The vacuolar H ؉ -ATPase (V-ATPase) along with ion channels and transporters maintains vacuolar pH. V-ATPase ATP hydrolysis is coupled with proton transport and establishes an electrochemical gradient between the cytosol and vacuolar lumen for coupled transport of metabolites. Btn1p, the yeast homolog to human CLN3 that is defective in Batten disease, localizes to the vacuole. We previously reported that Btn1p is required for vacuolar pH maintenance and ATP-dependent vacuolar arginine transport. We report that extracellular pH alters both V-ATPase activity and proton transport into the vacuole of wild-type Saccharomyces cerevisiae. V-ATPase activity is modulated through the assembly and disassembly of the V 0 and V 1 V-ATPase subunits located in the vacuolar membrane and on the cytosolic side of the vacuolar membrane, respectively. V-ATPase assembly is increased in yeast cells grown in high extracellular pH. In addition, at elevated extracellular pH, S. cerevisiae lacking BTN1 (btn1-⌬), have decreased V-ATPase activity while proton transport into the vacuole remains similar to that for wild type. Thus, coupling of V-ATPase activity and proton transport in btn1-⌬ is altered. We show that down-regulation of V-ATPase activity compensates the vacuolar pH imbalance for btn1-⌬ at early growth phases. We therefore propose that Btn1p is required for tight regulation of vacuolar pH to maintain the vacuolar luminal content and optimal activity of this organelle and that disruption in Btn1p function leads to a modulation of V-ATPase activity to maintain cellular pH homeostasis and vacuolar luminal content.The neuronal ceroid-lipofuscinoses (NCLs) 2 are the most common group of progressive neurodegenerative diseases in children, with an incidence as high as 1 in 12,500 live births (1, 2). The NCL disorders are inherited in an autosomal recessive manner, with mutations in seven distinct genes resulting in pathologically similar disease with a different age of onset (3, 4). The NCLs are characterized by the accumulation of autofluorescent hydrophobic material in the lysosomes of neurons, and to lesser extent, other cell types (5, 6); however, the molecular basis behind this storage and the disease remains unknown. The juvenile form of NCL results from mutations in the CLN3 gene, which codes for a lysosomal transmembrane protein (7-9).We have previously reported that the Saccharomyces cerevisiae BTN1 gene product has high sequence similarity with the human CLN3 gene product. BTN1 encodes a non-essential protein that is 39% identical and 59% similar to human CLN3 (10). Studies have revealed that Btn1p is located in the vacuolar membrane (11, 12) and, although the primary function of this protein remains unclear, it has been implicated in several cellular pathways. Lack of BTN1 resulted in resistance to D-(Ϫ)-threo-2-amino-1-[p-nitrophenyl]-1,3-propanediol (ANP), and this phenotype is complemented by expression of human Cln3p, indicating that yeast Btn1p and human Cln3p likely have a conserved function (13). Resistance of btn1-⌬...