Time course analysis of genes regulated by E. coli sigma 32 (rpoH) after overexpression

DNA microarray analysis of genes regulated by the alternative sigma factor, sigma 32 (rpoH). Sigma 32-dependent genes were initially identified by comparing a wild type (wt) E. coli K-12 strain that has a low level of sigma 32, with a strain over-expressing sigma 32 (following induction of rpoH from an inducible promoter by IPTG). We monitored changes in gene expression in 4 separate time-courses. Because sigma 32 is negatively regulated, its activity decreases 10 min after overexpression. Consequently, to identify genes regulated by sigma 32 we analyzed the expression data for 10 min after overexpression using SAM (Statistical Analysis of Microarrays). We identified 105 genes organized in 66 separate transcription units. This study is detailed in Nonaka et al 2006 (submitted). Keywords: time course This series consists of 4 replicated time courses from separate biological samples. Each time course consists of a comparison between wild type E.coli MG1655 that has a low level of sigma 32, and an over-expressing sigma 32 strain following induction of rpoH 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, and 20 min after induction. To correct for changes in growth state, control and over-expressed samples were always compared from the same time point. Note time course 4 only contains the 10 min samples.