Post-translational modifications are known to be widely involved in the regulation of various biological processes, through the extensive diversification of each
protein function at the cellular network level. In order to unveil the system-wide function of the
protein lysine modification in
cancer cell signaling, we performed global acetylation and ubiquitination
proteome analyses of human
cancer cells, based on high-resolution nanoflow liquid chromatography-tandem mass spectrometry, in combination with the efficient biochemical enrichment of target modified
peptides. Our large-scale proteomic analysis enabled us to identify more than 5000 kinds of ubiquitinated sites and 1600 kinds of acetylated sites, from representative human
cancer cell lines, leading to the identification of approximately 900 novel
lysine modification sites in total. Very interestingly, 236
lysine residues derived from 141
proteins were found to be modified with both ubiquitination and acetylation. As a consequence of the subsequent motif extraction analyses,
glutamic acid (E) was found to be highly enriched at the position (-1) for the
lysine acetylation sites, whereas the same
amino acid was relatively dispersed along the neighboring residues of the
lysine ubiquitination sites. Our pathway analysis also indicated that the
protein translational control pathways, such as the
eukaryotic initiation factor 2 (
EIF2) and the
ubiquitin signaling pathways, were highly enriched in both of the acetylation and ubiquitination
proteome data at the network level. This report provides the first integrative description of the
protein acetylation and ubiquitination-oriented systematic regulation in human
cancer cells.