Chemical Proteomic Profiling of the Interacting Proteins of Isoprenoid Pyrophosphates

Isoprenoid pyrophosphates
are involved in protein prenylation and assume regulatory roles in
cells; however, little is known about the cellular proteins that can
interact with isoprenoid pyrophosphates. Here, we devised a chemical
proteomic strategy, capitalizing on the use of a desthiobiotin–geranyl
pyrophosphate (GPP) acyl phosphate probe for the enrichment and subsequent
identification of GPP-binding proteins using liquid chromatography-tandem
mass spectrometry (LC-MS/MS). By combining stable isotope labeling
by amino acids in cell culture (SILAC) and competitive labeling with
low vs high concentrations of GPP probe, with ATP vs GPP acyl phosphate
probes, or with the GPP probe in the presence of different concentrations
of free GPP, we uncovered a number of candidate GPP-binding proteins.
We also discovered, for the first time, histone deacetylase 1 (HDAC1)
as a GPP-binding protein. Furthermore, we found that the enzymatic
activity of HDAC1 could be modulated by isoprenoid pyrophosphates.
Together, we developed a novel chemical proteomic method for the proteome-wide
discovery of GPP-binding proteins, which sets the stage for a better
understanding about the biological functions of isoprenoids.