Transcription profiling of E. coli response to 0.2 mM Zn
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli
SUBMITTER: Lucy Lee
PROVIDER: E-MEXP-222 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Genome-wide transcriptional response of chemostat-cultured Escherichia coli to zinc.
Lee Lucy J LJ Barrett Jason A JA Poole Robert K RK
Journal of bacteriology 20050201 3
Zinc is an essential trace metal ion for growth, but an excess of Zn is toxic and microorganisms express diverse resistance mechanisms. To understand global bacterial responses to excess Zn, we conducted transcriptome profiling experiments comparing Escherichia coli MG1655 grown under control conditions and cells grown with a toxic, sublethal ZnSO4 concentration (0.2 mM). Cultures were grown in a defined medium lacking inorganic phosphate, permitting maximum Zn bioavailability, and in glycerol-l ...[more]
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Project description:Escherichia coli strain MG1655 was grown in a Zn-depleted custom-built chemostat. Culture volume (120 ml), temperature (37 oC) and stirring speed (440 rpm) were maintained. Steady state values for pH and OD600 were 6.9 and 0.6, respectively. Chemostats were grown for 50 h to allow five culture volumes to pass through the vessel and allow an apparent (pseudo-)steady state to be reached. At this point, ZnSO4.7H2O in water was added to a final concentration of 0.2 M in the chemostat. A 10 ml sample of culture was taken using a polypropylene pipette tip immediately prior to Zn addition and 2.5, 7, 10 and 30 min after addition. Samples were harvested into RNAprotect and total RNA was purified using QiagenM-bM-^@M-^Ys RNeasy Mini kit (using the supplierM-bM-^@M-^Ys protocol) prior to use in microarray analysis. A control experiment was also carried out in which water was added. 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The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 or Cy5/Cy3 (test/reference) fluorescent ratios were calculated from the normalized values. Biological experiments (i.e. a comparison of adequate versus low Zn in chemostat culture) were carried out three times, and a dye swap performed for each experiment, providing two technical repeats for each of the three biological repeats. Data from the independent experiments were combined. Data from the independent experiments were combined. Genes that were differentially expressed â?¥ twofold and displayed and P value of < 0.05 (as determined by a t-test) were defined as being statistically significantly differentially transcribed.
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2010-06-24 | E-GEOD-12878 | biostudies-arrayexpress
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2010-06-24 | E-GEOD-13048 | biostudies-arrayexpress
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2010-06-24 | E-GEOD-12877 | biostudies-arrayexpress