Saline-alkali soil is a major environmental constraint impairing plant growth and crop productivity. In this study, we identified a Ca²⁺ sensor/kinase/plasma membrane (PM) H⁺-ATPase module as a central component conferring alkali tolerance in Arabidopsis (Arabidopsis thaliana). We report that the SCaBP3 (SOS3-LIKE CALCIUM BINDING PROTEIN3)/CBL7 (CALCINEURIN B-LIKE7) loss-of-function plants exhibit enhanced stress tolerance associated with increased PM H⁺-ATPase activity and provide fundamental mechanistic insights into the regulation of PM H⁺-ATPase activity. Consistent with the genetic evidence, interaction analyses, in vivo reconstitution experiments, and determination of H⁺-ATPase activity indicate that interaction of the Ca²⁺ sensor SCaBP3 with the C-terminal Region I domain of the PM H⁺-ATPase AHA2 (Arabidopsis thaliana PLASMA MEMBRANE PROTON ATPASE2) facilitates the intramolecular interaction of the AHA2 C terminus with the Central loop region of the PM H⁺-ATPase to promote autoinhibition of H⁺-ATPase activity. Concurrently, direct interaction of SCaPB3 with the kinase PKS5 (PROTEIN KINASE SOS2-LIKE5) stabilizes the kinase-ATPase interaction and thereby fosters the inhibitory phosphorylation of AHA2 by PKS5. Consistently, yeast reconstitution experiments and genetic analysis indicate that SCaBP3 provides a bifurcated pathway for coordinating intramolecular and intermolecular inhibition of PM H⁺-ATPase. We propose that alkaline stress-triggered Ca²⁺ signals induce SCaBP3 dissociation from AHA2 to enhance PM H⁺-ATPase activity. This work illustrates a versatile signaling module that enables the stress-responsive adjustment of plasma membrane proton fluxes.

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