Dekel, E., Mangan, S. & Alon, U. Environmental selection of the feed-forward loop circuit in gene-regulation networks. Phys. Biol. 2, 81-88

Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, 76100, Israel.
Physical Biology (Impact Factor: 2.54). 07/2005; 2(2):81-8. DOI: 10.1088/1478-3975/2/2/001
Source: PubMed


Gene-regulation networks contain recurring elementary circuits termed network motifs. It is of interest to understand under which environmental conditions each motif might be selected. To address this, we study one of the most significant network motifs, a three-gene circuit called the coherent feed-forward loop (FFL). The FFL has been demonstrated theoretically and experimentally to perform a basic information-processing function: it shows a delay following ON steps of an input inducer, but not after OFF steps. Here, we ask under what environmental conditions might the FFL be selected over simpler gene circuits, based on this function. We employ a theoretical cost-benefit analysis for the selection of gene circuits in a given environment. We find conditions that the environment must satisfy in order for the FFL to be selected over simpler circuits: the FFL is selected in environments where the distribution of the input pulse duration is sufficiently broad and contains both long and short pulses. Optimal values of the biochemical parameters of the FFL circuit are determined as a function of the environment such that the delay in the FFL blocks deleterious short pulses of induction. This approach can be generally used to study the evolutionary selection of other network motifs.

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    • "Living organisms respond to changes in their surroundings by sensing the environmental context and by orchestrating the expression of sets of genes to utilize available resources and to survive stressful conditions Dekel et al. (2005); Shahrezaei & Swain (2008); Pour Safaei et al. (2012). We consider a model for the lac operon regulatory network in E. Coli bacterium. "
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    • "Networks are information processing centres of the cell (Fraser et al., 2013). Developments in the last decade or so have demonstrated that living cells exhibit a distinct preference for certain network topologies over others (Dekel et al., 2005; Mangan and Alon, 2003). This results in an overrepresentation of these topologies among a large number of available options to the cell. "
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    • "Since the introduction of this concept by Milo et al. in a seminal paper [1], a considerable number of researches have been conducted on this subject. Some of these researches focused on the biological aspects [2] [3] [4] and others concentrated on computational facets [5] [6] [7] [8] [9] [10]. The first group has endeavored to interpret the motifs detected in biological networks by the existing motif detection tools. "
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