In the current concept of phototransduction, the concentration of cGMP in retinal rod outer segments is controlled by the balance of two enzyme activities: cGMP phosphodiesterase (PDE) and guanylyl cyclase (GC). However, no protein directly mediates these two enzyme systems. Here we show that RGS9, which is suggested to control PDE activity through regulation of transducin GTPase activity (He, W., Cowan, C. W., and Wensel, T. G. (1998) Neuron 20, 95-102), directly interacts with GC. When proteins in the Triton X-100-insoluble fraction of bovine rod outer segments were isolated by two-dimensional gel electrophoresis and binding of GC to these proteins was examined using a GC-specific antibody, proteins (55 and 32 kDa) were found to interact with GC. However, the activity of GC bound to the 55-kDa protein was not detected. This observation was elucidated by the finding that the 55-kDa protein inhibited GC activity in a dose-dependent manner. Amino acid sequence showed that five peptides derived from the 55-kDa protein were identical to corresponding peptides of RGS9. Together with other biochemical characterization of the 55-kDa protein, these observations indicate that the 55-kDa protein is RGS9 and that RGS9 inhibits GC. RGS9 may serve as a mediator between the PDE and GC systems.In the prevailing model of phototransduction (1-3), illuminated rhodopsin stimulates GTP/GDP exchange on T ␣ , 1 which in turn activates PDE through release or dislocation of P ␥ from P ␣ by GTP/T ␣ . The resulting decrease of cytoplasmic [cGMP] leads to closure of cGMP-gated channels and hyperpolarization of photoreceptor plasma membranes. The closure of channels also blocks Ca 2ϩ influx, whereas Ca 2ϩ efflux by Na ϩ /Ca 2ϩ exchangers continues. The resulting decline in free [Ca 2ϩ ] activates GC. With inactivation of GTP/T ␣ -activated PDE by GTP hydrolysis on T ␣ and return of P ␥ to P ␣ , the GC activation serves to restore [cGMP] to the dark level. It has never been reported that any protein directly mediates between the PDE system and the GC system.Recent studies have shown that regulation of PDE for the restoration of [cGMP] to the dark level is really complicated. Kawamura and Murakami (4) have suggested a mechanism to regulate the lifetime of GTP/T ␣ -activated PDE. He et al. (5) have suggested that RGS9, a retina-specific member of RGS family, accelerates hydrolysis of GTP bound to T ␣ and that this acceleration may shorten the lifetime of GTP/T ␣ -activated PDE. Phosphorylation by cyclin-dependent protein kinase 5 of P ␥ complexed with GTP/T ␣ may also be involved in the regulation of lifetime of GTP/T ␣ -activated PDE.2 This phosphorylation could account for the turn-off of visual excitation without GTP hydrolysis that has been observed in vivo (6 -8). We have also suggested that PDE is involved to increase cytoplasmic [cGMP] to the dark level by release of cGMP from noncatalytic sites on P ␣ in amphibian photoreceptors (9).As we suggested in our initial study about GC (10), the regulatory mechanism of GC is also co...