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A. fumigatus wild type and delta phoB(PHO80) strains transcriptome analysis for growth upon minimal medium 0.1 mM Pi

ABSTRACT: Phosphate is an essential ion for fungal growth, required for proper DNA and phospholipids biosyntesis, energetic metabolism and signal transduction. The systems for inorganic phosphate (Pi) acquisition in eukaryotic cells (PHO) have been characterized as a low-affinity (that assures a supply of Pi at normal or high external Pi concentrations) and a high-affinity (activated in response to Pi starvation). Here, as an initial step to understand the PHO pathway in A. fumigatus, we characterized the PHO80 homologue, phoB(PHO80). We showed that the delta phoB(PHO80) mutant has a severe polar growth defect and there is an interaction between PhoB(PHO80), calcineurin and calcium metabolism. Microarray hybridizations carried out with RNA obtained from wild type and delta phoB(PHO80) mutant cells showed that Afu4g03610 [phoD(PHO84)], Afu7g06350 [phoE9(PHO89)], Afu4g06020 [phoCPHO81)], and Afu2g09040 (vacuolar transporter Vtc4) were more expressed either in the delta phoB(PHO80) mutant background or in 0.1 mM Pi. Keywords: gene expression array-based (log2 ratio)

ORGANISM(S): Aspergillus fumigatus

PROVIDER: GSE9548 | GEO | 2007/11/09

SECONDARY ACCESSION(S): PRJNA105183

REPOSITORIES: GEO

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Project description:Binding of transcription factors to DNA is a key regulatory step in the control of gene expression. DNA sequences with high affinity for transcription factors occur more frequently in the genome than instances of genes bound or regulated by these factors. How specific gene regulation is achieved by transcription factors remains unclear. We used genome-wide approaches to study how trans factors shape the binding and regulatory landscape of Pho4, a budding yeast transcription factor that activates gene expression in response to phosphate limitation. In no phosphate (0mM phosphate) medium, Pho4 is transported into the nucleus and activates transcription of a set of genes (PHO) that are necessary for cell survival in phosphate limited environment. In high phosphate (10mM phosphate) medium, Pho4 is transported outside of the nucleus and the transcription program of PHO genes are turned off. Here we examined the transcription profiling of S. cerevisiae (W303) in various strains treated in media with 10mM or 0mM inorganic phosphate, to study the the transcription activation by Pho4 its cooperative binding factor Pho2, and its competitive binding factor Cbf1. (I) To infer how much Pho4 itself, Pho2 itself, and the interaction between Pho2 and Pho4 contribute to transcriptional activation in response to Pi starvation, we applied mutant cycle analysis to compare wild type, pho2Δ, pho4Δ and pho2Δ pho4Δ strains in both 10 mM and 0 mM Pi conditions. Mutant cycle analysis is a cyclic comparison among all various mutants. For example, by comparing pho2Δ and pho2Δ pho4Δ, we can directly infer the contribution from Pho4 alone to gene activation. And by comparing wild type and pho2Δ, we can infer the contribution from Pho2 alone together with that from the interaction between Pho2 and Pho4. (II) Compare two strains or one strain in two treatments in multiple replicates with dye-swap method. wt no vs high Pi, to identify genes that are induced in response to Pi starvation. cbf1Δ vs wt in high Pi, to identify the influence of Cbf1 on gene expression in high Pi condition. cbf1Δpho4Δ vs wt in high Pi, to identify the influence of Cbf1 on gene expression that is mediated through Pho4, in high Pi condition. rtg3Δtye7Δ vs wt in high Pi, to identify the influence of Rtg3 and Tye7 on gene expression in high Pi condition. pho80Δ vs pho80Δpho4Δ, to identify the genes that are activated Pho4 when Pho4 is fully nuclear localized. pho80Δcbf1Δ vs pho80Δcbf1Δpho4Δ, to identify the influence of Cbf1 on gene expression that is mediated through Pho4, when Pho4 is fully nuclear localized.

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A. fumigatus wild type and delta phoB(PHO80) strains transcriptome analysis for growth upon minimal medium 0.1 mM Pi

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