Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in Saccharomyces cerevisiae

Abstract

Post-translational modification of proteins by lysine acetylation plays important regulatory roles in living cells. The budding yeast Saccharomyces cerevisiae is a widely used unicellular eukaryotic model organism in biomedical research. S. cerevisiae contains several evolutionary conserved lysine acetyltransferases and deacetylases. However, only a few dozen acetylation sites in S. cerevisiae are known, presenting a major obstacle for further understanding the regulatory roles of acetylation in this organism. Here we use high resolution mass spectrometry to identify about 4000 lysine acetylation sites in S. cerevisiae. Acetylated proteins are implicated in the regulation of diverse cytoplasmic and nuclear processes including chromatin organization, mitochondrial metabolism, and protein synthesis. Bioinformatic analysis of yeast acetylation sites shows that acetylated lysines are significantly more conserved compared with nonacetylated lysines. A large fraction of the conserved acetylation sites are present on proteins involved in cellular metabolism, protein synthesis, and protein folding. Furthermore, quantification of the Rpd3-regulated acetylation sites identified several previously known, as well as new putative substrates of this deacetylase. Rpd3 deficiency increased acetylation of the SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex subunit Sgf73 on K33. This acetylation site is located within a critical regulatory domain in Sgf73 that interacts with Ubp8 and is involved in the activation of the Ubp8-containing histone H2B deubiquitylase complex. Our data provides the first global survey of acetylation in budding yeast, and suggests a wide-ranging regulatory scope of this modification. The provided dataset may serve as an important resource for the functional analysis of lysine acetylation in eukaryotes.

The Arabidopsis Class II Sirtuin Is a Lysine Deacetylase and Interacts with Mitochondrial Energy Metabolism

“…Seven of the 11 acetylated Lys residues are highly conserved between species and were also shown to be Lys acetylated in yeast, rat, mouse, and human tissue, respectively (Supplemental Fig. S5; Choudhary et al, 2009;Weinert et al, 2011;Henriksen et al, 2012;Lundby et al, 2012;Sol et al, 2012). Furthermore we detected a 1.6-to 2-fold increase in Lys acetylation of the AAC carriers in the srt2 mutants (Fig.…”

Acetylome Profiling Reveals Overlap in the Regulation of Diverse Processes by Sirtuins, Gcn5, and Esa1

“…An earlier study examining global acetylation in yeast identified a similar number of sites (4208) (12). Surprisingly, only 21% of the total acetylation sites identified in these two studies were found in both data sets (supplemental Fig.…”

“…Although recent efforts have demonstrated that acetylation is a frequent post-translational modification, little is known about the regulation of most of these marks (12)(13)(14)(15). Moreover, although recruitment to chromatin is seen as the key step in acetylation of histone tails, little is known about the mechanism behind non-histone substrate selection.…”

Systematic identification of signal integration by protein kinase A

“…6C), suggesting that the coupling between carbohydrate storage and aging (38) is mediated in part by acetylation of the PKA at a conserved residue. Although significant, the effects measured with both mammalian and yeast mutants are small, suggesting that other acetylation sites reported in both the regulatory and catalytic subunits (34)(35)(36) or other indirect mechanisms may contribute to PKA regulation. …”

“…S5). Five residues are acetylated in Bcy1 (34,35), and at least two of them are conserved and acetylated in mammals (Fig. 5A) (36).…”