The N-end Rule Pathway and Ubr1 enforce protein compartmentalization via N-terminally-encoded cellular location signals

The Arg/N-end rule pathway, a mechanism of protein degradation conserved from yeast to humans, is involved in cellular protein quality control, but its role has only been vaguely understood. Through systematic examination of single residue mutants of model misfolded substrates, and global analyses of yeast proteins, we discovered that Ubr1, an E3 ligase of the Arg/N-end rule, degrades organellar proteins that fail to reach their intended subcellular compartments. We determined that recognition by Ubr1 is dependent on location signals that are naturally embedded into the 2nd amino acid residue of the majority of proteins. The N-end rule pathway is thus likely to have been critical to the evolution of endosymbiotic relationships which paved the way for advanced eukaryotic cellular life. Significance Statement This work elucidates a novel role for the N-end Rule Pathway, a protein degradation pathway highly conserved from yeast to humans. We demonstrate that the N-end rule pathway enforces the cellular compartmentalization of ER and mitochondrial proteins by degrading them when they fail to successfully translocate into their intended destinations and thus become mislocalized to the cytosol. This mechanism prevents the accumulation of toxic foreign proteins within the cytosol. Recognition of the displaced proteins is dependent on cellular location signals programmed into the 2 nd residue of the target proteins, as well as the tendency for the proteins to misfold in a foreign environment. These findings have significant relevance to research on the mechanisms causing human diseases involving protein misfolding.