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

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 Overall design: This series consists of 4 replicated time courses. Each time course consists of a comparison between wild type E.coli MG1655 that has a low level of sigma E, and an over-expressing sigma E strain following induction of rpoE from an inducible promoter by IPTG. Both strains were grown to mid log and then induced with IPTG and incubation resumed. Samples were removed for comparative microarray analysis immediately prior to induction, and at 2.5, 5, 10, 15, 20, 30 and 60 min after induction. To correct for changes in growth state, control and over-expressed samples were always compared from the same time point.