TABLE 4 .

Transcription of genes that showed decreased distribution of RpoZ-defective RNAP inside prophages (qRT-PCR assay)^b

Designation	Gene	rpoZ/WT	Ratioa	Function	Prophage
1	yagM	10.29 ± 0.5	0.0972	Phage protein with unknown function	CP4-6
2	yffL	4.48 ± 0.5	0.2233	Phage protein with unknown function	CPZ-55
3	yagN	2.44 ± 0.6	0.4093	Phage protein with unknown function	CP4-6
4	ymfJ	1.62 ± 0.6	0.6184	Phage protein with unknown function	e14
5	yagL	1.54 ± 0.6	0.6405	Predicted transcription factor	CP4-6
6	intF	1.47 ± 0.5	0.6816	Putative phage integrase	CP4-6
7	nmpC	0.99 ± 0.9	1.0141	Putative OM protein	DPL
8	afuB	0.86 ± 0.6	1.1638	Predicted ferric transporter	CP4-6
a	yjhH	0.95 ± 0.7	1.0494	Putative lyase	KpLE2
b	ykfC	0.87 ± 0.5	1.1436	Phage protein with unknown function	CP4-6

^aRatio 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.

^bThe 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 3 and Fig. 3). As references, two genes (a and b) were selected from the list of genes with increased distribution of RpoZ-defective RNAP (Table 2 and Fig. 2).