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Phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2) is a low-abundance signaling lipid associated with endo-lysosomal and vacuolar membranes in eukaryotic cells. Recent studies on Arabidopsis indicated a critical role of PI(3,5)P2in vacuolar acidification and morphology during ABA-induced stomatal closure, but the molecular targets in plant cells remained unknown. By using patch-clamp recordings on Arabidopsis vacuoles, we show here that PI(3,5)P2does not affect the activity of vacuolar H+-pyrophosphatase or vacuolar H+-ATPase. Instead, PI(3,5)P2at low nanomolar concentrations inhibited an inwardly rectifying conductance, which appeared upon vacuolar acidification elicited by prolonged H+pumping activity. We provide evidence that this novel conductance is mediated by chloride channel a (CLC-a), a member of the anion/H+exchanger family formerly implicated in stomatal movements in Arabidopsis. H+-dependent currents were absent in clc-a knock-out vacuoles, and canonical CLC-a-dependent nitrate/H+antiport was inhibited by low concentrations of PI(3,5)P2. Finally, using the pH indicator probe BCECF, we show that CLC-a inhibition contributes to vacuolar acidification. These data provide a mechanistic explanation for the essential role of PI(3,5)P2and advance our knowledge about the regulation of vacuolar ion transport
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