TABLE 5.
AbrC3 overlapping targets in ChIP-chip and transcriptome analysesd
| Gene | Enrichment ratioa | Predicted function of regulated gene | Time (h)b | Predicted binding site sequencec |
|---|---|---|---|---|
| SCO0736 | 1.50 | Putative secreted protein | 36 | −53-GAAGGCGACC-−44 |
| SCO2113 | 1.59 | Bfr, putative bacterioferritin | 48 | −26-GTTCCCGTTC-−17 |
| SCO3328 | 1.48 | BdtA, hypothetical protein | 48 | −46-GAAGGGGAAG-−37 |
| SCO4596 | 2.24 | AbrC3, TCS response regulator | 60 | −137-CTTCCCGTTC-−128 |
| SCO4709 | 1.89 | RplP, 50S ribosomal protein L16 | 36 | Not found |
| SCO5085 | 2.23 | ActII-ORF4, ACT cluster activator protein | 36 | 72-GAAGGCGACC-81 |
| SCO6809 | 1.77 | Putative integral membrane transport protein | 48 | −112-GAAGGCGGAC-−103 |
| SCO6992 | 2.78 | AbsR1, regulatory protein | 48 | −321-GAAGGGGACG-−312 |
a
AbrC3-DNA interaction affinity by ChIP-chip analysis.
b
Time in the ChIP-chip assay at which the shown enrichment ratio was found.
c
The consensus binding site sequence is 5′-GAASGSGRMS-3′. Numbers indicate the position of the sequence related to the start codon of the corresponding gene.
d
The genes shown in bold are upregulated. The other genes in the table are downregulated.