Backgrounds

Protein Metabolism: The Ubiquitin Proteasome System

The Ubiquitin System

1. Developing Methods to Decipher the Ubiquitin Code

Ubiquitylation is involved in numerous important cellular processes such as proteasomal degradation, DNA repair, protein sorting, and signal transduction. The ubiquitin function is relied on eight structurally distinct ubiquitin chains of different lengths, but our knowledge of the relationship between their topology and functional outcomes is still insufficient. To understand the ubiquitin code, it is essential to develop new methods for analyzing linkage types, chain lengths, and complexity of ubiquitylation.

We have developed a highly sensitive MS/MS-based quantification method for ubiquitin chains. The method allows us to analyze linkage-type selectivity of ubiquitin decoder proteins at endogenous experimental setting. We recently identified the main pathway targeting the K48-linked ubiquitylated substrates for proteasomal degradation (Fig. 3). We are further analyzing the decoder proteins throughout the ubiquitin-mediated pathways to reveal the ubiquitin network.

2. Roles of Novel Ubiquitin Codes

Using quantitative mass spectrometry, we recently identified multiple chemical modifications of ubiquitin itself. Acetylation of ubiquitin inhibits the elongation of particular ubiquitin chains, whereas phosphorylation of S65 ubiquitin stimulates ubiquitin chain synthesis for mitophagy. More recently, we identified more complexed ubiquitin chains branched at K48 and K63. The K48/K63 branched chains act as a unique coding signal that specifically affects recognition by downstream reader proteins to enhance NF- κB signaling. These novel ubiquitin codes greatly expand ubiquitin functions. We further explore additional roles and regulatory mechanisms of these novel ubiquitin codes.