Comprehensive Analysis of Lysine Acetylome Reveals a Site-Specific Pattern in Rapamycin-Induced Autophagy
journal contributionposted on 2018-12-28, 00:00 authored by Zhuo Zhou, Yu Chen, Mengqi Jin, Jianqin He, Ayiding Guli, Chunlan Yan, Shiping Ding
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.
site-specific acetylation patternsautophagic processmechanism-focused studies1081 proteins2135 sitesacetylome analysiselucidate site-specific protein networksmass spectrometry421 sitesMotif enrichment analysisLysine Acetylomecell culturesites downregulatedComprehensive Analysisacetylation sites296 proteinsdeacetylation-preponderant profileK 1549motifRapamycin-Induced Autophagy Protein acetylationrapamycin-induced autophagySite-Specific PatternIn-depth analysisdownregulated sitesp 300