ArticleNature chemical biology2011
Deciphering the transcriptional regulatory logic of amino acid metabolism.
Article in Nature chemical biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
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- Rewiring Amino Acid Flux for Efficient Transglutaminase Production inJournal of agricultural and food chemistry · 2026Article
- FFoods (Basel, Switzerland) · 2026Article
- The Algorithm for Reversible Jump Inference of Motifs.bioRxiv : the preprint server for biology · 2025Article
- A Pair of Promiscuous Surrogates forBiochemistry · 2025Article
- Feeling hormonal? Insights into bacterial auxin sensing and its physiological effects.mSystems · 2024Article
- Enhanced metabolic entanglement emerges during the evolution of an interkingdom microbial community.Nature communications · 2024Article
- Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacteriummSystems · 2024Article
- Biological functions at high pressure: transcriptome response ofFrontiers in microbiology · 2024Article
- The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets.Nucleic acids research · 2023Article
- How It All Begins: Bacterial Factors Mediating the Colonization of Invertebrate Hosts by Beneficial Symbionts.Microbiology and molecular biology reviews : MMBR · 2022Review
- Protein engineering for feedback resistance in 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase.Applied microbiology and biotechnology · 2022Article
- Homeostasis of the biosyntheticiScience · 2022Article
- Advances and prospects in metabolic engineering of Escherichia coli for L-tryptophan production.World journal of microbiology & biotechnology · 2022Review
- Global coordination of metabolic pathways in Escherichia coli by active and passive regulation.Molecular systems biology · 2021Article
- Global Transcriptional Regulators Fine-Tune the Translational and Metabolic Efficiency for Optimal Growth of Escherichia coli.mSystems · 2021Article
- Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites.Nucleic acids research · 2021Article
- Redefining fundamental concepts of transcription initiation in bacteria.Nature reviews. Genetics · 2020Review
- Systematic identification of metabolites controlling gene expression in E. coli.Nature communications · 2019Article
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5 authors.
Funding
Abstract
Although metabolic networks have been reconstructed on a genome scale, the corresponding reconstruction and integration of governing transcriptional regulatory networks has not been fully achieved. Here we reconstruct such an integrated network for amino acid metabolism in Escherichia coli. Analysis of ChIP-chip and gene expression data for the transcription factors ArgR, Lrp and TrpR showed that 19 out of 20 amino acid biosynthetic pathways are either directly or indirectly controlled by these regulators. Classifying the regulated genes into three functional categories of transport, biosynthesis and metabolism leads to the elucidation of regulatory motifs that constitute the integrated network's basic building blocks. The regulatory logic of these motifs was determined on the basis of relationships between transcription factor binding and changes in the amount of transcript in response to exogenous amino acids. Remarkably, the resulting logic shows how amino acids are differentiated as signaling and nutrient molecules, revealing the overarching regulatory principles of the amino acid stimulon.
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