Bovine photoreceptor (rod outer segment) proteins were selectively degraded by an ATP- and ubiquitin-dependent mechanism in rabbit reticulocyte lysate and human retinal pigment epithelial cell supernatant. Proteolysis of 37, 40, 58, 68 and approximately 100 kDa proteins was accompanied by the formation of high mass (> 150 kDa) species (putative ubiquitin-protein conjugates. To identity degraded substrates, the photoreceptor GTP-binding protein, transducin (Gt alpha beta gamma), was purified by GTP elution. Degradation of transducin (> or = 50% loss of each subunit) by retinal pigment epithelial cell supernatant was ubiquitin-dependent (EC50 = 1.2 microM). Formation of high mass transducin species was coincident with degradation. These data identify a selective proteolytic mechanism that may regulate the photoreceptor GTP-binding protein.