Fig. 3
The nrdA 5’ UTR region as a potential reservoir of upstream open reading frames (uORFs), small non-coding RNAs (sRNA) and sRNA binding sites. (a) In silico analysis using the Coding potential calculator (CCP2) and BLAST tools. A 49-amino acid peptide predicted by CCP2 was analysed via Blastp, and the entire 5’ UTR sequence was examined using tBlastn. (b) SDS-PAGE (4–20% acrylamide) of crude extracts from P. aeruginosa PAO1 WT harbouring pJN106 (5’-3’ orientation from the 5’ UTR) and pJN107 (3’-5’ orientation from the 5’ UTR), before (not-induced) and after induction with 0.4% L-arabinose. (c) Bioinformatic, bibliographic and experimental exploration of potential regulatory elements across the nrdA upstream and downstream regions. These include putative promoters or σ70 binding sites (P1 and P2, arrows), transcription start sites (TSSs, coloured triangles), Rho-independent terminators (hairpin structure), small RNAs (sRNA, curved red arrow) and sRNA binding sites (curved purple line with tick marks)43,44,46,47. Positions are shown relative to the translation start codon (ATG, + 1) with original genome coordinates also provided. The original and cropped version of the gel are provided in the Supplementary Material Figure S6 and are also available in the public repository (https://doi.org/10.34810/data2361).
