TABLE 4.
AbrC3 ChIP-chip targets selected by high enrichment ratiose
| Regulated genea | Enrichment ratiob | Predicted function of regulated gene | Time (h)c | Predicted binding site sequenced |
|---|---|---|---|---|
| SCO0167 | 2.45 | Conserved hypothetical protein SCJ1.16c | 36 | 354-GAAGGGGGCG-363 |
| SCO0951 | 2.22 | Putative transport system permease protein | 36 | −329-GGTCGCCTTC-−318 |
| SCO1391 | 5.44 | Crr, phosphoenolpyruvate-protein phosphotransferase | 48 | 1113- GAAGGCGGCG-1122 |
| SCO3020 | 4.22 | Putative integral membrane protein | 48 | Not found |
| SCO3263 | 2.60 | Conserved hypothetical protein | 36 | −240-GTTCGCCTTC-−231 |
| SCO3334 | 5.70 | TrpS, tryptophanyl tRNA synthetase | 48 | −387-GGCCGCGTTC-−378 |
| SCO3590 | 2.54 | VanR, putative TCS response regulator | 36 | Not found |
| SCO3992 | 2.45 | Hypothetical protein | 36 | Not found |
| SCO4075 | 6.32 | RagA, ABC transport protein, ATP-binding subunit | 48 | Not found |
| SCO4123 | 5.02 | Putative TCS response regulator | 48 | −674-GAACGCGACC-−665 |
| SCO4596 | 2.24 | AbrC3, TCS response regulator | 60 | −137-CTTCCCGTTC-−128 |
| SCO4630 | 2.78 | Hypothetical protein | 36 | Not found |
| SCO5085 | 2.23 | ActII-ORF4, ACT cluster activator protein | 36 | 72-GAAGGCGACC-81 |
| SCO5236 | 2.86 | NagB, putative glucosamine phosphate isomerase | 48 | −213-GGTCGCGTTC-−204 |
| SCO5330 | 3.26 | Hypothetical protein SC6G9.03c | 36 | −975-GAAGGGGGCG-−966 |
| SCO5332 | 2.21 | Hypothetical protein | 36 | 1134-CTTCGCCTTC-1143 |
| SCO5632 | 2.36 | Hypothetical protein SC6A9.3 | 36 | −1261-GAACGGGACG-−1252 |
| SCO5638 | 2.76 | Integral membrane protein | 36 | Not found |
| SCO5691 | 2.24 | Putative secreted sugar hydrolase | 48 | −777-GAACGCGGCG-−768 |
| SCO5729 | 2.33 | Conserved hypothetical protein SC3C3.15c | 36 | Not found |
| SCO5912 | 4.30 | Probable secreted protease | 48 | −54-CTCCCCCTTC-−45 |
| SCO5966 | 2.24 | Putative oxidase | 48 | −803-GAAGGCGGAC-−794 |
| SCO6273 | 2.18 | CpkC, putative type I polyketide synthase | 48 | 3138-CGCCCCGTTC-3147 |
| SCO6732 | 2.29 | Putative fatty acid oxidative multifunctional enzyme | 36 | 1140-GAAGGCGGCC-1149 |
| SCO6820 | 2.94 | Putative oxidoreductase | 48 | −519-GAACGCGGCC-−510 |
| SCO6941 | 2.55 | CvnC8, hypothetical protein SC1G8.13c | 36 | −306-GGCCGCCTTC-−297 |
| SCO6951 | 2.55 | Conserved hypothetical protein | 36 | −411-CGCCGCGTTC-−402 |
| SCO6992 | 2.78 | AbsR1, regulatory protein | 48 | −321-GAAGGGGACG-−312 |
| SCO7077 | 2.24 | Putative integral membrane protein | 36 | −294-GAAGGCGGCG-−285 |
| SCO7545 | 2.45 | Putative ABC transport protein, ATP-binding component | 48 | −369-GGCCGCGTTC-−360 |
a
Putative AbrC3 target genes indicated by the ChIP-chip analysis.
b
AbrC3-DNA interaction affinity.
c
Time in the ChIP-chip assay at which the shown enrichment ratio was found.
d
The consensus binding site sequence is 5′-GAASGSGRMS-3′. Numbers indicate the position of the sequence relative to the start codon of the corresponding gene.
e
Genes that also had differential transcription profiles are shown in bold.