We next examined the co-localization of AIPL1 and the EB SP600125 proteins in primary cilia in cell culture and in the structurally and functionally specialized cilia of photoreceptor cells of the human and mouse retina. Recent studies have revealed that the localization of EB1 to the base of primary cilia of cultured cells, as shown here, is necessary for microtubule minus-end anchoring at the centrosome or basal body and for effective vesicular trafficking to the cilia base, and is therefore required for the assembly of primary cilia. AIPL1 did not co-localize with primary cilia markers, suggesting that the interaction of AIPL1 and EB1 is also not related to the function of EB1 in primary cilia assembly, but must be a specific feature of photoreceptor cell biology. In accordance with this idea, AIPL1 and the EB proteins, EB1 and EB3, localized to the connecting cilia of retinal photoreceptors. Interestingly, EB1 localized to the base of the connecting cilium in the region of the basal body and to the proximal axoneme, whereas EB3 localization was restricted to the cilia-associated centrioles and basal bodies at the base of the connecting cilium. In comparison, EB1 and EB3 both localize to the base of non-motile primary cilia in cultured mammalian cells, and EB3 additionally localizes to the distal tip of some but not all motile cilia where it might promote persistent growth of microtubule axonemes. The distinct localization of the EB proteins in the photoreceptor connecting cilium might reflect a unique photoreceptor-specific function in microtubule minus-end anchoring and vesicular trafficking at the base of the cilium or in axonemal microtubule turnover. Like the EB proteins, AIPL1 co-localized with cilia markers in the photoreceptor connecting cilia. However, while AIPL1 was dispersed throughout the photoreceptor cells, the EB proteins were prominently expressed in the photoreceptor connecting cilia. Therefore, it is likely that only a small fraction of the total cellular pool of AIPL1 associates with the EB proteins at the photoreceptor connecting cilium. In addition to AIPL1 and the EB proteins, proteomic analysis of photoreceptor connecting cilia also detected Hsp90 and proteasome components. Therefore, we propose that the AIPL1-Hsp90 photoreceptor-specific heterocomplex may indeed interact dynamically or transiently with EB proteins at the connecting cilium, and thereby have an EB-targeted role in the connecting cilium. However, whether this association occurs via direct or indirect interaction with the EB proteins has yet to be shown. In conclusion, an interaction between AIPL1 and the EB proteins has been shown by yeast twohybrid analysis and co-immunoprecipitation. AIPL1 did not co-localize with the EB proteins or the microtubule network in cultured cells, suggesting that AIPL1 is not involved in EB-mediated microtubule dynamics or ciliogenesis. However, AIPL1 is not normally expressed in these cells as it is photoreceptor-specific. Our data also show the co-localization of the EB proteins and AIPL1 at the photoreceptor connecting cilium. This suggests an indirect or direct association of AIPL1 and the EB proteins is photoreceptor-specific, with the function of this association yet to be resolved. Besides association with the A and B subunits, the C subunit also forms a complex with other proteins, such as a4, which appears to be the mammalian homologue of the yeast Tap42 protein. The target of rapamycin Bortezomib kinase regulates Tap42 binding with the yeast protein phosphatase catalytic subunits Pph21/22 and SIT4, which are the yeast homologues of mammalian PP2A and PP6, respectively. In mammalian cells, a4 associates with the C subunit in the absence of the A and B subunits, and participates in a wide array of cellular activities such as apoptosis, DNA damage response, and cell migration.