Figure 5.

Transcriptome profiling of E. coli cells under Rtc-inducing conditions

Transcriptome profiling of E. coli wild-type cells, cells lacking gor, mazF or srmB, and Hpx-[RtcON] and Hpx-[RtcOFF] cells was performed by NGS and followed by differential gene expression analysis. Transcriptome profiling of E. coli cells lacking rtcA or rtcB was described previously by Engl et al. (2016).¹⁵

(A) Venn diagram of the genes differentially expressed in cells lacking gor or mazF compared to the wild-type and associated GO terms (Tables S7 and S8).

(B) Principal component analysis of the transcriptional profiling of the wild-type, Hpx-[RtcON] and Hpx-[RtcOFF] strains.

(C) Venn diagram of the genes differentially expressed in Hpx-[RtcON[ and Hpx-[RtcOFF] as compared to wild-type cells at 8 and 24 hpi, and associated GO terms and KEGG pathways.

(D) Heat maps of 5S (left; log₂fold expression ±5), 23S (left; log₂fold expression ±7) and 16S (left; log₂fold expression ±6) ribosomal (r) RNA abundance levels in a range of mutants, as shown by NGS; rows and columns have been grouped based on a hierarchical clustering algorithm. Limma/DESeq2 ∗ adjusted p-value < 0.05; ∗∗ adjusted p-value < 0.01; ∗∗∗∗ adjusted p-value < 0.0001.