N-degron and C-degron pathways of protein degradation

Abstract

This perspective is partly review and partly proposal. N-degrons and C-degrons are degradation signals whose main determinants are, respectively, the N-terminal and C-terminal residues of cellular proteins. N-degrons and C-degrons include, to varying extents, adjoining sequence motifs, and also internal lysine residues that function as polyubiquitylation sites. Discovered in 1986, N-degrons were the first degradation signals in short-lived proteins. A particularly large set of C-degrons was discovered in 2018. We describe multifunctional proteolytic systems that target N-degrons and C-degrons. We also propose to denote these systems as "N-degron pathways" and "C-degron pathways." The former notation replaces the earlier name "N-end rule pathways." The term "N-end rule" was introduced 33 years ago, when only some N-terminal residues were thought to be destabilizing. However, studies over the last three decades have shown that all 20 amino acids of the genetic code can act, in cognate sequence contexts, as destabilizing N-terminal residues. Advantages of the proposed terms include their brevity and semantic uniformity for N-degrons and C-degrons. In addition to being topologically analogous, N-degrons and C-degrons are related functionally. A proteolytic cleavage of a subunit in a multisubunit complex can create, at the same time, an N-degron (in a C-terminal fragment) and a spatially adjacent C-degron (in an N-terminal fragment). Consequently, both fragments of a subunit can be selectively destroyed through attacks by the N-degron and C-degron pathways.

Keywords: N-end rule; degron; proteasome; proteolysis; ubiquitin.

Fig. 1.

N-degron pathways. Nt-residues are indicated by single-letter abbreviations. A yellow oval denotes the rest of a protein substrate. (A) Twenty amino acids of the genetic code are arranged to delineate specific N-degrons. Nt-Met is cited three times because it can be recognized by the Ac/N-degron pathway (as Nt-acetylated Ac-Met), by the Arg/N-degron pathway (as unacetylated Nt-Met), and by the fMet/N-degron pathway (as Nt-formylated fMet). Nt-Cys is cited twice, because it can be recognized by the Ac/N-degron pathway (as Nt-acetylated Cys) and by the Arg/N-degron pathway (as an oxidized, arginylatable Nt-Cys sulfinate or sulfonate, formed in multicellular eukaryotes but apparently not in unstressed S. cerevisiae). (B) The eukaryotic (S. cerevisiae) fMet/N-degron pathway (39); 10-fTHF, 10-formyltetrahydrofolate. (C) The bacterial (E. coli) fMet/N-degron pathway (38). (D) The bacterial (V. vulnificus) Leu/N-end rule pathway (51). (E) The eukaryotic (S. cerevisiae) Pro/N-degron pathway (–37). (F) The eukaryotic (S. cerevisiae) Ac/N-degron pathway (, –48). (G) The eukaryotic (S. cerevisiae) Arg/N-degron pathway (26, 31). Modified with permission from ref. .

Fig. 2.

Structural basis of N-degron recognition. The upper diagrams schematically depict the substrate-binding sites of different N-recognins, with corresponding space-filling images indicating electrostatic potential (red, negative; blue, positive) below the diagrams. (A) The substrate-binding site of the human Gid4 Pro/N-recognin (–37). (B) One of substrate-binding sites (the UBR box, which recognizes basic Nt-residues) of the S. cerevisiae Ubr1 Arg/N-recognin. (C) The substrate-binding site of the E. coli ClpS Leu/N-recognin, which recognizes bulky hydrophobic Nt-residues (30, 52, 53). Modified with permission from ref. .