TABLE 2

Transcription of genes that showed increased distribution of RpoZ-defective RNAP in prophages (qRT-PCR assay)b

GeneRatioaFunctionProphage
ydbA7.66 ± 6.24Predicted autotransporter
ybhJ5.96 ± 1.93Predicted hydratase
yfjQ4.79 ± 1.44OM protein assembly complexCP4-57
paaE4.69 ± 2.161,2-Phenylacetyl-CoA epoxidase
ydaY4.69 ± 0.91Phage proteinRac
ybcH4.54 ± 0.21Predicted protein
yhcD4.53 ± 0.46Predicted OM usher porin protein
ymfN3.42 ± 0.50DNA-binding transcription regulatore14
basS3.27 ± 0.42BasST TCS histidine kinase
yaiP2.87 ± 1.18Predicted glucosyltransferase
ybhA2.32 ± 0.07Pyridoxal phosphate/fructose-2P phosphatase
ycfK2.29 ± 1.31Predicted protein (e14 prophage)
ymfK2.05 ± 0.08DNA-binding transcription regulatore14
nfrB1.81 ± 0.35NtrBC TCS histidine kinase (N4 receptor)
flu1.74 ± 0.60Ag43 autotransporterCP4-44
isrC1.68 ± 0.49IsrC sRNA (flu gene attenuation)
rcsD1.07 ± 0.19RcsCDB phosphorelay phosphotransferase
  • a Ratio indicates the relative level of mRNA (rpoZ mutant/wild type). When the target gene is located inside a prophage, the name of the prophage is given.

  • b The level of mRNA was determined for E. coli K-12 mutants lacking the rpoZ gene by using the qRT-PCR method. The genes were selected from the list showing the decreased distribution of RpoZ-defective RNAP (Table 1 and Fig. 3).