GEO DataSets

(Submitter supplied) The stringent response is initiated by rapid (p)ppGpp synthesis, which leads to a profound reprogramming of gene expression in most bacteria. The stringent phenotype seems to be species specific and may be mediated by fundamentally different molecular mechanisms. In Staphylococcus aureus, (p)ppGpp synthesis upon amino acid deprivation is achieved through the synthase domain of the bifunctional enzyme RSH (RelA/SpoT homolog). more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL10537

12 Samples

Download data: 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) More than 200 direct CodY target genes in Staphylococcus aureus were identified by genome-wide analysis of in vitro DNA binding. This analysis, which was confirmed for some genes by DNase I footprinting assays, revealed that CodY is a direct regulator of numerous transcription units associated with amino acid biosynthesis, transport of macromolecules and virulence. The virulence genes regulated by CodY fell into three groups. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL1339

17 Samples

Download data: CEL, CHP

(Submitter supplied) CodY is a conserved regulator in gram-positive organisms described to repress metabolic genes mainly involved in nitrogen metabolism but also to control the expression of virulence genes in pathogens. We constructed codY gene-replacement mutants in three unrelated S. aureus strains (Newman, UAMS-1, RN1HG). codY mutants grew slower in a chemically defined medium compared to the wild type strains. However, only codY mutants were able to grow in medium lacking threonine. more...

Organism:

Staphylococcus aureus subsp. aureus COL; Staphylococcus aureus subsp. aureus MW2; Staphylococcus aureus; Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus subsp. aureus N315; Staphylococcus aureus subsp. aureus USA300; Staphylococcus aureus subsp. aureus Mu50; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476; Staphylococcus aureus subsp. aureus str. Newman

Type:

Non-coding RNA profiling by array

Platform:

GPL7137

8 Samples

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(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) CodY is a conserved broad acting transcriptional factor that regulates the expression of genes related to amino acid metabolism and virulence in Staphylococcus aureus. CodY target genes have been studied by using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). In this study we performed the first in vivo determination of CodY target genes using a novel CodY monoclonal antibody in established ChIP-exo protocols. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25144

4 Samples

Download data: CSV

(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) 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) 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) We sequenced a total of 16 cDNA libararies derived from fragmented total mRNA and ribosome protected mRNAs from S. aureus hpf mutant (NE838) and its parental strain JE2 grown in tryptic soy broth (TSB) or minimal medium (MM). The data represented 2 independent biological replicates.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17452

16 Samples

Download data: TXT

(Submitter supplied) To measure S. aureus gene expression during growth phase and/or S. aureus–PMN interaction. Keywords: other

Organism:

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

Type:

Expression profiling by array

Platform:

GPL2129

159 Samples

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(Submitter supplied) Transcriptional profiling of the small colony variant (SCV) S. aureus isolate (JKD6229) compared to the parent isolate with a normal phenotype (JKD6210). Both isolates were from a patient with persistent S. aureus infection, and the SCV strain arose during failed antibiotic therapy.

Organism:

Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL10229

4 Samples

Download data: TXT

(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 melitensis; Brucella suis 1330

Type:

Expression profiling by array

Platform:

GPL7612

4 Samples

Download data: TXT

(Submitter supplied) Background The catabolite control protein A (CcpA) is a member of the LacI/GalR family of transcriptional regulators controlling carbon-metabolism pathways in low-GC Gram positive bacteria. It functions as a catabolite repressor or activator, allowing the bacteria to utilize the preferred carbon source over secondary carbon sources. This study is the first CcpA-dependent transcriptome and proteome analysis in S. more...

Organism:

Staphylococcus aureus subsp. aureus str. Newman; Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL3931

6 Samples

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(Submitter supplied) Transcriptome analysis of D39 rel+Spn and delta-relSpn strains treated with mupirocin revealed relSpn-independent (translation stress), relSpn-dependent (stringent response), and delta-relSpn-dependent changes suggesting that relSpn and (p)ppGpp amount play wide-ranging homeostatic roles in pneumococcal physiology, besides adjusting macromolecular synthesis and transport in response to nutrient availability.

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by array

Platform:

GPL536

12 Samples

Download data: GPR

(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 OG1RF; Enterococcus faecalis V583

Type:

Expression profiling by array

Platform:

GPL10534

12 Samples

Download data: TXT