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Expression analysis of Saccharomyces cerevisiae INVSc1 under accumulation of the bacterial alarmone ppGpp

ABSTRACT: 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(S): Saccharomyces cerevisiae S288C Saccharomyces cerevisiae

PROVIDER: GSE38239 | GEO | 2012/05/31

SECONDARY ACCESSION(S): PRJNA167742

REPOSITORIES: GEO

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Expression analysis of Saccharomyces cerevisiae INVSc1 under accumulation of the bacterial alarmone ppGpp

Project description: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. A two chip study using total RNA recoverd from the Saccharomyces cerevisiae TN2080 (accumulating ppGpp) and TN2077 (vector control) grown to mid-growth phase (8h) in SC-uracil medium. The plasmid pYC2/CT (V5-epitope tag vector) was used as a vector to express Sj-RSH.

2012-05-30 | E-GEOD-38239 | biostudies-arrayexpress

The RelA hydrolase domain acts as a molecular switch for (p)ppGpp synthesis

Project description:Bacteria synthesize guanosine tetra- and penta phosphate (commonly referred to as (p)ppGpp) in response to environmental stresses. (p)ppGpp reprograms cell physiology and is essential for stress survival, virulence and antibiotic tolerance. Proteins of the RSH superfamily (RelA/SpoT Homologues) are ubiquitously distributed and hydrolyze or synthesize (p)ppGpp. Structural studies have suggested that the shift between hydrolysis and synthesis is governed by conformational antagonism between the two active sites in RSHs. RelA proteins of γ-proteobacteria exclusively synthesize (p)ppGpp and encode an inactive pseudo-hydrolase domain. Escherichia coli RelA synthesizes (p)ppGpp in response to amino acid starvation with cognate uncharged tRNA at the ribosomal A-site, however, mechanistic details to the regulation of the enzymatic activity on the ribosome remain elusive. Here, we show a novel role of the enzymatically inactive hydrolase domain in modulating the activity of the synthetase domain of RelA. Using random mutagenesis screening and functional studies, we identify a loop region (residues 114-130) in the hydrolase domain, which controls the synthetase activity. We show that a synthetase-inactive loop mutant of RelA is not affected for tRNA binding, but binds the ribosome less efficiently than wildtype RelA. Our data provide strong evidence to support the model that the hydrolase domain acts as a molecular switch to regulate the synthetase activity.

2021-03-31 | GSE150416 | 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

(p)ppGpp controls stringent factors by exploiting antagonistic allosteric coupling between catalytic domains

Project description:Escherichia coli RelA is a ribosomal factor with strong (p)ppGpp synthesis activity that is dramatically activated in the presence of deacylated tRNA in the ribosomal A-site. RelA is a unique enzyme in that it is directly positively regulated by its product, alarmone nucleotide (p)ppGpp. Using HDX-MS, mulecular docking, biochemsitry, and microbiology approaches, we localise the (p)ppGpp binding site of E. coli RelA and uncover the molecular mechanism of RelA regulation by the alarmone.

2021-08-11 | PXD019953 | Pride

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

Project description:The stringent response is an adaptive physiological response triggered by different conditions of nutritional or environmental stress and aimed at increasing survival under harsh conditions. This response is mediated the signalling nucleotides guanosine tetraphosphate (ppGpp) and pentaphospate (pppGpp), collectively known as (p)ppGpp. In this study we aim to identify genome-wide targets of regulation by the stringent-response associated alarmone (p)ppGpp in Pseudomonas putida by performing RNA-seq experiments using the wild-type KT2440tel strain and a KT2440tel-derivative bearing deletions of the (p)ppGpp synthetase-encoding genes relA and spoT (ppGpp0 mutant).

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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.

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

2015-08-08 | GSE70092 | GEO

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

Transcription profiling of Streptomyces coelicolor strain M653 in a time series after ppGpp synthesis activation by thiostrepton

Project description:ppGpp synthesis was activated in exponentially growing cells of Streptomyces coelicolor in the absence of amino acid starvation by using a strain (M653 [DrelA tipAp::relA(1.46kb)]) that expresses a truncated portion of relA under the control of a thiostrepton-inducible promoter. Samples were harvested at 30 min intervals following induction for comparison to a control set of samples from aliquots of the same cultures that were not induced.

2007-08-01 | E-MEXP-1119 | biostudies-arrayexpress

The Role of RelA of Streptococcus mutans in Global Control of Gene Expression

Project description: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. Mupirocin (MUP) was shown to induce high levels of (p)ppGpp production in S. mutans in a relA-dependent manner, with a concommitant reduction in GTP pools. Keywords: (p)ppGpp, nutrient starvation, biofilm, virulence, stress

2007-11-14 | GSE9382 | GEO

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