TABLE 1

Genes that showed increased binding of RpoZ-defective RNAP (ChIP-chip assay)a

GeneLevelFunctionProphage
flu82.5Ag43 autotransporterCP4-44
lsrA45.4Predicted AI-2 ABC transporter
ymfN42.8Putative TFe14
ymfK32.2Putative repressore14
lsrC31.6Predicted AI-2 ABC transporter
nfrA31.3OM N4 receptor
paaE30.6Predicted phenylacetyl-CoA epoxidase
ydbA29.8Putative OM protein
ykfC22.8Conserved proteinCP4-6
ykfI21.9YfkI-YafW T-AT toxinCP4-6
ybcH21.7Hypothetical protein
paaF21.6Putative dehydroadipyl-CoA hydratase
modC18.4Molybdate ABC transporter
rcsD17.6RcsBC TCS phosphotransfer intermediate
yjhH16.3Predicted lyase/synthaseKpLE2
galT16.2Galactose-1-phosphate uridylyltransferase
ydaY15.8PseudogeneRac
stfR15.1Predicted tail fiber proteinRac
modF15.1Putative ABC transporter
ybhJ14.6Putative hydratase
ycfK13.4Putative proteine14
ydaV12.9Putative DNA replication proteinRac
intE12.1Putative integrasee14
ymfM12.0Putative proteine14
yjhG11.6d-Xylonate dehydrogenaseKpLE2
yfjP11.2Predicted GTP-binding proteinCP4-57
nfrB11.0NtrBC TCS sensor kinase
modA11.0Molybdate ABC transporter
yhcD11.0Putative fimbrial usher protein
ydbA10.9Putative protein
  • a ChIP-chip assay was performed for E. coli K-12 wild type and its rpoZ-defective mutant. After tiling array analysis, the levels of RNAP binding were compared between two strains. The ratio between the binding of RpoZ-defective RNAP and that of wild-type RNAP was calculated for the entire probe along the genome. These values are listed in decreasing order in the Level column. When the gene is located inside prophages, the name of the prophage is given. OM, outer membrane; CoA, coenzyme A.