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. 2023 Jul 21;13:11771. doi: 10.1038/s41598-023-38924-x

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Transcriptome analysis and differentially expressed regulons. (A) Venn-diagrams of differentially expressed genes (DEGs). Venn diagrams representing the number of DEGs in the indicated pairwise comparisons. pnp⁺, C-1a; Δpnp, C-5691; PNPT1_Ec, C-6001. (B) Differentially expressed regulons (P < 0.5; dotted line) in pairwise comparison. Enrichment analysis was performed with the Pathway tool available at the EcoCyc website⁵¹. Colour code and strain tags are as in (A). (C) Northern blotting analysis of gene expression. RNA was extracted from exponential cultures of C-1a (Ec), C-5691 (Δ) and C-6001 (Hs). 20 and 10 µg of RNA were run on 1.5% denaturing agarose gel (recA panel) or 6% denaturing polyacrylamide gel (cpxQ and soxS panels), respectively, blotted onto nylon filters and hybridized with radiolabelled oligonucleotides complementary to the mRNAs under analysis. 5S and 23S rRNA signals were used as loading controls.