| Deciphering the transcriptional regulatory logic of amino acid metabolism. | |
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MedLine Citation:
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PMID: 22082910 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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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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Authors:
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Byung-Kwan Cho; Stephen Federowicz; Young-Seoub Park; Karsten Zengler; Bernhard Ø Palsson |
Publication Detail:
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Type: JOURNAL ARTICLE Date: 2011-11-13 |
Journal Detail:
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Title: Nature chemical biology Volume: - ISSN: 1552-4469 ISO Abbreviation: - Publication Date: 2011 Nov |
Date Detail:
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Created Date: 2011-11-15 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101231976 Medline TA: Nat Chem Biol Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
Affiliation:
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1] Department of Bioengineering, University of California at San Diego, La Jolla, California, USA. [2] Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejoen, Korea (B.-K.C.) and Mogam Biotechnology Research Institute, Yongin, Korea (Y.-S.P.). |
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