Protein degradation is essential to regulate levels of proteins according to cellular needs and to protect cells from misfolded, aggregated or other abnormal proteins. Degradation of short-lived proteins is mediated by the ubiquitin-proteasome system (UPS) and by autophagy-endosome-lysosome pathways. In the UPS, the key players are E3 ligases, which recognize exposed sequence motifs, known as degrons, in target proteins and attach ubiquitin (Ub; an 8kDa protein) to nearby lysine residues. Ubiquitinated proteins are then degraded by the multi-subunit protease, the 26S proteasome. While degrons can be located anywhere within a protein, the first ones discovered, in 1986, were located at the N-terminus of proteins - these are referred to as N-degrons. E3 ligases that recognize N-degrons are called N-recognins.
Recent studies, including ours, suggest that there are many more E3 ligases involved in N-degron pathways than previously identified and that there is an extensive interplay between Nt-modifying enzymes and N-recognins. To identify and characterize new N-degron pathways, we are employing peptide pull-downs combined with quantitative mass spectrometry (MS).