Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate and has many biological functions in prokaryotic and eukaryotic organisms. To investigate polyP localization, we developed a novel technique using the affinity of the recombinant polyphosphate binding domain (PPBD) of Escherichia coli exopolyphosphatase to polyP. An epitope-tagged PPBD was expressed and purified from E. coli. Equilibrium binding assay of PPBD revealed its high affinity for long-chain polyP and its weak affinity for short-chain polyP and nucleic acids. To directly demonstrate polyP localization in Saccharomyces cerevisiae on resin sections prepared by rapid freezing and freeze-substitution, specimens were labeled with PPBD containing an epitope tag and then the epitope tag was detected by an indirect immunocytochemical method. A goat anti-mouse immunoglobulin G antibody conjugated with Alexa 488 for laser confocal microscopy or with colloidal gold for transmission electron microscopy was used. When the S. cerevisiae was cultured in yeast extract-peptone-dextrose medium (10 mM phosphate) for 10 h, polyP was distributed in a dispersed fashion in vacuoles in successfully cryofixed cells. A few polyP signals of the labeling were sometimes observed in cytosol around vacuoles with electron microscopy. Under our experimental conditions, polyP granules were not observed. Therefore, it remains unclear whether the method can detect the granule form. The method directly demonstrated the localization of polyP at the electron microscopic level for the first time and enabled the visualization of polyP localization with much higher specificity and resolution than with other conventional methods.Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate (P i ) connected by high-energy bonds. PolyP occurs in a wide range of organisms, including prokaryotes and eukaryotes. PolyP has various biological functions; for example, it acts as a P i reservoir, as an alternative source of highenergy bonds, and as a buffer against alkaline conditions and metals (25). Furthermore, polyP also has regulatory functions such as competence for transformation (18), motility (36, 37), gene expression under stressed conditions (24,35,46), and protein degradation in amino acid starvation (28, 29) in prokaryotic organisms. The regulatory functions of polyP in eukaryotes are less clear, but some important facts are known. Recently, involvement of polyP in apoptosis (43) and enhancement of the mitogenic activities of acidic and basic fibroblast growth factors by polyP (45) have been suggested to occur in mammalian cells.The presence of polyP in cells can be visualized by staining with toluidine blue O (TBO) or 4Ј,6-diamidino-2-phenylindole (DAPI). DAPI is usually used for DNA detection, because blue fluorescence is apparent when the stained tissues are viewed under UV light. However, DAPI-polyP fluoresces yellow at high concentrations when viewed under UV (48). These staining methods have often been used for detecting polyPaccumulating bacteria in activated...