Fig. 4: Genome-wide PRSEs, genome instability, and mutagenesis triggered by gentamicin. | Nature Communications

Fig. 4: Genome-wide PRSEs, genome instability, and mutagenesis triggered by gentamicin.

From: RNA polymerase stalling-derived genome instability underlies ribosomal antibiotic efficacy and resistance evolution

Fig. 4

a Dynamics of the dominant 3′ termini in the Δmfd strain (left), together with the wild-type strain (right, the same data as in Fig. 3d). b Distributions of fold changes of 3′ termini of the wild-type and the Δmfd strain without gentamicin treatment (shown in black and blue respectively, P = 3.60 × 10−13, one-sided MWU test). The inset zooms in on the right tail of the distribution. c 3′-end-seq profiles across the groSL operon in the wild-type strain (upper) and the Δmfd strain (lower) after 60 min of gentamicin treatment. d R-loop accumulation after gentamicin treatment in the wild-type and the Δmfd strain. Left penal shows the Western blot of the R-loop in the genomic DNA of both strains across gentamicin treatment. Right penal shows the quantification of bands using ImageJ, with all the signals normalized to the wild-type strain’s signal at 0 min (white for wild type, blue for Δmfd). A biological replicate is shown in Supplementary Fig. 7. e DNA damage level of the Δmfd strain (red) overlaid with the wild-type strain (gray, the same data as in Fig. 2b) after gentamicin treatment. Representative of 2 biological replicates. f DNA damage in the wild-type, Δmfd, and ΔuvrD strains after gentamicin treatment. DNA damage levels after 0 min and 40 min gentamicin treatment were measured by PFGE analysis (n = 6 biological replicates). P-values (two-tailed t-test) were labeled on the columns respectively. Error bars, ± std. g Distributions of PRSE intensities of coding genes carrying gentamicin-induced mutations (21 genes from Fig. 2c) and spontaneous mutations (8 genes from Fig. 2d) respectively (P = 6.87 × 10−3, one-sided MWU test). Shown are PRSE intensities after 60 min of gentamicin treatment, calculated from 3′ termini numbers per nt of each gene (see “Methods” section). Box plots: horizontal lines within boxes, medians; upper and lower box edges, first and third quartiles, respectively; whiskers, 1.5 times the interquartile range; circles, data for mutation genes. Source data are provided as a Source Data file.

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