The economy of chromosomal distances in bacterial gene regulation

Eda Cakir (1) , Annick Lesne (2, 3) , Marc-Thorsten Hütt (1)

1 Jacobs University = Constructor University [Bremen]
2 LPTMC - Laboratoire de Physique Théorique de la Matière Condensée
3 IGMM - Institut de Génétique Moléculaire de Montpellier

In the transcriptional regulatory network (TRN) of a bacterium, the nodes are genes and a directed edge represents the action of a transcription factor (TF), encoded by the source gene, on the target gene. It is a condensed representation of a large number of biological observations and facts. Non-random features of the network are structural evidence of requirements for a reliable systemic function. For the bacterium Escherichia coli we here investigate the (Euclidean) distances covered by the edges in the TRN when its nodes are embedded in the real space of the circular chromosome. Our work is motivated by 'wiring economy' research in Computational Neuroscience and starts from two contradictory hypotheses: (1) TFs are predominantly employed for longdistance regulation, while local regulation is exerted by chromosomal structure, locally coordinated by the action of structural proteins. Hence long distances should often occur. (2) A large distance between the regulator gene and its target requires a higher expression level of the regulator gene due to longer reaching times and ensuing increased degradation (proteolysis) of the TF and hence will be evolutionarily reduced. Our analysis supports the latter hypothesis.

Domaines: Bio-Informatique, Biologie Systémique [q-bio.QM]; Mécanique statistique [cond-mat.stat-mech]; Réseaux moléculaires [q-bio.MN]; Bactériologie

Eda Cakir, Annick Lesne, Marc-Thorsten Hütt. The economy of chromosomal distances in bacterial gene regulation. npj Systems Biology and Applications, 2021, 7, pp.49. ⟨10.1038/s41540-021-00209-2⟩. ⟨hal-03411512v2⟩