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

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journal contribution
posted on 2023-07-31, 03:59 authored by BLB Almeida, MNM Bahrudeen, V Chauhan, S Dash, V Kandavalli, A Häkkinen, J Lloyd-Price, PSD Cristina, ISC Baptista, A Gupta, J Kesseli, E Dufour, OP Smolander, M Nykter, P Auvinen, Howard JacobsHoward Jacobs, SMD Oliveira, AS Ribeiro
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.


Jane and Aatos Erkko Foundation [10-10524-38 to A.S.R.]; Finnish Cultural Foundation [50201300 to S.D., and 00200193, 00212591 to I.S.C.B.]; EDUFI Fellowship [TM-19-11105 to S.D.]; Suomalainen Tiedeakatemia (to C.S.D.P.); Tampere University Graduate Program [to V.C., M.N.M.B., B.L.B.A.]; TTU development program 20162022 [2014-2020.4.01.16-0032 to O.P.S.]; Academy of Finland [307856 and 323576 to P.A., 322927 to A.H., and 272376 and 256615 to H.T.J.].


Publication Date



Nucleic Acids Research






(p. 6801-6819)


Oxford University Press



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© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.