Regulation of global transcription in E. coli by Rsd and 6S RNA

In Escherichia coli, the housekeeping sigma factor σ70 directs RNA polymerase to transcribe growth-related genes, whereas the alternative sigma factor σ38 directs it to transcribe stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase activity are Rsd, which sequesters free σ70, and 6S RNA, which sequesters the RNA polymerase-σ70 holoenzyme. Despite multiple studies, their function remains controversial. Here we use genome-wide expression studies in five phases of growth, along with theoretical modeling, to investigate the functions of Rsd and 6S RNA. We show that 6S RNA and Rsd act as global regulators of gene expression throughout bacterial growth, and that both increase transcription of σ38 dependent genes. We also find several instances of crosstalk between 6S RNA and Rsd, and propose a model in which this crosstalk is important in regulating sigma factor competition.