Biology subjects

Jo, L.

Publications and source records attributed to Jo, L..

6 recordsLinked to original sources

bioRxiv2025

Progressive oxygenation of developing leaves directs morphogenesis

Oxygen availability underpins energy production in multicellular organisms, yet internal oxygen gradients arise in both plants and animals. Plants sense these variations via the PLANT CYSTEINE OXIDASE branch of the N-degron pathway, which regulates the stability of key transcription factors. Originally linked to metabolic control, this pathway recently emerged as a development regulator. While the shoot apical meristem was shown to be hypoxic, the oxygen dynamics of organs originating from this low-oxygen niche remain unknown. Here we show that developing leaves form a spatiotemporal oxygen gradient that is sensed through the oxygen sensing machinery. This pathway integrates local oxygen availability to regulate leaf morphogenesis: early hypoxia restricts cell expansion, while subsequent distal-to-proximal oxygenation enables specialized cell fates acquisition. Our findings reveal that oxygen acts as a positional cue in normal growth, guiding developmental trajectories. Our work highlights opportunities to harness oxygen gradients or sensing to direct plant form and function.

plant biology↗

bioRxiv2025

Cell-type-specific execution of effector-triggered immunity

Effector-triggered immunity (ETI) is a central component of host defense, but whether all cell types execute ETI similarly remains unknown. We combined chemically imposed immune activation with single-cell transcriptomics to profile ETI responses across all leaf cell types in Arabidopsis. Despite uniform ETI perception, we find striking divergence between transcriptional outputs: a core set of defense genes is broadly induced, while distinct cell types activate specialized immune modules. We infer that downstream immune execution is shaped not only by immune receptor activation, but also by cell identity and its associated transcriptional regulatory context, including local transcription factor availability and chromatin accessibility. We further demonstrate that transcriptional regulators preferentially induced in epidermal cells are required to restrict invasion by non-adapted pathogens. Their absence permits pathogen entry into deeper tissues despite intact recognition, revealing a spatial division of immune functions. Our findings uncover a layered immune architecture in plants, challenges the assumption of uniform immune execution, and provides a framework for exploring cell-type-specific resistance logic in multicellular hosts.

plant biology↗

bioRxiv2025

ABA-induced MYB transcriptional module regulates the differentiation trajectory of chickpea exodermis

Abscisic acid (ABA) regulates plant responses to stress and influences the differentiation of root barrier cell types, such as the endodermis and exodermis. Despite the importance of the exodermis in limiting water and solute fluxes, its regulation remains poorly understood in legumes. Here, we characterize the ABA-induced suberization and lignification of root tissues across eight galegoid legumes to identify exodermis-forming species in the clade. Chickpea deposited suberin lamella specifically in the outermost cortex and formed a functional apoplastic barrier, i.e. an exodermis. Transcriptomics of chickpea roots revealed ABA-induced programs that were temporally separated, specifically, a rapid program with the general ABA response, and a delayed programs of suberin and lignin biosynthesis. We identified WRKY and MYB transcription factors that putatively link the ABA response to the suberin biosynthesis, and using single-cell RNA-seq of chickpea roots we inferred an exodermis-expressed WRKY-MYB regulatory unit upstream of the suberin biosynthetic genes. Transactivation assays supported an ABA-dependent transcription factor activity upstream of suberin biosynthesis pathway in chickpea. Our results reveal a cell-type specific transcription factor hierarchy that coordinates hormone perception into an important mechanism of root plasticity in legumes.

plant biology↗

bioRxiv2024

Transcription factors SlMYB41, SlMYB92 and SlWRKY71 regulate gene expression in tomato exodermis

Root barrier cell types, like the endodermis and exodermis, are crucial for plant acclimation to environmental stresses. Deposition of suberin, a hydrophobic polymer, in these cell layers restricts the movement of molecules and plays a vital role in stress responses. This study investigates the role of SlMYB41, SlMYB92 and SlWRKY71 transcription factors (TFs) in regulating suberin biosynthesis in the tomato (Solanum lycopersicum) root exodermis by genetic perturbation. Genetic perturbation of these TFs altered exodermal suberin deposition patterns, indicating the SlMYBs as positive and SlWRKY71 negative regulators of suberization. RNA sequencing revealed a significant overlap between differentially expressed genes regulated by these TFs, suggesting a shared regulatory network. Gene set enrichment analyses highlighted their role in lipid and suberin biosynthesis as well as overrepresentation of exodermis-enriched transcripts. Furthermore, transactivation assays demonstrated that these two MYBs promote the expression of suberin-related genes, while SlWRKY71 represses them. These results indicate a complex antagonistic relationship, advancing our understanding of the regulatory mechanisms controlling exodermis suberization in tomato roots. HighlightMYB and WRKY transcription factors collaboratively regulate suberin biosynthesis in the tomato root exodermis. Antagonistic interactions may fine-tune suberization or act as a break to stop overaccumulation.

plant biology↗

bioRxiv2024

Genome-Wide Profiling of Soybean WRINKLED1 Transcription Factor Binding Sites Provides Insight into the Regulation of Fatty Acid and Triacylglycerol Biosynthesis Program in Seeds

Understanding the regulatory mechanisms controlling storage lipid accumulation will inform strategies to enhance seed oil quality and quantity in crop plants. The WRINKLED1 transcription factor (WRI1 TF) is a central regulator of lipid biosynthesis. We characterized the genome-wide binding profile of soybean (Gm)WRI1 and show that the TF directly regulates genes encoding numerous enzymes and proteins in the fatty acid and triacylglycerol biosynthetic pathways. GmWRI1 binds primarily to regions downstream of target gene transcription start sites. We showed that GmWRI1 bound regions are enriched for the canonical WRI1 DNA binding element, the AW Box (CNTNGNNNNNNNCG), and another DNA motif, the CNC Box (CNCCNCC). Functional assays showed that both DNA elements mediate transcriptional activation by GmWRI1. We also show that GmWRI1 works in concert with other TFs to establish a regulatory state that promotes fatty acid and triacylglycerol biosynthesis. In particular, comparison of genes targeted directly by GmWRI1 and by GmLEC1, a central regulator of the maturation phase of seed development, reveals that the two TFs act in a positive feedback subcircuit to control fatty acid and triacylglycerol biosynthesis. Together, our results provide new insights into the genetic circuitry in which GmWRI1 participates to regulate storage lipid accumulation during seed development. Significance StatementWe report the genome-wide profiling of DNA sequences bound by and the genes directly- regulated by soybean WRINKLED1, a central regulator of storage lipid accumulation in oilseed plants. The information offers new insights into the mechanisms by which WRINKLED1 regulates genes encoding lipid biosynthetic enzymes and establishes a regulatory environment that promotes oil accumulation, and it may aid in the design of strategy to alter storage lipid accumulation in oilseeds.

plant biology↗

bioRxiv2023

ggPlantmap: an R package for creation of informative and quantitative ggplot maps derived from plant images.

As plant research generates an ever-growing volume of spatial quantitative data, the need for decentralized and user-friendly visualization tools to explore large and complex datasets tools becomes crucial. Existing resources, such as the Plant eFP (electronic Fluorescent Pictograph) browsers, have played a pivotal role on the communication of gene expression data across many plant species. However, although widely used by the plant research community, the Plant eFP browser lacks open and user-friendly tools for the creation of customized expression maps independently. Plant biologists with less coding experience can often encounter challenges when attempting to explore ways to communicate their own spatial quantitative data. We present ggPlantmap an open-source R package designed to address this challenge by providing an easy and user-friendly method for the creation of ggplot representative maps from plant images. ggPlantmap is built in R, one of the most used languages in biology to empower plant scientists to create and customize eFP-like browsers tailored to their experimental data. Here, we provide an overview of the package and tutorials that are accessible even to users with minimal R programming experience. We hope that ggPlantmap can assist the plant science community, fostering innovation and improving our understanding of plant development and function. HighlightggPlantmap, a new addition to the plant data visualization toolbox, allows users to create graphical maps from plant images for the representation of spatial quantitative data in R.

plant biology↗