Fig. 1: AlpA positively regulates the expression of genes in two operons in P. aeruginosa.

a Plot of RNA-Seq data comparing gene expression in PAO1 ∆alpA to PAO1 WT. Cells were treated with 1 µg/mL ciprofloxacin for 2 h to induce DNA damage. Brown dots are statistically significantly differentially regulated genes, beige dots are genes that are not significantly differentially regulated. Genes shown to be most highly positively regulated by AlpA are labeled. b RNA-Seq data from PAO1 WT and PAO1 ∆alpA mutant cells (upper panels) treated with ciprofloxacin, and ChIP-Seq data from cells synthesizing AlpA-TAP (lower panels) depicting reads over the PA0807–PA0830 region. For RNA-Seq, only reads mapping to the plus strand (indicated +strand) are shown (in blue). ChIP-Seq of AlpA-TAP shows AlpA associates with the PA0807 promoter region and operon. Significantly enriched peaks are indicated by a dark gray box below the read density plot (in beige), red line within this dark gray box indicates site of maximum enrichment. Control (indicated mock) is the mock IP control performed with PAO1 cells that synthesize AlpA without a TAP-tag. Genes are depicted in yellow at the bottom of the panel. Genomic location in kb is provided at the top of the panel.