The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Bilena L.B. Almeida, Mohamed N.M. Bahrudeen, Vatsala Chauhan, Suchintak Dash, Vinodh Kandavalli, Antti Häkkinen, Jason Lloyd-Price, Palma S.D. Cristina, Ines S.C. Baptista, Abhishekh Gupta, Juha Kesseli, Eric Dufour, Olli-Pekka Smolander, Matti Nykter, Petri Auvinen, Howard T. Jacobs, Samuel M.D. Oliveira, Andre Sanches Ribeiro

Research output: Contribution to journalArticleScientificpeer-review


The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene's numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.

Original languageEnglish
Pages (from-to)6801-6819
Number of pages19
JournalNucleic Acids Research
Issue number12
Publication statusPublished - 8 Jul 2022
Publication typeA1 Journal article-refereed

Publication forum classification

  • Publication forum level 2

ASJC Scopus subject areas

  • Genetics


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