FIG. 2.

DnaA binding at loci with clustered DnaA boxes. Data are shown for specific regions from Fig. 1, plotted for ∼8-kb regions centered around clustered DnaA boxes, where DnaA binding increased substantially upon inhibition of replication. Chromosomal positions are listed as distances (in kilobases) from oriC, and enrichment is shown as described in the legend to Fig. 1. DnaA box locations are indicated by diamonds below the data traces; filled and open diamonds represent perfect and single-mismatch boxes, respectively. Gene locations and orientations are indicated with arrows. Expression of genes with asterisks is altered after inhibition of replication (15). Expression of all genes indicated with asterisks decreases after replication inhibition, except for that of sda, which increases. Data are shown in the vicinities of dnaA (A), ywlC (B), ywcI (C), yydA (D), gcp (E), and sda (F). Filled squares with solid lines represent wild-type cells (AG174) 60 min after treatment with HPUra, filled circles with dotted lines represent untreated wild-type cells (AG174), gray open circles and lines represent dnaA null mutant cells (AIG200), and filled triangles with solid lines represent dnaD(Ts) cells (KPL73) after 90 min at 47°C.