Fig. 1
Analysis of the nrdA upstream region and identification of long 5’ untranslated region (5’ UTR). (a) Schematic representation of the nrdAB promoter, 5’ UTR, and its genetic context. The AlgR transcriptional factor binding site is shown in green, and NrdR binding sites are indicated in red. The ribosome binding site (RBS), translational start codon (Met, ATG), and the − 35 and − 10 promoter regions are underlined. Transcriptional start sites (TSSs) identified by different methods are marked with coloured triangles, as detailed in panel (b). The long 5’ UTR of nrdA (408–411 bp) is highlighted in light orange. (b) Identification of TSSs using various approaches, including bioinformatic analysis, primer extension and 5’rapid amplification of cDNA ends (5’ RACE) performed in our laboratory, as well as transcriptomic data from a previously published differential RNA-seq (dRNA-seq) experiment (PRJNA169508)59. Coloured triangles correspond to the TSS identified by each method and are mapped in panel (a). (c) Primer extension analysis showing the identified TSS (blue triangle in panels (a-b)), marked with an asterisk (*). (d) 5’RACE analysis of the nrdA, with the identified TSS (pink triangle in panels (a,b)). The percentage indicates the proportion of sequenced colonies that matched the same region, with the number in parentheses corresponding to the exact number of colonies showing that specific base pair. 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).
