The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress

Alejandro-Osorio, Adriana L; Huebert, Dana J.; Porcaro, Dominic T; Sonntag, Megan E; Nillasithanukroh, Songdet; Will, Jessica L.; Gasch, Audrey P.

doi:10.1186/gb-2009-10-5-r57

Cited by 75 publications

(73 citation statements)

References 77 publications

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“…Moreover, network analysis showed that the HOG pathway plays a central role in transcriptome changes at the onset of dough fermentation. The enrichment of the genes involved in chromatin modification in the network is consistent with a known role of chromatin-modifying enzymes and histone modifications in the regulation of transcriptional changes in response to environmental changes and stress (65,66).…”

Section: Fig 4 (A)supporting

confidence: 82%

Dynamics of the Saccharomyces cerevisiae Transcriptome during Bread Dough Fermentation

Aslankoohi

Zhu

Rezaei

et al. 2013

Appl Environ Microbiol

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The behavior of yeast cells during industrial processes such as the production of beer, wine, and bioethanol has been extensively studied. In contrast, our knowledge about yeast physiology during solid-state processes, such as bread dough, cheese, or cocoa fermentation, remains limited. We investigated changes in the transcriptomes of three genetically distinct Saccharomyces cerevisiae strains during bread dough fermentation. Our results show that regardless of the genetic background, all three strains exhibit similar changes in expression patterns. At the onset of fermentation, expression of glucose-regulated genes changes dramatically, and the osmotic stress response is activated. The middle fermentation phase is characterized by the induction of genes involved in amino acid metabolism. Finally, at the latest time point, cells suffer from nutrient depletion and activate pathways associated with starvation and stress responses. Further analysis shows that genes regulated by the high-osmolarity glycerol (HOG) pathway, the major pathway involved in the response to osmotic stress and glycerol homeostasis, are among the most differentially expressed genes at the onset of fermentation. More importantly, deletion of HOG1 and other genes of this pathway significantly reduces the fermentation capacity. Together, our results demonstrate that cells embedded in a solid matrix such as bread dough suffer severe osmotic stress and that a proper induction of the HOG pathway is critical for optimal fermentation.

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Section: Fig 4 (A)supporting

confidence: 82%

Dynamics of the Saccharomyces cerevisiae Transcriptome during Bread Dough Fermentation

Aslankoohi

Zhu

Rezaei

et al. 2013

Appl Environ Microbiol

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“…6D), suggesting that other proteins recruit Rpd3 to these targets. The Rpd3(L) complex regulates genes in response to diverse stresses (13)(14)(15)(16), including oxidative stress (12), and may recruit Rpd3 to these regions. RNAseq analysis identified 309 H 2 O 2 -enriched target genes that changed expression in wild-type cells in response to H 2 O 2 and were either up-or downregulated when SNT2 was deleted (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, cells lacking Snt2 have higher levels of phosphorylation of the stress MAPK Slt2 (20), and a bioinformatics study suggested that Snt2 might function to activate genes in response to stress (22). Rpd3 is known to regulate the response to numerous stresses, including oxidative stress, often as a part of the Rpd3(L) complex (12)(13)(14)(15). On the basis of these data, we hypothesized that Snt2, Ecm5, and Rpd3 might function as an additional regulator of the oxidative stress response.…”

Section: Snt2 Physically Associates With Ecm5 and The Rpd3 Deacetylasementioning

confidence: 99%

“…Rpd3 is a lysine deacetylase known to associate with two other well-characterized complexes, Rpd3 large [Rpd3(L)] and Rpd3 small [Rpd3(S)] (9-11). The Rpd3(L) complex has been reported to function in numerous pathways and notably has been linked to ESR regulation (12)(13)(14)(15)(16). However, the function of Snt2, either on its own or in association with Ecm5 and Rpd3, remains unclear.…”

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confidence: 99%

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The Yeast Snt2 Protein Coordinates the Transcriptional Response to Hydrogen Peroxide-Mediated Oxidative Stress

Baker

Ueberheide

Dewell

et al. 2013

Molecular and Cellular Biology

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dRegulation of gene expression is a vital part of the cellular stress response, yet the full set of proteins that orchestrate this regulation remains unknown. Snt2 is a Saccharomyces cerevisiae protein whose function has not been well characterized that was recently shown to associate with Ecm5 and the Rpd3 deacetylase. Here, we confirm that Snt2, Ecm5, and Rpd3 physically associate. We then demonstrate that cells lacking Rpd3 or Snt2 are resistant to hydrogen peroxide (H 2 O 2 )-mediated oxidative stress and use chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) to show that Snt2 and Ecm5 recruit Rpd3 to a small number of promoters and in response to H 2 O 2 , colocalize independently of Rpd3 to the promoters of stress response genes. By integrating ChIP-seq and expression analyses, we identify target genes that require Snt2 for proper expression after H 2 O 2 . Finally, we show that cells lacking Snt2 are also resistant to nutrient stress imparted by the TOR (target of rapamycin) pathway inhibitor rapamycin and identify a common set of genes targeted by Snt2 and Ecm5 in response to both H 2 O 2 and rapamycin. Our results establish a function for Snt2 in regulating transcription in response to oxidative stress and suggest Snt2 may also function in multiple stress pathways.

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“…The TORC1 and ras/PKA/cyclic AMP pathways converge on the Sch9p kinase and Sfp1 that targets the rRNA and ribosome biosynthesis (RRB) transcriptional repressors Stb3p, Dot6p, and Tod6p (12,13,14,15). These proteins in turn recruit the Rpd3L histone deacetylase complex to the promoters of RRB genes and mediate the budding yeast stress response (16). TOR kinase signaling also regulates the activity of the RP promoter binding transcription factor Fhl1 through controlling the subcellular location of the corepressor Crf1 (17).…”

mentioning

confidence: 99%

Dissecting the cis and trans Elements That Regulate Adjacent-Gene Coregulation in Saccharomyces cerevisiae

et al. 2014

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The relative positions that genes occupy on their respective chromosomes can play a critical role in determining how they are regulated at the transcriptional level. For example, a significant fraction of the genes from a variety of coregulated gene sets, including the ribosomal protein (RP) and the rRNA and ribosome biogenesis (RRB) regulons, exist as immediate, adjacent gene pairs. These gene pairs occur in all possible divergent, tandem, and convergent orientations. Adjacent-gene pairing in these regulons is associated with a tighter transcriptional coregulation than is observed for nonpaired genes of the same regulons. In order to define the cis and trans factors that regulate adjacent-gene coregulation (AGC), we conducted a mutational analysis of the convergently oriented RRB gene pair MPP10-YJR003C. We observed that coupled corepression of the gene pair under heat shock was abrogated when the two genes were separated by an actively expressed RNA polymerase (Pol) II transcription unit (the LEU2 gene) but not when the inserted LEU2 gene was repressed. In contrast, the insertion of an RNA Pol III-transcribed tRNA (Thr) gene did not disrupt the coregulated repression of MPP10 and YJR003C. A targeted screen of mutants defective in regulating chromosome architecture revealed that the Spt20, Snf2, and Chd1 proteins were required for coupling the repression of YJR003C to that of MPP10. Nucleosome occupancy assays performed across the MPP10 and YJR003C promoter regions revealed that the mechanism of corepression of the gene pair was not related to the repositioning of nucleosomes across the respective gene promoters.

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The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress

Cited by 75 publications

References 77 publications

Dynamics of the Saccharomyces cerevisiae Transcriptome during Bread Dough Fermentation

Dynamics of the Saccharomyces cerevisiae Transcriptome during Bread Dough Fermentation

The Yeast Snt2 Protein Coordinates the Transcriptional Response to Hydrogen Peroxide-Mediated Oxidative Stress

Dissecting the cis and trans Elements That Regulate Adjacent-Gene Coregulation in Saccharomyces cerevisiae

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