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. 2017 Dec 8;7:17213. doi: 10.1038/s41598-017-17408-9

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© The Author(s) 2017

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Calculated delays can explain measured regulation delays in stringent response. (a) Calculated delays are matching measured up-regulation delays better than down-regulation delays. Genes down-regulated first have the longest calculated delays. (b) Genes whose pool of mRNA has a large share of nascent mRNA (RNAP density >1.8 % and mRNA copy number <0.97). These genes seem to form a group in our data set and consist mainly of flagellar genes. (c) Confusion matrix for prediction of down-regulation interval from calculated regulation delay of flagellum genes. Numbers from bottom left to top right count correct predictions. The four wrongly predicted operons are fliE, tsr (top left), fliFGHIJK and fliLMNOPQR (bottom right).