Glucose regulates transcription in yeast through a network of signaling pathways

The reversible nature of protein phosphorylation dictates that any protein kinase activity must be counteracted by protein phosphatase activity. How phosphatases target specific phosphoprotein substrates and reverse the action of kinases, however, is poorly understood in a biological context. We address this question by elucidating a novel function of the conserved PP4 family phosphatase Pph3-Psy2, the yeast counterpart of the mammalian PP4c-R3 complex, in the glucose-signaling pathway. Our studies show that Pph3-Psy2 specifically targets the glucose signal transducer protein Mth1 via direct binding of the EVH1 domain of the Psy2 regulatory subunit to the polyproline motif of Mth1. This activity is required for the timely dephosphorylation of the downstream transcriptional repressor Rgt1 upon glucose withdrawal, a critical event in the repression of HXT genes, which encode glucose transporters. Pph3-Psy2 dephosphorylates Mth1, an Rgt1 associated corepressor, but does not dephosphorylate Rgt1 at sites associated with inactivation, in vitro. We show that Pph3-Psy2 phosphatase antagonizes Mth1 phosphorylation by protein kinase A (PKA), the major protein kinase activated in response to glucose, in vitro and regulates Mth1 function via putative PKA phosphorylation sites in vivo. We conclude that the Pph3-Psy2 phosphatase modulates Mth1 activity to facilitate precise regulation of HXT gene expression by glucose.

Section: Discussionsupporting

confidence: 92%

Psy2 Targets the PP4 Family Phosphatase Pph3 To Dephosphorylate Mth1 and Repress Glucose Transporter Gene Expression

Han

Guaderrama

et al. 2014

“…Expression of the TCA cycle and OXPHOS genes is regulated by glucose levels independently of PKA and SNF1 by the Hap2/3/4/5p transcription complex, suggesting that the Hap2/3/4/5p complex provides an additional mechanism of transcriptional regulation of mitochondrial respiration (5). The Hap2/3/4/5p complex binds to DNA through the Hap2, -3, and -5 subunits, which are constitutively expressed.…”

Section: Resultsmentioning

confidence: 99%

“…The preferred sources of carbon and energy for the yeast Saccharomyces cerevisiae are fermentable sugars such as glucose (3)(4)(5). When yeast cells are grown in liquid cultures in rich media containing glucose under aerobic conditions, the cells metabolize glucose predominantly by glycolysis, producing pyruvate.…”

mentioning

confidence: 99%

Reduced Histone Expression or a Defect in Chromatin Assembly Induces Respiration

Galdieri

Zhang

Rogerson

et al. 2016

Regulation of mitochondrial biogenesis and respiration is a complex process that involves several signaling pathways and transcription factors as well as communication between the nuclear and mitochondrial genomes. Here we show that decreased expression of histones or a defect in nucleosome assembly in the yeast Saccharomyces cerevisiae results in increased mitochondrial DNA (mtDNA) copy numbers, oxygen consumption, ATP synthesis, and expression of genes encoding enzymes of the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS). The metabolic shift from fermentation to respiration induced by altered chromatin structure is associated with the induction of the retrograde (RTG) pathway and requires the activity of the Hap2/3/4/5p complex as well as the transport and metabolism of pyruvate in mitochondria. Together, our data indicate that altered chromatin structure relieves glucose repression of mitochondrial respiration by inducing transcription of the TCA cycle and OXPHOS genes carried by both nuclear and mitochondrial DNA.

“…The observation that glucose but not Snf1 inhibition caused a rapid dissociation of ADH2 from polysomes suggested that a glucose-dependent signaling pathway might be required for this process. cAMP-dependent protein kinase (protein kinase A [PKA]) is a major regulator of pathways active during fermentation (5,76), and low PKA activity inhibits translation during glucose starvation (73). Whether PKA plays a role in glucose-induced mRNA decay is unknown.…”

Section: Figmentioning

confidence: 99%

“…as , TPK2 as , and TPK3 as (76), were derepressed for 4 h either in the presence or in the absence of the inhibitor 2NM-PP1. Then, samples of both cultures were removed for RNA isolation and quantitation.…”

Section: Figmentioning

confidence: 99%

Snf1-Dependent Transcription Confers Glucose-Induced Decay upon the mRNA Product

Braun

Dombek

Young

2016

In the yeast Saccharomyces cerevisiae, the switch from respiratory metabolism to fermentation causes rapid decay of transcripts encoding proteins uniquely required for aerobic metabolism. Snf1, the yeast ortholog of AMP-activated protein kinase, has been implicated in this process because inhibiting Snf1 mimics the addition of glucose. In this study, we show that the SNF1-dependent ADH2 promoter, or just the major transcription factor binding site, is sufficient to confer glucose-induced mRNA decay upon heterologous transcripts. SNF1-independent expression from the ADH2 promoter prevented glucose-induced mRNA decay without altering the start site of transcription. SNF1-dependent transcripts are enriched for the binding motif of the RNA binding protein Vts1, an important mediator of mRNA decay and mRNA repression whose expression is correlated with decreased abundance of SNF1-dependent transcripts during the yeast metabolic cycle. However, deletion of VTS1 did not slow the rate of glucose-induced mRNA decay. ADH2 mRNA rapidly dissociated from polysomes after glucose repletion, and sequences bound by RNA binding proteins were enriched in the transcripts from repressed cells. Inhibiting the protein kinase A pathway did not affect glucose-induced decay of ADH2 mRNA. Our results suggest that Snf1 may influence mRNA stability by altering the recruitment activity of the transcription factor Adr1. T he regulation of gene expression by nutritional conditions inSaccharomyces cerevisiae yeast, particularly the availability of glucose, has been a paradigm of transcriptional control (1-7). Glucose deprivation leads to a global reorganization of transcription (8). Numerous genes are upregulated to allow the cell to switch to a respiratory mode of metabolism, and a large number of genes are downregulated as the cells adapt to a lower rate of growth. Snf1, the yeast ortholog of AMP-activated protein kinase (AMPK) (6), is responsible for upregulating the expression of over 400 genes after glucose depletion (9). Snf1, together with the cyclic AMP (cAMP)-dependent protein kinase A (PKA) and target of rapamycin (TOR) pathways, coordinates many of the nutrientresponsive metabolic pathways in yeast (10). Despite the preponderance of evidence indicating altered transcription as the major factor determining the increase in mRNA abundance when yeast cells are depleted of glucose, there is considerable evidence indicating that posttranscriptional changes, particularly an increase in mRNA stability, are also important in determining gene expression levels (11)(12)(13)(14)(15). A recent study demonstrated that promoter sequences influence the subcellular location and efficiency of translation of transcripts upregulated by glucose starvation (16). Thus, promoter sequences appear to have a role in gene expression that includes both transcriptional and posttranscriptional processes.Glucose-induced mRNA decay is a process that leads to rapid loss of mRNAs encoding enzymes required for efficient aerobic respiration when glucose is replenished. ...