Escherichia coli
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ABSTRACT:
PROVIDER: PRJNA108269 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:gene expression profiles by overexpressing Hha from pCA24N-hha using 2 mM IPTG induction in BW25113 wild type suspension cells in LB medium at 37C relative to BW25113 carrying the empty vector plasmid in the same test conditions. Experiment Overall Design: Strains: E. coli K12 BW25113/pCA24N, BW25113/pCA24N-hha Experiment Overall Design: Growth conditions: grow culture in LB medium at 37C to OD600 0.1 and add 2 mM IPTG to induce, and grow to OD600 0.5 to collect cells. RNA was extraction, and gene expression profiles were evaluated.
2008-10-20 | E-GEOD-10116 | biostudies-arrayexpress
Project description:gene expression profiles by overexpressing Hha from pCA24N-hha using 2 mM IPTG induction in BW25113 wild type suspension cells in LB medium at 37C relative to BW25113 carrying the empty vector plasmid in the same test conditions. Keywords: overexpression, gene expression profiles
2008-06-17 | GSE10116 | GEO
Project description:This Series involves two studies: 1) The gene expression of E. coli K-12 BW25113 ompA mutant strain vs. wild type strain glasswool biofilm cells and E. coli K-12 BW25113 ompA mutant vs. wild type polystyrene biofilm cells. 2) The gene expression of E. coli BW25113 ompA/pCA24N_ompA vs. ompA/pCA24N suspension cells. Strains: E. coli K-12 BW25113 wild type, ompA mutant Medium: LB Cell type: Biofilm cells grown on glasswool and polystyrene surfaces Time: 15 h Temperature: 37C Strains: BW25113 ompA/pCA24N_ompA and ompA/pCA24N Medium: LB Time: 7 h Temperature: 37C Cell type: suspension cells, induced by 0.1 mM IPTG
2010-11-03 | E-GEOD-14064 | biostudies-arrayexpress
Project description:The global regulator, H-NS, controls genes related to stress response, biofilm formation, and virulence expression by recognizing the curved DNA and silences gene transcription acquired from lateral gene transfer. Here, we rewired H-NS to control biofilm formation using protein engineering. One H-NS variant, H-NS K57N was obtained to reduce biofilm formation 10-fold compared to H-NS wild-type. Whole-transcriptome analysis (BW25113 hha hns / pCA24N-hns K57N vs. BW25113 hha hns / pCA24N-hns) revealed that H-NS K57N represses biofilm formation through the interactinon with other nucleoid proteins, Cnu and StpA. Remarkably, H-NS K57N enhanced the excision of defective prophage Rac while H-NS wild-type represses it, and H-NS controlled only Rac excision among E. coli prophages. These results imply that the repression of Rac excision is one of the silencing manner for foreign genes by H-NS. Also, the prophage excision not only led to the change of biofilm formation but also resulted in cell lysis through the expression of toxin protein HokD with reduced viability, which are important for cell physiology in response to the change of environmental conditions. Hence, H-NS regulatory system may be evolved easily with specialized functions in terms of biofilm formation, prophage control, and cell lysis. For the whole transcriptome study of BW25113 hha hns / pCA24N-hns K57N versus BW25113 hha hns / pCA24N-hns, cells were grown in 250 mL LB containing 1 mM IPTG for 7 h with 10 g of glass wool (Corning Glass Works, Corning, N.Y.) in 1 L Erlenmeyer flasks to form a robust biofilm. Biofilm cells were obtained by rinsing and sonicating the glass wool in sterile 0.85% NaCl solution at 0°C, and RNALater buffer® (Applied Biosystems, Foster City, CA) was added for RNA stabilization and protection during the RNA preparation steps. Total RNA was isolated from biofilm cells. The E. coli GeneChip Genome 2.0 array (Affymetrix, Lot# 4059655) containing 10,208 probe sets for four E. coli strains (MG1655, CFT073, O157:H7-Sakai, and O157:H7-EDL933) was used for DNA microarray. cDNA synthesis, fragmentation, and hybridizations were performed.
2010-02-27 | E-GEOD-17853 | biostudies-arrayexpress
Project description:Fifty five genes were induced or reduced (2.5-fold) by the absence of rodZ genes Among them, curli production-, cell division-, and biofilm-associated genes as well as phage-related genes were regulated by the RodZ, significantly Three-condition experiment, BW25113 WT/pCA24N vs. rodZ/pCA24N vs. rodZ/pCA24N-RodZ. For preparing the total RNA, each cells were grown at 37°C upto OD600=0.5 and then keep growing with 1 mM IPTG for additional 6 h
2015-11-05 | E-GEOD-63052 | biostudies-arrayexpress
Project description:This Series involves two studies: 1) The gene expression of E. coli K-12 BW25113 ompA mutant strain vs. wild type strain glasswool biofilm cells and E. coli K-12 BW25113 ompA mutant vs. wild type polystyrene biofilm cells. 2) The gene expression of E. coli BW25113 ompA/pCA24N_ompA vs. ompA/pCA24N suspension cells.
2010-01-20 | GSE14064 | GEO
Project description:The global transcriptional regulator Hha of Escherichia coli controls hemolysin activity, biofilm formation, and virulence expressions. Earlier, we have reported that Hha represses initial biofilm formation and disperses biofilms as well as controls prophage excision in E. coli. Since biofilm dispersal is a promising area to control biofilms, here we rewired Hha to control biofilm dispersal and formation. The Hha variant Hha13D6 was obtained to have enhanced biofilm dispersal activity along with increased toxicity compared to wild-type Hha (Hha13D6 induces dispersal 60%, whereas wild-type Hha induces dispersal at early biofilms but not at mature biofilms). Toxic Hha13D6 caused cell death probably by the activation of proteases HslUV, Lon, and PrlC, and deletion of protease gene hslV with overproducing Hh13D6 repressed biofilm dispersal, indicating Hha13D6 induces biofilm dispersal through the activity of protease HslV. Furthermore, another Hha variant Hha24E9 was also obtained to decrease biofilm formation 4-fold compared to wild-type Hha by regulation of gadW, glpT, and phnF. However, the dispersal variant Hha13D6 did not decrease biofilm formation, while the biofilm variant Hha24E9 did not induce biofilm dispersal. Hence, Hha may have evolved two ways in response to environmental factors to control biofilm dispersal and formation, but both controlling mechanisms come from different regulatory systems. For the whole-transcriptome study of BW25113 hha/pCA24N-hha13D6 versus BW25113 hha/pCA24N-hha biofilm dispersal, cells were grown in 250 mL of LB glucose (0.2%) for 16 h at 125 rpm with 10 g of glass wool (Corning Glass Works, Corning, NY, USA) in 1 L Erlenmeyer flasks to form a robust biofilm (Ren et al., 2004) and incubated an additional 1 h with 1 mM IPTG to induce wild-type Hha and Hha13D6. Similarly, for the whole transcriptome study of BW25113 hha/pCA24N-hha24E9 versus BW25113 hha/pCA24N-hha biofilm formation, cells were grown in 250 mL of LB glucose (0.2%) containing 1 mM IPTG for 7 h at 250 rpm with 10 g of glass wool to form biofilms. Biofilm cells were obtained by rinsing and sonicating the glass wool in sterile 0.85% NaCl solution at 0°C, and RNALater buffer® (Applied Biosystems, Foster City, CA, USA) was added to stabilize RNA during the RNA preparation steps. Total RNA was isolated from biofilm cells using a bead beater (Biospec, Bartlesville, OK, USA). cDNA synthesis, fragmentation, and hybridizations to the E. coli GeneChip Genome 2.0 array (Affymetrix, Santa Clara, CA, USA; P/N 511302). Genes were identified as differentially expressed if the expression ratio was higher than the standard deviation: 2.0-fold (induced and repressed) cutoff for Hha13D6 DNA microarrays (standard deviation 1.3-fold) and 10.0-fold (induced) or 4.0-fold (repressed) for Hha24E9 DNA microarrays (standard deviation 4.0-fold), and if the p-value for comparing two chips was less than 0.05.
2010-10-31 | E-GEOD-21604 | biostudies-arrayexpress
Project description:To provide more evidence of the specificity of the RNase activity of GhoS, we performed a whole-transcriptome study for the production of GhoS vs. an empty plasmid so that we could investigate all of the cellM-bM-^@M-^Ys transcripts for cleavage with GhoS, in vivo (i.e., BW25113/pCA24N-ghoS vs. BW25113/pCA24N with 1 mM IPTG induction of ghoS for 90 min). Under these conditions, only 20 genes were found to be repressed by more than 4-fold; there were no induced genes. These GhoS-repressed genes were all involved in the biosynthesis/transport of purines and pyrimidines; among them, pyrI was most highly repressed (-20 fold). These results suggest that GhoS selectively cleaves only a few cellular targets. Overnight cultures of E. coli strains BW25113-pCA24N-ghoS and BW25113-pCA24N (emtpy plasmid) were inoculated into fresh LB medium to a turbidity of 0.05 at 600 nm and grown at 37M-BM-0C. IPTG (1 mM) induction was performed when turbidity reached 0.2 and continued for 90 min. Total RNAs were isolated from the cultures and converted to cDNA for the application on E. coli genome 2.0 array.
2012-08-30 | E-GEOD-36779 | biostudies-arrayexpress
Project description:To provide more evidence of the specificity of the RNase activity of GhoS, we performed a whole-transcriptome study for the production of GhoS vs. an empty plasmid so that we could investigate all of the cell’s transcripts for cleavage with GhoS, in vivo (i.e., BW25113/pCA24N-ghoS vs. BW25113/pCA24N with 1 mM IPTG induction of ghoS for 90 min). Under these conditions, only 20 genes were found to be repressed by more than 4-fold; there were no induced genes. These GhoS-repressed genes were all involved in the biosynthesis/transport of purines and pyrimidines; among them, pyrI was most highly repressed (-20 fold). These results suggest that GhoS selectively cleaves only a few cellular targets.
2012-08-30 | GSE36779 | GEO
Project description:The global regulator, H-NS, controls genes related to stress response, biofilm formation, and virulence expression by recognizing the curved DNA and silences gene transcription acquired from lateral gene transfer. Here, we rewired H-NS to control biofilm formation using protein engineering. One H-NS variant, H-NS K57N was obtained to reduce biofilm formation 10-fold compared to H-NS wild-type. Whole-transcriptome analysis (BW25113 hha hns / pCA24N-hns K57N vs. BW25113 hha hns / pCA24N-hns) revealed that H-NS K57N represses biofilm formation through the interactinon with other nucleoid proteins, Cnu and StpA. Remarkably, H-NS K57N enhanced the excision of defective prophage Rac while H-NS wild-type represses it, and H-NS controlled only Rac excision among E. coli prophages. These results imply that the repression of Rac excision is one of the silencing manner for foreign genes by H-NS. Also, the prophage excision not only led to the change of biofilm formation but also resulted in cell lysis through the expression of toxin protein HokD with reduced viability, which are important for cell physiology in response to the change of environmental conditions. Hence, H-NS regulatory system may be evolved easily with specialized functions in terms of biofilm formation, prophage control, and cell lysis.
2010-02-22 | GSE17853 | GEO