ArticleJournal of molecular biology2008
Functional organisation of Escherichia coli transcriptional regulatory network.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
- Dynamic heterogeneity in an E. coli stress response regulon mediates gene activation and antimicrobial peptide tolerance.Cell reports · 2026Article
- Gene regulation inMicrobiology and molecular biology reviews : MMBR · 2025Review
- Evaluating the predictive power of combined gene expression dynamics from single cells on antibiotic survival.mSystems · 2025Article
- Topology-based metrics for finding the optimal sparsity in gene regulatory network inference.Bioinformatics (Oxford, England) · 2025Article
- Complexity reduction by symmetry: Uncovering the minimal regulatory network for logical computation in bacteria.PLoS computational biology · 2025Article
- Article
- Inferred regulons are consistent with regulator binding sequences in E. coli.PLoS computational biology · 2024Article
- Competition and evolutionary selection among core regulatory motifs in gene expression control.Nature communications · 2023Article
- Retron-mediated multiplex genome editing and continuous evolution in Escherichia coli.Nucleic acids research · 2023Article
- Review
- The role of replication-induced chromosomal copy numbers in spatio-temporal gene regulation and evolutionary chromosome plasticity.Frontiers in microbiology · 2023Article
- Understanding the Genome-Wide Transcription Response To Various cAMP Levels in Bacteria Using Phenomenological Models.mSystems · 2022Article
- The Spatial Organization of Bacterial Transcriptional Regulatory Networks.Microorganisms · 2022Article
- Molecular basis for lethal cross-talk between two unrelated bacterial transcription factors - the regulatory protein of a restriction-modification system and the repressor of a defective prophage.Nucleic acids research · 2022Article
- Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa.Nucleic acids research · 2022Article
- An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control.NPJ systems biology and applications · 2022Article
- The transcription factor network of E. coli steers global responses to shifts in RNAP concentration.Nucleic acids research · 2022Article
- HyfF subunit of hydrogenase 4 is crucial for regulating FJournal of bioenergetics and biomembranes · 2022Article
- The Fis Nucleoid Protein Negatively Regulates the Phase VariationFrontiers in microbiology · 2022Article
- An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851.Memorias do Instituto Oswaldo Cruz · 2022Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Taking advantage of available functional data associated with 115 transcription and 7 sigma factors, we have performed a structural analysis of the regulatory network of Escherichia coli. While the mode of regulatory interaction between transcription factors (TFs) is predominantly positive, TFs are frequently negatively autoregulated. Furthermore, feedback loops, regulatory motifs and regulatory pathways are unevenly distributed in this network. Short pathways, multiple feed-forward loops and negative autoregulatory interactions are particularly predominant in the subnetwork controlling metabolic functions such as the use of alternative carbon sources. In contrast, long hierarchical cascades and positive autoregulatory loops are overrepresented in the subnetworks controlling developmental processes for biofilm and chemotaxis. We propose that these long transcriptional cascades coupled with regulatory switches (positive loops) for external sensing enable the coexistence of multiple bacterial phenotypes. In contrast, short regulatory pathways and negative autoregulatory loops enable an efficient homeostatic control of crucial metabolites despite external variations. TFs at the core of the network coordinate the most basic endogenous processes by passing information onto multi-element circuits. Transcriptional expression data support broader and higher transcription of global TFs compared to specific ones. Global regulators are also more broadly conserved than specific regulators in bacteria, pointing to varying functional constraints.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.