Chemoproteomic Profiling of Isoprenoid Pyrophosphate Interacting Proteins with Photoaffinity Probes

Isoprenoid pyrophosphates are key
intermediates in the biosynthesis
of many biologically important molecules and in the prenylation of
proteins involved in various biological processes. Except for these
well-studied functions, new roles of isoprenoid pyrophosphates have
been reported continuously. To study their functions on the proteome
scale, we developed a series of isoprenoid pyrophosphate photoaffinity
probes for the covalent labeling of their interacting proteins. Through
“click” reaction with the alkyne handle on the probes,
fluorophores could be attached to the labeled proteins for the gel-based
fluorescence analysis or cell imaging. A biotin moiety could be used
instead to enrich labeled protein. Combining with SILAC-based quantitative
proteomic analysis, several known and putative interacting proteins
for farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate
(GGPP) were identified, including many nucleocytoplasmic transport
proteins. We have validated the interaction between transportin-1
with FPP and GGPP in vitro, suggesting potential
new function of FPP and GGPP in protein transportation. This probe-labeling
method could be further applied for evaluating other isoprenoid interacting
proteins and exploring their cellular functions and localization,
which will greatly facilitate biochemical research of isoprenoids.