Protein acetylation reportedly acts
as a key regulator of autophagy.
However, up to now, the relationship between acetylome and autophagy
has remained unclear. Here stable isotope labeling of amino acids
in cell culture and high-throughput quantitative mass spectrometry
were used to perform an acetylome analysis of rapamycin-induced autophagy
in vitro. Our data revealed that 2135 sites were quantified on 1081
proteins. During autophagy, 421 sites were significantly regulated
on 296 proteins, with 80.8% of sites downregulated and 19.2% upregulated.
Motif enrichment analysis revealed five main motifs. Most of the downregulated
sites conformed to the classical functional motif of p300/CBP [G-AcK].
Furthermore, acetylation targeted proteins involved mainly in ribosomes,
spliceosomes, and AcCoA-related metabolic process. In-depth analysis
indicated that most of the acetylation sites were in the critical
domain, were functional sites, or could change their enzymatic activity
by acetylation, highlighting the importance of site-specific acetylation
patterns. Subsequently, we demonstrated that K1549 of p300 was also
a functional site that could regulate the autophagic process in vitro.
In conclusion, our data reveal a deacetylation-preponderant profile
with autophagy. The specificity of the related motifs and the identification
of site-specific acetylation patterns will assist searches for potential
targets or subsequent mechanism-focused studies to elucidate site-specific
protein networks in autophagy.