Deciphering the CK2-dependent phosphoproteome and its integration with regulatory PTM networks
Abstract
Protein functions are regulated by the post-translational addition of covalent modifications on certain amino acids. Depending on their distance within the 3-dimensional structure, addition/removal of individual post translational modifications (PTMs) can be impacted by others. This PTM interplay constitutes an essential regulatory mechanism that interconnects the molecular networks in the cell. Protein CK2, a clinically relevant acidophilic Ser/Thr kinase, may be responsible for 10-20% of the human phosphoproteome. Such estimates agree with the number of known substrates, which continues to expand. Furthermore, the demonstration that CK2 participates in hierarchical phosphorylation and has similar sequence determinants to caspases suggest extensive PTM interplay in CK2-dependent signaling.
In this thesis, we explore the role of lysine acetylation in the vicinity of the phosphorylatable residue(s) as a modulator of phosphorylation by CK2. To explore this association a biochemistry approach was followed to decipher the impact of lysine acetylation in CK2 specificity and a proteomics approach was employed for profiling the affected sites in cells. In solution peptides conforming to the CK2 consensus containing lysine or acetyllysine at positions +1, +2, or +3 downstream the phosphorylatable site, were found only to be phosphorylated by CK2 when either determinant was present at position +2. Linear patterns were generated to reflect this specificity and the PTM databases and the human proteome were searched for substrate hits. The boundaries and cellular conditions of the hits were assessed including conservation, mutations, regulatory role, and enzyme-substrate relationships. Several hits matching the patterns were observed in the cells to be both acetylated and phosphorylated. Since chromatin organization proteins were hits the regulatory role of CK2 in this process was summarized. The data processing and analysis steps followed were incorporated in a data-driven R Shiny web application visualRepo.
Collectively, our work shows how CK2-dependent phosphorylation and lysine acetylation network integration could contribute to the complexity of cellular processes. It also provides a computational and analytical framework for further studies exploring the PTM interplay occurring at a kinase consensus sequence. Finally, given the druggability of CK2, our results offer new molecular insights for exploring the combination of CK2 and lysine deacetylase inhibitors.