Bypassing the Requirement for an Essential MYST Acetyltransferase

Abstract

Histone acetylation is a key regulatory feature for chromatin that is established by opposing enzymatic activities of lysine acetyltransferases (KATs/HATs) and deacetylases (KDACs/HDACs). Esa1, like its human homolog Tip60, is an essential MYST family enzyme that acetylates histones H4 and H2A and other nonhistone substrates. Here we report that the essential requirement for ESA1 in Saccharomyces cerevisiae can be bypassed upon loss of Sds3, a noncatalytic subunit of the Rpd3L deacetylase complex. By studying the esa1Δ sds3Δ strain, we conclude that the essential function of Esa1 is in promoting the cellular balance of acetylation. We demonstrate this by fine-tuning acetylation through modulation of HDACs and the histone tails themselves. Functional interactions between Esa1 and HDACs of class I, class II, and the Sirtuin family define specific roles of these opposing activities in cellular viability, fitness, and response to stress. The fact that both increased and decreased expression of the ESA1 homolog TIP60 has cancer associations in humans underscores just how important the balance of its activity is likely to be for human well-being.T HE genetic information of DNA is packed into chromatin, which is predominantly composed of the H3, H4, H2A, and H2B core histone proteins that together with DNA form nucleosomes, the basic subunits of the genome (Kornberg and Lorch 1999). Chromatin structure regulates many cellular processes including gene expression, DNA replication, DNA damage repair, and recombination (Felsenfeld and Groudine 2003). Nucleosomes themselves are tightly regulated by mobilization and positioning that are mediated by ATP-dependent chromatin-remodeling machines (Rando and Winston 2012) and by multiple types of histone posttranslational modifications that include acetylation and many other marks (Campos and Reinberg 2009).Nucleosome acetylation is a highly dynamic modification that is promoted by HATs and removed by HDACs. HATs are classified by sequence into different families (Allis et al. 2007). ESA1/KAT5 belongs to the widely conserved MYST HAT family, named for its founding members (MOZ-YBF2/ SAS3-SAS2-TIP60) (Lafon et al. 2007). Esa1 is an essential HAT in yeast (Smith et al. 1998;Clarke et al. 1999) and the catalytic subunit of two distinct multi-protein complexes: NuA4 and Piccolo (Boudreault et al. 2003). Notably, the human homolog of Esa1 is Tip60, which is also essential in vertebrates and has been linked to multiple human diseases (Squatrito et al. 2006;Avvakumov and Côté 2007;Lafon et al. 2007), thus increasing the relevance of gaining a deeper understanding of essential HAT functions.Esa1 primarily acetylates H4 and H2A in vivo (Clarke et al. 1999;Lin et al. 2008) and regulates the expression of active protein-encoding genes (Reid et al. 2000;Lin et al. 2008). It plays a crucial role in cell cycle progression and ribosomal DNA (rDNA) silencing (Clarke et al. 1999(Clarke et al. , 2006 and is recruited to DNA double-strand breaks (DSBs) to promote damage repair by acetylati...

NuA4 acetyltransferase is required for efficient nucleotide excision repair in yeast

“…The esa1 Δ sds3 Δ double mutant strain was viable, consistent with a previous report [54], so we tested whether the NER defect associated with loss of Esa1 acetyltransferase activity is rescued by a compensatory deletion of the Sds3 subunit of the Rpd3L HDAC complex. The sds3 Δ mutant alone did not significantly affect repair of CPD lesions relative to the WT control following UV irradiation (Figure S3).…”

“…Previous studies have implicated the Rpd3L and Set3/Hos2 histone deacetylase complexes as opposing the activity of NuA4/Esa1. Deletion of the Sds3 subunit of Rpd3L histone deacetylase complex rescues the lethality of esa1 Δ mutant [53, 54], while deletion of Hos2 rescues many of the DNA damage sensitivities of the esa1 partial loss-of-function mutants [55]. Hence, we tested whether the NER defect associated with mutations in NuA4 subunits could be rescued by a compensatory loss-of-function mutation in either SDS3 or HOS2 .…”

Merge and separation of NuA4 and SWR1 complexes control cell fate plasticity in Candida albicans

“…NuA4 (nucleosome acetyltransferase of H4) is a multi-subunit HAT (histone acetyltransferase) complex that is highly conserved in eukaryotes and has important roles in cell cycle progression, cell transformation, development, apoptosis, transcription, and DNA repair 3 – 9 . Saccharomyces cerevisiae NuA4 is composed of 13 subunits 9 , 10 , including the essential acetyltransferase subunit Esa1 11 – 13 and the platform protein Eaf1, which has a crucial function in NuA4 complex integrity and assembly 14 , 15 (Fig. 1a ).…”

Chromatin Regulation by the NuA4 Acetyltransferase Complex Is Mediated by Essential Interactions Between Enhancer of Polycomb (Epl1) and Esa1

“…Because Esa1 is essential, much of our early understanding of it came from studying hypomorphic alleles, where Esa1 is only partially or conditionally functional (Clarke et al 1999;Decker et al 2008). Recently, the first bypass suppressor of Esa1 was identified, where esa1D is rescued by loss of the Rpd3L HDAC complex (Torres-Machorro and Pillus 2014). This bypass of Esa1 is promoted by establishing a relatively balanced cellular acetylation state.…”