S-Palmitoylation is the covalent attachment
of
C14:0–C22:0 fatty acids (mainly C16:0 palmitate) to cysteines
via thioester bonds. This lipid modification is highly abundant in
neurons, where it plays a role in neuronal development and is implicated
in neurodegenerative diseases, such as Alzheimer’s disease,
Parkinson’s disease, and Huntington’s disease. The knowledge
ofS-palmitoylation in neurodevelopment is limited
due to technological challenges in analyzing this highly hydrophobic
protein modification. Here, we used two orthogonal methods, acyl-biotin
exchange (ABE) and lipid metabolic labeling (LML), to identifyS-palmitoylated proteins and sites during retinoic acid-induced
neuronal differentiation of SH-SY5Y cells. We identified 2002 putativeS-palmitoylated proteins in total, of which 650 were found
with both methods. Significant changes in the abundance ofS-palmitoylated proteins were detected, in particular for
several processes and protein classes that are known to be important
for neuronal differentiation, which include proto-oncogene tyrosine-protein
kinase receptor (RET) signal transduction, SNARE protein-mediated
exocytosis, and neural cell adhesion molecules. Overall,S-palmitoylation profiling by employing ABE and LML in parallel during
RA-induced differentiation of SH-SY5Y cells revealed a subset of high
confidence bona fideS-palmitoylated proteins and
suggested an important role forS-palmitoylation
in neuronal differentiation.