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Aminopeptidases trim Xaa-Pro proteins, initiating their degradation by the Pro/N-degron pathway

Significance The Gid4 protein of the yeast proline (Pro)/N-degron pathway targets proteins for degradation by recognizing their N-terminal (Nt) Pro residue. This proteolytic pathway can also target proteins that bear Nt-Pro at position 2 instead of position 1. In the present study, we used genetic and biochemical approaches to discover that Fra1 and Icp55 are specific aminopeptidases that trim the Nt-Ala (A) and Nt-Ser (S) residues from AP-Aro10 and SP-Pck1 proteins, respectively, thereby yielding Nt-Pro and initiating degradation of these proteins by the Pro/N-degron pathway. In addition to discovering the mechanism of targeting of XP proteins, these insights have also expanded the diversity of substrates of the Pro/N-degron pathway. N-degron pathways are proteolytic systems that recognize proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Our previous work identified Gid4 as a recognition component (N-recognin) of the Saccharomyces cerevisiae proteolytic system termed the proline (Pro)/N-degron pathway. Gid4 is a subunit of the oligomeric glucose-induced degradation (GID) ubiquitin ligase. Gid4 targets proteins through the binding to their Nt-Pro residue. Gid4 is also required for degradation of Nt-Xaa-Pro (Xaa is any amino acid residue) proteins such as Nt-[Ala-Pro]-Aro10 and Nt-[Ser-Pro]-Pck1, with Pro at position 2. Here, we show that specific aminopeptidases function as components of the Pro/N-degron pathway by removing Nt-Ala or Nt-Ser and yielding Nt-Pro, which can be recognized by Gid4-GID. Nt-Ala is removed by the previously uncharacterized aminopeptidase Fra1. The enzymatic activity of Fra1 is shown to be essential for the GID-dependent degradation of Nt-[Ala-Pro]-Aro10. Fra1 can also trim Nt-[Ala-Pro-Pro-Pro] (stopping immediately before the last Pro) and thereby can target for degradation a protein bearing this Nt sequence. Nt-Ser is removed largely by the mitochondrial/cytosolic/nuclear aminopeptidase Icp55. These advances are relevant to eukaryotes from fungi to animals and plants, as Fra1, Icp55, and the GID ubiquitin ligase are conserved in evolution. In addition to discovering the mechanism of targeting of Xaa-Pro proteins, these insights have also expanded the diversity of substrates of the Pro/N-degron pathway.