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Global gene expression analysis of Bacillus cereus to proanthocyanidin exposure

ABSTRACT: B. cereus RNA isolation were taken at OD 0.5 just before addition of 0.02 mg/mL EEC, and at 30 min of exposure. Water was added instead of EEC for control. Total RNA was isolated and we performed DNA microarray for genome-wide transcriptional analysis of B. cereus ATCC 14579 in the presence or absence of EEC. The microarray used in this study was custom-made B. cereus ATCC 14579 developed by Agilent Technologies (https://earray.chem.agilent.com/earray/). The B. cereus microarray design was based on the predicted chromosomal open reading frames (NCBI Accession No. AE016877). It targets the 5234 annotated CDS, three non-overlapping probes were designed, low-quality probes were eliminated, and finally 15242 could be spotted. Microarray data was normalized to 75th percentile and the difference was found to be significant by unpaired T-test (P = 0.05). Next, ratio changes of 2-fold (for up-regulated genes in the EEC stress condition) and 0.5-fold (for down-regulated genes in the EEC stress condition) were regarded as biologically significant. 596 were up-regulated and 495 were down-regulated. Bacillus cereus was selected at 0, 30 min exposure for RNA extraction and hybridization on Agilent microarrays.

ORGANISM(S): Bacillus cereus

SUBMITTER: Tomoko TAMURA

PROVIDER: E-GEOD-68767 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global gene expression analysis of Bacillus cereus to proanthocyanidin exposure

Project description:B. cereus RNA isolation were taken at OD 0.5 just before addition of 0.02 mg/mL EEC, and at 30 min of exposure. Water was added instead of EEC for control. Total RNA was isolated and we performed DNA microarray for genome-wide transcriptional analysis of B. cereus ATCC 14579 in the presence or absence of EEC. The microarray used in this study was custom-made B. cereus ATCC 14579 developed by Agilent Technologies (https://earray.chem.agilent.com/earray/). The B. cereus microarray design was based on the predicted chromosomal open reading frames (NCBI Accession No. AE016877). It targets the 5234 annotated CDS, three non-overlapping probes were designed, low-quality probes were eliminated, and finally 15242 could be spotted. Microarray data was normalized to 75th percentile and the difference was found to be significant by unpaired T-test (P = 0.05). Next, ratio changes of 2-fold (for up-regulated genes in the EEC stress condition) and 0.5-fold (for down-regulated genes in the EEC stress condition) were regarded as biologically significant. 596 were up-regulated and 495 were down-regulated.

2015-05-12 | GSE68767 | GEO

Gene transcription from the linear plasmid pBClin15 leads to cell lysis and extracellular DNA dependent aggregation of B. cereus ATCC 14579 in response to quinolone induced stress

Project description:Several members of the Bacillus cereus group of bacteria carry lysogenic phages of the family Tectiviridae. The Bacilus cereus reference strain (ATCC 14579) harbor a linear plasmid (pBClin15) that is highly similar to the genomes of the Tectiviruses. Production of active phages has however never been reported for pBClin15 and the role of pBClin15 in B. cereus physiology has been enigmatic. We have for the first time demonstrated an effect of pBClin15 on the physiology of B. cereus ATCC 14579 whereby the wild type is more sensitive to DNA damaging antibiotics compared to a pBClin15 cured strain. The microarray experiments in this study were designed to highlight transcriptional differences between the B. cereus ATCC 14579 wild type and a plasmid cured variant that potentially could explain the impact of pBClin15 on the B. cereus physiology. Microarray experiments were carried out under non-stressful conditions (growth in logarithmic phase in LB medium) under which there were no phenotypic difference between the wild type and pBClin15 cured strain as well as under stressful conditions under which there were phenotypic differences between the two strain (growth in LB medium supplemented with 0.5M-5g norfloxacin per ml).

2013-09-10 | E-MEXP-3894 | biostudies-arrayexpress

Insight into the response of Bacillus cereus towards the polysaccharide chitosan

Project description:Comparison of chitosan-treated B. cereus ATCC 14579 cells with non-treated B. cereus ATCC 14579 cells. 2 chitosans with similar molecular weight (Mw) but different degrees of acetylation (Fa) were used: chitosan B (Mw: 28.4 kDa, Fa: 0.16) (samples 1-3) and chitosan A (Mw: 36.0 kDa, Fa: 0.01) (samples 4-6).

2011-10-19 | GSE29024 | GEO

Multiple roles for CodY in the type strain Bacillus cereus ATCC 14579

Project description:Comparison of the B cereus codY deletion mutant with wild type strain (ATCC 14579)

2012-07-05 | GSE31017 | GEO

Comparative transcriptome analysis of biofilm and planktonic cells of Bacillus cereus ATCC 10987

Project description:Planktonic and biofilm cells of Bacillus cereus ATCC 14579 and ATCC 10987 were studied using microscopy and transcriptome analysis. By microscopy, clear differences could be observed between biofilm and planktonic cells as well as between the two strains. By using hierarchical clustering of the transcriptome data, little difference was observed between the biofilm cells of B. cereus ATCC 14579 and ATCC 10987. Different responses between biofilm and planktonic cells could be identified using transcriptome analysis. Biofilm formation seemed to cause a shift in metabolism with up- or down-regulation of genes involved in different metabolic pathways. Genes involved in motility were down-regulated. No clear up-regulation related to capsular or extracellular polysaccharides was observed. Sporulation was observed in biofilm cells using microscopy, which was corroborated with up-regulation of genes involved in sporulation in biofilm cells. The results obtained in this study provide insight in general and strain specific behavior of B. cereus cells in multicellular communities.

2015-10-10 | GSE24620 | GEO

Comparative transcriptome analysis of biofilm and planktonic cells of Bacillus cereus ATCC 14579

2015-10-10 | GSE24619 | GEO

Comparative transcriptome and phenotype analysis of acid-stressed Bacillus cereus strains

Project description:This SuperSeries is composed of the following subset Series: GSE13711: Comparative transcriptome and phenotype analysis of acid-stressed Bacillus cereus strain ATCC 14579 GSE13729: Comparative transcriptome and phenotype analysis of acid-stressed Bacillus cereus strain ATCC 10987 Refer to individual Series

2010-06-25 | E-GEOD-13773 | biostudies-arrayexpress

Monitoring the ethanol stress response of a sigM deletion strain of B. cereus ATCC 14579.

Project description:Here, the role of σM and its regulon in stress response and survival of B. cereus ATCC 14579 was assessed by comparative transciptome and phenotypic analysis of this strain and its sigM deletion strain. Exposure of B. cereus ATCC 14579 to a wide range of stresses revealed expression of sigM, encoding σM, to be up-regulated mainly in the presence of ethanol and after alkaline pH-shock. Next to this, disc diffusion tests showed the sigM deletion strain to be more sensitive to oxidizing agents and to be more resistant to cell-wall targeting antibiotics than the wild-type strain. The σM regulon was subsequently determined by comparative transcriptional analyses of the wild-type and its sigM-deletion strain after exposure to ethanol. The putative σM-regulon was shown to consist of 29 genes, several of these genes are predicted to be involved in counteracting oxidative stress, such as an NADH oxidase, a ferredoxin, and a lysine decarboxylase or could encode enzymes involved in methionine metabolism, leading toward L-cysteine production, including luxS. Screening of promoter upstream regions allowed for the assessment of a B. cereus consensus promoter binding site for σM. Since the consensus promoter binding site for B. cereus ATCC 14579 σM, its regulon and the predicted functionalities are different from the corresponding features in B. subtilis, it can be concluded that σM plays a unique role in B. cereus stress response and survival. The sigM deletion strain of B. cereus ATCC 14579 was cultured to an OD600 of ~0.6. Here the first RNA sample was taken, 0 min. After sampling 4% of ethanol was added (v/v), and samples were taken after 10, 30 and 60 minutes of exposure. Comparisons performed were 0 min - 10 min, 0 min - 30 min, and 0 min - 60 min.

2008-05-11 | E-GEOD-9856 | biostudies-arrayexpress

Gene induction by ethanol stress in B. cereus ATCC 14579

Project description:The stress response of B. cereus ATCC 14579 is monitored true time, showing an enormous response in gene expression. The wild-type strain of B. cereus ATCC 14579 was cultured to an OD600 of ~0.6. Here the first RNA sample was taken, 0 min. After sampling 4% of ethanol was added (v/v), and samples were taken after 10, 30 and 60 minutes of exposure. Comparisons performed were 0 min - 10 min, 0 min - 30 min, and 0 min - 60 min.

2008-05-11 | E-GEOD-9855 | biostudies-arrayexpress

Gene induction by ethanol stress in B. cereus ATCC 14579

Project description:The stress response of B. cereus ATCC 14579 is monitored true time, showing an enormous response in gene expression. Keywords: Stress response, comparative transcriptome analysis.

2008-05-11 | GSE9855 | GEO

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