Collaboration Between the Essential Esa1 Acetyltransferase and the Rpd3 Deacetylase Is Mediated by H4K12 Histone Acetylation in Saccharomyces cerevisiae

Abstract

Histone modifications that regulate chromatin-dependent processes are catalyzed by multisubunit complexes. These can function in both targeting activities to specific genes and in regulating genomewide levels of modifications. In Saccharomyces cerevisiae, Esa1 and Rpd3 have opposing enzymatic activities and are catalytic subunits of multiple chromatin modifying complexes with key roles in processes such as transcriptional regulation and DNA repair. Esa1 is an essential histone acetyltransferase that belongs to the highly conserved MYST family. This study presents evidence that the yeast histone deacetylase gene, RPD3, when deleted, suppressed esa1 conditional mutant phenotypes. Deletion of RPD3 reversed rDNA and telomeric silencing defects and restored global H4 acetylation levels, in addition to rescuing the growth defect of a temperature-sensitive esa1 mutant. This functional genetic interaction between ESA1 and RPD3 was mediated through the Rpd3L complex. The suppression of esa1's growth defect by disruption of Rpd3L was dependent on lysine 12 of histone H4. We propose a model whereby Esa1 and Rpd3L act coordinately to control the acetylation of H4 lysine 12 to regulate transcription, thereby emphasizing the importance of dynamic acetylation and deacetylation of this particular histone residue in maintaining cell viability.

Bypassing the Requirement for an Essential MYST Acetyltransferase

“…Rpd3 was recently reported in a third complex, Rpd3m, along with the Snt2 and Ecm5 subunits ( Figure 1A) (Shevchenko et al 2008;McDaniel and Strahl 2013). This complex is enriched at promoter regions and has a role in the response to oxidative stress (Baker et al 2013), but little else is yet known about its function.Genetic, biochemical, and genome-wide studies suggest that Rpd3 and Hda1 are the most relevant opposing activities to Esa1 (Vogelauer et al 2000;Lin et al 2008;Chang and Pillus 2009); yet important questions remain. Rpd3 has been directly identified as the deacetylase for some histone and nonhistone targets of Esa1 (Lu et al 2011;Rando and Winston 2012;Yi et al 2012), whereas genetic interaction networks point to deletion of HDA1 as the most prominent alleviating hub for NuA4 (Lin et al 2008).…”

“…Genetic, biochemical, and genome-wide studies suggest that Rpd3 and Hda1 are the most relevant opposing activities to Esa1 (Vogelauer et al 2000;Lin et al 2008;Chang and Pillus 2009); yet important questions remain. Rpd3 has been directly identified as the deacetylase for some histone and nonhistone targets of Esa1 (Lu et al 2011;Rando and Winston 2012;Yi et al 2012), whereas genetic interaction networks point to deletion of HDA1 as the most prominent alleviating hub for NuA4 (Lin et al 2008).…”

“…The esa1-414 allele is a frameshift mutation in codon 414 that leads to a C-terminal sequence change in 10 amino acids and truncation of the last 22 amino acids. Although esa1-414 cells have a growth rate similar to wild type at 30°, they are sensitive to DNA damage (Chang and Pillus 2009). The phenotypes of esa1-414 cells can be exacerbated by growth at elevated temperatures, conditions under which histone H4 acetylation is decreased and cells slow and/or stop growth by blocking cell cycle progression in G2/M (Clarke et al 1999;Chang and Pillus 2009).…”

The Role of SAS-I in Mediating Crosstalk Between Histone Modifications

“…The majority of H4K16 acetylation is performed by Sas2 (Kimura et al 2002, Suka et al 2002 while Esa1, a HAT contained in the NuA4 complex, can acetylate H4K16, but it mostly targets H4K5, 8, and12 (Chang and Pillus 2009, Suka et al 2002, Suka et al 2001, Grant et al 1997. In fact, upon deletion of Sas2, H4K16ac is reduced significantly while Esa1 deletion mutants only show a slight decrease in H4K16ac.…”

“…In yeast, the majority of H4K16 acetylation is performed by Sas2, a MYST family HAT contained in the SAS-I complex with Sas4 and Sas5 (Kimura et al 2002, Suka et al 2002. While Esa1, an essential HAT contained in the NuA4 complex, can acetylate H4K16, it mostly targets H4K5 and H4K12 (Suka et al 2001, 2002, Chang and Pillus 2009). To determine which HAT was responsible for the transition, the same immunoblotting experiment was performed on histones isolated from cells lacking SAS-I subunits or containing Esa1 mutants (Figure 2-3) (Decker et al …”