FIG. 4.
Confirmation of lineage I or lineage II σB-dependent genes by TaqMan qRT-PCR and comparison of promoter regions. (A) Normalized log copy numbers of transcripts for five genes (inlA, opuCA, lmo0398, lmo1539, and lmo2668) in lineage I and II strains and their isogenic ΔsigB mutants. The bars indicate the average log-transformed levels of transcripts (normalized to rpoB) for three independent replicates (i.e., three RNA isolations performed on different days); the error bars indicate one standard deviation from the mean. For each gene, one-sided t tests were used to determine if the transcript levels in the ΔsigB mutants were significantly different from those in the wild-type strains (*, P < 0.05). (B) Putative σB promoter sequences for five genes determined to be σB dependent by microarray analyses in either lineage I or lineage II or in both lineages. Bold type indicates nucleotide differences between lineage I and II putative σB promoter sequences. RACE, random amplification of cDNA ends.