The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally
Figure 3
Bioinformatic analysis of the sequence regions bound by ArcA in vivo.
(A) The 18-bp ArcA box sequence logo was constructed from the alignment of 128 ArcA boxes identified with a motif search of the 146 regions bound by ArcA in both ChIP-seq replicates (Table S3). The sequence conservation (bits) is depicted by the height of the letters with the relative frequencies of each base depicted by its relative heights [113]. The total sequence conservation is 15.6±0.07 bits in the range from positions −3 to +14. The crest of the sine wave represents the major groove of B-form DNA. (B) Sequence logo for a single direct repeat element. The total sequence conservation is 7.6±0.03 bits in the range from −3 to +6. The sequence regions surrounding each ArcA box (158) were scanned with this 10 bp PWM. (C) The distribution of two, three, four and five direct repeat binding sites in the regions bound by ArcA in vivo (See also Table S4). (D) Examples of some common multiple DR sites displayed using sequence walkers [100]. The number of sites with this same binding site architecture is listed in parentheses and the Ri (bits) for each DR element is indicated under the sequence walker.