GEO DataSets

(Submitter supplied) Transcriptional profiling to define the stringent response regulon and significance of basal (p)ppGpp levels in E. faecalis OG1RF.

Organism:

Enterococcus faecalis; Enterococcus faecalis OG1RF

Type:

Expression profiling by array

Platform:

GPL15039

48 Samples

Download data: MEV

(Submitter supplied) In Firmicutes, the nutrient-sensing regulators (p)ppGpp, the effector molecule of the stringent response, and CodY work in tandem to maintain bacterial fitness during infection. Here, we tested (p)ppGpp and codY mutant strains of Enterococcus faecalis in a catheter-associated urinary tract infections (CAUTI) mouse model and used global transcriptional analysis to investigate the (p)ppGpp and CodY relationship. more...

Organism:

Enterococcus faecalis OG1RF

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26706

6 Samples

Download data: TXT

(Submitter supplied) Changes in Enterococcus faecalis OG1RF(pCF10) gene expression at 4 hours post-infection in a rabbit model of subdermal abscess formation were studied using RNA-seq analysis.

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18799

2 Samples

Download data: TXT

(Submitter supplied) Changes in Enterococcus faecalis OG1RF gene expression during infection in a rabbit model of subdermal abscess formation were studied using microarray analysis.

Organism:

Enterococcus faecalis V583; Enterococcus faecalis OG1RF

Type:

Expression profiling by array

Platform:

GPL10534

12 Samples

Download data: TXT

(Submitter supplied) Growth curves and (p)ppGpp accumulation assays showed that RelA inactivation could influence S. suis growth and led to incapacity of (p)ppGpp synthesis during glucose starvation. To identify the roles of RelA/(p)ppGpp in global gene regulation in S. suis, we compared the transcriptional profiles of SC-19 [a (p)ppGpp+ strain] and ΔrelA [a (p)ppGpp0 strain during glucose starvation] in both glucose-abundant and -deficient CDM in exponential phase by microarray analysis. more...

Organism:

Streptococcus suis

Type:

Expression profiling by array

Platform:

GPL20080

12 Samples

Download data: TXT

(Submitter supplied) Transcriptomic profiles of Pseudomonas protegens H78 and its (p)ppGpp0 relA/spoT mutant, which were grown to the late exponential phase (OD600 = 5.0 to 6.0) in the KMB media at 28 °C, were assessed by deep sequencing (RNA-seq) on Illumina 2500.

Organism:

Pseudomonas protegens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22592

6 Samples

Download data: XLS

(Submitter supplied) In this report, codY mutant strains were constructed and used to demonstrate the relationship of (p)ppGpp synthesized by RelP and RelQ with the activation of CodY. In addition, because CodY has not been studied in S. mutans, we used microarrays to demonstrate that this protein function as a global regulator of gene expression in S. mutans. Keywords: stress response, gene knockout analysis

Organism:

Streptococcus mutans

Type:

Expression profiling by array

Platform:

GPL4340

8 Samples

Download data: MEV

(Submitter supplied) The impact on gene expression by the alarmone (p)ppGpp during growth and non-growth was determined by comparing the transcriptome of R. etli CFN42 wild type and rel mutant. This allowed us to better understand the pleiotropic stress phenotype of the rel mutant as well as identifying specific (p)ppGpp-dependent stress regulators.

Organism:

Rhizobium etli CFN 42

Type:

Expression profiling by genome tiling array

Platform:

GPL9409

6 Samples

Download data: GFF, TXT

(Submitter supplied) The stringent response is characterized by the synthesis of the messenger molecules pppGpp, ppGpp or pGpp (collectively designated (pp)pGpp). The phenotypic consequences resulting from (pp)pGpp accumulation vary among species and can be mediated by different underlying mechanisms. Most genome-wide analyses were performed under stress conditions, which often mask the immediate effects of (pp)pGpp mediated regulatory circuits. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24034

12 Samples

Download data: XLS

(Submitter supplied) Transcription profiling of wild type, relA-, and relA-spoT-, crp-, dksA-, rpoS-, lrp- mutant strains of E. coli starved for isoleucine Bacteria comprehensively reorganize their global gene expression when faced with nutrient exhaustion. In Escherichia coli and other free-living bacteria, the alarmone ppGpp facilitates this massive response by directly or indirectly coordinating the down-regulation of genes of the translation apparatus, and the induction of biosynthetic genes and the general stress response. more...

Organism:

Bacillus anthracis; Escherichia coli CFT073; Bacteroides thetaiotaomicron VPI-5482; Escherichia coli O157:H7 str. Sakai; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli str. K-12 substr. MG1655; Escherichia coli; Escherichia coli O157:H7 str. EDL933; Enterococcus faecalis V583

Type:

Expression profiling by array

Platforms:

GPL3154 GPL6702

30 Samples

Download data: CEL, TXT

(Submitter supplied) The stringent stress response, mediated by the signalling molecule guanosine penta(tetra)-phosphate (p)ppGpp, has recently gained more attraction as a potential new therapeutic target. However, interference of a global mediator could lead to unwanted side effects, therefore warrants detailed mechanistic understanding. We used RNA-Seq to investigate the transcriptional landscape of a Pseudomonas aeruginosa ppGpp-deficient strain under non-stressful conditions. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

6 Samples

Download data: TXT

(Submitter supplied) The production of (p)ppGpp by Streptococcus mutans UA159 is catalyzed by three gene products, RelA, RelP and RelQ. Here, we investigate the role of the RelA (Rel) homologue of S. mutans in the stringent response and in global control of gene expression. RelA of S. mutans was shown to synthesize pppGpp in vitro from GTP and ATP in the absence of added ribosomes, as well as in vivo in an E. coli relA-spoT mutant. more...

Organism:

Streptococcus mutans

Type:

Expression profiling by array

Platform:

GPL4340

16 Samples

Download data: MEV

(Submitter supplied) Guanosine 3 ,5 -bispyrophosphate (ppGpp), also known as ‘‘magic spot,’’ has been shown to bind prokaryotic RNA polymerase to down-regulate ribosome production and increase transcription of amino acid biosynthesis genes during the stringent response to amino acid starvation. Because many environmental growth perturbations cause ppGpp to accumulate, we hypothesize ppGpp to have an overarching role in regulating the genetic program that coordinates transitions between logarithmic growth (feast) and growth arrest (famine). more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL4995

136 Samples

Download data: TXT

(Submitter supplied) ppGpp accumulation caused by ectopic expression of RelA in Saccharomyces cerevisiae gave rise to marked changes in gene expression with both upregulation and downregulation, including changes in mitochondrial gene expression. The most prominent upregulation (38-fold) was detected in the function-unknown hypothetical gene YBR072C-A, followed by many other known stress-responsive genes. ppGpp acuumulation resulted in enhancement of tolerance against various stress stimuli, such as osmotic stress, ethanol, hydrogen peroxide, and high temperature.

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:

Expression profiling by array

Platform:

GPL15609

2 Samples

Download data: CALLS, PAIR, TXT

(Submitter supplied) We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in light/dark conditions. We performed ChIP-seq experiments using wild type and the rel- strain at dusk, during exposure to 12 h of darkness and at dawn. We show that the RNA polymerase pausing index is globally lower in the rel- strain.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16957

12 Samples

Download data: XLSX

(Submitter supplied) We investigated the role of basal ppGpp levels in Synechococcus elongatus PCC7942 in adaptation to darkness. We performed RNA-seq experiments using the rel- relA+ and the rel- relAE335Q strain at dusk and during exposure to 12 h of darkness. We show that basal ppGpp levels is not sufficient for restoration of appropriate transcriptional shutdown in response to darkness.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16957

36 Samples

Download data: XLS

(Submitter supplied) We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in light/dark conditions. We performed RNA-seq experiments using wild type and the rel- strain at dusk and during exposure to 12 h of darkness. We show that ppGpp is required for correct response to darkness.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16957

36 Samples

Download data: XLS

(Submitter supplied) We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in constant light. We performed RNA-seq experiments using wild type + relA+ and wild type + relAE335Q strains after induction with theophylline starting at subjective dusk. We show that ppGpp induction inhibits global transcription in light.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16957

6 Samples

Download data: XLS

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16957

106 Samples

Download data

(Submitter supplied) We investigated the role of the basal levels of ppGpp in Synechococcus elongatus PCC7942 in constant light. We performed RNA-seq experiments using the rel- + relA+ and rel- + relAE335Q strains and show that basal levels of ppGpp are required for regulation of global transcription in light.

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16957

8 Samples

Download data: XLS