Figure 1.

The classical N-end rule pathway in various eukaryotes and prokaryotes. (a) The N-end rule pathway in mammals, flies, and plants. In mammals and other multicellular eukaryotes, the tertiary destabilizing residues Asn and Gln are, respectively, deamidated into the secondary destabilizing residues Asp and Glu by NTAN1 Nt^N-amidase and NTAQ1 Nt^Q-amidase, which in turn are arginylated by ATE1-encoded arginyl (R)-transferase isoforms generating the degron Arg. In mammals, N-terminal Cys is converted to a substrate of arginylation through its oxidation into CysO₂(H) or CysO₃(H) prior to arginylation. N-terminal Arg, together with other type 1 and type 2 residues, are recognized and bound by the N-recognin family members, which mediate ubiquitylation and proteasomal degradation, characterized by the UBR box in mammals. Although the components of the plant Arabidopsis and fly Drosophila N-end rule pathways are not fully characterized, their hierarchical structures appear to be more similar to the mammalian pathway compared to the yeast pathway. In contrast to mammals, the plant Arabidopsis genome expresses two distinct R-transferases, AtATE1 and AtATE2, from separate genes. To date, two plant N-recognins, PRT1 and PRT6, have been identified. (b) The S. cerevisiae N-end rule pathway. A single N-terminal amidohydrolase, Nta1 (Nt^N,Q-amidase), mediates deamidation of N-terminal Asn and Gln into Asp and Glu, which in turn are arginylated by a single Ate1 R-transferase, generating the degron Arg. N-terminal Arg and other primary degrons are recognized by a single N-recognin Ubr1. (c) The bacterial N-end rule pathway. The secondary destabilizing residues Arg, Lys, and Met are conjugated with Leu or Phe by the Aat leucyl/pheylalanyl-tRNA-protein (L/F)-transferase, generating the degrons Leu and Phe. The secondary destabilizing residues Asp and Glu can also be conjugated with Leu by Bpt leucyl-tRNA-protein (L)-transferase, generating the degron Leu. The primary destabilizing residues (Leu, Phe, Trp, and Tyr) are recognized and bound by the N-recognin ClpS, which delivers substrates to the ClpAP protease complex without involving Ub or Ub-like molecules. Abbreviations: Aat, aminoacyl transferase; Bpt, bacterial protein transferase; C*, oxidized Cys; E1, Ub activating enzyme; E2, Ub conjugating enzyme; E3, Ub protein ligase; E4, Ub conjugation factor; L/F-ylation, leucylation/phenylalanylation; N, asparagine; Q, glutamine; Uba1 and Uba6, Ub activating enzymes 1 and 6; Ubc4, Ub conjugating enzyme 4; Ube2A/B, Ub conjugating enzyme E2 A/B; UBR box, Ub ligase N-recognin box; Ubr1, -2, -4, -5, Ub ligase N-recognin1, -2, -4, -5; Ufd4, Ub fusion degradation 4; Use1, Uba6-specific E2 1.