| Histone acetylation and deacetylation are among the principal mechanisms by which chromatin is regulated during transcription, DNA silencing, and DNA repair. We analyzed patterns of genetic interactions uncovered during comprehensive genome-wide analyses in Saccharomyces cerevisiae to probe how histone acetyltransferase (HAT) and histone deacetylase (HDAC) protein complexes interact. The genetic interaction data unveil an underappreciated role of HDACs in maintaining cellular viability, and led us to show that deacetylation of the histone variant Htz1p at lysine 14 is mediated by Hda1p. Studies of the essential nucleosome acetyltransferase of H4 (NuA4) revealed acetylation-dependent protein stabilization of Yng2p, a nonhistone substrate of NuA4 and Rpd3C, and led to a new functional organization model for this critical complex. We also found that DNA double-stranded breaks (DSBs) result in local recruitment of the NuA4 complex, followed by an elaborate NuA4 remodeling process concomitant with Rpd3p recruitment and histone deacetylation. These new characterizations of the HDA and NuA4 complexes demonstrate how systematic analyses of genetic interactions may help illuminate the mechanisms of intricate cellular processes.;HAT and HDAC protein complexes also conduct many critical functions through nonhistone substrates in metazoans, but only chromatin-associated nonhistone substrates have been reported in Saccharomyces cerevisiae. Using yeast proteome microarrays, we identified and validated many nonhistone substrates of the essential nucleosome acetyltransferase of H4 (NuA4) complex. Among these, the acetylation site (Lys 514) of phosphoenolpyruvate carboxykinase (Pck1p) was determined by tandem mass spectrometry. Acetylation at this lysine residue was crucial for the Pck1p enzymatic activity and the ability of yeast cells to grow on non-fermentable carbon sources such as ethanol. Moreover, loss of Pck1p activity blocked extension of yeast chronological life span caused by water starvation. Human PCK1 (hPCK1) could rescue the lethality of yeast cells lacking PCK1 on ethanol. In human hepatocellular carcinoma (HepG2) cells, human Pck1 acetylation and glucose production was dependent on TIP60, the human homolog of ESA1. Our results demonstrate a novel regulatory function for NuA4 in glucose metabolism and aging by acetylating a critical metabolic enzyme. |
