Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe
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ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe 972h-
SUBMITTER: Ian Carter-O'Connell
PROVIDER: E-GEOD-39499 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Genome-wide characterization of the phosphate starvation response in Schizosaccharomyces pombe.
Carter-O'Connell Ian I Peel Michael T MT Wykoff Dennis D DD O'Shea Erin K EK
BMC genomics 20121212
<h4>Background</h4>Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway, leading to expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway involving genetically identified positive (pho7+) and negative (csk1+) regulators. The genes ind ...[more]
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Project description:Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway leading to the expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway. The genes induced by phosphate limitation and the molecular mechanism by which the genetically identified positive (pho7+) and negative (csk1+) regulators function are not known. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response. We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response for the ScPHO5 (pho1+), ScPHO84 (spbc8e4.01c+), and ScGIT1 (spbc1271.09+) orthologs. We use ChIP-Seq to identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction. We provide a global analysis of the PHO pathway in S. pombe. Our results elucidate the conserved core regulon required for responding to phosphate starvation between distantly related ascomycetes and a better understanding of flexibility in environmental stress response networks. Schizosaccharomyces pombe 972 h- cells were starved for inorganic phosphate for 0, 30, 60, 120, or 240 minutes pior to microarray preparation to determine the extent and temporal resolution of the phosphate starvation response. At 120 minutes post-starvation we define a set of genes that are directly and specifically induced by phosphate starvation, providing a time-point at which all other experiments were performed. We characterize the pho7+- and csk1+- dependency of this PHO response at 120 minutes post-starvation in pho7+csk1+, pho7M-NM-^T, csk1M-NM-^T, and pho7M-NM-^Tcsk1M-NM-^T cells. In a seperate set of experiments we characterized the S. pombe stress response to copper limitation, iron limitation, and carbon switching at 120 minutes post-stress and osmotic shift at 20 minutes post-stress in both pho7+ and pho7M-NM-^T cells.
2013-01-02 | E-GEOD-39478 | biostudies-arrayexpress
Project description:Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway leading to the expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway. The genes induced by phosphate limitation and the molecular mechanism by which the genetically identified positive (pho7+) and negative (csk1+) regulators function are not known. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response. We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response for the ScPHO5 (pho1+), ScPHO84 (spbc8e4.01c+), and ScGIT1 (spbc1271.09+) orthologs. We use ChIP-Seq to identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction. We provide a global analysis of the PHO pathway in S. pombe. Our results elucidate the conserved core regulon required for responding to phosphate starvation between distantly related ascomycetes and a better understanding of flexibility in environmental stress response networks. ChIP Sequencing of the Schizosaccharomyces pombe 972h- transcription factor Pho7-TAP in high-Pi, no-Pi, and csk1M-NM-^T conditions
2013-01-02 | E-GEOD-39498 | biostudies-arrayexpress
Project description:Masson pine (Pinus massoniana) has evolved some adaptations for growth in low P soils. To elucidate these mechanisms, we investigated global gene expression profiles of the masson pine responding to long-term phosphorus starvation and different Pi levels (P1, 0.01 mM P; P2, 0.06 mM P). Analysis used phosphorus-sufficient treatment RNA as control samples for comparison to the experimental samples (P1 and P2) taken at 12, 24, 48 and 60 day. Indirect comparisons were made across multiple arrays with raw data pulled from different channels for data analysis and comparison to the control data.
2013-11-30 | E-GEOD-52835 | biostudies-arrayexpress
Project description:Changes in gene expression are hallmarks of cellular differentiation. Sexual differentiation in fission yeast (Schizosaccharomyces pombe) provides a model system for gene expression programs accompanying and driving cellular specialization. The expression of hundreds of genes is modulated in successive waves during meiosis and sporulation in S. pombe, and several known transcription factors are critical for these processes. We used DNA microarrays to investigate meiotic gene regulation by examining transcriptomes after genetic perturbations (gene deletion and/or overexpression) of rep1, mei4, atf21 and atf31, which encode known transcription factors controlling sexual differentiation. This analysis reveals target genes at a genome-wide scale and uncovers combinatorial control by Atf21p and Atf31p. We also studied two transcription factors that are upregulated during meiosis but had not been previously implicated in sexual differentiation : Rsv2p induces stress-related genes during spore formation, while Rsv1p acts as a repressor for glucose-metabolism genes. Our data further reveal negative feedback interactions: both Rep1p and Mei4p not only activate specific gene expression waves (early and middle genes, respectively), but are also required for repression of genes induced in the previous waves (Ste11p-dependent and early genes, respectively).
2008-01-01 | E-TABM-300 | biostudies-arrayexpress
Project description:Changes in gene expression are hallmarks of cellular differentiation. Sexual differentiation in fission yeast (Schizosaccharomyces pombe) provides a model system for gene expression programs accompanying and driving cellular specialization. The expression of hundreds of genes is modulated in successive waves during meiosis and sporulation in S. pombe, and several known transcription factors are critical for these processes. We used DNA microarrays to investigate meiotic gene regulation by examining transcriptomes after genetic perturbations (gene deletion and/or overexpression) of rep1, mei4, atf21 and atf31, which encode known transcription factors controlling sexual differentiation. This analysis reveals target genes at a genome-wide scale and uncovers combinatorial control by Atf21p and Atf31p. We also studied two transcription factors that are upregulated during meiosis but had not been previously implicated in sexual differentiation : Rsv2p induces stress-related genes during spore formation, while Rsv1p acts as a repressor for glucose-metabolism genes. Our data further reveal negative feedback interactions: both Rep1p and Mei4p not only activate specific gene expression waves (early and middle genes, respectively), but are also required for repression of genes induced in the previous waves (Ste11p-dependent and early genes, respectively).
2008-01-01 | E-TABM-298 | biostudies-arrayexpress
Project description:Plant vacuoles serve as the primary intracellular compartments for inorganic phosphate (Pi) storage. Passage of Pi across vacuolar membranes plays a critical role in buffering the cytoplasmic Pi level against fluctuations of external Pi and metabolic activities. Here we demonstrate that the SPX-MFS proteins, designated as Phosphate Transporter 5 family (PHT5), also named Vacuolar Phosphate Transporter (VPT), function as vacuolar Pi transporters. Based on 31P-magnetic resonance spectroscopy analysis, Arabidopsis pht5;1 loss-of-function mutants accumulate less Pi and exhibit a lower vacuolar-to-cytoplasmic Pi ratio than controls. Conversely, overexpression of PHT5 leads to massive Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. Furthermore, we show that heterologous expression of OsSPX-MFS1, the rice PHT5 homolog, mediates Pi influx to yeast vacuoles. Our findings uncover a group of Pi transporters in vacuolar membranes that regulate the cytoplasmic Pi homeostasis required for the fitness of plant growth. 10-day seedlings grown on Pi-sufficient medium or followed by 1-day or 3-day Pi starvation, shoot RNA and root RNA were extracted separately
2016-03-28 | E-GEOD-74856 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in Sphingomonas. sp A1 AlgO-deficient mutant grown on alginate compared with that on yeast extract AlgO is a possble transcriptional factor described in J. Bacteriol. (2000) 182(14):3998-4004 by Momma K, Okamoto M, Mishima Y, Mori S, Hashimoto W, and Murata K. A two chip study using total RNA recovered from two cultures of Sphingomonas. sp A1 AlgO-deficient mutant grown in 0.5% alginate medium and 0.5% yeast extract medium. Each chip measures the expression level of genes from Sphingomonas. sp A1.
2014-01-28 | E-GEOD-54410 | biostudies-arrayexpress
Project description:In E. coli the phosphate homeostasis is regulated by the Pst system and the two-component system PhoB/R. Pathogens like E. coli O157:H7 are responsible for many outbreaks and can be found and survive in poor inorganic phosphate (Pi) environments. To understand global EHEC O157:H7 EDL933 strain responses to Pi-starvation, we compared the transcriptomes of EDL933 the WT strain grown in MOPS Pi rich medium and that grown in MOPS Pi poor medium, using the Affymetrix GeneChip® E. coli Genome 2.0 Array. Also we investigated the EDL933 global response to the absence of PhoB by comparing the transcriptomes of the WT strain the ΔphoB mutant both grown in Low Pi EDL933WT strain and its isogenic mutant ΔphoB were grown in Pi- and/or in Pi+ conditions until the OD600 reached respectively 0.55 to 0.6. Samples equal to 5.108 CFU were taken from this mid log phase and processed for transcriptomes analysis. Ten µg of RNAs were extracted and retro-transcripted. One µg of the fragmented and biotinylated cDNAs, were hybridized onto Affymetrix GeneChip® E. coli. The data were processed using the FlexArray® software; RMA normalization and the levels of transcription obtained from 3 biological replicates of each experimental condition were compared using the EB (Wright & Simon) algorithm. We then conducted comparisons between EDL933WT grown in Pi- and in Pi+ conditions (comparison A) and between EDL933WT and EDL933∆phoB strains both grown in Pi- (comparison B). The differentially expression conditions corresponded to 2-fold change (FC) cut-off and p-value < 0.05.
2014-03-15 | E-GEOD-50529 | biostudies-arrayexpress
Project description:This study is aimed for the identification of novel small RNAs under different ethanol producing conditions. We have applied transcriptome analysis to facilitate identification and validation of 15 novel sRNAs in Zymomonas mobilis. We furthermore characterize their expression in the context of high and low levels of intracellular ethanol. Here, we report that 3 of the sRNAs (Zms2, Zms4 and Zms6) are differentially expressed under aerobic and anaerobic conditions, when low and high ethanol productions are observed respectively. These data suggests that in this organism regulatory RNAs can be associated with metabolic functions involved in ethanol stress responses. Z. mobilis was grown under aerobic and anaerobic conditions which showed low and high ethanol production, respectively. Each samples were sequenced for identification of small RNA candidates and differentially expressed candidates between two conditions.
2014-05-20 | E-GEOD-57773 | biostudies-arrayexpress
Project description:We used cDNA generated from total mRNA for RNA-Seq analysis (Genome Analyzer II at GATC Biotech AG) to monitore the gene expression of P. putida after a cold shock from 30M-BM-0C to 10M-BM-0C Culture was grown in minimal medium supplemented with succinate at 30M-BM-0C. In mid-exp. phase cells were harvested for subsequent RNA extraction (standard condition) and medium was cooled down to 10M-BM-0C. Two hrs after reaching the temperature, cells were again harvested for RNA extraction.
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