Fig. 5: Streptomycin exposure leads to increased de novo synthesis of rRNA molecules, some of which lack a subset of rRNA modifications. | Nature Communications

Fig. 5: Streptomycin exposure leads to increased de novo synthesis of rRNA molecules, some of which lack a subset of rRNA modifications.

From: Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites

Fig. 5: Streptomycin exposure leads to increased de novo synthesis of rRNA molecules, some of which lack a subset of rRNA modifications.

A Multiple sequence alignment (MSA) of the seven rRNA operons sequences in all regions identified by NanoConsensus upon antibiotic exposure. B IGV tracks of nanopore cDNA reads aligning to the ribosome sequence in all regions identified by NanoConsensus upon antibiotic exposure. Positions with mismatch frequencies greater than 0.1 are colored, whereas positions with mismatch frequencies lower than 0.1 are shown in gray. C Differential expression analysis results between treated and untreated samples. In gray, non-significant genes; in green, genes with abs(log2FC) > 2 and; in red, genes with abs(log2FC) > 2 and p adjusted value >=0.05. P-values were calculated using the two-sided Walsh test and corrected with Benjamini–Hochberg approach. Source data are provided as a Source Data file. D GO term enrichment analysis using molecular process terms using as input all genes with abs(log2FC) > 2, which corresponded to n = 195 (upregulated) and n = 214 (downregulated) genes upon streptomycin treatment, and n = 197 (upregulated) and n = 203 (downregulated) genes upon kasugamycin treatment. In orange, terms related to downregulated genes upon antibiotic exposure and; in green, related to upregulated genes. P-values were obtained with the Fisher’s Exact Test, followed by calculating the False Discovery Rate (FDR). Only terms with a FDR < 0.05 were included in the final results. Source data are provided as a Source Data file. E Cumulative distribution of summed basecalling errors at per read level from both untreated (n = 10,953 reads), str-treated (n = 3689 reads) and ksg-treated (n = 14,376 reads) samples. In the upper-left corner, p-values between distributions calculated with the two-sided KS test are shown.

Back to article page