Auxin-mediated Protein Degradation in Caenorhabditis elegans

The auxin-inducible degron (AID) technology was recently adapted for use in the nematode Caenorhabditis elegans. Rapid degradation of C. elegans proteins tagged with an AID is mediated by a plant-specific F-box protein, transport inhibitor response 1 (TIR1), and occurs only in the presence of the phytohormone auxin. The first iteration of this technology elicited protein degradation in C. elegans through a naturally occurring form of auxin, indole-3-acetic acid (IAA). Here, we present a protocol that uses 1-naphthaleneacetic acid, potassium salt (K-NAA), an indole-free synthetic auxin analog. At equal concentration, K-NAA is as effective as IAA in standard nematode growth media (NGM). K-NAA is also effective in physiological buffer (M9), allowing for high-throughput experimentation. The main advantages of K-NAA are twofold: first, its photostability prevents light-induced compound degradation during storage and the production of toxic indole-derivatives during fluorescence microscopy of live cells; and second, its water solubility eliminates the need of using ethanol to dissolve the auxin compound, a solvent that may confound C. elegans lifespan and behavioral assays. In this protocol, we describe our method of degrading C. elegans proteins using K-NAA on solid and in liquid media, as well as our method of analyzing protein degradation.