TABLE 3

Transcription of genes that showed decreased binding of RpoZ-defective RNAP inside prophages (ChIP-chip assay)a

GeneLevelFunctionProphage
yagM0.012Putative proteinCP4-6
yffL0.020Putative proteinCPZ-55
yagL0.023DNA-binding proteinCP4-6
yagB0.022Predicted proteinCP4-6
yagG0.026Xyloside transporterCP4-6
wzxB0.029O-antigen flippase
afuB0.030Predicted ferric transporterCP4-6
intF0.032Putative phage integraseCP4-6
wbbI0.036Putative GalF transferase
yagN0.041Putative proteinCP4-6
stfR0.044Putative membrane proteinRac
yehB0.047Putative OM fimbrial usher protein
yjjJ0.053Toxin-like protein
yagI0.060XynR TFCP4-6
wbbH0.061Putative O-antigen polymerase
napA0.065Periplasmic nitrate reductase
ygeM0.067Putative protein
waaI0.069UDP-glucose:LPS glucosyltransferase
ymfJ0.072Putative proteine14
nmpC0.075Predicted OM porin NmpCDLP
frvA0.077Fructose PTS enzyme IIA
yjiT0.078Conserved protein
yqiK0.082Putative protein
zraS0.083Zinc-sensing ZraSR TCS sensor kinase
ypjC0.085Pseudogene
yddG0.088Aromatic amino acid exporter
yjgL0.094Putative OM protein
yfjP0.095Predicted GTP-binding proteinCP4-57
waaP0.095LP core heptose kinase
yciC0.098Putative IM protein
chiA0.100Endochitinase
  • 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 of binding levels between the RpoZ-defective RNAP and wild-type RNAP was calculated for the entire probe along the genome. These values are listed in increasing order in the Level column. When the gene is located inside prophages, the name of the prophage is given. LPS, lipopolysaccharide; PTS, phosphotransferase; LP, lipoprotein; IM, inner membrane.