Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution

By L. Holt, Brian B. Tuch, J. Villén, Alexander Johnson, Steven P. Gygi, D. Morgan. Science, 2009

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Cataloging Kinase Targets Protein phosphorylation is a central mechanism in the control of many biological processes (see the Perspective by Collins). It remains a challenge to determine the complete range of substrates and phosphorylation sites altered by a kinase like cyclin-dependent kinase 1 (Cdk1), which controls cell division in yeast. Holt et al. (p. 1682) engineered a strain of yeast to express a modified Cdk1 molecule that could be inhibited by a specific small-molecule inhibitor. The range of Cdk1-dependent phosphorylation was assessed by quantitative mass spectrometry, which revealed many previously uncharacterized substrates for Cdk1. In addition to phosphorylation on serine and threonine residues, which appears to be evolutionarily ancient, tyrosine phosphorylation occurs primarily in multicellular organisms. Tan et al. (p. 1686, published online 9 July) compared the overall presence of tyrosine residues in human proteins (which are frequently phosphorylated) and in yeast proteins (which are not). Loss of tyrosine residues has occurred during evolution, presumably to reduce adventitious tyrosine phosphorylation. The range of sites phosphorylated by a protein kinase in yeast provides clues to the evolution of such regulatory mechanisms. To explore the mechanisms and evolution of cell-cycle control, we analyzed the position and conservation of large numbers of phosphorylation sites for the cyclin-dependent kinase Cdk1 in the budding yeast Saccharomyces cerevisiae. We combined specific chemical inhibition of Cdk1 with quantitative mass spectrometry to identify the positions of 547 phosphorylation sites on 308 Cdk1 substrates in vivo. Comparisons of these substrates with orthologs throughout the ascomycete lineage revealed that the position of most phosphorylation sites is not conserved in evolution; instead, clusters of sites shift position in rapidly evolving disordered regions. We propose that the regulation of protein function by phosphorylation often depends on simple nonspecific mechanisms that disrupt or enhance protein-protein interactions. The gain or loss of phosphorylation sites in rapidly evolving regions could facilitate the evolution of kinase-signaling circuits.

Subfields: Cell Biology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/1640dd43e4bca4224599e7660cfa1ece4df876b1

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Citations in the corpus

Decoding signalling networks by mass spectrometry-based proteomics (2010, background): “As an alternative approach to gene deletion, many new substrates of yeast Cdk1 (also known as Cdc28), an essential cell cycle kinase, were revealed by phosphoproteomic analysis of a yeast strain expressing an analogue-sensitive mutant of Cdk1 (Ref”
Differential network biology (2012, background): “…levels or protein post-translational modiﬁcations under different conditions or species has provided unique insight into the regulation of the cell (Gygi et al , 1999; Ong et al , 2002; Aebersold and Mann, 2003; Linding et al , 2007; Beltrao et al , 2009; Holt et al , 2009; Tan et al , 2009).”
A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction (2011, background): “Inthisanalysis Inthisanalysis,wecandifferentiatebetweenfirst-orderandsecond-orderphosphorylationevents,supportingtheobservationthatsecond-site ( 32 , 33 ).”
Partial inhibition of Cdk1 in G2 phase overrides the SAC and decouples mitotic events (2014, background): “Removal of these phosphorylations by the phosphatase Cdc25C activates Cdk1/ cyclin B1, allowing it to phosphorylate over 300 target substrates, including those involved in chromosome condensation, nuclear envelope breakdown (NEVB), and cytoskeleton reorganization, all of which drives cells into mito”