Biology subjects

Nobori, T.

Publications and source records attributed to Nobori, T..

9 recordsLinked to original sources

bioRxiv2026

A Pmk1-Regulated Mst12-Bip1 Network Coordinates Appressorium Function, Effector Deployment, and Invasive Growth by Magnaporthe oryzae

To cause rice blast disease, the filamentous fungus Magnaporthe oryzae develops a specialised infection cell called an appressorium, which generates enormous turgor to breach the rice leaf cuticle. Although key regulators of appressorium development have been identified, it is not known how they drive the extensive transcriptional reprogramming required for infection-related morphogenesis. Here, we show that the Pmk1 MAP kinase orchestrates plant infection by regulating a transcriptional network controlled by the Mst12 and Bip1 transcription factors. Bip1 is regulated both by Pmk1-dependent phosphorylation and at the transcriptional level, while Mst12 binds to a cis-acting element upstream of BIP1 essential for pathogenesis. Bip1 and Mst12 are both necessary for regulating a set of Pmk1-dependent appressorium-specific genes, including transcriptional regulators, cell wall-degrading enzymes, and effector proteins. In addition, Mst12 specifically regulates functions required for appressorium-mediated penetration, while Bip1 controls a distinct sub-set of effector genes deployed during invasion of plant tissue. When considered together, these findings define a Pmk1-dependent transcriptional network required for plant infection by the blast fungus.

molecular biology↗

bioRxiv2026

Transient cell states encode positional information to direct asymmetric growth

How tissues generate asymmetric growth from spatially and temporally restricted signals remains a fundamental challenge in developmental biology. We show that transient cell states encode positional information that instructs asymmetric growth in plants. Using spatial single-cell transcriptomics and multi-omics, we uncover a surprisingly complex landscape of transient cell states in the apical hook, including a previously unrecognized population in the apical hypocotyl region that integrates developmental and hormonal cues and bifurcates into opposing growth trajectories. Gene regulatory network analysis and functional perturbation establish GATA TRANSCRIPTION FACTOR 2 (GATA2) as a central regulator that promotes cell elongation through gibberellin signaling. These results reveal that diverse, spatially localized transient cell states function as regulatory hubs that convert positional information into divergent growth programs, providing a unifying framework for how dynamic cellular states shape organ morphology.

plant biology↗

bioRxiv2025

An embryo-derived peptide signal directs endosperm polarity in Arabidopsis

Angiosperm seed formation requires the coordinated development of the products of double fertilization, the embryo and the endosperm. The endosperm mediates efficient nutrient transfer from surrounding maternal tissues to the developing embryo. This function requires a polarized tissue organization, which manifests as early polar gene expression and polar cellularization dynamics. We show that the receptor kinase HAIKU2 acts in coordination with the transcription factor WRKY10/MINISEED3 to ensure robust endosperm polarity establishment through the activity of the homeodomain transcription factors WUSCHEL-RELATED HOMEOBOX 8 and 9. This process depends on egg cell fertilization and is mediated through the peptide PATHOGEN-INDUCED PEPTIDE-LIKE 7, which acts as a HAIKU2 ligand. Our results reveal how a molecular paracrine dialogue between the embryo and endosperm ensures optimal seed developmental coordination.

plant biology↗

bioRxiv2023

Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack

Plant leaf intercellular space provides a nutrient-rich and heterogeneous niche for microbes that critically impacts plant health. However, how individual plant cells respond to heterogeneous microbial colonization remains largely elusive. Here, by time-resolved simultaneous single-cell transcriptome and epigenome profiling of plants (Arabidopsis thaliana) infected by virulent and avirulent bacterial pathogens (Pseudomonas syringae), we present cell atlases with gene regulatory logic involving transcription factors, putative cis-regulatory elements, and target genes associated with disease and immunity. We also identify previously uncharacterized cell populations with distinct immune gene expression within major developmental cell types. Furthermore, we employ time-resolved spatial transcriptomics to reveal spatial heterogeneity of plant immune responses linked to pathogen distribution. Integrating our single-cell multiomics and spatial omics data enables spatiotemporal mapping of defense gene regulatory logic with pathogen cells. Our study provides a molecularly-defined spatiotemporal map of plant-microbe interaction at the single-cell resolution.

plant biology↗

bioRxiv2023

A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

Extensive studies of the reference plant Arabidopsis have enabled a deep understanding of tissues throughout development, yet a census of cell types and states throughout development is lacking. Here, we present a single-nucleus transcriptome atlas of seed-to-seed development employing over 800,000 nuclei, encompassing a diverse set of tissues across ten developmental stages, with spatial transcriptomic validation of the dynamic seed and silique. Cross-organ analyses revealed transcriptional conservation of cell types throughout development and heterogeneity within individual cell types influenced by organ-of-origin and developmental timing, including groups of transcription factors, suggesting gatekeeping by transcription factor activation. This atlas provides a resource for the study of cell type specification throughout the development continuum and a reference for stimulus-response and genetic perturbations at the single-cell resolution.

plant biology↗

bioRxiv2023

Drought Recovery Induced Immunity Confers Pathogen Resistance

All organisms experience stress as an inevitable part of life, from single-celled microorganisms to complex multicellular beings. The ability to recover from stress is a fundamental trait that determines the overall resilience of an organism, yet stress recovery is understudied. To begin unraveling the stress recovery process we studies recovery from drought stress in Arabidopsis thaliana. We performed a fine-scale time series of bulk RNA sequencing starting 15 minutes after rehydration following moderate drought. We reveal that drought recovery is a rapid process involving the activation of thousands of recovery-specific genes. To capture these rapid recovery responses in different leaf cell types, we performed single-nucleus transcriptome analysis at the onset of post-drought recovery, identifying a cell type-specific transcriptional state developing within 15 minutes of rehydration independently across cell types. Furthermore, we reveal a recovery-induced activation of the immune system that occurs independent of infection, which enhances pathogen resistance in vivo in A. thaliana, wild tomato (Solanum pennellii) and domesticated tomato (Solanum lycopersicum cv. M82). Since rehydration promotes microbial proliferation and thereby increases the risk of infection1-2, drought recovery-induced immunity may be crucial for plant survival in natural environments. These findings indicate that drought recovery coincides with a preventive defense response, unraveling the complex regulatory mechanisms that facilitate stress recovery in different plant cell types.

plant biology↗

bioRxiv2022

PHYTOMap: Multiplexed single-cell 3D spatial gene expression analysis in plant tissue

Retrieving the complex responses of individual cells in the native three-dimensional tissue context is crucial for a complete understanding of tissue functions. Here, we present PHYTOMap (Plant HYbridization-based Targeted Observation of gene expression Map), a multiplexed fluorescence in situ hybridization method that enables single-cell and spatial analysis of gene expression in whole-mount plant tissue in a transgene-free manner and at low cost. We applied PHYTOMap to simultaneously analyze 28 cell type marker genes in Arabidopsis roots and successfully identified major cell types, demonstrating that our method can substantially accelerate the spatial mapping of marker genes defined in single-cell RNA-seq datasets in complex plant tissue.

plant biology↗

bioRxiv2021

Dissecting the co-transcriptome landscape of plants and microbiota members

Interactions between plants and neighboring microbial species are fundamental elements that collectively determine the structure and function of the plant microbiota. However, the molecular basis of such interactions is poorly characterized. Here, we monocolonized Arabidopsis leaves with nine plant- associated bacteria from all major phyla of the plant microbiota and profiled co- transcriptomes of plants and bacteria. We detected both common and distinct co- transcriptome signatures among plant-commensal pairs. In planta responses of commensals were similar to those of a disarmed pathogen characterized by the suppression of genes involved in general metabolism in contrast to a virulent pathogen. We identified genes that are enriched in the genome of plant-associated bacteria and induced in planta, which may be instrumental for bacterial adaptation to the host environment and niche separation. This study provides insights into how plants discriminate among bacterial strains and lays the foundation for in- depth mechanistic dissection of plant-microbiota interactions.

plant biology↗

bioRxiv2019

In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions

Understanding how gene expression is regulated in plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a foliar bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana and identified a number of bacterial processes influenced by plant immunity at the mRNA and the protein level. We found instances of both concordant and discordant regulation of bacterial mRNAs and proteins. Notably, the tip component of bacterial type III secretion system was selectively suppressed by the plant salicylic acid pathway at the protein level, suggesting protein-level targeting of the bacterial virulence system by plant immunity. Furthermore, gene co-expression analysis illuminated previously unknown gene regulatory modules underlying bacterial virulence and their regulatory hierarchy. Collectively, the integrated in planta bacterial omics approach provides molecular insights into multiple layers of bacterial gene regulation that contribute to bacterial growth in planta and elucidate the role of plant immunity in controlling pathogens.

plant biology↗