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Comparison of the transcription profile of B. subtilis clpX strain with B. subtilis clpX spx strain, reporting on Spx activity

ABSTRACT: In B. subtilis the unusual transcription factor Spx controls the thiol stress response regulon (Nakano et al 2003 PNAS 100:13603; Rochat et a. 2012 NAR 40:9751). Under normal growth conditions Spx is constantly degraded by the AAA+ protease complex ClpXP (Nakano et al 2001 MolMi 42:383). Comparing a B. subtilis clpX strain, where Spx levels are high, with a B. subtilis clpX spx double mutant strain which lacks Spx, will report on Spx dependent transcriptional control. We prepared total RNA of exponentially grown B. subtilis clpX and of B. subtilis clpX spx cells.

ORGANISM(S): Bacillus subtilis

PROVIDER: GSE50102 | GEO | 2014/09/01

SECONDARY ACCESSION(S): PRJNA216053

REPOSITORIES: GEO

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Comparison of the transcription profile of B. subtilis clpX strain with B. subtilis clpX spx strain, reporting on Spx activity

Project description:In B. subtilis the unusual transcription factor Spx controls the thiol stress response regulon (Nakano et al 2003 PNAS 100:13603; Rochat et a. 2012 NAR 40:9751). Under normal growth conditions Spx is constantly degraded by the AAA+ protease complex ClpXP (Nakano et al 2001 MolMi 42:383). Comparing a B. subtilis clpX strain, where Spx levels are high, with a B. subtilis clpX spx double mutant strain which lacks Spx, will report on Spx dependent transcriptional control. We prepared total RNA of exponentially grown B. subtilis clpX and of B. subtilis clpX spx cells. Using a merged dye swap experiments of red or green labelled cDNA of the above described RNA preparations-

2014-09-01 | E-GEOD-50102 | biostudies-arrayexpress

The regulon of the pleiotropic transcription factor Spx in Bacillus subtilis

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The regulon of the pleiotropic transcription factor Spx in Bacillus subtilis

Project description:The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress. Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished. Wild-type strain and spx mutant cells exposed or not to diamide stress were subjected to tiling array gene expression analysis. To distinguish direct and indirect effects, the genomic sites bound by the Spx-RNAP complex were mapped using a chromatine immunoprecipitation approach. This allowed the identification of 144 transcription units comprising 275 genes under direct Spx regulation. This data set contains 4 samples. Immunoprecipitated (IP) DNA from Bacillus subtilis Bas044 strain (BSB1, a tryptophan-prototrophic derivative 168 strain expressing a SPA-tagged Spx protein) were extracted from bacterial cultures in absence or presence of diamide. IP and whole cell extract DNA were hybridized on tiling array to generate ChIP-on-chip profiles. Two biological replicates were analyzed.

2012-09-06 | E-GEOD-35097 | biostudies-arrayexpress

Bacillus subtilis

Project description:Comparison of the transcription profile of B. subtilis clpX strain with B. subtilis clpX spx strain, reporting on Spx activity

| PRJNA216053 | ENA

Phenotype Enhancement Screen of a Regulatory spx Mutant Unveils a Role for the ytpQ Gene in the Control of Iron Homeostasis.

Project description:Spx is a global regulator of genes that are induced by disulfide stress in Bacillus subtilis. Most of the Spx-regulated genes (SRGs) are of unknown function, but many encode products conserved in low %GC Gram positive bacteria. Using a gene-disruption library of B. subtilis genomic mutations, the SRGs were screened for phenotypes related to Spx-controlled activities, such as growth in minimal medium and sensitivity to methylglyoxal, but nearly all of the SRG mutations showed little if any phenotype. To uncover SRG function, the mutations were rescreened in an spx mutant background to determine which mutant SRG allele would enhance the spx mutant phenotype. One of the SRGs, ytpQ, was the site of a mutation that, when combined with an spx null mutation, elevated the severity of the Spx mutant phenotype, as shown by reduced growth in a minimal medium and by hypersensitivity to methylglyoxal. Proteomic and transcriptomic data indicated that the ytpQ mutation caused the derepression of the Fur and PerR regulons, as well as heightened LexA-controlled gene expression. Our study suggests that the ytpQ gene, encoding a conserved DUF1444 protein, functions directly or indirectly in repairing or stabilizing Fe-bearing proteins, which are sensitive to thiol reactive agents and, therefore, likely influenced by Spx-controlled genes.

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Transcriptome analysis of miniBacillus PG10 and its parental strain B. subtilis 168

Project description:miniBacillus PG10 lacks ~36% of dispensible genentic material and has been derived from B. subtilis 168 (Reuß et al. 2017; PMID: 27965289). We performed RNA-seq analysis on mid-to-late exponential cultures and stationary phase cultures that were grown in LB medium. We specifically analyzed differential gene expression levels of lipid metabolic genes to compare to the lipidomic profiles of the two strains.

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Phenotype Enhancement Screen of a Regulatory spx Mutant Unveils a Role for the ytpQ Gene in the Control of Iron Homeostasis.

2011-10-24 | E-GEOD-28872 | biostudies-arrayexpress

A Chemical Disruptor of the ClpX Chaperone Complex Attenuates Multiresistant Staphylococcus aureus Virulence

Project description:The Staphylococcus aureus ClpXP protease is an important regulator of cell homeostasis and virulence. Here we utilize a high-throughput screen against the ClpXP complex and identify a specific inhibitor of the ClpX chaperone that disrupts its oligomeric state. Synthesis of 34 derivatives revealed that the molecular scaffold is restrictive for diversification with only minor changes tolerated. Subsequent analysis of the most active compound revealed strong attenuation of S. aureus toxin production which was quantified via a novel MS-based assay platform. Transcriptome and whole proteome studies further confirmed the global reduction of virulence and unraveled characteristic signatures of protein expression in compound treated cells. Although these partially matched the pattern of ClpX knockout cells, further depletion of toxins was observed leading to the intriguing perspective that additional virulence pathways may be directly or indirectly addressed by the small molecule.

2017-09-14 | PXD007259 | Pride

Effect of clpX overexpression in Synechococcus

Project description:In the unicellular cyanobacteriuIn the cyanobacterium, Synechococcus elongatus PCC 7942, most genes show rhythmic expression controlled by the Kai-based clock under continuous light conditions (LL). Overexpression of clpX led to a decrease in kaiBC promoter activity, disruption of circadian rhythm, and eventually cell death. We found that overexpression of clpX upregulated mRNA levels of ribosomal protein subunits, after which expression of other genes containing the clock genes was decreased. Wild type (WT) and inducible clpX-overexpressor (ox-clpX) S. elongatus PCC 7942 strains were analyzed under continuous light (LL) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: WT at hours 16 in LL (IPTG-free): WT under LL 20 in LL (addition of 100 µM IPTG for 4 hours): ox-clpX cells at hours 16 in LL (IPTG-free): ox-clpX cells at hours 20 in LL (addition of 100 µM IPTG for 4 hours)

2013-07-31 | E-GEOD-42542 | biostudies-arrayexpress

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