Comparison of the Changes in Global Gene Expression of <i>Escherichia coli</i> Induced by Four Bactericidal Agents

Abstract

DNA microarrays provide a global view of the physiological state of the cell by parallel analysis of the expression levels of all the genes in an organism. The effects of four bactericidal agents on the expression pattern of Escherichia coli MG1655 were assessed. Compounds were chosen on the basis of their different mechanisms of action and included inhibitors of DNA replication and recombination, translation, transcription and cell wall biosynthesis. The addition of rifampin resulted in increased expression of the target, rpoB, as well as several genes involved in nucleotide salvage and purine biosynthesis. The addition of ampicillin resulted in overall changes in gene expression that showed some similarity to changes induced by rifampin. The addition of the antibiotics kanamycin or norfloxacin resulted in the induction of unique gene expression signatures: a heat shock response to kanamycin and an SOS response to norfloxacin. Several genes of unknown function showed expression profiles similar to the genes associated with the SOS or the heat shock response. Thus, these profiles define families of genes with similar expression phenotypes that can be tested for related function.

RHAMM, a receptor for hyaluronan-mediated motility, compensates for CD44 in inflamed CD44-knockout mice: A different interpretation of redundancy

“…cDNA microarrays containing Ϸ13,000 mouse cDNA clones on three physically different slides were used in this study as described (31,32). cDNA clones were obtained commercially from Research Genetics (Huntsville, AL) (I.M.A.G.E.…”

Characterization of heterogeneity in the molecular pathogenesis of lupus nephritis from transcriptional profiles of laser-captured glomeruli

“…The cDNA synthesized from each control or SLE glomerular RNA sample was hybridized to two microarray slides that each contained a cDNA array spotted in duplicate, yielding a quadruplicate data set for each sample. Outliers were automatically excluded prior to normalization (44). For analysis, the intensities from each data set were scaled at the 75th percentile (the 75th percentile value of each data set was set to 100) followed by log transformation in base 2, and then were normalized in a two-step procedure (44).…”

“…Outliers were automatically excluded prior to normalization (44). For analysis, the intensities from each data set were scaled at the 75th percentile (the 75th percentile value of each data set was set to 100) followed by log transformation in base 2, and then were normalized in a two-step procedure (44). The first normalization step was performed across arrays within the same RNA sample.…”

Antibiotiques et réponse SOS bactérienne

“…Plusieurs antibiotiques, comme la ciprofloxacine (CIP), l'ampicilline (AMP) ou le triméthoprime (TMP), sont connus pour induire directement, à des concentrations sous-inhibitrices, la réponse SOS chez divers microorganismes [10,11]. Différentes études montrent que l'induction (ou le niveau d'induction) de la réponse SOS par les antibiotiques semble dépendre de la bactérie et de l'antibiotique.…”