Comparative study of the transcriptional regulatory networks of \textit{E. coli} and yeast: structural characteristics leading to marginal dynamic stability

DOI10.1016/J.JTBI.2007.07.001MaRDI QIDQ2211646zbMATH OpenOpenAlexWikidataFDO

Authors Deok-Sun Lee, Heiko Rieger

Publication date 11 November 2020

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/q-bio/0609033

zbMATH Keywords

Boolean modeldynamic stabilitygene regulatory network

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Microbiology (92C70)

Abstract: Dynamical properties of the transcriptional regulatory network of {it Escherichia coli} and {it Saccharomyces cerevisiae} are studied within the framework of random Boolean functions. The dynamical response of these networks to a single point mutation is characterized by the number of mutated elements as a function of time and the distribution of the relaxation time to a new stationary state, which turn out to be different in both networks. Comparison with the behavior of randomized networks reveals relevant structural characteristics other than the mean connectivity, namely the organization of circuits and the functional form of the in-degree distribution. The abundance of single-element circuits in {it E. coli} and the power-law in-degree distribution of {it S. cerevisiae} shift their dynamics towards marginal stability overcoming the restrictions imposed by their mean connectivities, which is argued to be related to the simultaneous presence of robustness and adaptivity in living organisms.

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Cites work

• Evolution of scale-free random graphs: Potts model formulation
• Superpolynomial growth in the number of attractors in Kauffman networks

Cited in

(6)

• Dynamical criticality in gene regulatory networks
• Anomalies in the transcriptional regulatory network of the yeast \textit{Saccharomyces cerevisiae}
• Regulatory dynamics of standard two-component systems in bacteria
• Broad edge of chaos in strongly heterogeneous Boolean networks
• Robustness of transcriptional regulation in yeast-like model Boolean networks
• Dynamic properties of cell-cycle and life-cycle networks in budding yeast

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