The transcription factor NF-kappaB is activated in cellular stress responses. This requires rapid regulation of its function, which is accomplished, in part, by various modes of phosphorylation. Even though diverse DNA binding subunits of NF-kappaB proteins may transactivate from distinct recognition sequences, the differential regulation of transcription from the large number of NF-kappaB responsive sites in various gene promoters and enhancers has been incompletely understood. The cyclic GMP-dependent kinase (PKG) is an important mediator of signal transduction that may induce gene expression through cAMP response element binding protein (CREB) and through other, yet undefined, mechanisms. We have previously characterized a signal transduction pathway that leads to activation-induced cell death in T-lymphocytes and involves the activation of PKG. Here we demonstrate that the NF-kappaB proteins p65, p49 (also called p52), and p50 are specific substrates for this kinase. PKG dose-dependently increases the transactivating activity of p65 from the NF-kappaB consensus sequence. It also mediates dose-dependently an increase in transcriptional activity by p49 or p50 from a unique CCAAT/enhance binding protein (C/EBP)-associated NF-kappaB site, but not from the consensus site. Phosphorylation of p65, p50, or p49 does not alter their subcellular distribution. Because the release of cytosolic p65/p50 heterodimers into the nucleus is by itself insufficient to differentiate all the numerous NF-kappaB promoter sequences, phosphorylation of the DNA-binding subunits reveals a form of differential regulation of NF-kappaB activity and it implies a novel pathway for PKG-induced gene transcription. These observations may bear on mechanisms of programmed cell death in T-lymphocytes. They may also be relevant to ongoing efforts to induce cancer cell apoptosis through activation of PKG.