Yeast fatty acid synthase consists of two independent polypeptide strains, alpha and beta. The functional multienzyme complex, composed of six alpha- and six beta-subunits, is rather stable against proteolysis in vivo. Mutations in one of the subunits or deletion of one subunit lead to degradation of the nonmutated remaining fatty acid synthase protein. We show that the unassembled alpha-subunit of this enzyme is short-lived, and degradation depends on the presence of active cytoplasmic proteinase yscE, the yeast proteasome. The unassembled beta-subunit is degraded by a nonvacuolar proteolytic system under vegetative growth conditions. However, starvation of a vacuolar proteinase mutant strain, which lacks the alpha-subunit of fatty acid synthase, leads to appearance of the unassembled beta-subunit is isolated vacuoles. This indicates that the major vacuolar peptidases proteinase yscA and yscB are at least partly involved in degradation of the beta-subunit of fatty acid synthase. In a proteinase yscA and yscB double mutant strain wild type for fatty acid synthase both subunits of fatty acid synthase, alpha and beta, are detectable in vacuoles. In addition, under the same starvation conditions other cytoplasmic proteins are found in the vacuole of a proteinase yscA and yscB double mutant strain. The experiments in conjunction with the previous finding of the appearance of vesicles in vacuoles of starved cells (Simeon, A., van der Klei, I.J., Veenhuis, M., and Wolf, D. H. (1992) FEBS Lett. 301, 231-235) indicate that transport of these tested cytoplasmic proteins into the vacuole is an unselective bulk process induced by nutritional stress.