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Transcriptome reprogramming of key transcription factor deletion strains of Saccharomyces cerevisiae compared with the wild type strain by RNA-Seq

ABSTRACT: Saccharomyces cerevisiae cells have evolved remarkably sophisticated and flexible transcriptional regulatory networks (TRNs) that allow them to survive and thrive in stress conditions, such as high temperature, osmotic and oxidative conditions, etc. Furthermore, transcription factor plays a central role in transcriptional regulatory networks of stress response. To achieve a thorough understanding of master transcription factors and transcriptional regulatory networks in specific response to prolonged thermal stress, we sequenced mRNA from the cultures of the wild type strain ScY01a as well as four key transcription factor deletion strains including ScY01a (ric1∆), ScY01a (srb2∆), ScY01a (sin3∆) and ScY01a (mig1∆) grown at 40ºC in biological duplicates. Differences in gene expression comparing the transcription factor deletion strains with the wild type strain by RNA deep sequencing revealed a hierarchical transcriptional regulatory network required for long-term thermal stress tolerance of S. cerevisiae, which is centered on these four transcription factors.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE104356 | GEO | 2022/02/08

REPOSITORIES: GEO

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Transcriptome reprogramming of key transcription factor deletion strains of Saccharomyces cerevisiae compared with the wild type strain grown at normal temperature by RNA-Seq

Project description:Saccharomyces cerevisiae cells have evolved remarkably sophisticated and flexible transcriptional regulatory networks (TRNs) that allow them to survive and thrive in stress conditions, such as high temperature, osmotic and oxidative conditions, etc. Furthermore, transcription factor plays a central role in transcriptional regulatory networks of stress response. To achieve a thorough understanding of master transcription factors and transcriptional regulatory networks in specific response to prolonged thermal stress, we previously sequenced mRNA from the cultures of the wild type strain ScY01a as well as three key transcription factor deletion strains including ScY01a (srb2∆), ScY01a (sin3∆) and ScY01a (mig1∆) grown at 40ºC in biological duplicates. Here, we further sequenced the corresponding samples cultured at 30ºC as a control. Differences in gene expression comparing the transcription factor deletion strains with the wild type strain by RNA deep sequencing revealed a hierarchical transcriptional regulatory network centered on these three transcription factors in S. cerevisiae.

2022-02-08 | GSE148213 | GEO

Base editing of general transcription factor Spt15 to enhance yeast stress tolerance

Project description:We aimed to explore the application of the Target-AID base editor in genomic in situ protein engineering by generating nonsynonymous mutations. A general transcription factor Spt15 (TATA-box binding protein) gene of Saccharomyces cerevisiae was selected as a target. Based on computational and experimental scanning mutagenesis of the Spt15 gene as well as flask-fermentation screening, three stress-tolerant Spt15 mutant strains (A140G, P169A and R238K) and two stress-sensitive Spt15 mutant strains (S118L and L214V) were obtained. To validate the regulatory mechanisms underlying these different Spt15 mutants, genome-wide transcriptome analysis by RNA sequencing was carried out to quantify global transcription changes in the Spt15 mutant strains compared to the wild type strain at the same culture conditions including the unstressed normal condition as well as hyperosmotic and thermal stress conditions. Results uncover the impacts of the Spt15 point mutations on global transcriptional regulation in response to hyperosmotic and thermal stresses, and provide insight into the applicability of the Target-AID base editor in genomic in situ protein engineering to alter yeast stress tolerance.

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The zinc finger protein Mig1 regulates mitochondrial function and azole drug susceptibility in the pathogenic fungus Cryptococcus neoformans

Project description:The opportunistic pathogen Cryptococcus neoformans causes fungal meningoencephalitis in immunocompromised individuals. In previous studies, we found that the Hap complex in this pathogen represses genes encoding mitochondrial respiratory functions and TCA cycle components under low-iron conditions. The orthologous Hap2/3/4/5 complex in Saccharomyces cerevisiae exerts a regulatory influence on mitochondrial functions and Hap4 is subject to glucose repression via the carbon catabolite repressor Mig1. In this study, we explored the regulatory link between a candidate ortholog of the Mig1 protein and the HapX component of the Hap complex in C. neoformans. This analysis revealed repression of MIG1 by HapX and activation of HAPX by Mig1 in low iron conditions, and Mig1 regulation of mitochondrial functions including respiration, tolerance for reactive oxygen species, and expression of genes for iron-consuming and iron-acquisition functions. Consistent with these regulatory functions, a mig1Î mutant had impaired growth on inhibitors of mitochondrial respiration and ROS inducers. Furthermore, deletion of MIG1 provoked a dysregulation in nutrient sensing via the TOR pathway and impacted the pathway for cell wall remodeling. Importantly, loss of Mig1 increased susceptibility to fluconazole thus further establishing a link between azole antifungal drugs and mitochondrial function. Mig1 and HapX were also required together for survival in macrophages, but Mig1 alone had a minimal impact on virulence in mice. Overall, these studies provide novel insights into a HapX/Mig1 regulatory network and reinforce an association between mitochondrial dysfunction and drug susceptibility that may provide new targets for the development of antifungal drugs. In this study, transcription profiles of WT and mig1D mutant strains of Cryptococcus neoformans were compared in a dye-swap experiment following 6hr exposure to Low Iron Medium (LIM) or LIM + 100mM FeCl3.

2015-12-17 | E-GEOD-76063 | biostudies-arrayexpress

Genetic reconstruction of a functional transcriptional regulatory network

Project description:Although global analyses of transcription factor binding provide one view of potential transcriptional regulatory networks, regulation also occurs at levels distinct from transcription factor binding. Here, we use a genetic approach to identify targets of transcription factors in yeast and reconstruct a functional regulatory network. First, we profiled transcriptional responses in S. cerevisiae strains with individual deletions of 263 transcription factors. Then we used directed-weighted graph modeling and regulatory epistasis analysis to identify indirect regulatory relationships between these transcription factors, and from this we reconstructed a functional transcriptional regulatory network. The enrichment of promoter motifs and Gene Ontology annotations provide insight into the biological functions of the transcription factors. Data values are X scores and corresponding p-values derived using an error model. We profiled transcriptional responses upon the individual deletion of more than 260 TFs. We used a directed-weighted graph modelling approach and regulatory epistasis analysis to identify indirect regulatory relationships, and thus constructed a refined, functional transcriptional regulatory network.

2010-07-02 | E-GEOD-4654 | biostudies-arrayexpress

Genetic reconstruction of a functional transcriptional regulatory network

Project description:Although global analyses of transcription factor binding provide one view of potential transcriptional regulatory networks, regulation also occurs at levels distinct from transcription factor binding. Here, we use a genetic approach to identify targets of transcription factors in yeast and reconstruct a functional regulatory network. First, we profiled transcriptional responses in S. cerevisiae strains with individual deletions of 263 transcription factors. Then we used directed-weighted graph modeling and regulatory epistasis analysis to identify indirect regulatory relationships between these transcription factors, and from this we reconstructed a functional transcriptional regulatory network. The enrichment of promoter motifs and Gene Ontology annotations provide insight into the biological functions of the transcription factors. Data values are X scores and corresponding p-values derived using an error model. Keywords: X scores and corresponding p-values derived using an error model

2007-04-01 | GSE4654 | GEO

Metabolic engineering of Saccharomyces cerevisiae and role of transcription factor Znf1

Project description:Agricultural wastes and other non-food sources can be used to produce biofuels. Despite multiple attempts using engineered yeast strains expressing exogenous genes, the native Saccharomyces cerevisiae produces low amount of second generations of biofuels. Here, we focused on Znf1, a non-fermentable carbon transcription factor and the suppressor protein Bud21 to overcome this challenge. Several mutants of engineered S. cerevisiae strains were engineered to enhance production of biofuels and xylose-derived compounds such as xylitol. This study demonstrates Znf1's novel transcriptional regulatory control of xylose and offer an initial step toward a more sustainable production of advanced biofuels from xylose.

2024-01-21 | PXD048648 | Pride

Ethanol cellular defense induce unfolded protein response in yeast

Project description:Ethanol is a valuable industrial product and a common metabolite used by many cell types. However, this molecule produces high levels of cytotoxicity affecting cellular performance at several levels. In the presence of ethanol, cells must adjust some of their components, such as the membrane lipids to maintain homeostasis. In the case of microorganism as Saccharomyces cerevisiae, ethanol is one of the principal products of their metabolism and is the main stress factor during fermentation. Although many efforts have been made, mechanisms of ethanol tolerance are not fully understood and very little evidence is available to date for specific signaling by ethanol in the cell. This work studied two Saccharomyces cerevisiae strains, CECT10094 and Temohaya-26, isolated from flor wine and traditional fermentations respectively, which differ in ethanol tolerance, in order to understand the molecular mechanisms underlying the ethanol stress response and the reasons for different ethanol tolerance. The transcriptome was analyzed after ethanol stress and, among others, an increased activation of genes related with the unfolded protein response (UPR) and its transcription factor, Hac1p, was observed in the tolerant strain CECT10094. We observed that this strain also resist more UPR agents than Temohaya-26 and the UPR-ethanol stress correlation was corroborated observing growth of 15 more strains and discarding UPR correlation with other stresses as thermal or oxidative stress. Furthermore, higher activation of UPR pathway in the tolerant strain CECT10094 was observed using a UPR mCherry reporter. Finally, we observed UPR activation in response to ethanol stress in other S. cerevisiae ethanol tolerant strains as the wine strains T73 and EC1118.

2016-02-03 | GSE44863 | GEO

The zinc finger protein Mig1 regulates mitochondrial function and azole drug susceptibility in the pathogenic fungus Cryptococcus neoformans

Project description:The opportunistic pathogen Cryptococcus neoformans causes fungal meningoencephalitis in immunocompromised individuals. In previous studies, we found that the Hap complex in this pathogen represses genes encoding mitochondrial respiratory functions and TCA cycle components under low-iron conditions. The orthologous Hap2/3/4/5 complex in Saccharomyces cerevisiae exerts a regulatory influence on mitochondrial functions and Hap4 is subject to glucose repression via the carbon catabolite repressor Mig1. In this study, we explored the regulatory link between a candidate ortholog of the Mig1 protein and the HapX component of the Hap complex in C. neoformans. This analysis revealed repression of MIG1 by HapX and activation of HAPX by Mig1 in low iron conditions, and Mig1 regulation of mitochondrial functions including respiration, tolerance for reactive oxygen species, and expression of genes for iron-consuming and iron-acquisition functions. Consistent with these regulatory functions, a mig1Δ mutant had impaired growth on inhibitors of mitochondrial respiration and ROS inducers. Furthermore, deletion of MIG1 provoked a dysregulation in nutrient sensing via the TOR pathway and impacted the pathway for cell wall remodeling. Importantly, loss of Mig1 increased susceptibility to fluconazole thus further establishing a link between azole antifungal drugs and mitochondrial function. Mig1 and HapX were also required together for survival in macrophages, but Mig1 alone had a minimal impact on virulence in mice. Overall, these studies provide novel insights into a HapX/Mig1 regulatory network and reinforce an association between mitochondrial dysfunction and drug susceptibility that may provide new targets for the development of antifungal drugs.

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