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Time course analysis of genes regulated by E. coli sigma E (rpoE) after overexpression

ABSTRACT: DNA microarray analysis of genes regulated by the alternative sigma factor, sigma E (rpoE). Sigma E-dependent genes were initially identified by comparing a wild type (wt) E. coli K-12 strain that has a low level of sigma E, with a strain over-expressing sigma E (following induction of rpoE from an inducible promoter by IPTG). We monitored changes in gene expression in 4 separate time-courses after induction and used SAM (Statistical Analysis of Microarrays) to identify 75 significantly induced and 8 significantly repressed genes. Some of these genes are part of operons in which other gene members were clearly induced but were not marked as significant in our strict selection criteria. Therefore, to fully describe the sigma E regulon we expanded this set by using the statistics from SAM to analyze the reproducibility and significance of the expression ratios of all the genes adjacent to and in the same orientation as the highly significant genes. This gave 96 genes organized in 50 sigma E-dependent transcription units (TUs), of which 42 were induced and 8 were repressed. This study is detailed in Rhodius et al 2006 (PLoS Biol 4(1): e2) Keywords: time course

ORGANISM(S): Escherichia coli

PROVIDER: GSE3437 | GEO | 2005/10/13

SECONDARY ACCESSION(S): PRJNA93475

REPOSITORIES: GEO

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Project description:Transcriptional profiling of S. mutans rpoE knockout mutant comparing to the wild type. The mutation of rpoE cause dramatic changes in phenotypes. The goal is to determine the genes affected by rpoE. The delta subunit of RNA polymerase, RpoE, is wide spread in low G+C Gram-positive bacteria and is thought to play a role in enhancing transcriptional specificity by blocking RNA polymerase binding at weak-promoter sites and stimulating RNA synthesis by accelerating core enzyme recycling. Despite the well-studied biochemical properties of RpoE, a role for this protein in vivo has not been defined in depth. In this study, we show that inactivation of rpoE in the human dental caries pathogen Streptococcus mutans causes impaired growth, and loss of important virulence traits, including biofilm formation, resistance to antibiotics, and tolerance to environmental stresses. Complementation of the mutant with rpoE expressed in trans restored its phenotype to wild type. The luciferase fusion reporter showed that rpoE was highly transcribed throughout growth, and that acid and hydrogen peroxide stresses repressed rpoE expression. Transcriptome profiling of wild type and ΔrpoE cells in the exponential and early stationary phase of growth, under acid and hydrogen peroxide stress and under both stresses combined revealed that genes involved in histidine synthesis, malolactic fermentation, biofilm formation, and antibiotic resistance were down-regulated in the ΔrpoE mutant in all conditions. Moreover, the loss of RpoE resulted in dramatic changes in transport and metabolism of carbohydrates and amino acids. Interestingly, differential expression, mostly up-regulation, of 330 non-coding regions was found. In conclusion, this study demonstrates that RpoE is an important global modulator of gene expression in S. mutans, which is required for optimal growth and environmental adaptation. 5 conditions, mutant vs wild type, biological replicates: 2, technical replicates: 2

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Time course analysis of genes regulated by E. coli sigma E (rpoE) after overexpression

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