Misfolded or orphaned ER membrane proteins are selectively targeted for degradation through a thermodynamically-driven partitioning mechanism in which hydrophilic residues within transmembrane segments partition into the locally thinned, aqueous cavity adjacent to the ubiquitin ligase Hrd1, with single-pass proteins requiring both Hrd1 and Der1 while multi-pass proteins depend on Hrd1 alone. The propensity for degradation correlates directly with the energetic cost of amino acid insertion into the lipid bilayer, providing a general quality control mechanism that distinguishes properly folded membrane proteins from those exposing energetically unfavorable hydrophilic residues to the phospholipid environment.

Misfolded or unassembled membrane proteins in the endoplasmic reticulum (ER) are polyubiquitinated, translocated into the cytosol, and degraded by the proteasome, a poorly understood process that is conserved in all eukaryotes. Here, we use S. cerevisiae to elucidate how ER membrane proteins are selected for degradation. We show that hydrophilic residues in a trans-membrane (TM) segment cause the TM to partition into a thinned membrane region next to the ubiquitin ligase Hrd1, which then leads to substrate polyubiquitination and degradation. In the case of single-pass membrane proteins, the Hrd1-associated Der1 protein contributes to partitioning and degradation. In contrast, multi-pass proteins require Hrd1 to function on its own. Our results provide a general mechanism by which ER membrane proteins are targeted for degradation.