Abstract
<title>Abstract</title> <p> Cellular compartmentalization is crucial for organelles to fulfill their key functions. Among these organelles, cilia possess the inherent ability to restrict the entry of non-ciliary components through the ciliary gate. Mutations in genes encoding components of the ciliary gate result in various cilia-related diseases known as Ciliopathy, further emphasizing its significance. The ciliary cargo but not non-ciliary residents is loaded onto the intraflagellar transport (IFT) train at the base of the cilia, and IFT transports them through the ciliary gate for delivery to cilia. Yet, how non-ciliary residents are prevented from accumulating in cilia remains unclear. Here, we observe ciliary accumulation of non-ciliary proteins in BBSome-deficient mutants (Bardet-Biedl Syndrome), a phenotype reminiscent of ciliary gate-defective mutants such as <italic>mks-5</italic> and <italic>nphp-4</italic> . Time-lapse imaging shows that these non-ciliary proteins move bidirectionally along cilia at IFT velocities, and bimolecular fluorescence complementation (BiFC) reveals that the non-ciliary protein ELMD-1 associates with the IFT component IFT-43 in BBSome-deficient mutants, indicating that they are mis-loaded onto IFT trains. This misloading allows them to bypass the ciliary gate. Fluorescence recovery after photobleaching (FRAP) suggests the gate remains largely functional, supporting a two-step model of ciliary composition control: cargo selection/loading and ciliary gating. We propose that defects in cargo selection/loading (and potentially export) alter ciliary composition, allowing unintended protein entry. </p>