Joubert syndrome (JS) and JS-related disorders (JSRD) are clinically heterogeneous, characterised by cerebellar malformation and hypervariable phenotypes such as cystic kidneys, retinitis pigmentosa and polydactyly. Emerging evidence indicate that JS/JSRD are caused by defects in primary cilia, which serve diverse sensory and signaling roles during chemo/mechano-sensation, phototransduction, and development. Although multiple JS/JSRD proteins are known, the molecular bases of their functions remain poorly understood. Here, we investigate the molecular functions of C. elegans ARL-13, a homologue of the small Ras G-protein Arl13b, which causes classical JS and is required for vertebrate cilium formation and sonic hedgehog signaling. First, we find that ARL-13 is mostly restricted to proximal (middle) segments of ciliary axonemes, does not undergo intraflagellar transport (IFT), and requires N-terminal palmitoylation lipid modification for its ciliary targeting/retention. Loss of ARL-13 function disrupts cilium chemosensory function, morphology, and ultrastructure, with defects including truncated axonemes, microtubule misplacement/malformation, enlarged middle segments and ciliary accumulation of matrix/membranous material. Consistent with these phenotypes,
arl-13mutants are defective in localisation and/or translocation of ciliary proteins, with ciliary transmembrane proteins partially mislocalised and IFT proteins exhibiting anterograde IFT motility defects, indicative of kinesin2 motor uncoupling, differential separation of IFT complex A/B components, and reduced OSM-3 translocation rates. Finally,
arl-13 interacts synthetically with
bbs-8,
dyf-5 and
nph-4, with double mutants exhibiting enhanced cilia integrity and IFT defects. Taken together, we propose that ARL-13 associates with the ciliary membrane where it maintains cilium structure/function and the localisation and motilities of ciliary transmembrane and IFT proteins, perhaps by regulating aspects of ciliary membrane biogenesis and/or turnover. We also suggest that defects in this function underlie the molecular basis of Arl13b-associated Joubert syndrome.