Illouz-Eliaz Lab

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 investigate how plants recover from drought, we examine a fine-scale time series of RNA sequencing starting 15 min 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 Arabidopsis thaliana (A. thaliana) leaf cell types, we perform a single-nucleus transcriptome analysis at the onset of drought recovery, identifying a cell type-specific transcriptional state developing independently across cell types. To further validate the cell-type specific transcriptional changes observed during drought recovery, we employ spatial transcriptomics using multiplexed error-robust fluorescence in situ hybridization (MERFISH), revealing anatomical localization of recovery-induced gene expression programs across Arabidopsis leaf tissues. Furthermore, we reveal a recovery-induced activation of the immune system that occurs autonomously, and 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 infection, the activation of 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.

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.Competing Interest StatementJ.R.E. serves on the scientific advisory board of Zymo Research, Inc. and Cibus, Inc. The other authors declare that they have no competing interests.Howard Hughes Medical Institute, https://ror.org/006w34k90

Leaf development is dynamic, enabling plants to modulate their growth in response to environmental cues. Under drought conditions, for instance, the model plant Arabidopsis thaliana restricts leaf growth to conserve water, a strategy that enhances water-use efficiency. While this stress avoidance response is well described physiologically, the underlying transcriptional changes that drive such developmental plasticity remain poorly understood. We investigated the transcriptional basis of how drought stress reshapes Arabidopsis leaf development. We profiled 1,226 leaves at various developmental stages and levels of drought stress, and generated a single-nucleus transcriptome atlas comprising ~1 million individual nuclei. We found that drought stress advances transcriptional programmes associated with leaf ageing in a dose-dependent manner, particularly within the mesophyll. These transcriptional shifts scale with stress intensity and correlate with reduced shoot growth, indicating that mesophyll-specific transcriptional changes underlie drought-induced restriction in leaf growth. Overexpression of FERRIC REDUCTION OXIDASE 6 (FRO6) in the mesophyll was sufficient to partially restore leaf growth under drought conditions. Our findings demonstrate how gene expression is reshaped by environmental cues to ensure that shoot architecture is adaptive to stress severity.