Fig. 5. FadZ is a 3’UTR-processed sRNA repressor of the OmpD porin.

a Schematic of the genomic context of the fadBA operon and FadZ in Salmonella. b FadZ was enriched by Hfq-coIP. Genome browser screenshot showing the genomic locations of FadZ fragments under ESP condition. c The sequence and predicted secondary structure of FadZ. d Alignment of FadZ genomic sequences from representative enterobacterial genera. Conserved nucleotides were marked in red. The processed 5’ end and Rho-independent terminator were indicated. e Expression of FadZ in Salmonella wild-type and FadZ-deletion strains. Total RNA was isolated at indicated time points and analyzed on northern blot. 5S rRNA was probed as a loading control. f Northern blot analysis of FadZ expression in a strain carrying a temperature-sensitive RNase E allele (rne-TS) and the wild-type allele (rne-WT). Bacteria were grown in LB-broth to OD 1.0 at 28 °C and then shifted to 28 °C or 44 °C for 30 min. Total RNA was extracted and separated on a 6% PAA gel. g Predicted binding sites between FadZ and OMP genes using RNAhybrid. Conserved nucleotides among OMP genes were marked in red. Amino acids corresponding to the binding sites were shown below. The mutated nucleotides were indicated. h Regulation of abundant major porins by FadZ. Salmonella strains containing control vector pJV300 or plasmids constitutively expressing the indicated RNA fragments were grown overnight in LB. Total proteins were analyzed by SDS-PAGE, and total RNAs were analyzed by northern blotting. i Relative fluorescence for translational OMP-sfGFP reporters. A ΔfadZ strain carrying either the control plasmid pXG-1 or pXG10-sfGFP with an in-frame fusion to the indicated genes, together with pJV300 or pPL-FadZ as indicated. j Regulation of ompD::GFP by FadZ. k Regulation of ompC::sfGFP by FadZ. Graph bars (i–k) represent mean relative fluorescence. Error bars indicate standard deviations from n = 3 biological replicates. Source data are provided as a Source Data file.