Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA396952 | ENA |
REPOSITORIES: ENA
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Project description:Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK
| PRJNA433655 | ENA
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: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:Investigation of whole genome gene expression changes at short (2 hours) and extended (24 hours) timepoints in wild-type Saccharomyces cerevisiae treated with 50 μM menadione during exponential growth compared to an rph1Δ strain Transient treatment with 50 μM menadione elevates mitochondrial ROS and extends chronological lifespan in yeast. Deletion of RPH1, a H3K36me3 histone demethylase, block chronological lifespan extension. This study aimed to identify Rph1p-dependent gene expression changes induced by menadione treatment that may support chronological lifespan extension. Reference: Bonawitz, N.D., Chatenay-Lapointe, M., Wearn, C.M., and Shadel, G.S. (2008). Expression of the rDNA-encoded mitochondrial protein Tar1p is stringently controlled and responds differentially to mitochondrial respiratory demand and dysfunction. Curr Genet 54, 83-94.
2013-03-22 | GSE45383 | GEO
Project description:Investigation of whole genome gene expression changes at short (2 hours) and extended (24 hours) timepoints in wild-type Saccharomyces cerevisiae treated with 50 μM menadione during exponential growth compared to an rph1Δ strain Transient treatment with 50 μM menadione elevates mitochondrial ROS and extends chronological lifespan in yeast. Deletion of RPH1, a H3K36me3 histone demethylase, block chronological lifespan extension. This study aimed to identify Rph1p-dependent gene expression changes induced by menadione treatment that may support chronological lifespan extension. Reference: Bonawitz, N.D., Chatenay-Lapointe, M., Wearn, C.M., and Shadel, G.S. (2008). Expression of the rDNA-encoded mitochondrial protein Tar1p is stringently controlled and responds differentially to mitochondrial respiratory demand and dysfunction. Curr Genet 54, 83-94. A 24 chip study using total RNA recovered from two separate cultures each of Saccharomyces cerevisiae wild-type DBY2006 and rph1Δ. Each chip measures expression levels of 5,777 transcripts from NCBI build June 2008 with 8 probes per transcript and 3 replicate probe sets.
2013-03-22 | E-GEOD-45383 | biostudies-arrayexpress
Project description:Snf1/AMPK functions as a heterotrimeric complex, consisting of a regulatory subunit that is senses the energy status, a catalytic subunit with the canonical kinase domain and a scaffolding subunit to secure the complex together. The high degree of conservation in the sequence, structure and function of yeast Snf1 and mammalian AMPK, it is only logical to investigate the extent of conservation in the downstream effects that are controlled by these kinases.
2020-12-18 | GSE29358 | GEO
Project description:Alkaline pH stress invokes in S. cerevisiae a potent and fast transcriptional response that includes many genes repressed by glucose. Certain mutants in the glucose-sensing and response pathways, such as those lacking the Snf1 kinase, are sensitive to alkalinization. We show that addition of glucose to the medium improves growth of wild type cells at high pH, fully abolish the snf1 alkali-sensitive phenotype and attenuates high pH-induced Snf1 phosphorylation at Thr210. The elm1 mutant, lacking one of the three upstream Snf1 kinases (tos3, elm1 and sak1), is markedly alkali sensitive, whereas the phenotype of the tos3 elm1 sak1 strain is even stronger than that of snf1 cells and it is not fully rescued by glucose supplementation. DNA microarray analysis reveals that about 75% of genes induced at short term by high pH are also induced by glucose scarcity. Snf1 mediates, in full or in part, the activation of a significant subset (38%) of short-term alkali-induced genes, including those coding high-affinity hexose transporters and phosphorylating enzymes. Induction of genes encoding enzymes involved in glycogen (but not trehalose) metabolism is largely dependent of the presence of Snf1. Therefore, the function of Snf1 in adaptation to glucose scarcity appears crucial for alkaline pH tolerance. Incorporation of micromolar amounts of iron and copper to a glucose-supplemented medium result in an additive effect and allows near normal growth at high pH, thus indicating that these three nutrients are key limiting factors for growth in an alkaline environment.
2012-03-02 | GSE25697 | GEO
Project description:Studies of aging and longevity are revealing how diseases that shorten life can be controlled to improve the quality of life and lifespan itself. Two strategies under intense study to accomplish this goal are rapamycin treatment and calorie restriction. New strategies are being discovered including one that uses low-dose myriocin treatment. Myriocin inhibits the first enzyme in sphingolipid synthesis in all eukaryotes and we showed recently that low-dose myriocin treatment increases yeast lifespan at least in part by down-regulating the sphingolipid-controlled Pkh1/2-Sch9 (ortholog of mammalian S6 kinase) signaling pathway. Here we show that myriocin treatment has global influences and modulates the evolutionarily conserved Snf1/AMPK, PKA and TORC1 signaling pathways to enhance yeast lifespan. These extensive affects of myriocin rival those of rapamycin and calorie restriction. Our studies in yeast along with other studies in mammals reveal the potential of myriocin or related compounds to lower the incidence of age-related diseases in humans. No-myriocin-treated cells and myriocin-treated cells; three biological replicates in each treatment
2014-09-22 | E-GEOD-41362 | biostudies-arrayexpress
Project description:Alkaline pH stress invokes in S. cerevisiae a potent and fast transcriptional response that includes many genes repressed by glucose. Certain mutants in the glucose-sensing and response pathways, such as those lacking the Snf1 kinase, are sensitive to alkalinization. We show that addition of glucose to the medium improves growth of wild type cells at high pH, fully abolish the snf1 alkali-sensitive phenotype and attenuates high pH-induced Snf1 phosphorylation at Thr210. The elm1 mutant, lacking one of the three upstream Snf1 kinases (tos3, elm1 and sak1), is markedly alkali sensitive, whereas the phenotype of the tos3 elm1 sak1 strain is even stronger than that of snf1 cells and it is not fully rescued by glucose supplementation. DNA microarray analysis reveals that about 75% of genes induced at short term by high pH are also induced by glucose scarcity. Snf1 mediates, in full or in part, the activation of a significant subset (38%) of short-term alkali-induced genes, including those coding high-affinity hexose transporters and phosphorylating enzymes. Induction of genes encoding enzymes involved in glycogen (but not trehalose) metabolism is largely dependent of the presence of Snf1. Therefore, the function of Snf1 in adaptation to glucose scarcity appears crucial for alkaline pH tolerance. Incorporation of micromolar amounts of iron and copper to a glucose-supplemented medium result in an additive effect and allows near normal growth at high pH, thus indicating that these three nutrients are key limiting factors for growth in an alkaline environment. We identified the changes in the expression profiles caused by alkalinization of the medium (pH8 vs. pH5.5 for 10 min) in several strains: wild type cells (4 chips), snf1 mutant cells (4 chips) We also identified the transcriptomic changes that occur after glucose deprivation (0.05% vs 2% for 15 min) in: wild type cells (2 chips) snf1 mutant cells (2 chips) Total: 12 chips
2012-03-02 | E-GEOD-25697 | biostudies-arrayexpress
Project description:The conserved Snf1/AMPK (AMP-activated protein Kinase) family is one of the central components in nutrient sensing and regulation of carbon metabolism in eukaryotes. It is also involved in several other processes such as stress resistance, invasive growth and ageing. Snf1 kinase is composed of a catalytic alpha-subunit Snf1, a regulatory gamma-subunit Snf4 and one of three possible beta-subunits, Sip1, Sip2 or Gal83. We used a systematic approach to study the role of the three beta-subunits by analyzing all 7 possible combinations of beta-subunit deletions together with the reference strain.
2010-05-27 | E-GEOD-20591 | biostudies-arrayexpress