A high-throughput assay for phosphoprotein-specific phosphatase activity in cellular extracts

Mol Cell Proteomics. 2013 Mar;12(3):797-806. doi: 10.1074/mcp.O112.024059. Epub 2012 Dec 11.

Abstract

Protein phosphatases undo the post-translational modifications of kinase-signaling networks, but phosphatase activation in cells is difficult to measure and interpret. Here, we report the design of a quantitative and high-throughput assay platform for monitoring cellular phosphatase activity toward specific phosphoprotein targets. Protein substrates of interest are purified recombinantly, phosphorylated in vitro using the upstream kinase, and adsorbed to 96-well plates. Total phosphatase extracts from cells are then added to trigger a solid-phase dephosphorylation reaction. After stopping the reaction, phosphoprotein levels are quantified by ELISA with a phospho-specific antibody, and the loss of phospho-specific immunoreactivity is used as the readout of phosphatase activity. We illustrate the generality of the method by developing specific phosphatase-activity assays for the three canonical mitogen-activated protein phospho-kinases: ERK, JNK, and p38. The assays capture changes in activity with a dynamic range of 25-100-fold and are sensitive to a limit of detection below 25,000 cells. When applied to cytokine-induced signaling, the assays revealed complex and dynamic regulation of phosphatases suggesting cross-communication and a means for cellular memory. Our assay platform should be beneficial for phosphoproteomic surveys and computational-systems models of signaling, where phosphatases are known to be important but their activities are rarely measured.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Blotting, Western
  • Cell Extracts*
  • Dual-Specificity Phosphatases / genetics
  • Dual-Specificity Phosphatases / metabolism
  • Enzyme Activation / drug effects
  • Enzyme Assays / instrumentation
  • Enzyme Assays / methods*
  • Enzyme-Linked Immunosorbent Assay
  • Epidermal Growth Factor / pharmacology
  • HT29 Cells
  • Humans
  • Interferon-gamma / pharmacology
  • Mice
  • Mitogen-Activated Protein Kinase Phosphatases / genetics
  • Mitogen-Activated Protein Kinase Phosphatases / metabolism
  • Mitogen-Activated Protein Kinases / metabolism*
  • Phosphoprotein Phosphatases / genetics
  • Phosphoprotein Phosphatases / metabolism*
  • Phosphoproteins / metabolism*
  • Phosphorylation / drug effects
  • Proteomics / methods
  • RNA Interference
  • Rats
  • Reproducibility of Results
  • Tumor Necrosis Factor-alpha / pharmacology

Substances

  • Cell Extracts
  • Phosphoproteins
  • Tumor Necrosis Factor-alpha
  • Epidermal Growth Factor
  • Interferon-gamma
  • Mitogen-Activated Protein Kinases
  • DUSP10 protein, human
  • Mitogen-Activated Protein Kinase Phosphatases
  • Phosphoprotein Phosphatases
  • DUSP16 protein, human
  • Dual-Specificity Phosphatases