Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)
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ABSTRACT:
PROVIDER: PRJNA601909 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10907640_1.fastq.gz | Fastqsanger.gz | |||
| SRR10907640_2.fastq.gz | Fastqsanger.gz | |||
| SRR10907641_1.fastq.gz | Fastqsanger.gz | |||
| SRR10907641_2.fastq.gz | Fastqsanger.gz | |||
| SRR10907642_1.fastq.gz | Fastqsanger.gz |
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Project description:Validated transcriptional regulatory roles for five two-component systems in E. coli (ChIP-exo dataset)
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Project description:Validated transcriptional regulatory roles for five two-component systems in E. coli
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Project description:Escherichia coli use two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts of E. coli’s global transcriptional regulatory network (TRN). Here, we identified the regulons of five TCSs in E. coli MG1655: BaeSR and CpxAR, which were stimulated by ethanol stress, and KdpDE, PhoRB, and ZraSR, which were stimulated by potassium, phosphate, and zinc, respectively. We analyzed RNA-seq data using independent component analysis (ICA). ChIP-exo data was used to validate condition-specific target gene binding sites. Based on this data we (1) identify the target genes for each TCS; (2) show how the target genes are transcribed in response to stimulus; and (3) reveal novel relationships between TCSs, which indicate non-cognate inducers for various response regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to cell envelope stress. Our understanding of the TRN in E. coli is thus notably expanded.
2020-10-21 | GSE143851 | GEO
Project description:Escherichia coli use two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts of E. coli’s global transcriptional regulatory network (TRN). Here, we identified the regulons of five TCSs in E. coli MG1655: BaeSR and CpxAR, which were stimulated by ethanol stress, and KdpDE, PhoRB, and ZraSR, which were stimulated by potassium, phosphate, and zinc, respectively. We analyzed RNA-seq data using independent component analysis (ICA). ChIP-exo data was used to validate condition-specific target gene binding sites. Based on this data we (1) identify the target genes for each TCS; (2) show how the target genes are transcribed in response to stimulus; and (3) reveal novel relationships between TCSs, which indicate non-cognate inducers for various response regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to cell envelope stress. Our understanding of the TRN in E. coli is thus notably expanded.
2020-10-21 | GSE143855 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2020-10-21 | GSE143856 | GEO
Project description:Group B Streptococcus (GBS), in its transition from commensal to pathogen, will encounter diverse host environments and thus require coordinately controlling its transcriptional responses to these changes. This work was aimed at better understanding the role of two component signal transduction systems (TCS) in GBS pathophysiology through a systematic screening procedure. We first performed a complete inventory and sensory mechanism classification of all putative GBS TCS by genomic analysis. Five TCS were further investigated by the generation of knock-out strains from WT strain CJB111, and in vitro transcriptome analysis identified genes regulated by these systems.
2014-06-03 | E-MTAB-2423 | biostudies-arrayexpress
Project description:Two-component signal transduction pathways are one of the primary means by which microorganisms respond to environmental signals. These signaling cascades originated in prokaryotes and were inherited by eukaryotes via endosymbiotic lateral gene transfer from ancestral cyanobacteria. We report here that the nuclear genome of pathogenic fungus Candida albicans contains elements of a two-component signaling pathway that seem to be targeted to the mitochondria. In C. albicans two-component response regulator protein Srr1(Stress Response Regulator) contains a mitochondrial targeting sequence at the N-terminus, and fluorescence microscopy reveals mitochondrial localization of GFP-tagged Srr1p. Moreover, phylogenetic analysis indicates that C. albicans Srr1p is more closely related to histidine kinases and response regulators found in marine bacteria compared to other two-component proteins present in the fungi. These data suggest conservation of this protein during the evolutionary transition from endosymbiont to a subcellular organelle. We used microarray analysis to determine if the phenotypes observed with srr1Δ/Δ mutant could be correlated with gene transcriptional changes. Expression of mitochondrial genes was altered in the srr1Δ/Δ null mutant in comparison to the wild type. Furthermore, apoptosis significantly increased in the srr1Δ/Δ mutant strain compared to wild type, suggesting activation of mitochondria dependent apoptotic cell death pathway in the srr1Δ/Δ mutant. This study shows for the first time that a lower eukaryote like C. albicans possesses a two-component response regulator protein that has survived in mitochondria and regulates a subset of genes whose functions are associated with oxidative stress response and programmed cell death (apoptosis).
2013-07-02 | GSE45438 | GEO
Project description:Two-component signal transduction pathways are one of the primary means by which microorganisms respond to environmental signals. These signaling cascades originated in prokaryotes and were inherited by eukaryotes via endosymbiotic lateral gene transfer from ancestral cyanobacteria. We report here that the nuclear genome of pathogenic fungus Candida albicans contains elements of a two-component signaling pathway that seem to be targeted to the mitochondria. In C. albicans two-component response regulator protein Srr1(Stress Response Regulator) contains a mitochondrial targeting sequence at the N-terminus, and fluorescence microscopy reveals mitochondrial localization of GFP-tagged Srr1p. Moreover, phylogenetic analysis indicates that C. albicans Srr1p is more closely related to histidine kinases and response regulators found in marine bacteria compared to other two-component proteins present in the fungi. These data suggest conservation of this protein during the evolutionary transition from endosymbiont to a subcellular organelle. We used microarray analysis to determine if the phenotypes observed with srr1M-NM-^T/M-NM-^T mutant could be correlated with gene transcriptional changes. Expression of mitochondrial genes was altered in the srr1M-NM-^T/M-NM-^T null mutant in comparison to the wild type. Furthermore, apoptosis significantly increased in the srr1M-NM-^T/M-NM-^T mutant strain compared to wild type, suggesting activation of mitochondria dependent apoptotic cell death pathway in the srr1M-NM-^T/M-NM-^T mutant. This study shows for the first time that a lower eukaryote like C. albicans possesses a two-component response regulator protein that has survived in mitochondria and regulates a subset of genes whose functions are associated with oxidative stress response and programmed cell death (apoptosis). Candida albicans wildtype or srr1 null cells were left untreated or were treated with either 8mM H2O2 for one hour prior to RNA isolation.
2013-07-02 | E-GEOD-45438 | biostudies-arrayexpress
Project description:Members of the Bacillus cereus group can adapt to a wide range of environmental challenges. In bacteria, these challenges are often translated into a transcriptional response via the cognate response regulators (RRs) of specialized two-component systems (TCSs). We have previously developed a phylogenetic footprinting approach that was successfully implemented to predict specific binding sites (operators) and target genes for the RRs of B. cereus and related species. In this study, this footprinting approach was integrated with transcriptome analyses of two B. cereus TCS deletion mutants, involving the TCSs YvrHG and YufLM. Comparison of mutant versus wild-type transcriptomes revealed that the respective TCSs were significantly active during the exponential growth phase in rich medium and that the footprinting-based predictions were accurate for the two TCSs. Moreover, the predicted specific operators were used in combination with the transcriptome data to guide the identification of more extended TCS regulons. This revealed new roles for the respective TCSs, including the participation in an intricate transcriptional network involved in antibiotic resistance, including the confirmed resistance to oxolinic acid (YvrHG) and the confirmed uptake and metabolism of fumarate and the repression of fermentative pathways (YufLM).
2014-12-31 | GSE18523 | GEO