The intercalated cells of the kidney collecting duct are specialized for physiologically regulated proton transport. In these cells, a vacuolar H+-ATPase is expressed at enormous levels in a polarized distribution on the plasma membrane, enabling it to serve in transepithelial H+ transport. In contrast, in most eukaryotic cells, vacuolar H+-ATPases reside principally in intracellular compartments to effect vacuolar acidification. To investigate the basis for the selective amplification of the proton pump in intercalated cells, we isolated and sequenced cDNA clones for two isoforms of the -56-kDa subunit of the H+-ATPase and examined their expression in various tissues. The predicted amino acid sequence of the isoforms was highly conserved in the internal region but diverged in the amino and carboxyl termini. mRNA hybridization to a cDNA probe for one isoform (the "kidney" isoformn) was detected only in kidney cortex and medulla, whereas mRNA hybridization to the other isoform of the -56-kDa subunit and to the H+-ATPase 31-kDa subunit was found in the kidney and other tissues. Immunocytochemistry of rat kidney with an antibody specific to the kidney isoform revealed intense staining only in the intercalated cells. Staining was absent from proximal tubule and thick ascending limb, where H+-ATPase was detected with a monoclonal antibody to the 31-kDa subunit of the H+-ATPase. This example ofspecific amplification ofan isoform of one subunit of the vacuolar H+-ATPase being limited to a specific cell type suggests that the selective expression of the kidney isoform of the -56-kDa subunit may confer the capacity for amplification and other specialized functions of the vacuolar H+-ATPase in the renal intercalated cell.Vacuolar H+-ATPases participate in a remarkably diverse variety of cellular functions. In the intracellular membrane compartments of eukaryotic cells, they acidify endosomes, lysosomes, and other components of the vacuolar system, serving in endocytosis and secretion (1). In cells specialized for H' transport, such as the renal intercalated cell (2, 3) and the osteoclast (4), vacuolar H+-ATPases reside in high densities in a polarized distribution on the plasma membrane, effecting transcellular proton transport. How the vacuolar class of H+-ATPases performs such diverse functions remains unknown. Accumulating evidence suggests that structural subsets of the vacuolar H+-ATPases exist that may have unique roles. In prior studies, we reported that a vacuolar H+-ATPase preparation isolated from bovine kidney microsomes could be resolved on an HPLC ion-exchange column as two peaks of activity that exhibited differences in the structure of their -56-kDa subunits on SDS/polyacrylamide gels (5). More recently, we found that H+-ATPase purified from different membrane compartments in the mammalian kidney varied in their structural and functional properties (6). Again, differences in the structure ofthe -56-kDa polypeptide subunit were noted. Work from several laboratories has subsequently revealed at least ...