Extended Data Fig. 7: Transcriptome analysis of darobactin treatment shows activation of envelope stress pathways.

E. coli BW25113 were treated with 1× MIC darobactin, and the RNA isolated and sequenced. a–c, Volcano plots illustrate differential gene expression (Fisher’s exact test in edgeR; results were deemed significant if |log₂(FC)| ≥ 2 and FDR-corrected P < 0.001; n = 3 biologically independent samples for each control or treatment sample) at time points t = 15 min (a), t = 30 min (b) and t = 60 min (c) after exposure. Grey region, not significant. d, Network visualization of differentially expressed genes at each time point. Nodes include genes (coloured circles) and time points (grey rectangles). Gene node colours represent relevant functional categories. Directed edges radiating from a time point node represent differentially expressed genes with respect to the given time point with weights reflecting the |log₂(FC)|. e, Right, heat map showing the differential expression (|log₂(FC)|) of genes of interest. Left, assignment to envelope stress pathways. Solid lines depict members of the same operon. In all panels, red indicates downregulation (lower expression in treatment relative to control) and blue indicates upregulation.