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Summary Flooding represents a major threat to global agricultural productivity and food security, but plants are capable of deploying a suite of adaptive responses that can lead to short‐ or longer‐term survival to this stress. One cellular pathway thought to help coordinate these responses is via flooding‐triggered Ca²⁺signaling.We have mined publicly available transcriptomic data from Arabidopsis subjected to flooding or low oxygen stress to identify rapidly upregulated, Ca²⁺‐related transcripts. We then focused on transporters likely to modulate Ca²⁺signals. Candidates emerging from this analysis includedAUTOINHIBITED Ca²⁺ATPASE 1andCATION EXCHANGER 2. We therefore assayed mutants in these genes for flooding sensitivity at levels from growth to patterns of gene expression and the kinetics of flooding‐related Ca²⁺changes.Knockout mutants inCAX2especially showed enhanced survival to soil waterlogging coupled with suppressed induction of many marker genes for hypoxic response and constitutive activation of others.CAX2mutants also generated larger and more sustained Ca²⁺signals in response to both flooding and hypoxic challenges.CAX2 is a Ca²⁺transporter located on the tonoplast, and so these results are consistent with an important role for vacuolar Ca²⁺transport in the signaling systems that trigger flooding response. 

Abstract The phytohormone ethylene controls plant growth and stress responses. Ethylene-exposed dark-grown Arabidopsis seedlings exhibit dramatic growth reduction, yet the seedlings rapidly return to the basal growth rate when ethylene gas is removed. However, the underlying mechanism governing this acclimation of dark-grown seedlings to ethylene remains enigmatic. Here, we report that ethylene triggers the translocation of the Raf-like protein kinase CONSTITUTIVE TRIPLE RESPONSE1 (CTR1), a negative regulator of ethylene signaling, from the endoplasmic reticulum to the nucleus. Nuclear-localized CTR1 stabilizes the ETHYLENE-INSENSITIVE3 (EIN3) transcription factor by interacting with and inhibiting EIN3-BINDING F-box (EBF) proteins, thus enhancing the ethylene response and delaying growth recovery. Furthermore, Arabidopsis plants with enhanced nuclear-localized CTR1 exhibited improved tolerance to drought and salinity stress. These findings uncover a mechanism of the ethylene signaling pathway that links the spatiotemporal dynamics of cellular signaling components to physiological responses.