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Cell type identity determines transcriptomic immune responses in Arabidopsis thaliana roots

ABSTRACT: Root pathogens are a major thread in global crop production and protection strategies are required to sustainably enhance the efficiency of root immunity. Our understanding of root immunity is still limited in comparison to the knowledge gained for the regulation of immune response in leaves. In an effort to reveal the organisation of root immunity in roots, we undertook a cell type-specific transcriptome analysis to identify gene networks in epidermis, cortex and pericycle cells of Arabidopsis roots upon treatment with two immunity elicitors, bacterial microbe-associated molecular pattern flagellin and the endogenous damage-associated molecular pattern Pep1. Our analyses revealed that both elicitors induced cell type-specific immunity gene networks. Interestingly, both elicitors did not alter cell identity determining gene networks. Using sophisticated paired motif promoter analyses, we identified key transcription factor pairs involved in the regulation of cell type-specific immunity networks. In addition, our data show that cell identity networks are liaised with cell immunity networks to activate cell type-specific immune response according to the functional capabilities of each cell type.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE112960 | GEO | 2020/08/10

REPOSITORIES: GEO

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Project description:Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Five different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in all radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to -Fe media for 24 hours. Little is known about how developmental cues affect the way cells interpret their environment. Here we characterize the transcriptional response of different cell layers and developmental stages of the Arabidopsis root to high salinity and find that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell-layers, several of which correspond to observable physiological changes. We show that known stress pathways primarily control semi-ubiquitous responses and use mutants that disrupt epidermal patterning to reveal cell-layer specific and inter-cell-layer effects. By performing a similar analysis using iron-deprivation we identify common cell-type specific stress responses and environment-independent biological functions that define each cell type. Experiment Overall Design: To gain a genome-scale understanding of the role that developmental processes play in regulating stimulus response, we examined the effect of -Fe stress on gene expression along the radial axis of the root. Cell identity is the main variable that changes along the radial axis with the epidermis representing the outermost tissue layer and the stele representing the inner most layer. 5 different GFP reporter lines were used to isolate specific populations of cells from the Arabidopsis root using FACS sorting of protoplasted cells. GFP-reporter lines were exposed to iron deficient (-Fe) conditions (0.3mM Ferrozine in MS media containing no ferrous sulfate) for 24 hours before hand.

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Cell type identity determines transcriptomic immune responses in Arabidopsis thaliana roots

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