Document Detail


Deciphering the transcriptional regulatory logic of amino acid metabolism.
MedLine Citation:
PMID:  22082910     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Byung-Kwan Cho; Stephen Federowicz; Young-Seoub Park; Karsten Zengler; Bernhard Ø Palsson
Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2011-11-13
Journal Detail:
Title:  Nature chemical biology     Volume:  8     ISSN:  1552-4469     ISO Abbreviation:  Nat. Chem. Biol.     Publication Date:  2012 Jan 
Date Detail:
Created Date:  2011-12-16     Completed Date:  2012-02-07     Revised Date:  2013-09-24    
Medline Journal Info:
Nlm Unique ID:  101231976     Medline TA:  Nat Chem Biol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  65-71     Citation Subset:  IM    
Affiliation:
Department of Bioengineering, University of California at San Diego, La Jolla, California, USA. bkcho01@gmail.com
Data Bank Information
Bank Name/Acc. No.:
GEO/GSE26054
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MeSH Terms
Descriptor/Qualifier:
Amino Acids / metabolism*
Escherichia coli / metabolism*
Gene Expression Regulation*
Genome-Wide Association Study
Transcription Factors / genetics
Transcription, Genetic*
Grant Support
ID/Acronym/Agency:
GM062791/GM/NIGMS NIH HHS; R01 GM062791/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Transcription Factors
Comments/Corrections
Comment In:
Nat Chem Biol. 2012 Jan;8(1):23-4   [PMID:  22173355 ]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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