator, optoTAT, which enables precise and rapid induction of microtubule acetylation within minutes in live cells. Using optoTAT, we observed striking and rapid responses at both molecular and cellular level. First, microtubule acetylation triggers release of the RhoA activator GEF-H1 from sequestration on microtubules. This release subsequently enhances actomyosin contractility and drives focal adhesion maturation. These subcellular processes collectively promote sustained directional cell migration. Our findings position GEF-H1 as a critical molecular responder to microtubule acetylation in the regulation of directed cell migration, revealing a dynamic crosstalk between the actin and microtubule cytoskeletal networks.

cell biology↗