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Comparative transcriptomic analysis of global gene expression mediated by (p)ppGpp reveals common regulatory networks in Pseudomonas syringae

ABSTRACT: Comparative transcriptomic analysis of global gene expression mediated by (p)ppGpp reveals common regulatory networks in Pseudomonas syringae

PROVIDER: PRJNA600017 | ENA |

REPOSITORIES: ENA

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Comparative transcriptomic analysis of global gene expression mediated by (p)ppGpp reveals common regulatory networks in Pseudomonas syringae

Project description: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.

2020-03-23 | GSE143325 | GEO

Comparative transcriptomic analysis of global gene expression mediated by (p) ppGpp reveals common regulatory networks in Pseudomonas syringae.

Project description: Not available

| S-EPMC7146990 | biostudies-literature

ppGpp signal plays critical role in pathogenesis of Acinetobacter baumannii 17978

Project description: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). We found that the expression of csu operon, which is important in pili biosynthesis for early biofilm formation, was significantly reduced in the ppGpp-deficient strain. Our findings showed that ppGpp signaling plays critical role in biofilm formation, surface motility, adherence and virulence of A baumannii. This study is the first demonstration of the association between ppGpp and pathogenicity of A. baumannii.

2021-05-01 | GSE173627 | GEO

Effect of ppGpp on Salmonella Typhimurium gene expression

2006-05-30 | GSE4631 | GEO

E.coli (p) ppGpp regulation.E. coli, ppGpp, growth rate

Project description:These two projects are about the proteome of wild type E. coli K-12 NCM3722 strain (RE198LQ) and its rpoS-null strain (XA00994LQ). Both projects include replicates of two conditions, the normal conditions and (p)ppGpp overproduction conditions via RelA* OE.

2023-12-20 | PXD042250 | Pride

The nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus

Project description: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. We identified PurR as a receptor of (p)ppGpp in Bacillus anthracis and revealed that (p)ppGpp strongly enhances PurR binding to its regulon in the Bacillus subtilis genome. A co-structure reveals that (p)ppGpp binds to a PurR pocket reminiscent of the active site of PRT enzymes that has been repurposed to serve a purely regulatory role, where the effectors (p)ppGpp and PRPP compete to allosterically control transcription. PRPP inhibits PurR DNA binding to induce transcription of purine synthesis genes, whereas (p)ppGpp antagonizes PRPP to enhance PurR DNA binding and repress transcription. A (p)ppGpp-refractory purR mutant fails to downregulate purine synthesis genes upon starvation. Our work establishes the precedent of (p)ppGpp as a classical effector of transcription repressors and reveals the key function of (p)ppGpp in regulating nucleotide synthesis through gene regulation, from the human intestinal tract to host-pathogen interfaces.

2021-12-10 | GSE185164 | GEO

(p)ppGpp promotes Enterococcus faecalis virulence in a murine model of catheter-associated urinary tract infection

Project description: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. Absence of (p)ppGpp or single inactivation of codY led to lower bacterial loads in catheterized bladders, and diminished biofilm formation on fibrinogen-coated surfaces under in vitro and in vivo conditions. Single inactivation of the bifunctional (p)ppGpp synthetase/hydrolase rel did not affect virulence supporting previous evidence that association of (p)ppGpp with enterococcal virulence is not dependent on activation of the stringent response. Inactivation of codY in the (p)ppGpp0 strain restored E. faecalis virulence in the CAUTI model as well as the ability to form biofilms in vitro. Transcriptome analysis revealed that inactivation of codY restores, for the most part, the dysregulated metabolism of (p)ppGpp0 cells. While a clear linkage between (p)ppGpp and CodY with expression of virulence factors could not be established, targeted transcriptional analysis indicate that a possible association between (p)ppGpp and c-di-AMP signaling pathways in response to the conditions found in the bladder may plays a role in enterococcal CAUTI. Collectively, this study identifies the (p)ppGpp-CodY network as an important contributor to enterococcal virulence in catheterized mouse bladder and supports that basal (p)ppGpp pools promote virulence through maintenance of a balanced metabolism during adverse conditions.

2019-05-25 | GSE131749 | GEO

Transcription profiling by array of Legionella pneumophila ppGpp knockout and relA over expression mutants.

Project description:Effect of ppGpp on transcript level after RelA overexpression (90 min). The cells are constructed in our lab. They are knock-out mutants in the production of ppGpp(guanosine tetraphosphate) of Legionella, complemented with an over-expression vector containing the relA gene to express the RelA protein (responsible for the ppGpp production). The aim is to follow the gene response in Legionella pneumophila after induction of ppGpp at different time points.

2010-04-14 | E-MTAB-211 | biostudies-arrayexpress

RelA/(p)ppGpp regulates the glucose-starvation induced stringent response in the zoonostic Streptococcus suis

Project description: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. A less stringent cut-off limit, 2-fold change, was used. qRT-PCR validation displayed the same trends observed in the microarrays

2015-08-08 | GSE70092 | GEO

Effect of ppGpp on Salmonella Typhimurium gene expression

Project description: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 Study comprised 4 separate experiments (with 2 strains and 4 replicates for each strain per growth condition). The experiments were indirect comparisons using Salmonella genomic DNA as the comparator which also acted as the control for spot quality.

2010-06-11 | E-GEOD-4631 | biostudies-arrayexpress

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