The ciliary membrane‐associated proteome reveals actin‐binding proteins as key components of cilia

Primary cilia are sensory, antennae‐like organelles present on the surface of many cell types. They have been involved in a variety of diseases collectively termed ciliopathies. As cilia are essential regulators of cell signaling, the composition of the ciliary membrane needs to be strictly regulated. To understand regulatory processes at the ciliary membrane, we report the targeting of a genetically engineered enzyme specifically to the ciliary membrane to allow biotinylation and identification of the membrane‐associated proteome. Bioinformatic analysis of the comprehensive dataset reveals high‐stoichiometric presence of actin‐binding proteins inside the cilium. Immunofluorescence stainings and complementary interaction proteomic analyses confirm these findings. Depolymerization of branched F‐actin causes further enrichment of the actin‐binding and actin‐related proteins in cilia, including Myosin 5a (Myo5a). Interestingly, Myo5a knockout decreases ciliation while enhanced levels of Myo5a are observed in cilia upon induction of ciliary disassembly. In summary, we present a novel approach to investigate dynamics of the ciliary membrane proteome in mammalian cells and identify actin‐binding proteins as mechanosensitive components of cilia that might have important functions in cilia membrane dynamics. Synopsis Primary cilia are important mediators of human disease and cell signaling. A local proximity labeling strategy to identify the ciliary membrane‐associated proteome (cmAPEX) reveals the close association of actin binding proteins (ABPs) with the ciliary membrane. cmAPEX and complementary affinity purification analyses identified association of actin‐binding proteins (ABPs) with cilia. cmAPEX resolves dynamic relocalization of ciliary proteins including ABPs upon inhibition of actin polymerization. Myo5a is a novel and essential ciliary protein that relocates into the cilium upon induction of ciliary disassembly. Graphical Abstract Primary cilia are important mediators of human disease and cell signaling. A local proximity labeling strategy to identify the ciliary membrane‐associated proteome (cmAPEX) reveals the close association of actin binding proteins with the ciliary membrane.