RNA-seq analysis of MG1655 Escherichia coli (Wild-type, and mutants lacking the glucose metabolism regulator TmaR) experiencing short- & long-term N starvation and following treatment with rifampicin during long-term N starvation in Gutnick minimal media

RNA-seq was carried out to compare the transcriptomes of wild-type MG1655 E coli with mutants lacking the glucose metabolism regulator TmaR , in bacteria that had been exposed to short-term (3hr) and long-term (24hr) nitrogen starvation in Gutnick minimal media. A rifampicin-chase experiment was performed following long-term (24hr) nitrogen starvation, with 150ug/ml rifampicin added at N-24, with samples taken 15 and 60 minutes following treatment. TmaR is required for the formation of Hfq foci, a novel sub-cellular feature that forms during long-term nitrogen starvation. The aim of this work was to use the mutant lacking TmaR to understand the functional role of the Hfq foci, and whether they play a role in sRNA stability during long-term nitrogen starvation.