Biology subjects

Sakurai, N.

Publications and source records attributed to Sakurai, N..

7 recordsLinked to original sources

bioRxiv2026

ChemoTrack: A comprehensive dataset linking single-cell migration trajectories to precisely defined chemotactic signals

Chemotaxis drives cell migration in processes ranging from wound healing to embryonic development and cancer metastasis, yet its quantitative understanding remains limited because responding cells change and degrade attractant gradients, and existing datasets are too small and imprecise to capture stochastic behaviour. We present ChemoTrack, a publicly accessible resource comprising 2 million measurements from 500,000 migration tracks, in which the chemoattractant gradient and concentration experienced by every cell at the time of observation are precisely determined. The dataset includes microscopy images and trajectories spanning a full range of biologically relevant chemotactic conditions. Analysis shows that cells steer according to absolute differences in active receptor number, not fractional receptor occupancy, and maximal chemotaxis is not predicted by half-maximal receptor occupancy. By combining scale, precision and accessibility, ChemoTrack shifts quantitative description of eukaryotic chemotaxis from experimental conditions to the instantaneous chemical signal experienced by individual cells, enabling future mathematical and mechanistic analyses.

Cell Biology↗

bioRxiv2025

Natural variation in IBF1 disrupts its interaction with CHS1 and affects metabolism of hulls in rice

Secondary metabolites in plants have various physiological functions, including antioxidant and antibacterial activities. Previous studies have suggested genes and associated molecular mechanisms involved in the production of diverse secondary metabolites. However, much less is known about the genetic bases underlying within-species diversity in metabolite accumulation patterns, particularly in less focused tissues such as rice hulls. In this study, we aimed to identify the causal variant that affects flavonoid accumulation in rice hulls. We identified an F-box containing protein IBF1 is causal for genotypic differences in hull color through positional cloning. The variety IR64, with straw-white hulls, harbors functional IBF1 proteins that interact with a chalcone synthase, CHS1. Conversely, frame-shift mutations of IBF1 in the variety DJ123, which has pigmented hull color, resulted in a lack of a Kelch domain essential for the IBF1-CHS1 interaction. As a result, the DJ123 variant of IBF1 (IBF1DJ123) no longer interacted with CHS1, which was further supported by deep learning-based protein structural modeling. Further metabolome and transcriptome analyses using IR64 and an IR64-based chromosomal segment substitution line (CSSL) carrying IBF1DJ123 revealed an increase in the content of multiple flavonoids (such as naringenin and luteolin), while suppressing the expression of CAD involved in lignin synthesis. Metabolites in the CSSL carrying IBF1DJ123 suppressed the growth and siderophore generation activity of Pantoea species, which can act as beneficial or pathogenic endophytes. This study highlights the impact of a single gene on diverse metabolite accumulation patterns and suggests that this change may provide defense against pathogens.

plant biology↗

bioRxiv2025

Pathological Angiogenesis Precedes the Onset of Aortic Dissection

Aortic dissection (AD) is a severe, life-threatening disease that occurs abruptly1. Although remodeling and inherent vulnerability of the aortic media, as observed in heritable connective tissue disorders such as Marfan syndrome, have been implicated in the onset of AD, the precise pathological mechanisms underlying the non-heritable form, which accounts for most cases, remains largely unknown2. Here, using hyperacute AD patient-derived samples, we show that pathological angiogenesis within the aortic media precedes the onset of dissection. Integrating single-cell transcriptomic analysis of aortic medial endothelial cells with high-resolution imaging revealed temporal changes preceding dissection. Hypoxic alterations in the media triggered osteochondrogenic changes in smooth muscle cells, promoted hydroxyapatite deposition, and induced angiogenesis via VEGF secretion from AD-specific CD14+CD68+CD163+MRC1(CD206)neg-low macrophages. Atomic force microscopy revealed that these processes culminated in the formation of a soft capillary layer, potentially concentrating stress on this region and contributing to AD onset. H&E staining of archived specimens revealed that non-heritable AD can be classified into angiogenic or non-angiogenic subtypes, with more than half exhibiting the former. In contrast, acute AD cases associated with Marfan syndrome typically exhibit a non-angiogenic pattern, suggesting distinct underlying mechanisms. This study reports angiogenesis as a key pathological driver in non-heritable AD and highlight potential targets for early diagnosis, prevention, and treatment.

pathology↗

bioRxiv2025

CRISPR/Cas9-mediated genome editing reveals the involvement of a polyphenol oxidase in the shikonin-specific biosynthesis in Lithospermum erythrorhizon

Shikonin, a 1,4-naphthoquinone derivative produced by several Boraginaceae species, exhibits unique pharmacological properties and is used as a natural dye. The regulatory factors of shikonin production have been demonstrated using a cell culture system of Lithospermum erythrorhizon. Among these factors, copper is known to be the strongest enhancer of shikonin production. Although shikonin biosynthesis has been studied for over 40 years, the steps of naphthalene ring formation are still unknown, as is the reason for the effect of copper. In this study, we explored candidate genes associated with shikonin production using a PCR-select subtraction experiment. Polyphenol oxidase (PPO), a dicopper-dependent oxidoreductase, was highlighted because it showed synchronous expression with shikonin production. Transcriptome analysis of hairy roots and cultured cells of this plant revealed that, of the five PPO genes expressed in L. erythrorhizon, only PPO1 showed a strong correlation with shikonin production. Next, we generated genome-edited hairy roots of LePPO1 using CRISPR/Cas9-mediated mutagenesis to analyze its impact on shikonin derivative and other specialized metabolite production. The results showed that shikonin content was markedly reduced in all LePPO1-ge lines. Interestingly, the content of deoxyshikonofuran, a hydroquinone derivative and shunt product that branches after GHQ-3''-OH in the shikonin biosynthetic pathway, remained unaffected in the LePPO1-ge lines. These findings suggest that LePPO1 participates in naphthalene ring formation and explain why a copper ion is crucial for shikonin biosynthesis.

biochemistry↗

bioRxiv2023

Identification of Core Yeast Species and Microbe-Microbe Interactions Impacting Larval Growth of Drosophila in the Wild

Microbiota consisting of various fungi and bacteria have a significant impact on the physiological functions of the host. However, it is unclear which species are essential to this impact and how they affect the host. This study analyzed and isolated microbes from natural food sources of Drosophila larvae, and investigated their functions. Hanseniaspora uvarum is the predominant yeast responsible for larval growth in the earlier stage of fermentation. As fermentation progresses, Acetobacter orientalis emerges as the key bacterium responsible for larval growth, although yeasts and lactic acid bacteria must coexist along with the bacterium to stabilize this host-bacterial association. By providing nutrients to the larvae in an accessible form, the microbiota contributes to the upregulation of various genes that function in larval cell growth and metabolism. Thus, this study elucidates the key microbial species that support animal growth under microbial transition.

developmental biology↗

bioRxiv2023

Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect akuBGL activity

The defensive-offensive associations between algae and herbivores determine marine ecology. Brown algae utilize phlorotannin as their chemical defense against the predator Aplysia kurodai, which uses {beta}-glucosidase (akuBGL) to digest the laminarin in algae to glucose. Moreover, A. kurodai employs Eisenia hydrolysis-enhancing protein (EHEP) as an offense to protect akuBGL activity from phlorotannin inhibition by precipitating phlorotannin. To underpin the molecular mechanism of this digestive-defensive-offensive system, we determined the structures of apo and tannic-acid (TNA, a phlorotannin-analog) bound form of EHEP, as well as apo akuBGL. EHEP consisted of three peritrophin-A domains formed in a triangle and bound TNA in the center without significant conformational changes. Structural comparison between EHEP and EHEP-TNA led us to find that EHEP can be resolubilized from phlorotannin-precipitation at an alkaline pH, which reflects a requirement in the digestive tract. akuBGL contained two GH1 domains, only one of which conserved the active site. Combining docking analysis, we propose the mechanisms by which phlorotannin inhibits akuBGL by occupying the substrate-binding pocket, and EHEP protects akuBGL against the inhibition by binding with phlorotannin to free the akuBGL pocket.

biochemistry↗

bioRxiv2020

Phosphorylation and dephosphorylation of Ser852 and Ser889 control clustering, localization, and function of PAR-3

Cell polarity is essential for various asymmetric cellular events, where the partitioning defective (PAR) protein, PAR3, plays a unique role as a cellular landmark to establish polarity. In epithelial cells, PAR3 localizes at the subapical border such as the tight junction in vertebrates and functions as an apical determinant. Although there is much information about the regulators of PAR3 localization, the mechanism involved in PAR3 concentration and localization to the specific membrane domain remains an important question to be clarified. In this study, we demonstrate that ASPP2, a stimulator of PAR3 localization, can link PAR3 and protein phosphatase 1 (PP1). The ASPP2-PP1 complex dephosphorylates a novel phosphorylation site, Ser852, of PAR3. Furthermore, Ser852- or Ser889-unphosphorylatable PAR3 mutants form protein clusters and ectopically localize to the lateral membrane. Concomitance of clustering and ectopic localization suggests that PAR3 localization is a consequence of local clustering. We also demonstrate that unphosphorylatable forms of PAR3 are static in molecular turnover and fail to coordinate rapid reconstruction of the tight junction, supporting that both phosphorylated and dephosphorylated states are essential for the functional integrity of PAR3. Summary statementWe show that phosphorylation and dephosphorylation regulate clustering of PAR-3, a cell polarity-regulating factor, and how the clustering regulation affects localization of PAR-3 and cell-cell junction formation.

cell biology↗