Proteins trafficking through the endoplasmic reticulum (ER) are topologically diverse. As such, multiple pathways collectively termed ER-associated degradation (ERAD) ensure that protein domains located in the lumen, membrane, and cytosol, are properly folded. The continuous nucleoplasm and cytosol also maintain a network of quality control mechanisms. These center on the Doa10, San1, and Ubr1 ubiquitin ligases. Unlike in the ER, the necessity for multiple pathways here is unclear. With all three factors localized in the nucleus, at least in part, how substrates are individually recognized is unknown. In this study, we show that the mode of biosynthesis can determine the system used for quality control. Targeting and integrating a misfolded protein to the ER membrane makes it an exclusive substrate of Doa10 whereas the soluble form of the same protein makes it a substrate of the San1/Ubr1 E3 system. (C) 2012 Elsevier Inc. All rights reserved.