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.
journal_name
Nat Chem Bioljournal_title
Nature chemical biologyauthors
Cho BK,Federowicz S,Park YS,Zengler K,Palsson BØdoi
10.1038/nchembio.710subject
Has Abstractpub_date
2011-11-13 00:00:00pages
65-71issue
1eissn
1552-4450issn
1552-4469pii
nchembio.710journal_volume
8pub_type
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