Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes

  1. Michael Snyder1,2,4,12
  1. 1Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;
  2. 2Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA;
  3. 3Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA;
  4. 4Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA;
  5. 5Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S3E1, Canada;
  6. 6Department of Computer Science, University of Toronto, Toronto, Ontario M5S3E1, Canada;
  7. 7Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA;
  8. 8Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA;
  9. 9Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S3E1, Canada;
  10. 10Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S3E1, Canada;
  11. 11Department of Computer Science, Yale University, New Haven, Connecticut 06520

    Abstract

    Protein kinases are key regulators of cellular processes. In spite of considerable effort, a full understanding of the pathways they participate in remains elusive. We globally investigated the proteins that interact with the majority of yeast protein kinases using protein microarrays. Eighty-five kinases were purified and used to probe yeast proteome microarrays. One-thousand-twenty-three interactions were identified, and the vast majority were novel. Coimmunoprecipitation experiments indicate that many of these interactions occurred in vivo. Many novel links of kinases to previously distinct cellular pathways were discovered. For example, the well-studied Kss1 filamentous pathway was found to bind components of diverse cellular pathways, such as those of the stress response pathway and the Ccr4–Not transcriptional/translational regulatory complex; genetic tests revealed that these different components operate in the filamentation pathway in vivo. Overall, our results indicate that kinases operate in a highly interconnected network that coordinates many activities of the proteome. Our results further demonstrate that protein microarrays uncover a diverse set of interactions not observed previously.

    Keywords

    Footnotes

    • Received October 3, 2010.
    • Accepted February 14, 2011.

    Freely available online through the Genes & Development Open Access option.

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