SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis

Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P₂ play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2–SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P₂, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2–SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.Polyphosphoinositides (PPIs) are a class of signaling membrane lipids, comprising the phosphorylated products of phosphatidylinositol (PtdIns). PPIs perform a dual function as scaffolding signals and precursors for other molecular messengers, which, together with their specific distribution at different intracellular membranes, makes PPIs important mediators of a wide variety of cellular processes, such as membrane trafficking and homeostasis, cytoskeleton organization, nuclear signaling, and stress responses (1–5). The metabolism of PPIs is regulated by specific kinases, phosphatases, and phospholipases to tightly control the concentration and intracellular localization of different lipid pools (2, 6, 7).In yeast, two phosphoinositide (PI) types, PtdIns3P and PtdIns(3,5)P₂, and their interconversion have been shown to play crucial roles in trafficking toward the vacuole, regulation of vacuolar pH, and vacuolar membrane fusion and fission (8–11). In yeast and mammals, production and degradation of PtdIns(3,5)P₂ involve the PtdIns3P 5-kinase Fab1p/PIKfyve and the antagonistic phosphatase factor-induced gene/suppressor of actin 3 (Fig4/Sac3), respectively (8, 12–14). Impairment of genes implicated in PtdIns(3,5)P₂ metabolism has deleterious consequences in yeast, plants, and mammals (8, 15–19), demonstrating an essential function of this minor phospholipid. Recent observations also hint at a role for PPIs in plant vacuoles (18–20), but the data are scarce and remain inconclusive.Advances in deciphering various cellular roles of PIs include insights into the phosphatases responsible for hydrolyzing PPIs. A group of phosphatases, designated suppressor of actin (SAC) domain phosphatases, has been identified in lower eukaryotes, mammals, and plants (21). Whereas yeast and humans have only five genes harboring the SAC domain, the genome of the model plant Arabidopsis thaliana contains nine genes, of which some have been functionally characterized and demonstrated to be involved in the regulation of stress responses (22–24), polarized root hair expansion (3), or cell wall formation (25).Here we show that the functionally uncharacterized group of Arabidopsis SAC2–SAC5 proteins that is orthologous to the yeast Fig4p is involved in PPI metabolism. SAC2–SAC5 localize along with PtdIns3P to the tonoplast and maintain the morphology of storage and lytic vacuoles. Our results demonstrate the crucial role of PPIs and SAC domain phosphatases in the function and morphology of vacuoles in plants.