A rare PRIMER cell state in plant immunity

Tatsuya Nobori, Alexander Monell, Travis A. Lee, Yuka Sakata, Shoma Shirahama, Jingtian Zhou, Joseph R. Nery, Akira Mine and Joseph R. Ecker ()
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Tatsuya Nobori: The Salk Institute for Biological Studies
Alexander Monell: The Salk Institute for Biological Studies
Travis A. Lee: The Salk Institute for Biological Studies
Yuka Sakata: Kyoto University
Shoma Shirahama: Kyoto University
Jingtian Zhou: The Salk Institute for Biological Studies
Joseph R. Nery: The Salk Institute for Biological Studies
Akira Mine: Kyoto University
Joseph R. Ecker: The Salk Institute for Biological Studies

Nature, 2025, vol. 638, issue 8049, 197-205

Abstract: Abstract Plants lack specialized and mobile immune cells. Consequently, any cell type that encounters pathogens must mount immune responses and communicate with surrounding cells for successful defence. However, the diversity, spatial organization and function of cellular immune states in pathogen-infected plants are poorly understood1. Here we infect Arabidopsis thaliana leaves with bacterial pathogens that trigger or supress immune responses and integrate time-resolved single-cell transcriptomic, epigenomic and spatial transcriptomic data to identify cell states. We describe cell-state-specific gene-regulatory logic that involves transcription factors, putative cis-regulatory elements and target genes associated with disease and immunity. We show that a rare cell population emerges at the nexus of immune-active hotspots, which we designate as primary immune responder (PRIMER) cells. PRIMER cells have non-canonical immune signatures, exemplified by the expression and genome accessibility of a previously uncharacterized transcription factor, GT-3A, which contributes to plant immunity against bacterial pathogens. PRIMER cells are surrounded by another cell state (bystander) that activates genes for long-distance cell-to-cell immune signalling. Together, our findings suggest that interactions between these cell states propagate immune responses across the leaf. Our molecularly defined single-cell spatiotemporal atlas provides functional and regulatory insights into immune cell states in plants.

Date: 2025
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DOI: 10.1038/s41586-024-08383-z

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