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

Abstract

Although histone acetylation and deacetylation machineries (HATs and HDACs) regulate important aspects of cell function by targeting histone tails, recent work highlights that non-histone protein acetylation is also pervasive in eukaryotes. Here, we use quantitative mass-spectrometry to define acetylations targeted by the sirtuin family, previously implicated in the regulation of non-histone protein acetylation. To identify HATs that promote acetylation of these sites, we also performed this analysis in gcn5 (SAGA) and esa1 (NuA4) mutants. We observed strong sequence specificity for the sirtuins and for each of these HATs. Although the Gcn5 and Esa1 consensus sequences are entirely distinct, the sirtuin consensus overlaps almost entirely with that of Gcn5, suggesting a strong coordination between these two regulatory enzymes. Furthermore, by examining global acetylation in an ada2 mutant, which dissociates Gcn5 from the SAGA complex, we found that a subset of Gcn5 targets did not depend on an intact SAGA complex for targeting. Our work provides a framework for understanding how HAT and HDAC enzymes collaborate to regulate critical cellular processes related to growth and division. Molecular & Cellular

Promotion of Cell Viability and Histone Gene Expression by the Acetyltransferase Gcn5 and the Protein Phosphatase PP2A in Saccharomyces cerevisiae

“…levels of these marks in vivo (Zhang et al 1998;Howe et al 2001;Pray-Grant et al 2005;Downey et al 2015). We asked if RTS1 mediated restoration of H3 acetylation.…”

Nicotinamide Suppresses the DNA Damage Sensitivity of Saccharomyces cerevisiae Independently of Sirtuin Deacetylases

“…Since cells lacking HST3 and HST4 are reported to display increased sensitivity to DNA damaging agents (Celic et al 2006;Maas et al 2006), we reasoned that the positive effects of nicotinamide observed in our assays were likely due to inhibition of the remaining sirtuins, Hst1, Hst2, and Sir2, which impact the acetylation status of many proteins within the cell (Downey et al 2013(Downey et al , 2015Downey and Baetz 2016). However, an hst1D hst2D sir2D triple mutant failed to phenocopy treatment with nicotinamide ( Figure 1B).…”

“…Since we previously found that multiple sirtuins regulate acetylations on the same substrates (Downey et al 2013(Downey et al , 2015, we used nicotinamide to inhibit these enzymes as a group ( Figure 1A). We found that plates that included nicotinamide at a concentration of 5 mM allowed for increased growth in the presence of high concentrations of MMS (i.e., 0.03% and above; Figure 1B).…”

“…Despite their names, these enzymes also have nonhistone targets that play critical roles in maintaining cellular homeostasis in organisms from bacteria to humans (Choudhary et al 2009;Weinert et al 2011;Henriksen et al 2012;Choudhary et al 2014;Downey et al 2015). In S. cerevisiae, for example, acetylation sites have been mapped on over a third of all proteins (Downey and Baetz 2016).…”

The Set3 Complex Antagonizes the MYST Acetyltransferase Esa1 in the DNA Damage Response

“…Additionally, it acts on nonhistone substrates, such as the NuA4 subunits Epl1 and Yng2 (7,12), the autophagy protein Atg3 (13), the RNA processing protein Nab3 (14,15), and nearly 200 other proteins (12,15,16). Notably, the Tip60 human ortholog of Esa1 has been linked to multiple human diseases (17)(18)(19), thus increasing the relevance of gaining a deeper understanding of Esa1 functions.…”