A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways

The present study addresses the regulatory network of Escherichia coli and offers a global view of the short- and long-term regulation of its metabolic pathways. The regulatory mechanisms responsible for key metabolic activities and the structure behind such mechanisms are detailed. Most metabolic functions are dependent on the activity of transcriptional regulators over gene expression--the so-called long-term regulation. However, enzymatic regulation--the so-called short-term regulation--often overlays transcriptional regulation and even, in particular metabolic pathways, enzymatic regulation may prevail. As such, understanding the balance between these two types of regulation is necessary to be able to predict and control cell responses, specifically cell responses to the various environmental stresses.

[1]  Peter D. Karp,et al.  EcoCyc: a comprehensive database of Escherichia coli biology , 2010, Nucleic Acids Res..

[2]  Araceli M. Huerta,et al.  Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles. , 2003, Genome research.

[3]  Pär Nordlund,et al.  Crystal structure of CaiB, a type-III CoA transferase in carnitine metabolism. , 2004, Biochemistry.

[4]  Adam M. Feist,et al.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.

[5]  A. Danchin,et al.  GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli. , 2004, Microbiology.

[6]  Adam M. Feist,et al.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.

[7]  An-Ping Zeng,et al.  Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph , 2004, Bioinform..

[8]  Nancy Argüelles,et al.  Author ' s , 2008 .

[9]  Ronan M. T. Fleming,et al.  Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization , 2009, PLoS Comput. Biol..

[10]  Ahmad A. Mannan,et al.  Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification , 2010, Microbial cell factories.

[11]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[12]  A. Emili,et al.  Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins , 2009, PLoS biology.

[13]  U. Alon Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.