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Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor

ABSTRACT: The Crabtree effect, in which fermentative metabolism is preferred at the expense of respiration, is a hallmark of budding yeast’s glucose response and a model for the Warburg effect in human tumors. While the glucose-responsive transcriptional repressors Mig1p and Mig2p play well-characterized roles in the Crabtree effect, little function for the related Mig3p transcription factor has been uncovered despite numerous investigations of laboratory yeast strains. Here we studied a wild isolate of Saccharomyces cerevisiae to uncover a critical role for Mig3p that has been lost in S288c-derived laboratory strains. We found that Mig3p affects the expression of hundreds of glucose-responsive genes in the oak strain YPS163, both during growth under standard conditions and upon ethanol treatment. Our results suggest that Mig3p may act as a multifunctional activator/repressor that plays separate roles under standard versus stress conditions, but this function has been largely lost in the lab strains. Population analysis suggests that the lab strain, and several wild strains, harbor mutations that diminish Mig3p function. Thus, by expanding our attention to multiple genetic backgrounds, we have uncovered an important missing link in a key metabolic response.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE40153 | GEO | 2012/11/01

SECONDARY ACCESSION(S): PRJNA172935

REPOSITORIES: GEO

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Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor

Project description:The Crabtree effect, in which fermentative metabolism is preferred at the expense of respiration, is a hallmark of budding yeast’s glucose response and a model for the Warburg effect in human tumors. While the glucose-responsive transcriptional repressors Mig1p and Mig2p play well-characterized roles in the Crabtree effect, little function for the related Mig3p transcription factor has been uncovered despite numerous investigations of laboratory yeast strains. Here we studied a wild isolate of Saccharomyces cerevisiae to uncover a critical role for Mig3p that has been lost in S288c-derived laboratory strains. We found that Mig3p affects the expression of hundreds of glucose-responsive genes in the oak strain YPS163, both during growth under standard conditions and upon ethanol treatment. Our results suggest that Mig3p may act as a multifunctional activator/repressor that plays separate roles under standard versus stress conditions, but this function has been largely lost in the lab strains. Population analysis suggests that the lab strain, and several wild strains, harbor mutations that diminish Mig3p function. Thus, by expanding our attention to multiple genetic backgrounds, we have uncovered an important missing link in a key metabolic response. We performed a series of microarray experiments comparing the gene expression response of unstressed or EtOH stressed wild-type or mig3∆ strains in either the BY4741 or YPS163 background (biological triplicates). We also compared gene expression for in reciprocal hemizygous strains (YPS163/BY4741mig3∆ and YPS163mig3∆/BY4742; biological duplicates). Lastly, we measured the gene expression of BY4741 over-expressing BY_MIG3 via galactose induction (biological triplicates).

2012-11-01 | E-GEOD-40153 | biostudies-arrayexpress

Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (gene expression)

Project description:Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain Keywords: Gene expression comparisons in different yeast strains

2008-09-05 | GSE10268 | GEO

Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (CGH)

Project description:Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain Keywords: comparative genomic hybridizations (CGH) comparing different yeast strains

2008-09-05 | GSE10267 | GEO

Comparison of the transcriptional response to ethanol in laboratory and wild yeast strains

2010-12-17 | GSE22904 | GEO

eQTL Mapping of the Yeast Ethanol Response

Project description:In a previous study, we identified extensive natural variation in the response to acute ethanol treatment in three yeast strains: a lab strain derived from the commonly used S288c (DBY8268), vineyard isolate M22, and oak soil strain YPS163. Many expression differences persisted across several modules of co-regulated genes, implicating trans-acting systemic differences in ethanol sensing and/or response. To understand the genetic basis for these expression differences, we performed eQTL mapping analysis of the response to acute ethanol stress in ~100 F2 strains from two crosses: DBY8268x M22 and DBY8268 x YPS163.

2014-10-02 | GSE54196 | GEO

Comparison of the transcriptional response to ethanol in laboratory and wild yeast strains

Project description:An S288c-derived lab strain of Saccharomyces cerevisiae has lower ethanol resistance than either the vineyard strain M22 or the oak strain YPS163. We performed a 60 minute time-course experiment in the presence of 5% ethanol and compared the transcriptional response to ethanol between strains. We additionally analyzed the time-point of maximal response (30 min.) in wild type cells, YPS163 msn2D, and YPS163 hap1D cells. The genomic expression response to 5% ethanol stress was measured in 3 different strain backgrounds, and 2 different mutant backgrounds. Basal gene expression was also compared in two non-lab strains to the S288c reference. A single replicate was performed for the time-course experiment. All of the single time-point experiments were performed using biological triplicates.

2010-12-17 | E-GEOD-22904 | biostudies-arrayexpress

Regulatory T and T helper cells from BXD mouse strains

Project description:Parental and BXD mouse lines were received from Jackson Laboratory and The Oak Ridge National Laboratory. Splenocytes were isolated and stained with anti-CD4 and anti-CD25 antibodies. CD4+ T cells were separated into CD4+CD25+ Treg and CD4+CD25- Th cells. Tregs and Th cell were collected from spleens of 31 BXD recombinant inbred strains and of the parental mouse strains DBA/2J and C57BL/6J. Gene expression was measured by microarrays. The comparative analysis of the transcriptomes from the two cell populations allowed us to identify many novel differentially expressed genes. Furthermore, the analysis of cis- and trans-expression Quantitative Trail Loci (eQTLs) showed that both common and unique regulatory mechanisms are active in the two cell types.

2011-12-15 | E-MTAB-836 | biostudies-arrayexpress

Transcriptomic comparison of WT and yebEFG mutant of Salmonella enterica ATCC 14028 strains grown in LB and in the presence of sublethal concentration of nalidixic acid

Project description:RNA-sequencing of two Salmonella enterica strains (WT, ∆yebEFG) in standard laboratory conditions (LB to ESP), and in SOS-response inducing conditions (LB+nalidixic acid)

2021-05-05 | GSE159310 | GEO

Adaptive laboratory evolution of chorismate synthase knockouts

Project description:We used RNA-seq to profile E. coli K-12 MG1655 strains subjected to adaptive laboratory evolution after chorismate synthase knockouts. Either isochorismate synthase (menF) or isochorismate synthase AND chorismate lyase (ubiC) was deleted from a strain of E. coli K-12 MG1655 that had already been previously adapted for growth on glucose minimal media. RNA-seq profiles of the original glucose-adapted strain, the 2 deletion strains, and 4 laboratory-evolved strains from each deletion are included in duplicate. ubiC catalyzes the first committed step of ubiquinone synthesis, an important molecule for the electron transport chain. Thus, these experiments allowed assessment of cellular adaptations to restore energy metabolism capability.

2023-02-08 | GSE224889 | GEO

Transcription profiling of rat insulinoma (INS-1 derived) cell lines that vary in their glucose responsiveness

Project description:The aim of this study was to identify the gene expression changes associated with glucose responsiveness in Rat INS-1 derived cell lines. RNA was prepared from cell lines which were shown to be highly glucose responsive and also lines which were shown to be poorly glucose responsive. Dr. Chris Newgard's lab quantified the RNA and sent it frozen in water. 3 biological replicates per condition were sent for the following conditions: (i) 832/13 and 833/15, robust glucose responsiveness; (ii)832/1 and 832/2 showed poor glucose responsiveness.

2007-09-11 | E-CBIL-35 | biostudies-arrayexpress

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