E. coli K-12 mutants yceP, trpE, and tnaA biofilm cell 24 hr for indole paper
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ABSTRACT:
ORGANISM(S): Escherichia coli Escherichia coli K-12
PROVIDER: GSE4562 | GEO | 2007/05/01
SECONDARY ACCESSION(S): PRJNA94487
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression of (i) K-12 yceP biofilms upon addition of 600 µM indole in LB glu medium, (ii) K-12 biofilms due to the trpE mutation in LB glu medium, and (iii) K-12 biofilms due to the tnaA mutation in LB medium. Experiment Overall Design: Strains:E. coli K12 BW25113 delta yceP, trpE, tnaA and wild type Experiment Overall Design: Medium:LB glu or LB Experiment Overall Design: Biofilm cells grown on glass wool Experiment Overall Design: Harvest time:24hr
2008-06-13 | E-GEOD-4562 | biostudies-arrayexpress
Project description:E. coli K-12 BW25113 mutant strain hha expression in biofilm cells relative to E. coli wild-type strain expression in biofilm cells. Samples were cultured in LB with glasswool at 37C for 4 hours and in LB glu with glasswool at 37C for 4, 15 and 24 hours. Hha is a temperature- and osmolarity-dependent modulator of gene expression that is induced 30-fold in Escherichia coli biofilms. Here we show through whole-transcriptome analysis that Hha decreases biofilm formation in both LB and LB glu media by (i) repressing fliC encoding the main structural flagellar protein flagellin, (ii) by repressing fimA encoding the major structural subunit of type I fimbriae, (iii) by repressing ihfA encoding a subunit of the transcriptional regulator IHF that induces the transcription of type I fimbriae genes, (iv) by regulating tnaA encoding tryptophanase that inhibits biofilms, and (v) by repressing ybaJ that forms an operon with hha. Corroborating the microarray data, hha deletion increased motility 3.2 ± 0.1-fold, decreased extracellular indole concentrations 12 ± 2-fold, and decreased type I fimbriae (as measured by yeast agglutination). Biofilm tests using single and double mutants of fimA and ihfA and transcriptional studies of the fimA, ihfA and ybaJ-hha promoters confirmed that Hha represses biofilm by inhibiting type I fimbriae production and that it negatively regulates its own transcription and that of ybaJ. Nickel-enhanced DNA microarrays to determine in vivo Hha binding sites confirmed that Hha binds the ybaJ-hha promoter, that it binds fimZ, a positive regulator of fimA, and that it binds to the rare codon tRNAs argU, ileXY, and proL. Sequence analysis of fimZ, fimB, fimE, and the type I fimbriae gene cluster fimAICDFGH revealed a high bias for the rare codons of arginine, isoleucine, proline, leucine, and threonine, and overexpressing Hha leads to cell death. Therefore, it appears Hha decreases biofilms by decreasing type I fimbriae production as a result of inhibiting synthesis of tRNAs for rare codons. Keywords: effect of hha deletion in biofilm formation 4 hr LB and 4,15 and 24 hr LB glu
2008-06-17 | GSE8708 | GEO
Project description:We have shown the quorum-sensing signals acylhomoserine lactones (AHLs), autoinducer-2 (AI-2), and indole influence the biofilm formation of Escherichia coli. Here, we investigate how the environment, i.e., temperature, affects indole and AI-2 signaling in E. coli. We show in biofilms that indole addition leads to more extensive differential gene expression at 30ï°C (186 genes) than at 37ï°C (59 genes), that indole reduces biofilm formation (without affecting growth) more significantly at 25ï°C and 30ï°C than at 37ï°C, and that the effect is associated with the quorum-sensing protein SdiA. The addition of indole at 30ï°C compared to 37ï°C most significantly repressed genes involved in uridine monophosphate (UMP) biosynthesis (carAB, pyrLBI, pyrC, pyrD, pyrF, and upp) and uracil transport (uraA). These uracil-related genes are also repressed at 30ï°C by SdiA, which confirms SdiA is involved in indole signaling. Also, compared to 37ï°C, indole more significantly decreased flagella-related qseB, flhD, and fliA promoter activity, enhanced antibiotic resistance, and inhibited cell division at 30ï°C. In contrast to indole and SdiA, the addition of (S)-4,5-dihydroxy-2,3-pentanedione (the AI-2 precursor) leads to more extensive differential gene expression at 37ï°C (63 genes) than at 30ï°C (11 genes), and, rather than repressing UMP synthesis genes, AI-2 induces them at 37ï°C (but not at 30ï°C). Also, the addition of AI-2 induces the transcription of virulence genes in enterohemorrhagic E. coli O157:H7 at 37oC but not at 30oC. Hence, cell signals cause diverse responses at different temperatures, and indole- and AI-2-based signaling are intertwined. Experiment Overall Design: We performed seven sets of microarray experiments in LB medium (Table 2): (i) biofilm cells of the BW25113 wild-type strain grown for 7 h at 30°C vs. 37°C to determine the effect of temperature on E. coli biofilm formation (initial absorbance of 0.05), (ii) biofilm cells of the tnaA mutant grown for 7 h with 1 mM indole vs. no indole at 30°C to determine the effect of temperature on indole signaling in E. coli (initial absorbance of 0.05), (iii) biofilm cells of the tnaA mutant grown for 7 h with 1 mM indole vs. no indole at 37°C to determine the effect of temperature on indole signaling in E. coli, (iv) suspension cells of the wild-type strain vs. the sdiA mutant at an absorbance of 4.0 at 600 nm at 30°C (since production of indole takes place primarily in the stationary phase) to discern the genes that SdiA controls (initial absorbance of 0.05), (v) biofilm cells of the sdiA mutant grown for 7 h with 1 mM indole vs. no indole at 30°C to determine gene expression in response to indole in the absence of SdiA, (vi) suspension cells of the luxS mutant with 100 micro M AI-2 vs. no AI-2 at 30°C for 3 h to determine the effect of temperature on AI-2 signaling in E. coli (initial absorbance of 0.5), and (vii) suspension cells of the luxS mutant with 100 micro M AI-2 vs. no AI-2 at 37°C for 3 h to determine the effect of temperature on AI-2 signaling in E. coli. Ten g of glass wool (Corning Glass Works, Corning, N.Y.) was used to form large amounts of biofilms (Ren et al., 2004a) in 250 mL LB in 1 L Erlenmeyer shake flasks. RNA was isolated from the suspension and biofilm cells as described previously (Ren et al., 2004b).
2008-06-18 | E-GEOD-9923 | biostudies-arrayexpress
Project description:We used DNA microarrays to investigate the impact of indole and 7-hdroxyindole on P. aeruginosa PAO1.For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures of P. aeruginosa PAO1 diluted that were 1:100. For P. aeruginosa with 7-hydroxyindole and indole, 500 uM 7-hydroxyindole in 250 uL DMF, 1000 uM indole in 250 uL DMF, or 250 uL DMF alone were added to cells grown in LB. The cells were shaken at 250 rpm and at 37oC for 7 h to form biofilms on the glass wool, and RNA was isolated from the biofilm cells. Keywords: comparison with E. coli signal indole on P. aeruginosa PAO1
2008-11-21 | GSE10065 | GEO
Project description:We used DNA microarrays to investigate the impact of indole and 7-hdroxyindole on P. aeruginosa PAO1.For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures of P. aeruginosa PAO1 diluted that were 1:100. For P. aeruginosa with 7-hydroxyindole and indole, 500 uM 7-hydroxyindole in 250 uL DMF, 1000 uM indole in 250 uL DMF, or 250 uL DMF alone were added to cells grown in LB. The cells were shaken at 250 rpm and at 37oC for 7 h to form biofilms on the glass wool, and RNA was isolated from the biofilm cells. Keywords: comparison with E. coli signal indole on P. aeruginosa PAO1 For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures of P. aeruginosa PAO1 diluted that were 1:100. For P. aeruginosa with 7-hydroxyindole and indole, 500 uM 7-hydroxyindole in 250 uL DMF, 1000 uM indole in 250 uL DMF, or 250 uL DMF alone were added to cells grown in LB. The cells were shaken at 250 rpm and at 37oC for 7 h to form biofilms on the glass wool, and RNA was isolated from the biofilm cells.
2010-10-23 | E-GEOD-10065 | biostudies-arrayexpress
Project description:Transcriptional profiling of Salmonella Typhimurium SL1344 wild type grown to OD600=1 in LB alone or in LB supplemented with 2mM Indole, or with 2mM indole for 15 min (called shock). The goal is to determine Salmonella response to indole at different time points.
2013-01-30 | GSE39760 | GEO
Project description:Transcriptional profiling of Salmonella Typhimurium SL1344 wild type grown to OD600=1 in LB alone or in LB supplemented with 2mM Indole, or with 2mM indole for 15 min (called shock). The goal is to determine Salmonella response to indole at different time points. Different conditions were tested. The reference on each hybridisation is the chromosome DNA of the wild type strain. 4 replicates each for LB and LB + Indole, 6 replicates for indole shock.
2013-01-30 | E-GEOD-39760 | biostudies-arrayexpress
Project description:The Escherichia coli quorum-sensing regulator, SdiA, belongs to the LuxR family of transcriptional regulators and is responsible for detecting signals from other bacteria. Previously we found that SdiA is necessary for E. coli to control its biofilm formation with indole just as SdiA is necessary for E. coli to alter its biofilm formation in the presence of N-acylhomoserine lactones (AHLs). Here we engineered SdiA by random mutagenesis to further control biofilm formation in the presence of indole and AHLs. After screening of 477?? mutants with indole and two AHLs (N-butyryl-DL-homoserine lactone, and N-(3-oxooctanoyl)-L-homoserine lactone, C6HSL), five SdiA variants were obtained that altered biofilm with and without signals of indole and AHLs. Two truncation variants (1E11 and 14C3) lacking the C-terminal DNA-binding domain of SdiA showed the reduction of biofilm formation by 5-fold and 10-fold in LB and LB glu, respectively. DNA microarrays show that the evolved SdiA (1E11) compared to wild-type SdiA influences indole synthesis genes, AI-2 uptake genes, acid-resistance genes, motility related genes, cold-shock protein genes, and several regulatory protein genes. Corroborating DNA microarrays, SdiA variants produced various amounts of indole which led to different survivals in low pH and influenced swimming motility and final cell density. Also, an AHL sensitive variant (2D10) 2-fold increased biofilm formation in the presence of C6HSL, while another variant (6B12) lowered biofilm formation in the presence of C6HSL. Hence, the results clearly showed that mutation of SdiA itself directly controls biofilm formation and SdiA variants could be further recognized by the inter-species signal AHLs. This is the first random protein engineering to control biofilm formation. Experiment Overall Design: For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms in 250 mL LB ( 1 mM IPTG + Cm30) in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures diluted that were 1:100. The cells were shaken at 250 rpm and 30C for 12 hours to form biofilms on the glass wool, and RNA was isolated from the the biofilm cells.
2009-02-09 | E-GEOD-11779 | biostudies-arrayexpress
Project description:Transcriptional profiling of Salmonella Typhimurium SL1344 wild type and deletion of the sdiA regulator-encoding gene grown to OD600=1 in LB alone or in LB supplemented with 2mM indole. The goal is to determine Salmonella response to indole and to define the SdiA-regulated genes in these conditions.
2013-01-30 | GSE36805 | GEO
Project description:Transcriptional profiling of Salmonella Typhimurium SL1344 wild type and deletion of the sdiA regulator-encoding gene grown to OD600=1 in LB alone or in LB supplemented with 2mM indole. The goal is to determine Salmonella response to indole and to define the SdiA-regulated genes in these conditions. 4 different conditions tested (wild type in LB, wild type in LB + 2mM indole, sdiA mutant in LB, sdiA mutant in LB + 2mM indole), 4 replicates for each condition. The reference on each hybridisation is the chromosomal DNA of the wild type strain.
2013-01-30 | E-GEOD-36805 | biostudies-arrayexpress