Membrane and soluble substrates of the Doa10 ubiquitin ligase are degraded by distinct pathways

The yeast Doa10 ubiquitin (Ub) ligase resides in the endoplasmic reticulum (ER)/nuclear envelope (NE), where it functions in ER-associated degradation (ERAD). Doa10 substrates include non-ER proteins such as the transcription factor Matα2. Here, we expand the range of Doa10 substrates to include a defective kinetochore component, a mutant NE membrane protein, and a substrate-regulated human ER enzyme. For all these substrates, Doa10 requires two Ub-conjugating enzymes, Ubc6 and Ubc7, as well as the Ubc7 cofactor Cuel. Based on a novel genomic screen of a comprehensive gene deletion library and other data, these four proteins appear to be the only nonessential and nonredundant factors generally required for Doa10-mediated ubiquitination. Notably, the Cdc48 ATPase facilitates degradation of membrane-embedded Doa10 substrates, but is not required for any tested soluble Doa10 substrates. This distinction is maintained even when comparing membrane and soluble proteins bearing the same degradation signal. Thus, while Doa10 ubiquitinates both membrane and soluble proteins, the mechanisms of subsequent proteasome targeting differ.