Identification of CDK1 substrates in mitosis by quantitative phosphoproteomics

ABSTRACT: Cyclin-dependent kinase 1 (Cdk1) is an essential regulator of many mitotic processes including the reorganization of the cytoskeleton, chromosome segregation, and formation and separation of daughter cells. Deregulation of Cdk1 activity results in defects in these processes. Although the role of Cdk1 in mitosis is well established, only a limited number of Cdk1 substrates have been identified in mammalian cells. Thus to increase our understanding of Cdk1-dependent phosphorylation pathways in mitosis, we conducted a quantitative phosphoproteomics analysis in mitotic HeLa cells using two small molecule inhibitors of Cdk1, Flavopiridol and RO-3306. In these analyses we identified a total of 24,900 phosphopeptides on 4,274 proteins of which 1215 phosphopeptides on 551 proteins that were significantly reduced by 2.5-fold or more upon Cdk1 inhibitor addition. Comparison of phosphopeptide quantification upon either inhibitor treatment revealed a high degree of correlation (R2 value of 0.87) between the different inhibitor datasets. Motif enrichment analysis of significantly regulated phosphopeptides revealed enrichment of canonical Cdk1 kinase motifs. Interestingly, the majority of proteins identified in this analysis contained 2 or more Cdk1 inhibitor-sensitive phosphorylation sites, are highly connected with other candidate Cdk1 substrates as determined by protein-protein network analysis, are enriched at specific subcellular structures, or are part of protein complexes as identified by the CORUM database. Furthermore, candidate Cdk1 substrates were enriched in G2 and M phase-specific genes. Finally, we validated a subset of candidate Cdk1 substrates by in vitro kinase assays. Our findings provide a valuable resource for the cell signaling and mitosis research community and greatly increase our knowledge of Cdk1 substrates and Cdk1-dependent signaling pathways.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Arminja Kettenbach 

PROVIDER: MSV000079528 | MassIVE | Wed Feb 24 14:34:00 GMT 2016

SECONDARY ACCESSION(S): PXD003681

REPOSITORIES: MassIVE