Ubp8 and SAGA Regulate Snf1 AMP Kinase Activity

Abstract

Posttranslational modifications of histone proteins play important roles in the modulation of gene expression. The Saccharomyces cerevisiae (yeast) 2-MDa SAGA (Spt-Ada-Gcn5) complex, a well-studied multisubunit histone modifier, regulates gene expression through Gcn5-mediated histone acetylation and Ubp8-mediated histone deubiquitination. Using a proteomics approach, we determined that the SAGA complex also deubiquitinates nonhistone proteins, including Snf1, an AMP-activated kinase. Ubp8-mediated deubiquitination of Snf1 affects the stability and phosphorylation state of Snf1, thereby affecting Snf1 kinase activity. Others have reported that Gal83 is phosphorylated by Snf1, and we found that deletion of UBP8 causes decreased phosphorylation of Gal83, which is consistent with the effects of Ubp8 loss on Snf1 kinase functions. Overall, our data indicate that SAGA modulates the posttranslational modifications of Snf1 in order to fine-tune gene expression levels.Ubiquitination of cellular targets regulates many biological processes, from intracellular trafficking to gene expression. Although ubiquitination by ubiquitin (Ub) ligases is widely studied, less is known about subsequent deubiquitination (DUB) of cellular substrates. The identification of genes coding 16 deubiquitinases in the Saccharomyces cerevisiae (yeast) genome and genes coding at least 60 deubiquitinases in the human genome suggests that not only is deubiquitination important but also that deubiquitination may also occur in a substratespecific manner to regulate specific cellular processes. Despite the lack of knowledge of the targets of many of these deubiquitinases, it is known that some of these enzymes impact cellular growth and function (3,21,46). Overexpression of certain deubiquitinases is associated with progression of malignancy in neuroblastomas and a variety of carcinomas, indicating that these enzymes may be oncogenic (27,31,38).USP22, a deubiquitinase associated with the SAGA histone acetyltransferase (HAT) complex, was identified as a member of an 11-gene "death-from-cancer" signature that serves as a predictor of treatment resistance, aggressive growth, and metastasis of human tumors when overexpressed (7,8). The SAGA complex is highly conserved, and its functions are best characterized in yeast (4,9,17,23,35). In addition to acetylating histone H3 via the Gcn5 subunit, SAGA also proteolytically cleaves ubiquitin moieties from histone H2B via the Ubp8 subunit, which is an ortholog of USP22 (13, 47). Ubp8-mediated deubiquitination of histone H2B regulates the expression of target genes by modulating the level of histone H3 lysine 4 methylation, a mark that is associated with active transcription (13). In addition, Ubp8 facilitates the recruitment of the Cterminal domain kinase (Ctk1) to target gene promoters via histone H2B deubiquitination, which facilitates the transition from transcription initiation to elongation (43).Interestingly, recent studies indicate that the functions of USP22 extend beyond histone H2B, as it also deubiquiti...

SUMOylation regulates the SNF1 protein kinase

“…Snf1 is ubiquitinylated, and its consequent degradation is best detected in a mutant missing the Ubp8 deubiquitinylase (55). We measured Snf1 levels in ubp8Δ cells to explore the effect of SUMOylation of Snf1 on its stability.…”

Poly(Q) Expansions in ATXN7 Affect Solubility but Not Activity of the SAGA Deubiquitinating Module

“…The best-characterized substrate for Ubp8 and USP22 is histone H2B, although other substrates have been identified in both yeast and mammalian cells (21)(22)(23)(24). In mammalian cells, genomewide analyses indicate that ubiquitinated H2B (H2Bub) is enriched at highly expressed genes (25), but this modification is associated with both gene activation and repression (26).…”

The SNF1 Kinase Ubiquitin-associated Domain Restrains Its Activation, Activity, and the Yeast Life Span

“…Further layers of regulatory finesse include the reversible physical allosteric association between the ␣ and ␥ regulatory subunits and the nuclear translocation of the active trimeric complex to alter gene expression that aims to preserve the energy balance of the cell (10,20,22). Also conserved is acetylation and ubiquitination, recently reported for both mammalian AMPK and yeast SNF1 kinase complexes (23)(24)(25)(26), that appear to have inhibitory roles in regulation of the kinase. Similarly, SUMOylation has been shown to be a negative regulator of Snf1 (27), clearly adding to the complexity of regulation of this central energy-sensing switch.…”