Bent DNA is found in some, but not all, regions recognized by the Bacillus subtilis AbrB protein

The AbrB protein of Bacillus subtilis is a transcriptional regulator of numerous genes in diverse metabolic pathways that commence expression at the onset of stationary phase. AbrB is a DNA-binding protein with specific affinity for defined DNA regions of its target genes. Analysis of these regions has failed to detect a readily apparent sequence determinant for AbrB binding and it is believed that AbrB recognizes a specific DNA structure formed by a finite subset of base sequences. We have examined six AbrB binding regions for intrinsic bending and found that three do not contain a detectable intrinsic bend, whereas three do. AbrB binding to these regions resulted in electrophoretic mobility patterns that were consistent with, but did not prove, that the DNA moieties were present in a bent configuration.