Targeted proteomic study of the cyclin-Cdk module

Mol Cell. 2004 Jun 18;14(6):699-711. doi: 10.1016/j.molcel.2004.05.025.


The cell division cycle of the yeast S. cerevisiae is driven by one Cdk (cyclin-dependent kinase), which becomes active when bound to one of nine cyclin subunits. Elucidation of Cdk substrates and other Cdk-associated proteins is essential for a full understanding of the cell cycle. Here, we report the results of a targeted proteomics study using affinity purification coupled to mass spectrometry. Our study identified numerous proteins in association with particular cyclin-Cdk complexes. These included phosphorylation substrates, ubiquitination-degradation proteins, adaptors, and inhibitors. Some associations were previously known, and for others, we confirmed their specificity and biological relevance. Using a hypothesis-driven mass spectrometric approach, we also mapped in vivo phosphorylation at Cdk consensus motif-containing peptides within several cyclin-associated candidate Cdk substrates. Our results demonstrate that this approach can be used to detect a host of transient and dynamic protein associations within a biological module.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenosine Triphosphatases
  • Amino Acid Sequence
  • Cell Cycle Proteins / analysis*
  • Cell Cycle Proteins / metabolism
  • Cyclin B
  • Cyclin-Dependent Kinases / antagonists & inhibitors
  • Cyclin-Dependent Kinases / genetics
  • Cyclin-Dependent Kinases / metabolism*
  • Cyclins / analysis
  • Cyclins / metabolism*
  • DNA-Binding Proteins / analysis
  • Mass Spectrometry
  • Molecular Sequence Data
  • Phosphorylation
  • Proteomics*
  • Saccharomyces cerevisiae Proteins / analysis*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Transcription Factors / analysis
  • Ubiquitins / analysis
  • Valosin Containing Protein


  • ACE2 protein, S cerevisiae
  • CLB3 protein, S cerevisiae
  • CLN2 protein, S cerevisiae
  • Cell Cycle Proteins
  • Cyclin B
  • Cyclins
  • DNA-Binding Proteins
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • Ubiquitins
  • Cyclin-Dependent Kinases
  • Adenosine Triphosphatases
  • CDC48 protein, S cerevisiae
  • Valosin Containing Protein