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Series GSE8706 Query DataSets for GSE8706
Status Public on Feb 22, 2008
Title E. coli BW25113 yncC vs wt biofilm cells in LB 15h 37C and MG1655 yncC vs wt colony cells in LB plates 15h 37C
Platform organisms Escherichia coli; Escherichia coli K-12
Sample organism Escherichia coli
Experiment type Expression profiling by array
Summary 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.
Keywords: biofilm gene expression and colony gene expression
 
Overall design Strains: E. coli K-12 BW25113 wild-type, mutant yncC
and E. coli K-12 MG1655 wild-type, mutant yncC
Medium: LB
Biofilm grown on glasswool or colony cells growth in LB plates
Time: 15 hours
Temperature: 37C
Cell type: biofilm or colony

For the biofilm arrays in BW25113 background:

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.
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.

for the colony arrays in MG1655 background:

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.
 
Contributor(s) Zhang X, Garcia-Contreras R, Wood TK
Citation(s) 18309357
Submission date Aug 06, 2007
Last update date Mar 08, 2019
Contact name Thomas K. Wood
E-mail(s) twood@engr.psu.edu
Phone 814-863-4811
Organization name Pennsylvania State University
Department Chemical Engineering & Biochemistry and Molecular Biology
Lab Dr. Wood's Lab
Street address Room 161 Fenske Laboratory, University Park
City State College
State/province PA
ZIP/Postal code 16802
Country USA
 
Platforms (2)
GPL199 [Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array
GPL3154 [E_coli_2] Affymetrix E. coli Genome 2.0 Array
Samples (4)
GSM215705 BW25113 w/t LB 15h 37C biofilm cells
GSM215706 BW25113 yncC deletion mutant LB 15h 37C biofilm cells
GSM252012 MG1655 WT colony 37C
Relations
BioProject PRJNA101941

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Supplementary file Size Download File type/resource
GSE8706_RAW.tar 5.1 Mb (http)(custom) TAR (of CEL, CHP)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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