The vacuolar proton-translocating ATPase is the principal energization mechanism that enables the yeast vacuole to perform most of its physiological functions. We have undertaken an examination of subunit-subunit interactions and assembly states of this enzyme. Yeast two-hybrid data indicate that Vma1p and Vma2p interact with each other and that Vma4p interacts with itself. Three-hybrid data indicate that the Vma4p self-interaction is stabilized by both Vma1p and Vma2p. Native gel electrophoresis reveals numerous partial complexes not previously described. In addition to a large stable cytoplasmic complex seen in wild-type, ⌬vma3 and ⌬vma5 strains, we see partial complexes in the ⌬vma4 and ⌬vma7 strains. All larger complexes are lost in the ⌬vma1, ⌬vma2, and ⌬vma8 strains. We designate the large complex seen in wild-type cells containing at least subunits Vma1p, Vma2p, Vma4p, Vma7p, and Vma8p as the definitive V 1 complex.The V-type proton-translocating ATPase is the cornerstone of the yeast vacuole. This multisubunit membrane-bound enzyme converts the energy of ATP into a proton electrochemical gradient that is essential for the majority of vacuolar functions, including ion homeostasis, accumulation of amino acids, and the correct targeting of vacuolar resident proteins (1-3). Enzymes of the V-ATPase class are found throughout the biological world serving many functions, oftentimes at different subcellular locations or with tissue-dependent activities (4).Many of the genes encoding ATPase subunits, as well as genes necessary for vacuolar acidification, have been identified (4, 5). Null mutations in the VMA (vacuolar membrane ATPase) genes result in a conditional phenotype characterized by several different traits. Growth of vma mutants is severely inhibited in media buffered to pH 7.0 or higher; best growth is obtained in media buffered to pH 5.5 (6). These mutants are sensitive to high concentrations of Ca 2ϩ (Ն50 mM) in the media (7). In vma strains that are also ade2, the reddish color caused by accumulation of fluorescent amino-imidazole ribotide conjugates in the vacuole is diminished, providing a convenient visual screen for ATPase mutants (8). Deacidification of the vacuolar lumen, which is normally maintained at pH 6 in wild-type cells, can be determined by direct fluorescent ratio measurements (9) and has been used as a screen for vacuolar ph mutants (5). Screens utilizing these characteristics have revealed the genes catalogued in Table I. Each of these genes is essential for vacuolar ATPase activity and most are required for proper assembly of the complete V-ATPase complex.Biochemical analyses have begun to elucidate the assembly and regulation of the enzyme (10, 11). The vacuolar ATPase is divided into two subcomplexes: a membrane-bound V 0 complex, which is responsible for the translocation of protons, and a peripheral membrane V 1 complex, which contains the ATPhydrolyzing subunits. In yeast, more extensive biochemical studies have lagged behind the more readily achieved genetic analyses. It has b...