Two clones from a A phage collection containing yeast genes regulated by inorganic phosphate were shown by lowstringency hybridization to select three mRNAs that direct the in vitro synthesis of repressible acid phosphatase (EC 3.1.3.2) polypeptides p60, p58, and p56. By higher stringency hybridization one yeast fragment [8 kilobases (kb)] selects p60 mRNA and the other (5 kb) selects p56 mRNA. These EcoRI digestion fragments were subcloned in yeast transformation vectors and hybridization selection assignments were confirmed by measuring enzyme and mRNA levels in transformants. Enzyme and mRNA levels in (8-kb) high copy number transformants grown in high inorganic phosphate medium revealed a hitherto undetected acid phosphatase protein, P57, which is believed to correspond to the constitutive enzyme encoded by PHO3. The identity of the 8-kb fragment purported to contain the PHO5/PH03 genes was confirmed by genetic mapping of an integrated copy of this fragment. The site of integration of the 5-kb fragment was demonstrated to be unlinked to the PHO5/PH03 genes.In Saccharomyces cerevisiae a complex genetic system controls the expression of a number of phosphohydrolases in response to cellular levels of inorganic phosphate (P) (1)(2)(3)(4). Included in these enzymes is a cytoplasmic repressible alkaline phosphatase (EC 3.1.3.1), a repressible acid phosphatase [APase; orthophosphoric-monoester phosphohydrolase (acid optimum), EC 3.1.3.2], and an acid phosphatase synthesized during high-Pi growth. Structural genes for these enzymes are PHO8, PHO5, and PHO3, respectively (2, 5, 6). The repressible acid phosphatase is an exocellular, multimeric glycoprotein with an average mass of 490 kilodaltons (7,8), consisting of several sequence-related polypeptides. These variant polypeptides, probably forming different isoenzymes in a heterologous quaternary structure, are encoded by three distinct mRNAs (9), distinguishable by their antigenic products in cell-free translation (p60, p58, and p56). We previously established that expression of these mRNAs is regulated by Pi and that repressible APase is synthesized de novo upon derepression (9), consistent with a transcriptional regulation model proposed by Oshima and colleagues (10). According to their genetic model, PH05 and PH08 are transcriptionally regulated by a coordinate mechanism involving the products of numerous regulatory genes that interact at the posttranslational level. PH03 expression is mediated by two genes independent of this mechanism.Recently, several yeast genes under Pi control were isolated by Kramer and Andersen (11). Two of these genes, defined by EcoRI restriction endonuclease fragments of 8 and 5 kilobases (kb), are regulated in a fashion characteristic of phosphatase structural genes. We have established the identity and chromosome location of these transcriptionally regulated genes, using yeast transformation and hybridization selection. We demonstrate here that the 8-kb EcoRI fragment contains two phosphatase structural genes, one encoding ...