A p53-like like transcription factor similar to Ndt80 controls the response to nutrient stress in the filamentous fungus, Aspergillus nidulans
Ontology highlight
ABSTRACT:
ORGANISM(S): Aspergillus nidulans
PROVIDER: GSE36235 | GEO | 2013/01/31
SECONDARY ACCESSION(S): PRJNA153149
REPOSITORIES: GEO
Similar Datasets
Project description:The xprG gene encodes a putative transcriptional activator involved in the regulation of extracellular proteases in response to nutrient stress in Aspergillus nidulans. To investigate whether XprG is required for expression of other genes in response to carbon starvation, we used microarrays provided by the PFGRC. These experiments indicate that the expression of many genes, including the sterigmatocystin gene cluster and other secondary metabolism genes, genes involved in asexual and sexual development and genes induced during autolysis, is altered in an xprGdelta mutant. Many of these genes are known to be regulated in response to carbon starvation. The results indicate that XprG may play a major role in the response to carbon limitation. An xprG+ (wt) strain and xprGdelta gene knockout strain (ko) were compared after transfer to medium containing 1% glucose (C) or carbon-free medium (NC) for 16 hours. The effect of the two nutrient conditions on each strain were also investigated.
2013-01-31 | E-GEOD-36235 | biostudies-arrayexpress
Project description:Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus.
2014-04-01 | GSE54940 | GEO
Project description:Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus. A one-chip study (data from 12 subarrays collected from a 12-plex Nimblegen microarray (ID 527890) using total RNA recovered from three separate glass-bead cultures of Paxillus involutus (ATCC200175) grown on Minimum Melin Norkrans medium (MMN) amended with ammonium (C/N ratio 3) and harvested at different times of carbon starvation.)
2014-04-01 | E-GEOD-54940 | biostudies-arrayexpress
Project description:Depending on the prevailing environmental, developmental and nutritional conditions Aspergillus nidulans produces different combinations of secondary metabolites (SMs). To activate the biosynthetic gene cluster (BGC) for a given SM global, chromatin-based de-repression must be integrated with pathway-specific induction signals. Here we describe a new global regulator affecting the set of starvation-induced SMs. We found a hitherto uncharacterized putative PAS-domain containing kinase to be upregulated in SM-producing cultures. The predicted protein is highly similar to yeast Rim15 which transmits nutritional and stress signals to downstream effectors involved in chromatin regulation, stress and starvation response. The putative kinase – termed RimO – is required for the transcription of a number of starvation-induced SMs including sterigmatocystin (ST). RimO regulates the pathway-specific transcription factor AflR both at the transcriptional and post-translational level. In the absence of RimO aflR is barely transcribed under SM conditions and the protein is not retained in the nucleus. Genome-wide transcriptional profiling showed that cells lacking rimO fail to correctly respond to carbon and nitrogen starvation and continue to transcribe genes of the basic metabolism to a high level. Conversely, overexpression of the kinase made cells largely insensitive to glucose repression and led to overproduction of several secondary metabolites. We propose a model that positions RimO downstream of PKA being necessary to transmit the starvation signal to downstream targets, including chromatin and transcriptional regulators of SM gene clusters. Additionally, it may also regulate signaling modules required for recognizing the starvation response.
2022-03-01 | GSE184618 | GEO
Project description:Glutathione (GSH) is an abundant and widely distributed antioxidant in fungi. Hence, understanding cellular GSH metabolism is of vital importance to deciphering redox regulation in these microorganisms. In this study, we generated dugB (AN1879), dugC (AN1092), and dugB dugC double deletion mutants which display disruption of the GSH degradation pathway in Aspergillus nidulans. Deletion of dugB, dugC or both resulted in a moderate increase in GSH content under growing conditions and substantially slowed down the depletion of GSH pools under carbon starvation. Inactivation of dug genes caused reduced accumulation of reactive oxygen species, decreased autolytic cell wall degradation and extracellular enzyme production, increased sterigmatocystin formation but decreased viability in starving cultures. Changes in the transcriptomes suggested that enzyme secretions were controlled at post transcriptional level. In contrast, secondary metabolite production was also regulated at the level of mRNA abundance. Based on these findings, we suggest that GSH connects starvation and redox regulation to each other: A. nidulans cells utilize GSH as stored carbon source during starvation. The reduction of GSH contents of cells alters the redox state activating regulatory pathways responsible for carbon starvation stress responses. Under glucose rich conditions, inactivation of dug genes reduced conidia production of surface cultures, disturbed sexual development and down-regulated the transcription of genes encoding MAP kinase pathway proteins (e.g. steC, sskB, pbsA, hogA, mkkA) or proteins involved in the regulation of conidiogenesis or sexual differentiation (e.g. flbA,C,E, nosA, rosA, nsdC,D). These finding indicates that the authority of redox regulation goes far beyond the protection against redox stress; it affects development, stress responses (other than redox stress) and secondary metabolism as well.
2021-03-02 | GSE151461 | GEO
Project description:Adaptation of Lactococcus lactis towards progressive carbon starvation is mediated by three different types of transcriptomic responses: i) global responses, i.e. general decrease of functions linked to bacterial growth and lack of induction of the general stress response, ii) specific responses functionally related to glucose exhaustion, i.e. under expression of central metabolism genes, induction of alternative sugars transport and metabolism genes, induction of arginine deiminase pathway genes and iii) other responses never described previously during carbon starvation. Keywords: stress response, time course
2008-02-23 | GSE5761 | GEO
Project description:Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that over a third of the genes induced after 6 h of exposure to wheat straw were also induced during 6 h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides.
2014-08-22 | GSE57315 | GEO
Project description:Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that over a third of the genes induced after 6 h of exposure to wheat straw were also induced during 6 h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides. Eight samples in total consisting of duplicate shake flask Aspergillus niger cultures from four conditions: 48h glucose, 6 h starvation, 6 h wheat straw, 24 h starvation
2014-08-22 | E-GEOD-57315 | biostudies-arrayexpress
Project description:Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. It results from both mRNA transcription and degradation controls. However, the contribution of transcript stability regulation in gene expression is poorly characterized. Using combined transcriptome and mRNA decay analyses, we investigated (i) how transcript stability changes in E. coli during the glucose-acetate-starvation transition and (ii) if these changes contribute to gene expression changes. Our work highlights that transcript stability increases along carbon depletion. Most of the stabilization occurs at glucose-acetate transition when glucose is exhausted, then stabilized mRNAs remain stable during acetate consumption and carbon starvation. Meanwhile, expression of most genes is downregulated and we observed three time less gene expression upregulation. Using control analysis theory on 375 genes, we show that most of gene expression regulation is driven by changes in transcription. Although mRNA stabilization is not the controlling phenomenon, it contributes to the emphasis or attenuation of transcription regulation. However, upregulation of 18 genes (33% of our studied upregulated set) is mainly governed by transcript stabilization. Because these genes are associated with response to nutrient changes and stress, this illustrates the importance of post-transcriptional regulations in bacterial response to nutrient starvation.
2020-05-12 | GSE144316 | GEO
Project description:Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. It results from both mRNA transcription and degradation controls. However, the contribution of transcript stability regulation in gene expression is poorly characterized. Using combined transcriptome and mRNA decay analyses, we investigated (i) how transcript stability changes in E. coli during the glucose-acetate-starvation transition and (ii) if these changes contribute to gene expression changes. Our work highlights that transcript stability increases along carbon depletion. Most of the stabilization occurs at glucose-acetate transition when glucose is exhausted, then stabilized mRNAs remain stable during acetate consumption and carbon starvation. Meanwhile, expression of most genes is downregulated and we observed three time less gene expression upregulation. Using control analysis theory on 375 genes, we show that most of gene expression regulation is driven by changes in transcription. Although mRNA stabilization is not the controlling phenomenon, it contributes to the emphasis or attenuation of transcription regulation. However, upregulation of 18 genes (33% of our studied upregulated set) is mainly governed by transcript stabilization. Because these genes are associated with response to nutrient changes and stress, this illustrates the importance of post-transcriptional regulations in bacterial response to nutrient starvation.
2020-05-12 | GSE144315 | GEO