Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK
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ABSTRACT:
PROVIDER: PRJNA433655 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6703550.fastq.gz | Fastqsanger.gz | |||
| SRR6703560.fastq.gz | Fastqsanger.gz | |||
| SRR6703570.fastq.gz | Fastqsanger.gz | |||
| SRR6703551.fastq.gz | Fastqsanger.gz | |||
| SRR6703561.fastq.gz | Fastqsanger.gz |
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Project description:Chronologically aging yeast cells are prone to adaptive regrowth, whereby mutants with a survival advantage spontaneously appear and re-enter the cell cycle in stationary phase cultures. Adaptive regrowth is especially noticeable with short-lived strains, including those defective for SNF1, the homolog of mammalian AMP-activated protein kinase (AMPK). SNF1 becomes active in response to multiple environmental stresses that occur in chronologically aging cells, including glucose depletion and oxidative stress. SNF1 is also required for the extension of chronological lifespan (CLS) by caloric restriction (CR) as defined as limiting glucose at the time of culture inoculation. To identify specific downstream SNF1 targets responsible for CLS extension during CR, we screened for adaptive regrowth mutants that restore chronological longevity to a short-lived snf1∆ parental strain. Whole genome sequencing of the adapted mutants revealed missense mutations in TPR motifs 9 and 10 of the transcriptional co-repressor Cyc8 that specifically mediate repression through the transcriptional repressor Mig1. Another mutation occurred in MIG1 itself, thus implicating the activation of Mig1-repressed genes as a key function of SNF1 in maintaining CLS. Consistent with this conclusion, the cyc8 TPR mutations partially restored growth on alternative carbon sources and significantly extended CLS compared to the snf1∆ parent. Furthermore, cyc8 TPR mutations reactivated multiple Mig1-repressed genes, including the transcription factor gene CAT8, which is responsible for activating genes of the glyoxylate and gluconeogenesis pathways. Deleting CAT8 completely blocked CLS extension by the cyc8 TPR mutations on CLS, identifying these pathways as key Snf1-regulated CLS determinants.
2018-03-28 | GSE110409 | GEO
Project description:Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK
| PRJNA396952 | ENA
Project description: Not available
| S-EPMC5961917 | biostudies-literature
Project description:The highly conserved heterotrimeric protein kinase SNF1 is important for metabolic adaptations in the pathogenic yeast Candida albicans. A key function of SNF1 is to inactivate the repressor protein Mig1 and thereby allow the expression of genes that are required for the the utilization of alternative carbon sources when the preferred carbon source glucose is absent or becomes limiting. However, how SNF1 controls Mig1 activity in C. albicans has remained elusive. Using a phosphoproteomic approach, we found that Mig1 is phosphorylated at multiple serine residues. Replacement of these serine residues by nonphosphorylatable alanine residues strongly increased the repressor activity of Mig1 in cells lacking a functional SNF1 complex, indicating that additional protein kinases are involved in the regulation of Mig1. Unlike wild-type Mig1, whose levels strongly decreased when the cells were grown on sucrose or glycerol instead of glucose, the levels of a mutant Mig1 protein lacking nine phosphorylation sites remained high under these conditions. Despite the increased protein levels and the absence of multiple phosphorylation sites, cells with a functional SNF1 complex could still sufficiently inhibit the hyperactive Mig1 to enable wild-type growth on alternative carbon sources. In line with this, phosphorylated forms of the mutant Mig1 were still detected in the presence and absence of a functional SNF1, demonstrating that Mig1 contains additional, unidentified phosphorylation sites and that downstream protein kinases are involved in the control of Mig1 activity by SNF1.
2023-10-27 | PXD045393 | Pride
Project description:The yeast Saccharomyces cerevisiae thrives in sugar-rich environments by rapidly consuming glucose and favoring alcoholic fermentation. This strategy is tightly regulated by the glucose repression pathway, which prevents the expression of genes required for the utilization of alternative carbon source. Central to this regulatory network is the yeast ortholog of the heterotrimeric 5′AMP-activated protein kinase (AMPK), which adjusts gene expression in response to glucose availability. The activity of the yeast AMPK complex is primarily regulated by the phosphorylation state of its catalytic subunit Snf1, a process orchestrated by a balance between upstream kinases and phosphatases. Among the latter, the Protein Phosphatase 1 (PP1) complex Reg1/Glc7 plays a critical role in inhibiting Snf1 activity under glucose-rich conditions. Despite its importance, the precise mechanism by which glucose availability leads to Snf1 inhibition remains incompletely understood. Evidence suggests that hexokinase 2 (Hxk2) participates in this pathway, potentially coupling the early steps of glucose metabolism to Snf1 signaling. Notably, the toxic glucose analog 2-deoxyglucose (2DG)- which is phosphorylated by Hxk2 but not further metabolized- mimics glucose in its ability to repress Snf1, implicating glucose or 2DG phosphorylation as a key regulatory signal. Additionally, yeast AMPK activity correlates with 2DG resistance through mechanisms that are incompletely described. In this study, we performed a large-scale 2DG-resistance genetic screen to explore both the molecular basis of 2DG resistance and AMPK regulation in yeast. The identified mutations confer resistance either by reducing 2DG phosphorylation (e.g., mutations in HXK2) or by enhancing constitutive Snf1 activity, via gain-of-function alleles in AMPK subunits or loss-of-function mutations in REG1 and GLC7. We also describe a novel series of REG1 missense mutations, including reg1-W165G, that maintain basal, glucose-regulated Snf1 activity but fail to mediate 2DG-induced Snf1 inhibition. These findings position Reg1 as a central mediator in glucose sensing, possibly by sensing 2DG-derived -and by extension, glucose-derived- metabolites.
2025-10-03 | PXD068555 | Pride
Project description:Histone modification affects life span in various organisms. The loss of Histone H3K36 methylation can shorten replicative life span in Saccharomyces cerevisiae. However, budding yeast, as a model organism for aging research, has replicative life span (RLS) and chronological life span (CLS). In this study, we showed that the loss of Histone H3K36 methylation can shorten CLS in Saccharomyces cerevisiae. We identified Ubc3/Bre1 mediates polyubiquitination of Set2 K25 and K530 at log phase and stationary phase, and Bre1 interacts with Ubc3 and Rad6 simultaneously. BRE1 knockout can stabilize Set2 protein to maintain H3K36me3 and regulate the transcription of aging related genes, such as DSE1/DSE2/SUN4/EGT2/SCW11. We also proved that Gcn5-mediated Set2 acetylation regulates Set2 protein stability and chronological aging. Altogether, our study showed that knockout of BRE1 and GCN5 regulate Set2 protein level by mediating the polyubiquitination of Set2 to influence the level of H3K36me3 and the transcription level of aging related genes enriched by H3K36me3, thereby extending the chronological life span.
2023-09-29 | GSE221025 | GEO
Project description:Histone modification affects life span in various organisms. The loss of Histone H3K36 methylation can shorten replicative life span in Saccharomyces cerevisiae. However, budding yeast, as a model organism for aging research, has replicative life span (RLS) and chronological life span (CLS). In this study, we showed that the loss of Histone H3K36 methylation can shorten CLS in Saccharomyces cerevisiae. We identified Ubc3/Bre1 mediates polyubiquitination of Set2 K25 and K530 at log phase and stationary phase, and Bre1 interacts with Ubc3 and Rad6 simultaneously. BRE1 knockout can stabilize Set2 protein to maintain H3K36me3 and regulate the transcription of aging related genes, such as DSE1/DSE2/SUN4/EGT2/SCW11. We also proved that Gcn5-mediated Set2 acetylation regulates Set2 protein stability and chronological aging. Altogether, our study showed that knockout of BRE1 and GCN5 regulate Set2 protein level by mediating the polyubiquitination of Set2 to influence the level of H3K36me3 and the transcription level of aging related genes enriched by H3K36me3, thereby extending the chronological life span.
2023-09-29 | GSE221024 | GEO
Project description:The Tup1-Cyc8 complex in Saccharomyces cerevisiae was one of the first global co-repressors of gene transcription discovered. The model for Tup1-Cyc8 function proposes that Tup1p mediates the repression activity, whilst Cyc8p recruits the complex to target genes. However, despite years of study, a full understanding of the contribution of Tup1p and Cyc8p to complex function is lacking. We examined TUP1 and CYC8 single and double deletion mutants and show that CYC8 represses more genes than TUP1, and there are genes subject to (i) unique repression by TUP1 or CYC8, (ii) redundant repression by TUP1 and CYC8, and (iii) there are genes at which de-repression in a cyc8 mutant is dependent upon TUP1, and vice-versa. We also reveal that Tup1p and Cyc8p can make distinct contributions to commonly repressed genes possibly via specific interactions with histone deacetylases. Furthermore, we show that Tup1p and Cyc8p can be found independently of each other to negatively regulate gene transcription and can persist at active genes to negatively regulate on-going transcription. Together, these data suggest that Tup1p and Cyc8p can associate with inactive and active genes to mediate distinct negative and positive regulatory roles when functioning within, and possibly out with the complex.
2023-07-05 | GSE230732 | GEO
Project description:The Saccharomyces cerevisiae Swi-Snf co-activator complex was the first ATP-dependent chromatin remodelling complex discovered which functions by altering promoter chromatin structure to enable gene transcription. Conversely, the yeast Tup1-Cyc8 complex was identified as the first global co-repressor which can repress transcription by establishing ordered arrays of hypoacetylated nucleosomes across gene promoters. Although studies have indicated potential cooperation between these archetypal complexes upon transcription regulation, the precise mechanism and global extent of this antagonistic interplay remains unclear. We have identified all of the genes subject to repression by Tup1-Cyc8 and activation by Swi-Snf in glucose-grown yeast. These antagonistically regulated genes are enriched for those involved in cell wall structure and sugar metabolism. The data reveals that some co-regulated genes are kept inactive by Tup1-Cyc8 in wt and are de-repressed in the absence of CYC8 in a SNF2-dependent manner. Conversely, other co-regulated genes are actively transcribed in wt at levels mediated by the net negative influence of CYC8 and the positive influence of SNF2. In all cases, co-regulated genes located nearest to telomeres are subject to the most robust regulation by Swi-Snf and Tup1-Cyc8. ChIP analysis suggests that Snf2p and Cyc8p are present at both the active and inactive co-regulated genes in wt, where SNF2 is required for full Tup1p occupancy. We show that Snf2p and Cyc8p can directly interact with each other, most likely in the context of their respective complexes, suggesting that Swi-Snf and Tup1-Cyc8 are present together at co-regulated genes. We demonstrate that the nucleosome remodelling activities by Swi-Snf and Tup1-Cyc8 are specific to each target gene and extend over the available upstream intergenic region, the length of which is dependent upon the genes chromosomal context. Together, these data/ provide a deeper insight into the interplay between Tup1-Cyc8 and Swi-Snf upon transcription regulation and /suggest their occupancy and activity are intimately intertwined to yield the target gene transcriptional outcome via chromosomal location-dependent chromatin remodelling covering the available upstream gene regions.
2026-06-04 | GSE327900 | GEO
Project description:The Saccharomyces cerevisiae Swi-Snf co-activator complex was the first ATP-dependent chromatin remodelling complex discovered which functions by altering promoter chromatin structure to enable gene transcription. Conversely, the yeast Tup1-Cyc8 complex was identified as the first global co-repressor which can repress transcription by establishing ordered arrays of hypoacetylated nucleosomes across gene promoters. Although studies have indicated potential cooperation between these archetypal complexes upon transcription regulation, the precise mechanism and global extent of this antagonistic interplay remains unclear. We have identified all of the genes subject to repression by Tup1-Cyc8 and activation by Swi-Snf in glucose-grown yeast. These antagonistically regulated genes are enriched for those involved in cell wall structure and sugar metabolism. The data reveals that some co-regulated genes are kept inactive by Tup1-Cyc8 in wt and are de-repressed in the absence of CYC8 in a SNF2-dependent manner. Conversely, other co-regulated genes are actively transcribed in wt at levels mediated by the net negative influence of CYC8 and the positive influence of SNF2. In all cases, co-regulated genes located nearest to telomeres are subject to the most robust regulation by Swi-Snf and Tup1-Cyc8. ChIP analysis suggests that Snf2p and Cyc8p are present at both the active and inactive co-regulated genes in wt, where SNF2 is required for full Tup1p occupancy. We show that Snf2p and Cyc8p can directly interact with each other, most likely in the context of their respective complexes, suggesting that Swi-Snf and Tup1-Cyc8 are present together at co-regulated genes. We demonstrate that the nucleosome remodelling activities by Swi-Snf and Tup1-Cyc8 are specific to each target gene and extend over the available upstream intergenic region, the length of which is dependent upon the genes chromosomal context. Together, these data/ provide a deeper insight into the interplay between Tup1-Cyc8 and Swi-Snf upon transcription regulation and /suggest their occupancy and activity are intimately intertwined to yield the target gene transcriptional outcome via chromosomal location-dependent chromatin remodelling covering the available upstream gene regions.
2026-06-04 | GSE302848 | GEO