RNAP binding effects following the replacement of RpoA^int with RpoA^del in the RNAP complex.

<p>(A) Typical RNAP binding profiles obtained from <i>rpoA</i>^<i>int</i>- and <i>rpoA</i>^<i>del</i>-expressing cells; <i>rpsU</i> and <i>yqeY</i> are indicated, with the RNAP binding signal of each probe mapped to the corresponding position in the <i>B</i>. <i>subtilis</i> chromosome. The binding intensity (shown by vertical bars) was determined as the relative ratio of the signal intensities obtained for the hybridization of labeled DNA fragments prepared from the affinity purification with RpoC or RpoA (ChAP DNA) versus whole cell extract (control DNA) fractions in each experiment. The RNAP binding intensities determined by affinity purification with RpoC as bait are shown in lanes 1 and 2. The RNAP binding intensities determined by affinity purification with RpoA as bait are shown in lanes 3 and 4. The RNAP binding intensities in the <i>rpoA</i>^<i>int</i>-expressing cells are shown in lanes 1 (SMS08) and 3 (SMS18), and those in <i>rpoA</i>^<i>del</i>-expressing cells are indicated in lanes 2 (SMS09) and 4 (SMS19). The arrangement of genes in the presented chromosomal region is indicated by thick arrows at the top of the figure. The RNAP binding profiles obtained from one (Exp. 1) of duplicate experiments are shown as representative. (B) Binding to the <i>mtl</i> operon is shown as a typical example of the reduced RNAP binding observed in <i>rpoA</i>^<i>del</i>-expressing cells. (C) Binding to the <i>srf</i> operon is shown as an example of the unique RNAP binding profile observed in <i>rpoA</i>^<i>del</i>-expressing cells, in which reductions were seen in the protein coding regions but not in the promoter proximal regions.