The H(+)-pyrophosphatase (V-PPase) of plant vacuolar membranes catalyzes the electrogenic translocation of H+ from the cytosol to vacuole lumen and, in parallel with the vacuolar H(+)-ATPase located in the same membrane, establishes the inside-acid, inside-positive H(+)-electrochemical potential difference responsible for energizing the H(+)-coupled transport of solutes into the vacuole. The results of previous investigations suggest that the gene encoding the substrate-binding subunit of the V-PPase is present in a single copy in the genome of Arabidopsis thaliana (V. Sarafian, Y. Kim, R.J. Poole, P.A. Rea [1992] Proc Natl Acad Sci USA 89: 1775-1779), but it is not known whether the situation in Arabidopsis is typical of most vascular plants. With the objective of assessing the general applicability of this finding and acquiring sequence data for structure-function analyses of the enzyme from Beta vulgaris, we have sought to isolate cDNAs encoding the V-PPase from this organism by screening a Beta cDNA library constructed in lambda ZAP with the Arabidopsis cDNA insert (AVP) encoding the V-PPase. The results of these investigations demonstrate that at least two genes encode the V-PPase in Beta. Restriction and sequence analyses of the cDNAs from Beta reveal two classes, designated BVP1 and BVP2. BVP1 and BVP2 encode closely related but distinct polypeptides with computed masses of 80,550 and 80,000 D, respectively, exhibiting 88% identity with each other and 89% identity with the corresponding polypeptide from Arabidopsis. The nucleotide sequences of BVP1 and BVP2, on the other hand, are 70% identical within their coding regions but less than 28 and 53% identical within their respective 5' and 3' noncoding regions. Southern analyses of Beta genomic DNA confirm that two genes encode the V-PPase, and northern analyses of polyadenylated RNA isolated from a range of tissue types and probed with RNAs transcribed from the 3' noncoding sequences of BVP1 or BVP2 indicate that both genes are expressed in the intact plant. On the basis of these findings and the recent demonstration of then sufficiency of the substrate-binding polypeptide, alone, for all of the known catalytic functions of the V-PPase (E.J. Kim, R.-G. Zhen, P.A. Rea [1994] Proc Natl Acad Sci USA [91:6128-6132]), the two cDNA species isolated from Beta are concluded to encode variant, possibly isoforms, of the enzyme.