TABLE 2.
ChIP-PCR analysis of DnaA binding at putative regulatory targetsa
| Locusb | No HPUra treatment
|
HPUra treatment
|
Overall P value | ||
|---|---|---|---|---|---|
| Mean enrichment ± SE | P value | Mean enrichment ± SE | P value | ||
| citZ | 1.3 ± 0.8 | 0.72 | 2.5 ± 0.4 | 0.03 | 0.40 |
| dnaB | 26.4 ± 9.2 | 0.01 | 0.9 ± 0.4 | 0.72 | 0.002 |
| flgB | 2.0 ± 1.1 | 0.32 | 1.0 ± 0.3 | 0.97 | 0.31 |
| kdgR | 1.8 ± 0.1 | 0.01 | 3.3 ± 1.6 | 0.17 | 0.34 |
| lysC | 1.7 ± 0.4 | 0.16 | 4.7 ± 1.1 | 0.02 | 0.05 |
| nrdI (nrdEF ymaB) | 1.8 ± 0.3 | 0.07 | 2.2 ± 1.1 | 0.18 | 0.69 |
| pyrP | 2.6 ± 0.6 | 0.04 | 3.5 ± 2.4 | 0.13 | 0.63 |
| spo0Jc (soj) | 3.9 ± 0.4 | 0.001 | 6.3 ± 1.7 | 0.02 | 0.62 |
| sunA (sunT) | 4.4 ± 1.7 | 0.06 | 8.6 ± 4.8 | 0.08 | 0.42 |
| yclN (yclOPQ) | 5.4 ± 1.6 | 0.03 | 6.8 ± 2.1 | 0.03 | 0.62 |
| ykuN (ykuOP) | 5.4 ± 1.2 | 0.02 | 4.8 ± 3.3 | 0.10 | 0.85 |
| yllB (ylxA ftsL pbpB) | 1.8 ± 0.5 | 0.18 | 1.7 ± 0.9 | 0.35 | 0.91 |
| ypvA | 3.1 ± 0.7 | 0.05 | 2.7 ± 0.3 | 0.02 | 0.65 |
| yurY (yurX csd yurVU) | 21.7 ± 5.2 | 0.01 | 5.2 ± 1.1 | 0.02 | 0.01 |
| ywzC (ywfO ywgA) | 4.2 ± 1.7 | 0.05 | 3.2 ± 1.6 | 0.12 | 0.62 |
Wild-type cells (AG174) left untreated or treated with HPUra for 60 min were harvested and analyzed by ChIP-PCR for DnaA binding at the indicated loci. Values presented are the mean enrichments ± standard errors for at least three independent biological replicates, normalized to the yabM locus, which is not specifically bound by DnaA. P values were determined by t test. The overall P value compares results with and without HPUra treatment.
Operons that respond transcriptionally to replication stress and have at least two potential DnaA binding sites were chosen for analysis. Loci are sorted alphabetically by the first gene. Additional genes in a given operon that are also affected by replication stress are indicated in parentheses.
Data for spo0J are taken from the ChIP-chip results (Fig. 1).