In Vivo Analysis of ER-Associated Protein Degradation and Ubiquitination in Arabidopsis thaliana

The endoplasmic reticulum (ER) is the cellular site for the biosynthesis of proteins and lipids. The ER is highly dynamic, whose homeostasis is maintained by proper ER shaping, unfolded protein response (UPR), ER-associated degradation (ERAD), and selective autophagy of the ER (ER-phagy). In ERAD and ER-phagy, unfolded/misfolded proteins are degraded in the 26S proteasome and the vacuole, respectively. Both processes are vital for normal plant development and plant responses to environmental stresses. While it is known that ubiquitination of a protein initiates EARD, recent research indicated that ubiquitination of a protein also promotes the turnover of the protein through ER-phagy. In this chapter, we describe in detail two in vivo methods for investigating (1) the degradation efficiency and (2) ubiquitination level of an ER-associated protein in Arabidopsis thaliana.