Functions for diverse metabolic activities in heterochromatin

Abstract

Growing evidence demonstrates that metabolism and chromatin dynamics are not separate processes but that they functionally intersect in many ways. For example, the lysine biosynthetic enzyme homocitrate synthase was recently shown to have unexpected functions in DNA damage repair, raising the question of whether other amino acid metabolic enzymes participate in chromatin regulation. Using an in silico screen combined with reporter assays, we discovered that a diverse range of metabolic enzymes function in heterochromatin regulation. Extended analysis of the glutamate dehydrogenase 1 (Gdh1) revealed that it regulates silent information regulator complex recruitment to telomeres and ribosomal DNA. Enhanced N-terminal histone H3 proteolysis is observed in GDH1 mutants, consistent with telomeric silencing defects. A conserved catalytic Asp residue is required for Gdh1's functions in telomeric silencing and H3 clipping. Genetic modulation of α-ketoglutarate levels demonstrates a key regulatory role for this metabolite in telomeric silencing. The metabolic activity of glutamate dehydrogenase thus has important and previously unsuspected roles in regulating chromatin-related processes.I n eukaryotic nuclei, DNA is wrapped around histones to form nucleosomes, the basic subunits of chromatin (1). The physical and chemical properties of chromatin are regulated by at least two types of enzymatic activities: chromatin remodeling and posttranslational modifications of histones and chromatin-associated proteins (2, 3). These enzymatic activities directly determine the accessibility of DNA for transcription, replication, and repair.In Saccharomyces cerevisiae, three genomic regions are known to contain loci repressed by chromatin-related activities. These include the HM silent mating-type loci (HMR and HML), regions within the ribosomal DNA (rDNA), and some telomeres. Transcriptional silencing at these loci is established and maintained by a number of factors, including the Sirtuin class III deacetylase activity of silent information protein 2 (Sir2). Notably, Sir2 uses NAD + as a cofactor to deacetylate histones H3 and H4 in newly deposited nucleosomes. Other than Sir2, the composition of the silencing complexes and the mechanisms of silencing are different for the three silenced regions, with the telomeres and the HM loci more similar to each other and the rDNA locus having distinct features (reviewed in ref. 4). Silencing at telomeres and the HM loci was long considered to follow a sequential model: initial deacetylation by Sir2 creates binding sites for Sir3 and Sir4, which in turn regulate the spreading of Sir2 across these regions (5). More recent high-resolution studies report a less uniform landscape for silenced chromatin (6), although the central importance of the Sir proteins remains clear. They, together with transcription factors including Rap1 and Abf1, form a multisubunit silencing complex known as the silent information regulator (SIR) complex. Silencing at the rDNA locus does not involve the SIR complex but ra...

Decoding the chromatin proteome of a single genomic locus by DNA sequencing

“…Furthermore, the binding scores of some metabolic enzymes changed upon treatment with HU (Supplementary Table 2), indicating that their interaction with chromatin is not constitutive. Indeed, there is a growing body of evidence that enzymes in the cytoplasm might have moonlighting functions in the nucleus, for example by local supply of co-factors of histone modifying enzymes 19,46,[51][52][53][54] . Alternatively, the interaction with chromatin could somehow influence the activity of metabolic enzymes.…”

“…RNA processing events such as capping, splicing, cleavage, and polyadenylation are all processes known to occur in close conjunction with RNA transcription and hence in proximity to DNA 17 , providing an explanation for the recovery of barcodes associated with RNA processing proteins. The presence of factors involved in cellular metabolism cannot be explained by general associations with transcription, although recent studies have suggested various roles of metabolic enzymes in the nucleus 4,[18][19] (and see discussion). Given the fact that some of these factors are known to be highly expressed, we investigated the possibility that their chromatin interactions were determined by protein abundance.…”

Proteomic Analysis of Saccharomyces cerevisiae Response to Oxidative Stress Mediated by Cocoa Polyphenols Extract

“…This novel epigenetic regulatory mechanism is actually an interesting research topic, as reflected in a recent review [38], and H3 modifications have been connected to different stress responses, including OS and lifespan in C. elegans and Drosophila [39,40]. Other amino acid metabolic enzymes could participate in chromatin regulation [41]. This is the case of one protein that was differently expressed in our study: Gdh1.…”

The pleiotropic effects of the glutamate dehydrogenase (GDH) pathway in Saccharomyces cerevisiae

“…Gdh3p was considered the molecular target of ebselen which ceased NADP-GDH activity through the formation of selenyl-sulfide bonds with cysteine residues. It was also observed that the NADP-GDH inactivation might had a critical function in the proteolysis of H3 histone in yeast [ 38 – 40 ], as discussed below.…”

“…The role of Gdh1p in transcriptional silencing was found to be crucial through the proteolysis of H3 histone in yeast (“H3-clipping” in the N-tail) [ 40 ]. This effect has been described previously in animal tissues [ 39 , 67 ].…”