Differential gene expression of ydgG mutant
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli Escherichia coli K-12
PROVIDER: GSE3514 | GEO | 2005/11/01
SECONDARY ACCESSION(S): PRJNA93559
REPOSITORIES: GEO
Similar Datasets
Project description:The E. coli Genechip antisense genome array was used to study the differential gene expression profile of E. coli K12 ydgG mutant compared to its isogenic wild type in a mature biofilm. Experiment Overall Design: Overnight cultures were diluted 100X into 1 L shake flasks containing 250 mL of LB + 0.2 % and 10 g of glass wool. The cells were shaken at 250 rpm and 37 C for 24 hours (final OD600=5 for the suspended cells), to form a biofilm on the glass wool, and RNA was isolated from the biofilm and Affymetrix protocol was used for preparing fragmented and labelled cDNA that was hybrizide to the chips.
2008-06-12 | E-GEOD-3514 | biostudies-arrayexpress
Project description:The gene expression of glasswool biofilm cells in E. coli yjgI mutant vs. E. coli wild type strain in LB. Strains: E. coli K12 BW25113 wild type, yjgI mutant Medium: LB Biofilm grown on glass wool Time: 15 h Cell type: biofilm
2011-05-29 | E-GEOD-22057 | biostudies-arrayexpress
Project description:Many reports show an association between the Pst system, the Pho regulon related genes and bacterial virulence. Our previous results showed that a functional Pst system is required for full virulence, resistance to serum, polymyxin B and acid shock. However, the interplay between the Pst system and virulence has an unknown molecular basis. To understand global APEC virulent strain responses to Pho regulon activation, we conducted transcriptome profiling experiments comparing the APEC chi7122 strain and its isogenic Pst mutant grown in rich phosphate medium using the Affymetrix GeneChip® E. coli Genome 2.0 Array. The Affymetrix GeneChip® E. coli Genome 2.0 Array contains the genome of the E. coli MG1655 and three pathogenic E. coli strain (EDL933, Sakai and CFT073) representing 20,366 genes. While comparing genes expression between Pst mutant and the wild type chi7122 strain, 471 genes are either up- (254) or down-regulated (217) of at least 1.5-fold, with a p-value inferior or equal to 0.05 and a false discovery rate of 2.71%. Keywords: Escherichia coli, phosphate starvation response, Pho regulon, Pst system, Affymetrix, transcriptional analysis
2008-09-15 | GSE9178 | GEO
Project description:Pathogens like E. coli O157:H7 are responsible for many outbreaks and can be found and survive in poor inorganic phosphate (Pi) environments. In E. coli the phosphate homeostasis is regulated by the Pst system and the two-component system PhoB/R. In a Δpst mutant, PhoB is constitutively activated and biofilm formation is increased. To understand how PhoB activation lead to biofilm increase, we compared the transcriptomes of EDL933 the WT strain and Δpst mutant both grown in MOPS Pi rich medium, using the Affymetrix GeneChip® E. coli Genome 2.0 Array.
2019-01-23 | GSE125488 | GEO
Project description:Leafy green vegetables, such as lettuce, have been increasingly implicated in outbreaks of foodborne illnesses due to contamination by Escherichia coli O157:H7. While E. coli can survive in soils, colonize plants, and survive on produce, very little is known about the interaction of E. coli with the roots of growing lettuce plants. In these studies, a combination of microarray analyses and surface enhanced Raman spectroscopy (SERS) were used to gain a comprehensive understanding of bacterial genes involved in the colonization and growth of E. coli O157:H7 on lettuce roots and compared to E. coli K12 using a hydroponic system (HS) which we have reported in the previous studies. Using microarray, after three days of interaction with lettuce roots, 94 and 109 genes of E. coli O157:H7 were significantly up-regulated and down-regulated at least 1.5 fold, respectively. Only 8 genes were also found in the E. coli K12 up-regulated genes. No genes were found in the down-regulated genes clusters between those two strains. For E. coli O157:H7, forty out of the 94 up-regulated genes (43%) were involved in protein synthesis and were highly repressed compared to 40 out of 193 (23%) E. coli K12 up-regulated genes associated with protein synthesis. The wildtype of E.coli O157:H7 colonized two log CFU per root less compared to E. coli K12. Genes involved in biofilm modulation (bhsA and ybiM) were significantly up-regulated in E. coli O157:H7 and curli production (crl and csgA) were found important for E. coli K12 to attach to lettuce roots in the previous studies. BhsA mutant of E. coli O157:H7 was impaired in the colonization of lettuce roots. The SERS spectra of E. coli K12 and O157 controls (cells without interacting with roots) were very similar. The spectra of E. coli K12 and O157 exposed to the hydroponic system (HS) showed some differences in the nucleic acid, protein, and lipid regions compared with controls. The spectra of E. coli K12 HS cells exhibited significant differences compared to spectra from E. coli O157 HS cells in the RNA and protein regions. The overall band intensity of amide regions declined for E. coli O157 HS cells, while it increased for E. coli K12 HS cells. The intensity of the RNA bands of E. coli K12 HS cells were also found much higher than those of E. coli O157 HS cells. These findings were in agreement to our Microarray data. Our microarray and SERS data showed that E. coli K12 and O157:H7 behavior dramatically differently in colonizing on lettuce roots. Compared to K12, E. coli O157:H7 colonized less efficiently on lettuce roots.
2012-03-29 | GSE36885 | GEO
Project description:E. coli K-12 BW25113 mutant strain yncC expression in biofilm cells relative to E. coli wild-type strain expression in biofilm cells. All samples were cultured in LB with glasswool at 37C for 15 hours and E. coli K-12 MG1655 mutant yncC colony cells vs wild type colony cells in LB plates 15h 37C. Quorum-sensing signal autoinducer 2 (AI-2) stimulates Escherichia coli biofilm formation through the motility regulator MqsR that induces expression of the putative transcription factor encoded by yncC. Here we show YncC increases biofilm formation by decreasing mucoidy (corroborated by decreased exopolysaccharide production and increased sensitivity to bacteriophage P1 infection). Differential gene expression and gel shift assays demonstrated that YncC is a repressor of the predicted periplasmic protein-encoding gene ybiM which was corroborated by the isogenic yncC ybiM double mutation which repressed the yncC phenotypes (biofilm formation, mucoidy, and bacteriophage resistance). Through nickel-enrichment microarrays and additional gel shift assays, we found that the putative transcription factor B3023 (directly upstream of mqsR) binds the yncC promoter. Overexpressing MqsR, AI-2 import regulators LsrR/LsrK, and AI-2 exporter TqsA induced yncC transcription whereas the AI-2 synthase LuxS and B3023 repressed yncC. MqsR has a toxic effect on E. coli bacterial growth which is partially reduced by the b3023 mutation. Therefore, AI-2 quorum-sensing control of biofilm formation is mediated through regulator MqsR that induces expression of the transcription factor YncC which serves to inhibit the expression of periplasmic YbiM; this inhibition of YbiM prevents it from overexpressing exopolysaccharide (causing mucoidy) and prevents YbiM from inhibiting biofilm formation. Experiment Overall Design: Strains: E. coli K-12 BW25113 wild-type, mutant yncC Experiment Overall Design: and E. coli K-12 MG1655 wild-type, mutant yncC Experiment Overall Design: Medium: LB Experiment Overall Design: Biofilm grown on glasswool or colony cells growth in LB plates Experiment Overall Design: Time: 15 hours Experiment Overall Design: Temperature: 37C Experiment Overall Design: Cell type: biofilm or colony Experiment Overall Design: For the biofilm arrays in BW25113 background: Experiment Overall Design: Overnight cultures (16 h, 2.5 mL) of wild type E. coli BW25113 and BW25113 yncC in LB and LB with kanamycin (50 μg/mL), respectively, were used to inoculate 250 mL LB with 10 g of glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubating at 37°C for 15 h with shaking (250 rpm), biofilm cells were prepared by rinsing and sonicating the glass wool in sterile 0.85% NaCl solution at 0°C as described before. The total RNA was isolated from biofilm cells as described previously. Experiment Overall Design: The E. coli Genechip antisense genome array (P/N 900381, Affymetrix, Santa Clara, CA) containing probes for more than 4200 open reading frames (ORFs) was used to analyze the complete E. coli transcriptome as described previously. Hybridizations were performed for 16 h and the total cell intensity was scaled automatically in the software to an average value of 630. The Gene Expression Technical Manual (Affymetrix) was followed for the procedures of DNA microarrays, and the GeneChip operating software (Affymetrix) was applied to analyze data of DNA microarrays. The data quality was assessed following the manufacturer's guidelines (GeneChip Expression Analysis: Data Analysis Fundamentals; Affymetrix) and also was based on the expected signals of E. coli BW25113 and the yncC mutant genotypes (e.g., signals of the deleted genes, araA and rhaA, were low for both BW25113 and BW25113 yncC, while the signal of yncC was low for the yncC mutant). A gene was identified as differentially-expressed when the P value based on the False Discovery Rate Method was less than 0.05 and the expression ratio was greater than threefold since the standard deviation for the expression ratio for all of genes was 2. Experiment Overall Design: for the colony arrays in MG1655 background: Experiment Overall Design: For the agar biofilm, fresh single colonies of wild-type E. coli MG1655 and MG1655 yncC were re-streaked on LB agar plates, incubated, and about 0.05 g of the colony cultures on LB plate were quickly transferred to 2-mL collection tubes. The total RNA was isolated from these colony cells as described previously. The E. coli GeneChip Genome 2.0 Array (Affymetrix, P/N 900551, Santa Clara, CA) containing 10,208 probe sets for open reading frames, rRNA, tRNA, and intergenic regions for four E. coli strains: MG1655, CFT073, O157:H7-Sakai, and O157:H7-EDL933, was used to analyze the complete E. coli transcriptome. A gene was identified as differentially-expressed when the P value based on the False Discovery Rate Method (Benjamini & Hochberg, 1995) was less than 0.05 and the expression ratio was greater than threefold since the standard deviation for the expression ratio for all of MG1655 genes (except the deleted yncC gene) was 2.
2008-04-07 | E-GEOD-8706 | biostudies-arrayexpress
Project description:Leafy green vegetables, such as lettuce, have been increasingly implicated in outbreaks of foodborne illnesses due to contamination by Escherichia coli O157:H7. While E. coli can survive in soils, colonize plants, and survive on produce, very little is known about the interaction of E. coli with the roots of growing lettuce plants. In these studies, a combination of microarray analyses and surface enhanced Raman spectroscopy (SERS) were used to gain a comprehensive understanding of bacterial genes involved in the colonization and growth of E. coli O157:H7 on lettuce roots and compared to E. coli K12 using a hydroponic system (HS) which we have reported in the previous studies. Using microarray, after three days of interaction with lettuce roots, 94 and 109 genes of E. coli O157:H7 were significantly up-regulated and down-regulated at least 1.5 fold, respectively. Only 8 genes were also found in the E. coli K12 up-regulated genes. No genes were found in the down-regulated genes clusters between those two strains. For E. coli O157:H7, forty out of the 94 up-regulated genes (43%) were involved in protein synthesis and were highly repressed compared to 40 out of 193 (23%) E. coli K12 up-regulated genes associated with protein synthesis. The wildtype of E.coli O157:H7 colonized two log CFU per root less compared to E. coli K12. Genes involved in biofilm modulation (bhsA and ybiM) were significantly up-regulated in E. coli O157:H7 and curli production (crl and csgA) were found important for E. coli K12 to attach to lettuce roots in the previous studies. BhsA mutant of E. coli O157:H7 was impaired in the colonization of lettuce roots. The SERS spectra of E. coli K12 and O157 controls (cells without interacting with roots) were very similar. The spectra of E. coli K12 and O157 exposed to the hydroponic system (HS) showed some differences in the nucleic acid, protein, and lipid regions compared with controls. The spectra of E. coli K12 HS cells exhibited significant differences compared to spectra from E. coli O157 HS cells in the RNA and protein regions. The overall band intensity of amide regions declined for E. coli O157 HS cells, while it increased for E. coli K12 HS cells. The intensity of the RNA bands of E. coli K12 HS cells were also found much higher than those of E. coli O157 HS cells. These findings were in agreement to our Microarray data. Our microarray and SERS data showed that E. coli K12 and O157:H7 behavior dramatically differently in colonizing on lettuce roots. Compared to K12, E. coli O157:H7 colonized less efficiently on lettuce roots. Escherichia coli O157:H7 strains were grown in the lettuce rhizosphere for three days. Transcriptional profiling of E. coli was compared between cells grown with and without rhizosphere . Three biological replicates of each treatment were prepared, and six microarray slides were used.
2012-03-28 | E-GEOD-36885 | biostudies-arrayexpress
Project description:Leafy green vegetables, such as lettuce, have been increasingly implicated in outbreaks of foodborne illnesses due to contamination by Escherichia coli O157:H7. While E. coli can survive in soils, colonize plants, and survive on produce, very little is known about the interaction of E. coli with the roots of growing lettuce plants. In these studies a combination of microarray analyses and microbial genetics were used to gain a comprehensive understanding of bacterial genes involved in the colonization and growth of E. coli K12 on lettuce roots using a hydroponic assay system. Here we report that after three days of interaction with lettuce roots, 193 and 131 genes were significantly up-regulated and down-regulated at least 1.5 fold, respectively. Forty-five out of the 193 up-regulated genes (23%) were involved in protein synthesis and were highly induced. Genes involved in stress response, attachment and biofilm formation were up-regulated in E. coli when they interacted with lettuce roots under conditions of hydroponic growth. In particular crl, a gene regulating the cryptic csgA gene for curli production, was significantly up regulated. The crl, csgA and fliN mutants had a reduced capacity to attach to roots as determined by bacterial counts and by confocal laser scanning microscopy. Our microarray data showed that E. coli K12 increased the synthesis of proteins indicated that a dramatic change was induced in the physiology of the microorganism. This study indicates that E. coli K12 can efficiently colonize lettuce roots by using attachment and biofilm modulation genes and can readily adapt to the rhizosphere of lettuce plants. Further studies are needed to better characterize this interaction in pathogenic strains of this species.
2011-11-17 | GSE33735 | GEO
Project description:We probed the mechanism of cross-regulation of osmotic and heat stress responses by characterizing the effects of high osmolarity (0.3M vs. 0.0M NaCl) and temperature (43oC vs. 30oC) on the transcriptome of Escherichia coli K12 using E. coli Genome 2 Array (Affymetrix, Inc.). Independent array hybridizations were carried out for 3 biological replicates (independent cultures). Total RNA was extracted using a hot phenol-chloroform method. cDNA synthesis, fragmentation and labeling, and washing and scanning of E. coli GeneChip Arrays were performed according to the instructions of the manufacturer (Affymetrix Technical Manual, Affymetrix, Inc., USA). Labeled cDNA was hybridized to E. coli Genome 2 Array (Affymetrix, Inc.). Independent array hybridizations were carried out for 3 biological replicates (independent cultures) of each condition. A number of genes in the SoxRS and OxyR oxidative stress regulons were up-regulated by high osmolarity, high temperature, and/or by the combination of both stresses. This result could account for cross-protection of osmotic stress against oxidative stress. The trehalose biosynthetic genes were induced by both stresses, in accord with the proposed protective role of this disaccharide against thermal and oxidative damage. Keywords: Affymetrix microarrays
2009-01-01 | GSE7656 | GEO
Project description:High-resolution transcriptional profiling of E. coli across nine timepoints of growth in rich media (LB). Samples collected from lag phase to stationary phase of growth. High-resolution tiling array to detect conditional operon isoforms. Custom Agilent array designed to detect condition-specific transcriptional isoforms. Array designed for E coli K12 MG1655 genome. Tiled using 23bp sliding window. Includes >10,000 probes surrounding predicted operon break sites at 6 bp resolution.
2014-07-22 | GSE55879 | GEO