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Comparing the transcriptional profiles of a Caulobacter crescentus CB15N (NA1000) wild-type to a SpoT null in carbon starvation.

ABSTRACT: SpoT is an Rsh (Rel / Spo homolog) protein, which synthesizes the alarmone ppGpp in response to starvation. This experiment is quantifying transcription in two Caulobacter strains after 5 minutes of glucose starvation: one strain is wild-type CB15N (NA1000); the other strain is NA1000 which has a chromosomal in-frame deletion of the spoT gene. The wild-type strain can synthesize the alarmone ppGpp in response to starvation and the spoT null strain cannot. Both strains were cultured in M2 defined medium with glucose as the sole carbon source, and then washed and incubated in M2 medium lacking glucose for 5 minutes before RNA isolation. Triplicate cultures of: 1) C. crescentus strain CB15N , and 2) CB15N ?SpoT, cultured in M2-glucose media, then starved for glucose for 5 minutes.

ORGANISM(S): Caulobacter vibrioides

SUBMITTER: Sean Crosson

PROVIDER: E-GEOD-21206 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comparing the transcriptional profiles of a Caulobacter crescentus CB15N (NA1000) wild-type to a SpoT null in carbon starvation.

Project description:SpoT is an Rsh (Rel / Spo homolog) protein, which synthesizes the alarmone ppGpp in response to starvation. This experiment is quantifying transcription in two Caulobacter strains after 5 minutes of glucose starvation: one strain is wild-type CB15N (NA1000); the other strain is NA1000 which has a chromosomal in-frame deletion of the spoT gene. The wild-type strain can synthesize the alarmone ppGpp in response to starvation and the spoT null strain cannot. Both strains were cultured in M2 defined medium with glucose as the sole carbon source, and then washed and incubated in M2 medium lacking glucose for 5 minutes before RNA isolation.

2011-05-01 | GSE21206 | GEO

Transcriptional regulation by the stringent response-associated alarmone (p)ppGpp in Pseudomonas putida

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Project description:The purpose of this experiment was to examine the differential transcriptional profiles of Caulobacter CB15N grown in M2-Glucose versus M2-Inositol. mRNA expression was compared between Caulobacter CB15N cells grown in M2-Glucose vs. M2-Inositol. Four arrays were run, two of each dye combination.

2010-06-30 | E-GEOD-12414 | biostudies-arrayexpress

RNAseq of the human gut commensal Bacteroides thetaiotaomicron wildtype, bt0700 and bt0700 bt3998 (ppGpp0) strains across three conditions: glucose minimal medium, 1h of carbon starvation, and mouse gut colonization

Project description:Transcriptional profiles of wildtype and mutant strains bt0700 and bt0700 bt3998 (ppGpp0) of human gut commensal B. thetaiotaomicron were collected to investigate the relevance of the stringent response mediated by the alarmone (p)ppGpp for growth and survival in three different conditions. RNAseq samples were taken during growth in glucose minimal medium, after 1h of carbon starvation, and after 6 days of monocolonizing germ-free mice (from cecum material).

2018-07-04 | E-MTAB-6412 | biostudies-arrayexpress

Caulobacter vibrioides CB15N mRNA expression in M2-Glucose Vs. M2-Inositol

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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 relA mutant strain and its parents strain SC-19 were cultured in both glucose-abundant CDM (CDM containing 1% glucose) and glucose-deficient CDM (CDM containing 2% glucose) respectively. The bacteriain in exponential phase were collected for microarray analysis. Three independent experiments were performed.

2015-08-08 | E-GEOD-70092 | biostudies-arrayexpress

The transcriptional response to MESH1 silencing

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2022-08-31 | GSE135358 | GEO

Transcriptional analysis of regulatory effects in Corynebacterium glutamicum and a derived (p)ppGpp0 mutant strain

Project description:The alarmone species ppGpp and pppGpp are an important part of bacterial physiology as they both coordinate the bacterial stress response to nutrient deficiency and also contribute to the maintenance of cell homeostasis. Recently, all components of the (p)ppGpp metabolism for the industrially relevant actinobacterial model organism Corynebacterium glutamicum could be functionally characterized by in vitro analysis and heterologous expression in the model system Escherichia coli. Based on these results, the strain C. glutamicum CR099 ΔrelΔrelSΔrelH is the first C. glutamicum (p)ppGpp0 strain available. The aim of this study was to investigate the effects of the alarmone species on transcriptome regulation in C. glutamicum by differential transcriptome analysis of the parental strain and the (p)ppGpp0 mutant. An RNAseq analysis of the early exponential growth phase was performed to analyze the (p)ppGpp basal level effects (Illumina TruSeq stranded mRNA libraries sequenced on Illumina HiSeq rapid mode 2 x 25nt PE). Due to the direct association of the alarmones with the bacterial stress response, the transcriptional response to the induction of a total starvation situation was investigated in form of a time series. Following an analysis of pooled replicates for 5 time points (Illumina TruSeq stranded mRNA libraries sequenced on Illumina HiSeq rapid mode 2 x 50nt PE), a detailed investigation was carried out for two stress exposure durations using three biological replicates per strain and time point each (Illumina TruSeq stranded mRNA libraries sequenced on Illumina HiSeq rapid mode 2 x 25nt PE).

2019-12-02 | E-MTAB-8070 | biostudies-arrayexpress

E. coli Isoleucine starvation and stringent response network

Project description: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. Such a large reorientation likely requires the cooperative activities of many different genetic regulators, yet the structure of the transcription network below the level of ppGpp remains poorly defined. Using isoleucine starvation as an experimental model system for amino acid starvation, we identified genes that required ppGpp, Lrp, and RpoS for their induction. Surprisingly, despite the fact that the overwhelming majority of genes controlled by Lrp and RpoS required ppGpp for their activation, we found that these two regulons were not induced simultaneously. The data reported here suggest that metabolic genes, such as those of the Lrp regulon, require only a low basal level of ppGpp for their efficient induction. In contrast, the RpoS-dependent general stress response is not robustly induced until relatively high levels of ppGpp accumulate. Here we describe a data-driven conceptual model that explains how bacterial cells allocate transcriptional resources between metabolic and stress survival processes by discretely tuning regulatory activities to a central indicator of cellular physiology. The regulatory structure that emerges is consistent with a rheostatic model of the stringent response that allows cells to efficiently adapt to a wide range of nutritional environments. Keywords: genetic modification design; stress response; isoleucine starvation

2008-04-08 | GSE11087 | GEO

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