Biology subjects

Tanokura, M.

Publications and source records attributed to Tanokura, M..

5 recordsLinked to original sources

bioRxiv2026

High-resolution temporal profiling reveals synchronized dynamics of the mouse gut microbiome

The gut microbiome is a highly dynamic ecosystem, yet its temporal organization remains poorly understood because microbiome sampling is typically limited to sparse time points. To overcome this challenge, we developed an automated device to enable continuous fecal sampling from individual mice at minute-to hour-scale resolution. Combining full-length 16S rRNA amplicon sequencing with a limited set of long-read metagenomic references, we economically reconstructed genome- and function-level trajectories at high temporal resolution. Automated hourly sampling over 14 consecutive days enabled phase analysis, revealing collective synchronization of taxa partitioned by carbohydrate utilization strategies between day and night, with microbial taxa and functional genes showing reproducible temporal succession across mice. Perturbations such as cage transfer or antibiotic treatment transiently disrupted this functional synchronization, followed by recovery toward a coherent dynamical state. This system and analytic frameworks will enable us to explore rapid microbiome dynamics in health and disease.

microbiology↗

bioRxiv2024

Tension-induced suppression of allosteric conformational changes explains coordinated stepping of kinesin-1

The dimeric motor protein kinesin-1 walks along microtubules by alternating ATP hydrolysis and movement of its two motor domains ("head"). The detached head preferentially binds to the forward tubulin-binding site after ATP binds to the microtubule-bound head, but the mechanism preventing premature binding to the microtubule while the partner head awaits ATP remains unknown. Here, we examined the role of the neck linker, the segment connecting the two heads, in this mechanism. High-resolution structural analyses of the nucleotide-free head revealed a bulge just ahead of the neck linkers base that creates an asymmetric constraint on its mobility. While the neck linker can stretch freely backward, it must navigate around this bulge to extend forward. Based on this finding, we hypothesized that premature binding of the tethered head is suppressed by an intolerable increase in neck linker tension. Molecular dynamic simulations and single-molecule fluorescent assays supported this model. These findings demonstrate a tension-based regulation mechanism where off-pathway conformational transitions are thermodynamically suppressed through entropy loss associated with neck linker stretching, suggesting that neck linker tension influences the allosteric conformational transition rather than directly affecting the nucleotide state.

biophysics↗

bioRxiv2023

Enhanced Ca2+ Binding to EF-Hands through Phosphorylation of Conserved Serine Residues Activates MpRBOHB and Chitin-Triggered ROS Production

NADPH oxidases/RBOHs catalyze apoplastic ROS production and act as key signaling nodes, integrating multiple signal transduction pathways regulating plant development and stress responses. Although RBOHs have been suggested to be activated by Ca2+ binding and phosphorylation by various protein kinases, a mechanism linking Ca2+ binding and phosphorylation in the activity regulation remained elusive. Chitin-triggered ROS production required cytosolic Ca2+ elevation and Ca2+ binding to MpRBOHB in a liverwort Marchantia polymorpha. Heterologous expression analysis of truncated variants revealed that a segment of the N-terminal cytosolic region highly conserved among land plant RBOHs encompassing the two EF-hand motifs is essential for the activation of MpRBOHB. Within the conserved regulatory domain, we have identified two Ser residues whose phosphorylation is critical for the activation in planta. Isothermal titration calorimetry analyses revealed that phosphorylation of the two Ser residues increased the Ca2+ binding affinity of MpRBOHB, while Ca2+ binding is indispensable for the activation, even if the two Ser residues are phosphorylated. Our findings shed light on a mechanism through which phosphorylation potentiates the Ca2+-dependent activation of MpRBOHB, emphasizing the pivotal role of Ca2+ binding in mediating the Ca2+ and phosphorylation-driven activation of MpRBOHB, which is likely to represent a fundamental mechanism conserved among land plant RBOHs.

molecular biology↗

bioRxiv2021

VISUAL network analysis reveals the role of BEH3 as a stabilizer in the secondary vascular development in Arabidopsis

During secondary growth in plants, vascular stem cells located in the cambium continuously undergo self-renewal and differentiation throughout the lifetime. Recent cell-sorting technique enables to uncover transcriptional regulatory framework for cambial cells. However, the mechanisms underlying the robust control of vascular stem cells have not been understood yet. By coexpression network analysis using multiple transcriptome datasets of an ectopic vascular cell transdifferentiation system using Arabidopsis cotyledons, VISUAL, we newly identified a cambium-specific gene module from an alternative approach. The cambium gene list included a transcription factor BES1/BZR1 homolog 3 (BEH3), whose homolog BES1 is known to control vascular stem cell maintenance negatively. Interestingly, the vascular size of the beh3 mutants showed a large variation, implying the role of BEH3 as a stabilizer. BEH3 almost lost the transcriptional repressor activity and functioned antagonistically with other BES/BZR members via competitive binding to the same motif BRRE. Indeed, mathematical modeling suggests that the competitive relationship among BES/BZRs leads to the robust regulation of vascular stem cells.

developmental biology↗

bioRxiv2018

Triazole ureas covalently bind to strigolactone receptors and regulate signaling

Strigolactones (SLs), a class of plant hormones with multiple functions, mediate plant-plant and plant-microorganism communications in the rhizosphere. In this study, we developed potent strigolactone antagonists, which covalently bind to the strigolactone receptor D14, by preparing an array of triazole urea compounds. Using yeast two-hybrid assays and rice tillering assays, we identified a triazole urea compound KK094 as a potent inhibitor of strigolactone receptors. The LC-MS/MS analysis and X-ray crystallography concluded that KK094 was hydrolyzed by D14, and that a reaction product of this degradation covalently binds to the Ser residue of the catalytic triad of D14. We also identified KK052 and KK073, whose effects on D14-D53/D14-SLR1 complex formation were opposite due to a trifluoromethyl group on its benzene ring. These results demonstrate that triazole urea compounds are potentially powerful tools for agricultural application and may be useful for the elucidation of the complicated mechanism underlying SL-perception.

plant biology↗