Ubiquitin (Ub) is an essential signal molecule regulating protein degradation, localization and other activities. Generally the C-terminus of the Ub molecule is covalently conjugated to lysine residues of protein substrates by the E1/E2/E3 reaction cascade, and the modification is reversed by the action of deubiquitinating enzymes (DUBs). PolyUb chains can be further assembled on the substrates by the linkage between lysine groups of the first Ub molecule and the C-terminus of the next. Our current proteomic analysis revealed that all seven lysine groups on the Ub molecule can be utilized for the formation of polyUb chains, including Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, and Lys63. We propose that the formation of functionally distinct polyUb chains is a regulatory step for ubiquitination and deubiquitination. To examine the function of these polyUb linkages, we will first develop a mass spectrometry technology for quantifying the abundance of all seven polyUb linkages, and then study the catalytic specificity between DUBs and polyUb chain topology. Moreover, we will focus on defining the function of Lys11 polyUb chains. Our studies will lead to the development of general proteomic tools for polyUb chain topology and better understanding of the diversity and function of polyUb chains.
