Cilia serve as motile or sensory devices on most eukaryotic cells surface. Defects in either cilia biogenesis or cilia function contribute to a wide spectrum of human diseases, also termed ciliopathies. ADP-ribosylaton factor (ARF)-like (ARL) proteins belong to the Ras superfamily of small GTP-binding proteins involved in diverse cellular functions. Comparative genomics study and molecular analysis indicate that, of dozens Arf/Arl proteins, three ARLs, ARL-3, ARL-6, and ARL-13B, are conserved ciliary proteins over the course of evolution from nematode to human. Remarkably,
arl-13b and
arl-6 (also called BBS-3) are each identified as one of the causal genes for Joubert Syndrome and BBS syndrome, respectively; while the molecular mechanisms underlying the functions of ARLs in cilia as well as the disease pathogenesis remain elusive. Using C. elegans as a model, we demonstrated that ARL-13B, ARL-6, and ARL-3 all localize to cilia per se and play critical roles in regulating cilia biogenesis and/or cilia sensory function in C. elegans. ARL-13B localizes primarily to ciliary middle segment and this localization is dependent on its C-terminus. We found PKD-2 ciliary mislocalization and mating behavior defects in
arl-13b;
arl-3 double knockout worms are worse than those in single knockouts. However, various ultrastructural cilia defects observed in
arl-13b knockout worms can be partially rescued by
arl-3 deletion. In addition, a constitutively active ARL-3 protein exacerbates the ultrastructural cilia defects in
arl-13b animals. Taken together, our data suggest an intriguing working model that ARL-13B and ARL-3 act in concert in cilia sensory functions, but surprisingly, function antagonistically in cilia biogenesis process.