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Longitudinal zone- and cell-type-specific immune responses sustain Arabidopsis roots against pathogen infections

ABSTRACT: The immunity is dynamically regulated to balance growth and defense. Roots consisting of diverse cell types across longitudinal developmental zones are vital for plant survival amidst most microbial challenges. Leveraging single-cell transcriptomics and imaging of Arabidopsis roots, here, we reveal that in contrast to microbe-associated molecular patterns (MAMPs), plant-derived phytocytokines elicit robust, coordinated immune responses across various root cell types and zones, ensuring the continuity of growth-defense trade-offs at the organismal level. The intensity of immune responses in different root zones tightly correlates with invasion sites of fungal and bacterial pathogens. Differential expression of receptors and key signaling modules in distinct cell types and zones dictates the response intensity to specific elicitors. Furthermore, motif-informed network inference identifies key transcriptional regulators targeting each root cell type, driving cell identity-based transcriptomic immune responses. Our findings reveal that distinct phytocytokines trigger potent and coordinated cell type- and stage-dependent transcriptional reprogramming. The contrasting availability of convergent signaling components and transcription regulators orchestrate cell-identity immune responses at the organ level.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE289716 | GEO | 2026/02/15

REPOSITORIES: GEO

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Project description:The organs of multicellular species are comprised of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change but little is known about how responses are tailored to specific cell types or coordinated among them on a global level. Here we use cellular profiling of five Arabidopsis root cell types in response to a limiting resource, nitrogen, to uncover a vast and predominantly cell-specific response that was largely undetectable using traditional methods. These methods reveal a new class of cell-specific nitrogen responses. As a proof-of-principle, we dissected one cell-specific response circuit that mediates nitrogen-induced changes in root branching from pericycle cells. Thus, cellular response profiling links gene modules to discrete functions in specific cell types. Experiment Overall Design: The whole experiment was carried out in triplicate with 84 chips in total (28 experiments). The nitrogen response in 5 FACS-sorted root cell types (LRC, lateral root cap; EpiC, epidermis and cortex; EndoP, endodermis and pericycle; Peri, pericycle; Stele, stele), protoplasts and Col-0 whole roots was assayed using microarrays. 5mM KNO3 was used as a nitrogen treatment for 2 hours. 5mM KCl was used as a control treatment for the same length of time. 1mM MSX in combination with 5mM KNO3 (or with 5mM KCl as a control) was used to block the assimilation of KNO3, and 5mM Gln added to restore it in order to separate KNO3 effects from assimilated-nitrogen effects. 5mM KNO3 was either maintained in the protoplast-generating solution (continuous treat) or not (transitory treat) to test how to best preserve the cellular nitrogen-response during the 1 hr protoplast generating procedure. As controls we used protoplasts, whole roots frozen directly after the 2hr treatment or 3.5hr treatment, or whole roots incubated in protoplast-generating solution (minus enzymes; transitory or continuous treated) and then frozen. After FACS-sorting or mock FACS-sorting cells were frozen.

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Longitudinal zone- and cell-type-specific immune responses sustain Arabidopsis roots against pathogen infections

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