Figure 3.

Characterization of the ygaVP promoter: (A) Primer extension analysis of the ygaVP promoter. Signal of the reverse transcripts and size markers are blue and red, respectively. ((A), bottom) The RNA polymerase σ-subunit recognition site (−10 and −35) and the translational start site of YgaV (blue) are shown. Reverse transcription was conducted with purified RNA and the fluorescent–labeled primer. The synthesized cDNA was mixed with the 600 LIZ Size Standard (Applied biosystem), and then analyzed using a 3730xl DNA analyzer (Applied biosystems). Finally, fragment analysis was conducted with Peak scanner software v.1.0 (Applied biosystem); (B) DNase I footprint analysis of YgaV. Binding to the ygaVP promoter DNA with different concentrations of reduced YgaV. Regions corresponding to the DNase I protection regions are shown in red. Motifs similar to the putative RcSqrR-recognition sequences are indicated by green boxes (for details, see text).