Flagellar dynein activity is regulated by phosphorylation. One critical phosphoprotein substrate in Chlamydomonas is the 138-kDa intermediate chain (IC138) of the inner arm dyneins (Habermacher, G., and Sale, W. S. (1997) J. Cell Biol. 136, 167-176). In this study, several approaches were used to determine that casein kinase I (CKI) is physically anchored in the flagellar axoneme and regulates IC138 phosphorylation and dynein activity. First, using a videomicroscopic motility assay, selective CKI inhibitors rescued dynein-driven microtubule sliding in axonemes isolated from paralyzed flagellar mutants lacking radial spokes. Rescue of dynein activity failed in axonemes isolated from these mutant cells lacking IC138. Second, CKI was unequivocally identified in salt extracts from isolated axonemes, whereas casein kinase II was excluded from the flagellar compartment. Third, Western blots indicate that within flagella, CKI is anchored exclusively to the axoneme. Analysis of multiple Chlamydomonas motility mutants suggests that the axonemal CKI is located on the outer doublet microtubules. Finally, CKI inhibitors that rescued dynein activity blocked phosphorylation of IC138. We propose that CKI is anchored on the outer doublet microtubules in position to regulate flagellar dynein.The dynein ATPase is a family of molecular motors responsible for diverse cellular functions including retrograde microtubule-based transport of organelles, assembly and function of the Golgi and mitotic apparatus, and movement of cilia and flagella (1, 2). One of the primary questions is how dynein activity is regulated. The focus of this report is based on a series of studies revealing that the flagellar central pair apparatus and radial spokes play a primary role in regulation of flagellar dynein activity (3, 4). The regulatory mechanism involves a structural network of axonemal kinases and phosphatases that control phosphorylation of key subunits within the inner arm dyneins (5-8). In particular, phosphorylation of a dynein intermediate chain subunit, IC138, 1 correlates with inhibition of flagellar dynein activity (7). This network of enzymes along with the central pair apparatus, radial spokes, and the inner arm dyneins operates to control flagellar waveform (9 -17). These conclusions are based on genetic analysis and in vitro functional studies of flagella from Chlamydomonas reinhardtii. For example, mutations that disrupt either the central pair or the radial spokes result in flagellar paralysis (2,3,18). These paralyzed axonemes undergo dynein-driven microtubule sliding in vitro (19) but at greatly reduced rates of sliding when compared with wild-type axonemes (20). Reconstitution and functional assays demonstrate that the radial spokes are required for wild-type dynein activity, and the velocity of dyneindriven microtubule sliding is mediated by posttranslational modification of the inner dynein arms (20). These results are consistent with other evidence indicating that the central pair/ radial spoke apparatus along with the dynein...