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Biology subjects

Sakai, K.

Publications and source records attributed to Sakai, K..

At least 19 recordsLinked to original sources

Conformational dynamics of an intrinsically disordered receptor enable signal transduction

Signal transduction is initiated when activated cell-surface receptors physically engage intracellular signaling proteins. Although structural and biochemical studies have established the molecular architecture of receptor tyrosine kinase (RTK) signaling, the earliest dynamic events that couple receptor activation to intracellular signal propagation have remained inaccessible because existing approaches provide static structural snapshots or ensemble-averaged measurements rather than direct observation of molecular motion. Here, using high-speed atomic force microscopy (HS-AFM), we directly visualize these initial molecular events at the single-molecule level in real time. Using fibroblast growth factor receptor 1 (FGFR1) as a model, we show that receptor autophosphorylation releases its intrinsically disordered juxtamembrane region, enabling extensive conformational dynamics of the kinase domain that permit productive engagement of the signaling adaptor FRS2, a key initiator of downstream RTK signaling. In contrast, a kinase-inactive mutation or the clinically approved FGFR inhibitor futibatinib restricts receptor motion, stabilizes a compact receptor configuration, and markedly reduces adaptor engagement. Molecular dynamics simulations suggest that the disruption of inhibitory interactions between the juxtamembrane region and the kinase domain provides a structural explanation for the observed receptor dynamics. Together, our findings uncover a previously inaccessible physical mechanism underlying the initiation of RTK signaling and establish HS-AFM as a powerful platform for visualizing receptor dynamics, providing a framework for mechanistic studies of signal transduction and for the development and mechanistic evaluation of compounds that modulate receptor signaling.

biophysics↗

Cortical TRPV1 modulates sensory processing through TRPA1-dependent mechanisms

Transient receptor potential vanilloid 1 (TRPV1) is classically recognised as a peripheral ion channel involved in nociception, but its physiological role in cortical sensory processing remains poorly understood. Here, we investigated whether cortical TRPV1 modulates tactile perception and sensory representations in the vibrissal primary somatosensory cortex (vS1) of mice. TRPV1 activation enhanced perceptual sensitivity, particularly for near-threshold tactile stimuli. In vS1, this was accompanied by stimulus-evoked responses that enhanced stimulus selectivity and discriminability. At the cellular level, activating TRPV1 increased excitability of pyramidal neurons in a TRPA1-dependent manner. Within vS1, TRPV1 activation reduced positive noise correlations and improved stimulus decoding through TRPA1-dependent changes in population activity. Together, these findings identify a TRPV1-TRPA1 signalling mechanism that regulates cortical gain, sharpens sensory representations and enhances perceptual sensitivity. Our results extend the established role of TRPV1 beyond peripheral sensory transduction to central sensory computation.

neuroscience↗

Calibrated ADAMTS13 inhibition prevents cardiovascular shear coagulopathy

Mechanical circulatory support essential for managing severe heart failure frequently triggers bleeding complications, driven by shear stress-induced over-proteolysis of von Willebrand factor (VWF) by ADAMTS13. Inhibiting ADAMTS13 presents a rationale to treat this condition, known as acquired von Willebrand syndrome (AVWS). However, conventional therapeutic strategies remain limited due to the risk of triggering thrombotic thrombocytopenic purpura. Here we show that HA10, a humanized anti-ADAMTS13 antibody, preserves a residual level of ADAMTS13 activity above the thrombosis-associated threshold. Multimodal structural and biophysical analyses--including NMR, SAXS, and SANS--revealed that HA10 bound to the disintegrin-like domain of ADAMTS13, dynamically competing with VWF while leaving 10- 20% residual enzymatic activity. The therapeutic efficacy and safety of HA10 were verified in non-human primate models of AVWS. Our findings establish a novel paradigm of enzymatic calibration rather than complete blockade, offering a mechanistically targeted and safe therapeutic approach for cardiovascular bleeding.

biochemistry↗

Fluorescence in situ hybridization reveals endophytic and epiphytic root colonization of the novel plant growth-promoting bacterium Citrobacter sedlakii CESi7

Plant growth-promoting bacteria are gaining significant attention as promising biofertilizers. However, the inconsistency between in vitro plant growth-promoting traits and actual field performance remains a challenge, driven partly by a limited understanding of in situ colonization. This study characterized the colonization patterns of Citrobacter sedlakii CESi7, a novel plant growth-promoting bacterium, isolated from oil palm waste compost, during Brassica rapa cultivation. The in situ behavior of CESi7 was observed in both sterilized medium and non-sterilized soil using fluorescence in situ hybridization with a strain-targeting probe. The results revealed that CESi7 can establish both epiphytic and endophytic populations that transiently colonize roots. In a sterilized medium, CESi7 was widely distributed throughout the root tissues. Conversely, in non-sterilized soil, the bacterium formed dense aggregates specifically at the root tips. This study provides direct microscopic evidence of the colonization strategy of CESi7, offering crucial insights for its development as an effective biofertilizer.

microbiology↗

Cell wall remodeling is required for crowding homeostasis during cell growth in S. cerevisiae

The cytoplasm is a densely crowded environment that plays essential roles in intracellular functions. Its biophysical properties can be markedly altered in response to environmental cues and changes in cellular state. Recent studies have shown that excessive growth leads to cytoplasmic dilution, contributing to cellular dysfunction. However, the molecular mechanisms regulating biophysical properties during excessive growth remain poorly understood. Here, we demonstrate that cell wall remodeling is crucial to maintain cytoplasmic crowding homeostasis during cell growth. Live-cell imaging and phosphoproteomic analysis showed that Mpk1, a component of Cell Wall Integrity (CWI) pathway, accumulates in the nucleus and its activity progressively increases as cells enlarge. Mpk1 is required to restrict cell volume expansion and maintain cytoplasmic crowding by adjusting cell wall thickness and mechanical resistance. Moreover, Mpk1 is essential for the survival of enlarged cells upon cell cycle re-entry. In addition to Mpk1, we identified multiple key components of the CWI pathway that are required to maintain physiological state of enlarged cells. Together, these findings establish the CWI signaling pathway as a key regulator of cell size homeostasis and cytoplasmic biophysical properties, providing a mechanistic link between cell wall remodeling and intracellular properties.

Cell Biology↗

Plasmin-mediated cleavage of GPIbα contributes to breakdown of platelet-von Willebrand factor complexes

Von Willebrand factor (VWF) is an essential contributor to hemostasis through its interaction with the platelet glycoprotein (GP) Ib receptor. VWF is cleaved by ADAMTS13 to limit its prothrombotic properties. Failure to do so can result in platelet-VWF complexes that occlude the microcirculation, as seen in thrombotic thrombocytopenic purpura (TTP). In this setting, plasmin becomes active to cleave VWF, forming a distinct plasmin-generated cleavage product of VWF (cVWF) that is detectable during acute attacks in patients with TTP and following therapeutic plasminogen activation in a mouse model of TTP. However, it remains unclear whether plasmin-mediated proteolysis of VWF alone accounts for the breakdown of platelet-VWF complexes. Using ristocetin-induced platelet agglutinations, we show that plasmin cleavage of VWF does not impair its platelet-binding capacity, whereas plasmin-mediated cleavage of GPIb reduces the ability of platelets released from agglutinates to bind VWF. Furthermore, platelets in suspension are relatively resistant to plasmin cleavage. We therefore propose that VWF binding may enhance GPIb cleavage by recruiting plasmin(ogen) to the platelet surface. In a TTP mouse model, plasminogen activation led to a VWF-dependent reduction in GPIb detectability, although to a lesser extent than observed in vitro. In patients with acute TTP, soluble GPIb levels were elevated, indicating increased GPIb shedding during attacks of thrombotic microangiopathy, although the extent to which this is plasmin-mediated remains unclear. Together, our findings demonstrate that plasmin cleavage of GPIb drives the disruption of ristocetin-induced agglutinates, while its contribution to the breakdown of platelet-VWF complexes in vivo appears limited.

biochemistry↗

Prenatal valproic acid-exposed autism marmosets increase mutual gaze and reduce inter-individual distance during dyadic social interactions

Autism spectrum disorder (ASD) is associated with differences in social interaction, including alterations in gaze behavior and interpersonal distance. Although most assessments of ASD remain individual-centric, emerging human studies indicate that social difficulties may arise from atypical dyadic coordination rather than from reduced social interest alone. We examined dyadic coordination in a non-human primate model of ASD, focusing on gaze and inter-individual distance during minimally constrained first encounters between prenatal valproic acid-exposed marmosets (VPA) and unexposed conspecifics (UE). Markerless pose estimation quantified frame-by-frame gaze direction and spacing, comparing VPA-UE with UE-UE dyads. VPA-UE pairs exhibited a higher proportion of mutual-gaze events than UE-UE pairs. VPA individuals showed more rapid looks in response to the partners gaze, yet spent less time looking at the partner when unobserved. VPA-UE dyads maintained shorter inter-individual distances than UE-UE dyads, and closer spacing was associated with decreased stability of mutual gaze. These findings reveal a dyadic coordination pattern in VPA-UE pairs, with rapid responsiveness coupled with distance-dependent fragility, paralleling features reported in human ASD. Our dyad-centric, markerless framework yields ecologically grounded readouts and potential intervention targets that leverage intact social responsiveness while accommodating altered spatial coordination.

neuroscience↗

Kinetic modeling of continuous meta-fermentation quantifies metabolic activity in a complex microbial system

One of the serious drawbacks of a complex microbial system is the difficulty in quantifying the metabolic activity of each microorganism. A kinetic model of predominant microbial species was constructed for continuous meta-fermentation in a complex microbial system at several dilution rates (D). The introduction of biomass and lactic acid inhibition terms improved model accuracies at D = 0.05 h-1 and 0.4 h-1, respectively. The coefficient of determination (R2) and root mean square error (RMSE) improved from 0.577 and 5.21 to 0.972 and 0.759, respectively, with the inhibition term at D = 0.05 h-1. The inhibition terms resulted in good R{superscript 2} (0.996) and RMSE (1.27) values at D = 0.4 h-1. By solving the Michaelis-Menten equation in the constructed models, the species flux (SF) was calculated to estimate the metabolic activity (formation and consumption) of each microorganism. At D = 0.05 h-1, Caldibacillus hisashii contributed to lactic acid production at 0.333 g/L/h, whereas Clostridium cochlearium consumed lactic acid at 0.203 g/L/h, suggesting cross-feeding of a metabolite. It is therefore possible to account for consumption that cannot be considered in gene-derived calculations, indicating that this is a promising analytical method for investigating the dynamic behavior of complex microbial systems. Kinetic models for continuous meta-fermentation at several D values were developed. A new metabolic analysis method is proposed to estimate the activity of microbial species in a complex microbial system.

bioinformatics↗

HDA19-mediated deacetylation of histone H3.3 lysine 27 and 36 regulates plant sensitivity to salt stress

Plants survive extreme environments through rapid chromatin reprogramming, yet the epigenetic marks that confer stress resilience remain poorly understood. Histone deacetylase HDA19 is a key epigenetic regulator in Arabidopsis, and hda19-deficient mutants display tolerance to multiple abiotic stresses, including drought, heat, and salinity. Using lysine acetylome profiling, we identified a non-canonical K27/K36 di-acetylation mark on histone H3.3, among nine H3 variants, as a specific substrate of HDA19. Under salinity stress, this mark decreased in wild-type plants but increased in hda19 mutants, while other known H3 modifications were similarly affected in both genotypes. Mimicking constitutive di-acetylation of H3.3 K27/K36 through lysine-to-glutamine substitutions promoted accumulation of stress-responsive late embryogenesis abundant (LEA) proteins and conferred salinity tolerance in seedlings, phenocopying hda19 mutants. Furthermore, generating the lea7-1/lea29-1/rab18-1 triple mutant abolished hda19-dependent salinity tolerance, confirming the LEA proteins role downstream of HDA19. Our findings demonstrate that H3.3 K27/K36 di-acetylation, modulated by HDA19, drives LEA protein accumulation and enables plants to withstand environmental stress, revealing a previously unknown core mechanism of plant stress resilience. Significance statementHistone acetylation is crucial for regulating chromatin states and transcription, yet the specific histone codes controlled by histone deacetylases and acetyltransferases during plant stress acclimation remain unclear. Arabidopsis mutants lacking histone deacetylase 19 show enhanced tolerance to drought, heat, and salinity. Using acetylome profiling and genetic analyses, we identify a previously unknown di-acetylation of histone H3.3 at lysines 27 and 36 as a key epigenetic switch activating late embryogenesis abundant proteins essential for salt tolerance in seedlings. This discovery reveals a novel mechanism linking histone H3.3 K27/K36 di-acetylation to stress-resilient protein accumulation, offering new insights into epigenetic control of plant stress responses and informing strategies to improve crop resilience under climate change.

plant biology↗

High-Speed AFM Reveals IDR-Mediated Structural Plasticity of EML4-ALK Modulated by ALK Inhibitors

EML4-ALK is a key oncogenic driver in lung cancer, but variant-specific chemoresistance limits the efficacy of current ALK inhibitors. Because the N-terminus contains an intrinsically disordered region (IDR), how ALK inhibitors affect the structure and dynamics of full-length EML4-ALK remains unclear. Here, using high-speed atomic force microscopy (HS-AFM), we visualize the overall structures of three full-length EML4-ALK variants (v1, v3, and v5) at the single-molecule level. We identified a transient globular subdomain (residues 191-217) within the v3 IDR that contributes to distinct oligomerization patterns. Notably, ALK inhibitors compact the IDR subdomain and reduce oligomerization, whereas this effect is abolished by the resistance mutation ALKG1202R, suggesting that ALK inhibitors not only affect kinase activity but also modulate IDR dynamics. Our findings shed new light on the structural regulation of EML4-ALK and provide a foundation for developing next-generation targeted therapies that account for IDR-driven molecular behavior. TeaserHigh-speed AFM revealed the full-length EML4-ALK structures and their IDR-mediated plasticity caused by ALK kinase inhibitors

cancer biology↗

The increase in cell volume and nuclear number of the koji-fungus Aspergillus oryzae contributes to its high enzyme productivity

While the ratio of nuclei to cell volume is well regulated, it remains largely unexplored in multinucleate organisms. The koji-fungus Aspergillus oryzae, traditionally used in Japanese brewing and fermentation for over a thousand years, is now widely utilized in modern biotechnology as a host for enzyme production. We discovered that, over time in culture, hyphae become thicker, resulting in a tenfold increase in cell volume, and the number of nuclei in hyphal cells also increases tenfold, exceeding 200. The increase in cell volume and nuclear number is unique among the investigated Aspergillus species and correlates with its high enzyme production capabilities. Since nuclear number and cell volume are correlated, both must increase simultaneously for either to expand. Our analyses identified genetic factors and nutritional environmental signals involved in each of these increases. Increases in nuclear number and cell volume were also observed in other fungi bred for industrial use. This study not only deepens our understanding of the evolutionary processes that promote high enzyme productivity through fungal breeding, but also provides insights into the molecular mechanisms regulating cell volume and nuclear number in multinucleate organisms.

microbiology↗

Dihydroxyhexanoic acid biosynthesis controls turgor in pathogenic fungi

Many plant pathogenic fungi penetrate host surfaces mechanically, using turgor pressure generated by appressoria, specialized infection cells. These appressoria develop semipermeable cell walls and accumulate osmolytes internally to create turgor by osmosis. While melanin is known to be important for turgor generation, the mechanism for wall semipermeability has remained unclear. Here we identify PKS2 and PBG13, by reverse genetics, as crucial for forming the semipermeable barrier in anthracnose and rice blast fungi. These genes encode enzymes that synthesize 3,5-dihydroxyhexanoic acid polymers essential for the cell wall properties. Deleting these enzymes impairs cell wall porosity, abolishing turgor and pathogenicity without affecting melanization. Our findings uncover a novel mechanism of turgor generation, linking enzyme function to pathogen penetration and disease potential, presenting new targets for disease control.

plant biology↗

Evolution of Tn4371 family ICE; traR mediated coordination of cargo gene upregulation and horizontal transfer

ICEKKS102Tn4677, which has been shown to transfer horizontally, carries bph operon for mineralization of PCBs/biphenyl and belongs to an ICE Tn4371 family. In this study we investigated the role of traR gene encoding a LysR-type transcriptional regulator, which is conserved in sequence, positioning, and directional orientation among Tn4371 family ICEs. The traR belonged to bph operon and its overexpression on solid medium resulted in modest upregulation of traG (3-fold) and marked upregulation of xis (80-fold), and enhanced ICE excision, and notably ICE transfer frequency. We propose the evolutional roles of traR, which upon insertion to the current position, connected the cargo gene activation and ICE-transfer. This property of ICE, transferring under environmental conditions that lead to cargo gene activation, would give fitness advantages to the host bacteria, thereby resulting in efficient dissemination of the Tn4371 family ICEs. SignificanceOnly ICEKKS102Tn4677 is proven to transfer among the widely disseminating Tn4371 family ICEs from {beta} and {gamma}-proteobacteria. We showed that the traR gene in ICEKKS102Tn4677 conserved in the ICE family with fixed location and direction is co-transcribed with the cargo gene and activates ICE transfer. We propose that capturing of traR by an ancestral ICE to the current position established ICE Tn4371 family ICEs. Our findings provide insights into the evolutionary processes that led to the widespread distribution of the Tn4371 family of ICEs across bacterial species.

molecular biology↗

Live-cell fluorescence imaging and optogenetic control of PKA kinase activity in fission yeast Schizosaccharomyces pombe.

The cAMP-PKA signaling pathway plays a crucial role in sensing and responding to nutrient availability in the fission yeast Schizosaccharomyces pombe. This pathway monitors external glucose levels to control cell growth and sexual differentiation. However, the temporal dynamics of the cAMP-PKA pathway in response to external stimuli remains unclear mainly due to the lack of tools to quantitatively visualize the activity of the pathway. Here, we report the development of the kinase translocation reporter (KTR)-based biosensor spPKA-KTR1.0, which allows us to measure the dynamics of PKA activity in fission yeast cells. The spPKA-KTR1.0 is derived from the transcription factor Rst2, which translocates from the nucleus to the cytoplasm upon PKA activation. We found that spPKA-KTR1.0 translocates between the nucleus and cytoplasm in a cAMP-PKA pathway-dependent manner, indicating that the spPKA-KTR1.0 is a reliable indicator of the PKA activity in fission yeast cells. In addition, we implemented a system that simultaneously visualizes and manipulates the cAMP-PKA signaling dynamics by introducing bPAC, a photoactivatable adenylate cyclase, in combination with spPKA-KTR1.0. This system offers an opportunity for investigating the role of the signaling dynamics of the cAMP-PKA pathway in fission yeast cells with higher temporal resolution. Take AwayO_LIspPKA-KTR1.0 allows visualization of PKA activity at the single-cell level C_LIO_LILive-cell imaging reveals the transient decrease in PKA activity after M-phase C_LIO_LIOptogenetics allows simultaneous visualization and manipulation of PKA activity C_LI

cell biology↗

Cytoplasmic fluidization triggers breaking spore dormancy in fission yeast.

The cytoplasm is a complex, crowded environment that influences myriad cellular processes including protein folding and metabolic reactions. Recent studies have suggested that changes in the biophysical properties of the cytoplasm play a key role in cellular homeostasis and adaptation. However, it still remains unclear how cells control their cytoplasmic properties in response to environmental cues. Here, we used fission yeast spores as a model system of dormant cells to elucidate the mechanisms underlying regulation of the cytoplasmic properties. By tracking fluorescent tracer particles, we found that particle mobility decreased in spores compared to vegetative cells, and rapidly increased at the onset of dormancy breaking upon glucose addition. This cytoplasmic fluidization depended on glucose sensing via the cAMP-PKA pathway. PKA activation led to trehalose degradation through trehalase Ntp1, thereby increasing particle mobility as the amount of trehalose decreased. In contrast, the rapid cytoplasmic fluidization did not require de novo protein synthesis, cytoskeletal dynamics, or cell volume increase. Furthermore, the measurement of diffusion coefficients with tracer particles of different sizes suggests that the spore cytoplasm impedes the movement of larger protein complexes (40-150 nm) such as ribosomes, while allowing free diffusion of smaller molecules ([~]3 nm) such as second messengers and signaling proteins. Our experiments have thus uncovered a series of signaling events that enable cells to quickly fluidize the cytoplasm at the onset of dormancy breaking. Significance statementCellular processes are influenced by the biophysical properties of the cytoplasm such as crowding and viscoelasticity. Although it has been suggested that cells tune the cytoplasmic properties in response to environmental changes, the molecular mechanisms remain unclear. Here, we used the dormant fission yeast spores and uncovered signaling pathways that facilitate cytoplasmic fluidization during dormancy breaking. Furthermore, we tracked the mobility of intracellular tracer particles, and found that the spore cytoplasm impedes the mobility of larger protein complexes, while allowing free diffusion of smaller molecules. These results suggest that small signaling proteins can diffuse relatively freely in the spore cytoplasm and have the ability to transmit dormancy breaking signals, while the motion of large complexes, such as ribosomes, is restricted.

cell biology↗

Yeast-based heterologous production of the Colletochlorin family of fungal secondary metabolites

Transcriptomic studies have revealed that fungal pathogens of plants activate the expression of numerous biosynthetic gene clusters (BGC) exclusively when in presence of a living host plant. The identification and structural elucidation of the corresponding secondary metabolites remain challenging. Here we adapted a polycistronic vector for efficient, seamless and cost-effective cloning of biosynthetic genes using in vivo assembly (also called transformation-assisted recombination) directly in Escherichia coli followed by heterologous expression in Saccharomyces cerevisiae. Two vectors were generated with different auto-inducible yeast promoters and selection markers. The effectiveness of these vectors was validated with fluorescent proteins. As a proof-of-principle, we applied our approach to the Colletochlorin family of molecules. These polyketide secondary metabolites were known from the phytopathogenic fungus Colletotrichum higginsianum but had never been linked to their biosynthetic genes. Considering the requirement for an halogenase, and by applying comparative genomics, we identified a BGC putatively involved in the biosynthesis of Colletochlorins in C. higginsianum. Following the expression of those genes in S. cerevisiae, we could identify the presence of the precursor Orsellinic acid, Colletochlorins and their non-chlorinated counterparts, the Colletorins. In conclusion, the polycistronic vectors described herein were adapted for the host S. cerevisiae and allowed to link the Colletochlorin compound family to their corresponding biosynthetic genes. This system will now enable the production and purification of infection-specific secondary metabolites of fungal phytopathogens. More widely, this system could be applied to any fungal BGC of interest.

microbiology↗

Imbalance of circuit plasticity and consolidation in autism model marmosets is adjusted by oxytocin administration

Alterations in the experience-dependent and autonomous elaboration of neural circuits are assumed to underlie autism spectrum disorder (ASD), though it is unclear what synaptic traits are responsible. Here, we used a valproic acid-induced ASD marmoset model, which shares common molecular features with idiopathic ASD, to investigate the structural dynamics of tuft dendrites of upper-layer pyramidal neurons and adjacent axons in the dorsomedial prefrontal cortex using two-photon microscopy. In model marmosets, dendritic spine turnover was upregulated, and spines were actively generated in clusters and subsequently survived more often than in control marmosets. Presynaptic boutons in local axons but not in commissural long-range axons showed hyperdynamic turnover in model marmosets, suggesting alterations in projection-specific plasticity. Intriguingly, nasal administration of oxytocin reduced the clustered spine emergence. Enhanced clustered spine generation, possibly unique to certain presynaptic partners, may be associated with ASD and may be a potential therapeutic target.

neuroscience↗

Alcanivorax borkumensis Biofilms Enhance Oil Degradation By Interfacial Tubulation

Alcanivorax borkumensis are prominent actors in oil spill bioremediation; however, the interfacial dynamics of their biofilms and its role in oil degradation remain unclear. Longitudinal tracking of biofilm-covered oil microdroplets using microfluidics reveals a spontaneous morphological transition from a thick biofilm phenotype to a thin dendritic phenotype optimized for high oil consumption rates. We show experimentally that biofilm dendrites emerge from aster-like nematic defects in the thin biofilms. We develop a theoretical model that elucidates the transition between phenotypes, linking tubulation to decreased interfacial tension and increased cell hydrophobicity, which we verify experimentally. We demonstrate positional control over the nematic defects on the droplets using microfluidics, causing the biofilm to dimple the droplets. Our results reveal how A. borkumensis biofilms utilize topological defects to increase oil access to achieve superior oil consumption rates, which may be a general strategy in oil-consuming bacteria. ONE SENTENCE SUMMARYA. borkumensis adapt their interfacial properties over time to evolve their biofilm phenotype and increase their oil consumption

biophysics↗