Proteomic Identification of Common SCF Ubiquitin Ligase FBXO6-Interacting Glycoproteins in Three kinds of Cells

FBOX6 ubiquitin ligase complex is involved in the endoplasmic
reticulum-associated
degradation pathway by mediating the ubiquitination of glycoproteins.
FBXO6 interacts with the chitobiose in unfolded N-glycoprotein, pointing
glycoproteins toward E2 for ubiquitination. Although the glycoprotein-recognizing
mechanism of FBXO6 is well documented, its bona fide interacting glycoproteins are largely unknown. Here we utilized
a protein purification approach combined with LC–MS to systematically
identify the FBXO6-interacting glycoproteins. Following identification
of 39 proteins that specifically interact with FBXO6 in all three
different cell lines, 293T, HeLa and Jurkat cells, we compared the
protein complex organization between wild-type FBXO6 and its mutant,
which fails to recognize glycoproteins. Combining these databases,
29 highly confident glycoproteins that interact with FBXO6 in an N-glycan
dependent manner are identified. Our data provide valuable information
for the discovery of the interacting glycoproteins of FBXO6 and also
demonstrate the potential of these approaches as general platforms
for the global discovery of interacting glycoproteins of other FBAs
(F-box associated regions) containing F-box proteins.