Vma9p (subunit e) is an integral membrane Vo subunit of the yeast V-ATPase

The Saccharomyces cerevisiae vacuolar proton-translocating ATPase (V-ATPase) is composed of 14 subunits distributed between a peripheral V-1 subcomplex and an integral membrane V-0 subcomplex. Genome-wide screens have led to the identification of the newest yeast V-ATPase subunit, Vma9p. Vma9p ( subunit e) is a small hydrophobic protein that is conserved from fungi to animals. We demonstrate that disruption of yeast VMA9 results in the failure of V-1 and V-0 V-ATPase subunits to assemble onto the vacuole and in decreased levels of the subunit a isoforms Vph1p and Stv1p. We also show that Vma9p is an integral membrane protein, synthesized and inserted into the endoplasmic reticulum ( ER), which then localizes to the limiting membrane of the vacuole. All V-0 subunits and V-ATPase assembly factors are required for Vma9p to efficiently exit the ER. In the ER, Vma9p and the V-0 subunits interact with the V-ATPase assembly factor Vma21p. Interestingly, the association of Vma9p with the V-0-Vma21p assembly complex is disrupted with the loss of any single V-0 subunit. Similarly, Vma9p is required for V-0 subunits Vph1p and Vma6p to associate with the V-0-Vma21p complex. In contrast, the proteolipids associate with Vma21p even in the absence of Vma9p. These results demonstrate that Vma9p is an integral membrane subunit of the yeast V-ATPase V-0 subcomplex and suggest a model for the arrangement of polypeptides within the V-0 subcomplex.