RT Journal Article
SR Electronic
T1 The transcription factor network of <em>E. coli</em> steers global responses to shifts in RNAP concentration
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.03.07.483226
DO 10.1101/2022.03.07.483226
A1 Bilena L B Almeida
A1 Mohamed N M Bahrudeen
A1 Vatsala Chauhan
A1 Suchintak Dash
A1 Vinodh Kandavalli
A1 Antti Häkkinen
A1 Jason Lloyd-Price
A1 Cristina S D Palma
A1 Ines S C Baptista
A1 Abhishekh Gupta
A1 Juha Kesseli
A1 Eric Dufour
A1 Olli-Pekka Smolander
A1 Matti Nykter
A1 Petri Auvinen
A1 Howard T Jacobs
A1 Samuel M D Oliveira
A1 Andre S Ribeiro
YR 2022
UL http://biorxiv.org/content/early/2022/03/08/2022.03.07.483226.abstract
AB 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.Competing Interest StatementThe authors have declared no competing interest.