1
|
Gyenis L, Menyhart D, Cruise ES, Jurcic K, Roffey SE, Chai DB, Trifoi F, Fess SR, Desormeaux PJ, Núñez de Villavicencio Díaz T, Rabalski AJ, Zukowski SA, Turowec JP, Pittock P, Lajoie G, Litchfield DW. Chemical Genetic Validation of CSNK2 Substrates Using an Inhibitor-Resistant Mutant in Combination with Triple SILAC Quantitative Phosphoproteomics. Front Mol Biosci 2022; 9:909711. [PMID: 35755813 PMCID: PMC9225150 DOI: 10.3389/fmolb.2022.909711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
Casein Kinase 2 (CSNK2) is an extremely pleiotropic, ubiquitously expressed protein kinase involved in the regulation of numerous key biological processes. Mapping the CSNK2-dependent phosphoproteome is necessary for better characterization of its fundamental role in cellular signalling. While ATP-competitive inhibitors have enabled the identification of many putative kinase substrates, compounds targeting the highly conserved ATP-binding pocket often exhibit off-target effects limiting their utility for definitive kinase-substrate assignment. To overcome this limitation, we devised a strategy combining chemical genetics and quantitative phosphoproteomics to identify and validate CSNK2 substrates. We engineered U2OS cells expressing exogenous wild type CSNK2A1 (WT) or a triple mutant (TM, V66A/H160D/I174A) with substitutions at residues important for inhibitor binding. These cells were treated with CX-4945, a clinical-stage inhibitor of CSNK2, and analyzed using large-scale triple SILAC (Stable Isotope Labelling of Amino Acids in Cell Culture) quantitative phosphoproteomics. In contrast to wild-type CSNK2A1, CSNK2A1-TM retained activity in the presence of CX-4945 enabling identification and validation of several CSNK2 substrates on the basis of their increased phosphorylation in cells expressing CSNK2A1-TM. Based on high conservation within the kinase family, we expect that this strategy can be broadly adapted for identification of other kinase-substrate relationships.
Collapse
Affiliation(s)
- Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Daniel Menyhart
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Edward S Cruise
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Kristina Jurcic
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Scott E Roffey
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Darren B Chai
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Flaviu Trifoi
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Sam R Fess
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Paul J Desormeaux
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | | | - Adam J Rabalski
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Stephanie A Zukowski
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Jacob P Turowec
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Paula Pittock
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Gilles Lajoie
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - David W Litchfield
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| |
Collapse
|
2
|
Turowec JP, Zukowski SA, Knight JDR, Smalley DM, Graves LM, Johnson GL, Li SSC, Lajoie GA, Litchfield DW. An unbiased proteomic screen reveals caspase cleavage is positively and negatively regulated by substrate phosphorylation. Mol Cell Proteomics 2014; 13:1184-97. [PMID: 24556848 PMCID: PMC4014278 DOI: 10.1074/mcp.m113.037374] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Post-translational modifications of proteins regulate diverse cellular functions, with mounting evidence suggesting that hierarchical cross-talk between distinct modifications may fine-tune cellular responses. For example, in apoptosis, caspases promote cell death via cleavage of key structural and enzymatic proteins that in some instances is inhibited by phosphorylation near the scissile bond. In this study, we systematically investigated how protein phosphorylation affects susceptibility to caspase cleavage using an N-terminomic strategy, namely, a modified terminal amino isotopic labeling of substrates (TAILS) workflow, to identify proteins for which caspase-catalyzed cleavage is modulated by phosphatase treatment. We validated the effects of phosphorylation on three of the identified proteins and found that Yap1 and Golgin-160 exhibit decreased cleavage when phosphorylated, whereas cleavage of MST3 was promoted by phosphorylation. Furthermore, using synthetic peptides we systematically examined the influence of phosphoserine throughout the entirety of caspase-3, -7, and -8 recognition motifs and observed a general inhibitory effect of phosphorylation even at residues considered outside the classical consensus motif. Overall, our work demonstrates a role for phosphorylation in controlling caspase-mediated cleavage and shows that N-terminomic strategies can be tailored to study cross-talk between phosphorylation and proteolysis.
Collapse
Affiliation(s)
- Jacob P Turowec
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|