Jump to main content
Jump to site search

Issue 4, 2015
Previous Article Next Article

Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli

Author affiliations

Abstract

Transcription factors (TFs) modulate gene expression as a consequence of internal or exogenous changes in cell signaling. TFs can bind to DNA either with their effector bound (holo conformation), or as free proteins (apo conformation). With the aim of contributing to the understanding of the evolutionary fitness and organizational principles behind the different TF conformations, we inquire into the origins of these conformational differences by analyzing these two TF conformations from the perspective of Savageau's demand theory. For the control of a gene whose function is in high demand, we found that evolutionary constraints are responsible for activator TFs binding to DNA mainly in holo conformation whereas apo activation is under-represented. The mathematically controlled comparison of the apo and holo conformations reveals formal and evolutionary arguments in favor of this TF control asymmetry, which suggests that evolution favors holo activation under environmental conditions commonly found by E. coli in the human digestive tract. Specifically, the sensibility analysis performed for the holo conformation, in the positive mode of regulation, shows that the wild-type is more robust for situations where realizable changes in the model's parameters favored a better performance under non-stressful environmental conditions commonly found by E. coli in the human digestive tract. By contrast, the positive apo conformation is better adapted to adverse situations. On the other hand, the sensibility analysis performed for the negative mode of regulation showing none of the TF active conformations presents an advantage.

Graphical abstract: Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli

Back to tab navigation

Supplementary files

Publication details

The article was received on 21 Sep 2014, accepted on 30 Jan 2015 and first published on 02 Feb 2015


Article type: Paper
DOI: 10.1039/C4MB00561A
Author version
available:
Download author version (PDF)
Citation: Mol. BioSyst., 2015,11, 994-1003
  •   Request permissions

    Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli

    F. J. Alvarez-Vasquez, J. A. Freyre-González, Y. I. Balderas-Martínez, M. I. Delgado-Carrillo and J. Collado-Vides, Mol. BioSyst., 2015, 11, 994
    DOI: 10.1039/C4MB00561A

Search articles by author

Spotlight

Advertisements