Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach

Abstract

network structure <p>The <it>E. coli</it> transcriptional regulatory network is shown to have a nonpyramidal architecture of independent modules governed by transcription factors, whose responses are integrated by intermodular genes.</p> AbstractBackground: Previous studies have used different methods in an effort to extract the modular organization of transcriptional regulatory networks. However, these approaches are not natural, as they try to cluster strongly connected genes into a module or locate known pleiotropic transcription factors in lower hierarchical layers. Here, we unravel the transcriptional regulatory network of Escherichia coli by separating it into its key elements, thus revealing its natural organization. We also present a mathematical criterion, based on the topological features of the transcriptional regulatory network, to classify the network elements into one of two possible classes: hierarchical or modular genes.

The GlxR regulon of the amino acid producer Corynebacterium glutamicum: Detection of the corynebacterial core regulon and integration into the transcriptional regulatory network model

“…The carbon metabolism module, for instance, features carbon source specific transcription factors, such as FruR, LldR, GntR1/R2, and the many regulators involved in aromatic compound degradation. The hierarchical and modular structure of the C. glutamicum supercluster reflects the typical topology of bacterial transcriptional regulatory networks (Ma et al, 2004;Resendis-Antonio et al, 2005), and is similar to that of recent E. coli models (Freyre-González et al, 2008;Martínez-Antonio et al, 2008).…”

“…In this organism, the synthesis of cAMP by adenylate cyclase is stimulated by a component of the phosphoenolpyruvate:sugar phosphotransferase system, and cAMP levels are coupled to cellular energy levels (Park et al, 2006;Bettenbrock et al, 2007). Crp E. coli has consistently been recognized as global regulator in the transcriptional regulatory network of E. coli, being involved in the regulation of about 400 genes in distinct cellular functionality (Freyre-González et al, 2008;Martínez-Antonio et al, 2008). In this way, Crp E. coli serves as regulatory hub, connecting several functional modules to the network and mediating the cellular response to a high-level signal conveyed by the varying concentrations of cAMP (Kolb et al, 1993).…”

The transcriptional regulatory repertoire of Corynebacterium glutamicum: Reconstruction of the network controlling pathways involved in lysine and glutamate production

“…This comprehensive network reconstruction revealed a modular and hierarchical structure of regulatory interactions at the transcriptional level (Ma et al, 2004;Resendis-Antonio et al, 2005). Recent results indicated that different organizational levels of the TRN of E. coli are bridged by the presence of positive and negative feedback loops (Freyre-González et al, 2008). The modularity of the TRN accounts for the robustness of the entire system in that way that damage is kept in a certain part of the network (Aderem, 2005).…”

Extensive cross-talk and global regulators identified from an analysis of the integrated transcriptional and signaling network in Escherichia coli

“…It is worth noting that each of the highlighted TFs has been described as a global regulator in the transcriptional network of E. coli by at least one of the previously published studies. 15,37,38 This observation suggests that dynamical outliers (which are also identified as structural outliers) are very likely to be global transcription factors. Many distinct features distinguish these factors from the rest of the integrated network: (i) all the factors have a much higher out-degree than in-degree, i.e.…”

“…[19][20][21] Consequently, questions have been raised on the generality of the trends. 15 Also of relevance in this context is the link between the structure and dynamics of a network which is most often neglected when studying global properties. Understanding this link becomes important as is demonstrated in the case of network synchronization in cortical network analyses.…”