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Published October 26, 2021 | Published + Supplemental Material
Journal Article Open

Aminopeptidases trim Xaa-Pro proteins, initiating their degradation by 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.

Additional Information

© 2021 National Academy of Sciences. Published under the PNAS license. Contributed by Alexander Varshavsky, September 8, 2021 (sent for review August 21, 2021; reviewed by Ulrich Hartl and William P. Tansey). We thank members of the laboratories of H.K.S. and A.V., particularly Jin Seok Shin for initial preparation and analysis of Pck1, and also Chang-Seok Lee and Cheol-Sang Hwang (Postech, Pohang, Korea) for some of yeast strains used in this study. This work was supported by National Research Foundation of Korea Grants NRF-2020R1A2C3008285 (to H.K.S.) and NRF-2020R1A5A1019023 (to H.K.S.) and by NIH Grants DK039520 (to A.V.) and GM031530 (to A.V.). Data Availability: All relevant data in the paper are entirely available through both text and figures in the manuscript and SI Appendix. Author contributions: S.-J.C., L.K., H.K.S., and A.V. designed research; S.-J.C. and L.K. performed research; S.-J.C., L.K., H.K.S., and A.V. analyzed data; and S.-J.C., L.K., H.K.S., and A.V. wrote the paper. Reviewers: U.H., Max Planck Institute of Biochemistry; and W.P.T., Vanderbilt University. The authors declare no competing interest. This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2115430118/-/DCSupplemental.

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Published - e2115430118.full.pdf

Supplemental Material - pnas.2115430118.sapp.pdf


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