Genome-wide Identification of ResD, NsrR, and Fur Binding in Bacillus subtilis during Anaerobic Fermentative Growth by in vivo Footprinting. Bacillus subtilis

Upon oxygen limitation transcription of genes that are required for anaerobic growth are upregulated in Bacillus subtilis. The ResE sensor kinase and the cognate ResD response regulator play a primary role in transcriptional activation of genes involved in aerobic and anaerobic respiration. The nitric oxide (NO)-sensitive NsrR repressor functions in controlling transcription to support nitrate respiration under oxygen-limited conditions. In addition, the ferric uptake repressor (Fur), which is essential for maintaining iron homeostasis, is involved in modulating anaerobic transcription. These transcription factors (TFs) often coordinately control gene expression in response to an individual environmental cue. However, whether the control is direct or indirect has been investigated mostly for specific genes. To gain a genome view of anaerobic gene expression, we determined the genome-wide, in vivo DNA binding of ResD, NsrR, and Fur transcription factors (TFs) using in situ DNase I footprinting.