GEO DataSets

(Submitter supplied) This RNA-seq analysis mainly examined the global effect of stringent resonse in E. amylovora under the T3SS-inducing condition. The (p)ppGpp mutant showed differential expression of more than 30% genes in the genome, which include significant down-regulation of T3SS genes and gene related to motiliey. On the other hand, genes involved in amino acid biosynthesis, translation, SOS response, DNA replication, chromosome segregation, as well as nucleotide metabolism, fatty acid and lipid biosynthesis were significantly up-regulated in (p)ppGpp mutant. more...

Organism:

Erwinia amylovora

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26279

6 Samples

Download data: TXT

(Submitter supplied) This RNA-seq analysis examined the global effect of CsrA and its non-coding small RNA (ncsRNA) csrB in E. amylovora under the T3SS-inducing condition. The csrA mutant showed differential expression of more than 20% genes in the genome, which include significant down-regulation of T3SS genes and those required for cell growth and viability. On the other hand, the csrB mutant exhibited significant up-regulation of most major virulence genes, suggesting antagonistic effect of csrB on CsrA targets.

Organism:

Erwinia amylovora

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26279

9 Samples

Download data: TXT

(Submitter supplied) This RNA-seq analysis examined the global effect of (p)ppGpp in P. syringae under the T3SS-inducing condition. The (p)ppGpp mutant showed differential expression of more than 30% genes in the genome, which include significant down-regulation of T3SS genes and those required for cell growth and viability.

Organism:

Pseudomonas syringae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27977

12 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis was performed to examine the sRNA transcripts in wild type E. amylovora 1189 and in the deletion mutant of hfq, at 6 and 12 hours of culture in hrp-inducing minimal medium.

Organism:

Erwinia amylovora

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18131

12 Samples

Download data: GTF, TXT

(Submitter supplied) We conducted genome-wide microarray analyses to determine the regulons of RcsB and RcsC in liquid medium and, for the first time, on immature pear fruit. Our array analyses identified a total of 648 genes differentially regulated by the RcsCB in vitro and in vivo. Consistent with our previous findings, RcsB acts as a positive regulator in both conditions, while RcsC positively controls amylovoran biosynthetic gene expression in vivo, but negatively in vitro. more...

Organism:

Erwinia amylovora

Type:

Expression profiling by array

Platform:

GPL13939

12 Samples

Download data: GPR

(Submitter supplied) Microarray analysis of E. amylovora treated with compounds no. 3 and no. 9 identified a total of 588 significantly differentially expressed genes. Among them, 95 and 78 genes were, respectively, induced and suppressed by both compounds as compared to DMSO control. Majority of T3SS genes in E. amylovora including hrpL and avrRpt2 effector gene were suppressed by both compounds. Compound no. 3 also suppressed the transcription of amylovoran precursor and biosynthesis genes. more...

Organism:

Erwinia amylovora

Type:

Expression profiling by array

Platform:

GPL13939

8 Samples

Download data: GPR

(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) Microarray analysis was used to identify genes that were controlled by AmyR in minimal and on immature pear fruits. Consistent with amylovoran production, an inverse correlation was observed between amyR expression and the expression level of amylovoran biosynthetic genes in liquid media. Interestingly, over-expression of AmyR suppressed the expression of type III secretion system genes including hrpA, hrpN and dspEF after pear fruit infection. more...

Organism:

Erwinia amylovora

Type:

Expression profiling by array

Platform:

GPL13939

14 Samples

Download data: GPR

(Submitter supplied) The experiment was carried out to study the effect of loss of (p)ppGpp or cyclic di-GMP on the gene expression pattern of Mycobacterium smegmatis MC2 155 strains. The cells were cultured in MB7H9 broth containing 0.2% glycerol and 0.05% Tween 80. The transcriptome analysis was performed using GeneSpring GX12 software. Fold changes were calculated with respect to the median expression of wild type replicates. more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by array

Platform:

GPL20299

6 Samples

Download data: TXT

(Submitter supplied) The pathogenic spirochete Borrelia burgdorferi senses and responds to diverse environmental challenges, including changes in nutrient availability, throughout its natural infectious cycle in Ixodes spp. ticks and mammalian hosts. This study examined the role of the putative DnaK suppressor protein (DksA) in the transcriptional response of B. burgdorferi to starvation. Wild-type and dksA-deficient B. more...

Organism:

Coxiella burnetii; Streptococcus pyogenes; Borreliella burgdorferi; Chlamydia trachomatis; Staphylococcus aureus; Yersinia pestis

Type:

Expression profiling by array

Platform:

GPL2129

12 Samples

Download data: CEL, CHP

(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) The nucleotide messenger (p)ppGpp allows bacteria to adapt to fluctuating environments by reprogramming the transcriptome. Despite its well-recognized role in gene regulation, (p)ppGpp is only known to directly affect transcription in Proteobacteria by binding to the RNA polymerase. Here we reveal a different mechanism of gene regulation by (p)ppGpp in Firmicutes from soil bacteria to pathogens: (p)ppGpp directly binds to the transcription factor PurR to downregulate purine biosynthesis. more...

Organism:

Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30809

25 Samples

Download data: RDATA, TXT

(Submitter supplied) Acinetobacter baumannii is a major cause of nosocomial infections which can survive in different hospital environments and its multidrug-resistant capacity is major concern now-a-days. ppGpp dependent stringent response mediates reprogramming of gene expression with diverse function in many bacteria. A baumannii A1S_0579 gene is responsible for ppGpp production. Transcriptome analysis of early stationary phase cultures represents several differentially expressed genes in ppGpp deficient strain (∆A1S_0579). more...

Organism:

Acinetobacter baumannii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22143

2 Samples

Download data: XLSX

(Submitter supplied) This RNA-seq analysis examined the global effect of the RNA binding RsmA proteins in P. syringae under the T3SS-inducing condition and in KB medium. The results showed differential expression of more than 50% genes in the genome, which include significant down-regulation of T3SS genes.

Organism:

Pseudomonas syringae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29440

18 Samples

Download data: TXT

(Submitter supplied) The expression profile of an S. Typhimurium mutant strain unable to synthesise ppGpp (relAspoT deletions) was compared to the wild-type strain. The effect of ppGpp on virulence gene expression was studied under 4 different growth conditions that induce virulence gene expression. Keywords: genetic modification

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by array

Platforms:

GPL3586 GPL3612

32 Samples

Download data: GPR

(Submitter supplied) In the intracellular pathogen Brucella spp., the activation of the stringent response, a global regulatory network providing rapid adaptation to a variety of growth-affecting stress conditions such as nutrient deficiency, is essential for replication in the host. A single, bi-functional enzyme Rsh catalyzes synthesis and hydrolysis of the alarmone (p)ppGpp, responsible for differential gene expression under stringent conditions. more...

Organism:

Brucella suis 1330; Brucella melitensis

Type:

Expression profiling by array

Platform:

GPL7612

4 Samples

Download data: TXT

(Submitter supplied) YbjN, an enterobacteria-specific protein, is a multicopy suppressor of ts9 temperature sensitivity in Escherichia coli. Microarray study revealed that the expression level of ybjN was inversely correlated with the expression of flagellar, fimbrial and acid resistance genes. Over-expression of ybjN significantly down-regulated genes involved in the citric acid cycle, glycolysis, the glyoxylate shunt, oxidative phosphorylation, and amino acid and nucleotide metabolism. more...

Organism:

Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655; Escherichia coli; Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by array

Platform:

GPL13359

8 Samples

Download data: TXT

(Submitter supplied) In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). In Caulobacter crescentus, SpoT synthesizes the secondary messengers (p)ppGpp, which affect transcriptional reprogramming by binding to RNA polymerase to downregulate anabolic gene transcription. (p)ppGpp can also impact the expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24555

9 Samples

Download data: XLSX