Snf1/AMPK regulates Gcn5 occupancy, H3 acetylation and chromatin remodelling at S. cerevisiae ADY2 promoter

Abate, Georgia; Bastonini, Emanuela; Braun, Katherine A.; Verdone, Loredana; Young, Elton T.; Caserta, Micaela

doi:10.1016/j.bbagrm.2012.01.009

Cited by 43 publications

(30 citation statements)

References 59 publications

(86 reference statements)

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“…Snf1 is recruited to the GAL1 promoter by Gal4 (88) and to the INO1 promoter (89). A Snf1 complex containing the activating subunit Gal83 is found at the SNF1-and ADR1-dependent ADY2 promoter (90). The mammalian ortholog of Snf1, AMPK, is found at the promoters and in the ORFs of several mammalian genes (91).…”

Section: Discussionmentioning

confidence: 99%

“…Xrn1 might be one such protein, because it is found in the nucleus (92; but see reference 59 for a conflicting report) and its activity appears to be regulated by Snf1-dependent phosphorylation (27). Although the known nuclear role of AMPK and Snf1 is to modify chromatin through activation of histone acetyltransferases (89,90,93), they could also influence posttranscriptional gene regulation by one of the mechanisms described above.…”

Section: Discussionmentioning

confidence: 99%

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

Braun

Dombek

Young

2016

Molecular and Cellular Biology

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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. ...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

Braun

Dombek

Young

2016

Molecular and Cellular Biology

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“…7. At the transcriptional level, promoter binding of Adr1 is regulated by Snf1-dependent histone hyperacetylation that occurs when glucose is depleted (20,32). Adr1 binding is also regulated by inhibitory phosphorylation of Ser-98 within its DNA binding domain, the reversal of which is Snf1-dependent (18).…”

Section: Discussionmentioning

confidence: 99%

“…ADR1 is transcribed constitutively, and the Adr1 protein is present but inactive during growth in the presence of high levels of glucose or other fermentable sugars (29,30). Relief from glucose repression (derepression) is accompanied by promoter binding of Adr1 in a Snf1-dependent fashion (31) and requires Snf1-dependent histone H3 hyperacetylation of promoter nucleosomes (20,32). Chromatin remodeling precedes and is required for gene activation and requires Snf1, Adr1, and Cat8, which recruit the Swi/Snf chromatin remodeling complex as well as the SAGA (Spt-Ada-Gcn5 acetyltransferase), and NuA4 histone acetyltransferase complexes (33,34).…”

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confidence: 99%

The AMP-activated Protein Kinase Snf1 Regulates Transcription Factor Binding, RNA Polymerase II Activity, and mRNA Stability of Glucose-repressed Genes in Saccharomyces cerevisiae

Young

Zhang

Shokat

et al. 2012

Journal of Biological Chemistry

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“…In S. cerevisiae, Snf1p (TR_45998, TA_227921, and TV_40990) regulates transcription of genes required for growth in different carbon sources, i.e., low-glucose medium or sucrose, through H3S10pho, which leads the acetylation of promoters mediated by Gcn5p and recruiting of TATA binding protein (268,276,277).…”

Section: Figmentioning

confidence: 99%

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Schmoll

Dattenböck

Carreras-Villaseñor

et al. 2016

Microbiol Mol Biol Rev

163

195

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SUMMARYThe genusTrichodermacontains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism inT. reesei,T. atroviride, andT. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of eachTrichodermaspecies discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theTrichodermagenus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique toT. atrovirideis the duplication of the alternative sulfur amino acid synthesis pathway.

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Snf1/AMPK regulates Gcn5 occupancy, H3 acetylation and chromatin remodelling at S. cerevisiae ADY2 promoter

Cited by 43 publications

References 59 publications

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

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

The AMP-activated Protein Kinase Snf1 Regulates Transcription Factor Binding, RNA Polymerase II Activity, and mRNA Stability of Glucose-repressed Genes in Saccharomyces cerevisiae

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

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