Combining auxin-induced degradation and RNAi screening identifies novel genes involved in lipid bilayer stress sensing in Caenorhabditis elegans

Abstract

Alteration of the lipid composition of biological membranes interferes with their function and can cause tissue damage by triggering apoptosis. Upon lipid bilayer stress, the endoplasmic reticulum mounts a stress response that is similar to the unfolded protein response. However, only a few genes are known to regulate lipid bilayer stress. Here, we performed a suppressor screen that combined the auxin-inducible degradation (AID) system with conventional RNAi in C. elegans to identify members of the lipid bilayer stress response. AID-mediated knockdown of the mediator MDT-15, a protein required for the upregulation of fatty acid desaturases, caused activation of a lipid bilayer stress sensitive reporters. We screened through almost all C. elegans kinases and transcription factors using RNAi by feeding. We report the identification of 8 genes that have not been implicated previously with lipid bilayer stress before in C. elegans. These suppressor genes include skn-1/NRF1,2,3 and let-607/CREB3. Our candidate suppressor genes suggest a network of transcription factors and the integration of multiple tissues for a centralized lipotoxicity response in the intestine. Additionally, we propose and demonstrate the proof-of-concept for combining AID and RNAi as a new screening strategy.