Comprehensive Analysis of Lysine Acetylome Reveals a Site-Specific Pattern in Rapamycin-Induced Autophagy

• Published in: Journal of proteome research Vol. 18; no. 3; pp. 865 - 877
• Main Authors: Zhou, Zhuo, Chen, Yu, Jin, Mengqi, He, Jianqin, Guli, Ayiding, Yan, Chunlan, Ding, Shiping
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 01.03.2019
• Subjects: Acetylation; Autophagy - drug effects; Binding Sites; Humans; Isotope Labeling - methods; Lysine - metabolism; Protein Processing, Post-Translational; Proteomics - methods; Sirolimus - pharmacology; Tandem Mass Spectrometry - methods; acetylation; autophagy; acetylome; acetyltransferase; rapamycin
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/acs.jproteome.8b00533

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.