Fig. 4.

Expression of cytochrome o oxidase and cytochrome d oxidase is dysregulated in ∆actR.

A) Plot of the absolute values of log₂ fold changes in gene expression upon 100 µM PYO treatment in WT against absolute values of log₂ fold changes in gene expression upon 100 µM PYO treatment in ∆actR. Only genes that were statistically significantly differentially expressed (adjusted p-value < 0.01) upon PYO treatment in at least one strain are plotted. Each point represents a single gene. The black line is y = x. B) Volcano plots of RNA-seq data comparing gene expression levels in ∆actR to WT, with either 0 µM PYO or 100 µM PYO. The vertical dashed lines mark a log₂ fold change of −2 or 2, and the horizontal dashed line marks an adjusted p-value of 0.01. Only genes with statistical significance below the adjusted p-value cutoff are plotted. C) qRT-PCR data confirming the expression patterns of the cyo and cyd operons in ∆actR vs. WT. The + PYO condition represents treatment with 100 µM PYO. Only cyoA and cydA are shown for brevity, as they are co-transcribed with other members of these operons. Expression levels were normalized to the housekeeping gene rpoD. ** p < 0.01 (Welch’s t-test followed by the Benjamini-Hochberg procedure for controlling the false discovery rate; n = 3). Error bars represent standard deviations of biological replicates.