Sign up for PNAS Online eTocs
Link: Info for AuthorsLink: Editorial BoardLink: AboutLink: SubscribeLink: AdvertiseLink: ContactLink: Sitemap Link: PNAS Home
Proceedings of the National Academy of Sciences
Link: Current Issue "" Link: Archives "" Link: Online Submission ""  Link: Advanced Search

Published online on December 15, 2005, 10.1073/pnas.0505231102
PNAS | December 27, 2005 | vol. 102 | no. 52 | 19103-19108


This Article
Right arrow Figures Only
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supporting Information
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a colleague
Right arrow Related articles in PNAS
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My File Cabinet
Right arrow Download to citation manager
Right arrow Request Copyright Permission
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via ISI Web of Science (19)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Barrett, C. L.
Right arrow Articles by Palsson, B. O.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Barrett, C. L.
Right arrow Articles by Palsson, B. O.
Social Bookmarking
Add to CiteULike   Add to Complore   Add to Connotea   Add to Del.icio.us   Add to Digg  
What's this?

 Previous Article  | Table of Contents |  Next Article 

MICROBIOLOGY
The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states

Christian L. Barrett, Christopher D. Herring, Jennifer L. Reed, and Bernhard O. Palsson *

Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412

Edited by Philip P. Green, University of Washington School of Medicine, Seattle, WA and approved November 1, 2005 (received for review June 24, 2005)

A principal aim of systems biology is to develop in silico models of whole cells or cellular processes that explain and predict observable cellular phenotypes. Here, we use a model of a genome-scale reconstruction of the integrated metabolic and transcriptional regulatory networks for Escherichia coli, composed of 1,010 gene products, to assess the properties of all functional states computed in 15,580 different growth environments. The set of all functional states of the integrated network exhibits a discernable structure that can be visualized in 3-dimensional space, showing that the transcriptional regulatory network governing metabolism in E. coli responds primarily to the available electron acceptor and the presence of glucose as the carbon source. This result is consistent with recently published experimental data. The observation that a complex network composed of 1,010 genes is organized to achieve few dominant modes demonstrates the utility of the systems approach for consolidating large amounts of genome-scale molecular information about a genome and its regulation to elucidate an organism's preferred environments and functional capabilities.

systems biology | transcriptional regulation

Author contributions: C.L.B. designed research; C.L.B. and C.D.H. performed research; C.L.B. and C.D.H. analyzed data; C.L.B. and B.O.P. wrote the paper; and J.L.R. reconstructed the organism.

Conflict of interest statement: University of California at San Diego has a related patent application (U.S. Patent Application 20040072723) that has been licensed.

This paper was submitted directly (Track II) to the PNAS office.

Abbreviation: TF, transcription factor.

* To whom correspondence should be addressed. E-mail: palsson{at}ucsd.edu.

© 2005 by The National Academy of Sciences of the USA


Add to CiteULike CiteULike   Add to Complore Complore   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg    What's this?

Related articles in PNAS:

This Week in PNAS

PNAS 2005 102: 18765-18766. [Full Text]  



This article has been cited by other articles in HighWire Press-hosted journals:


Home page
 J. Physiol.Home page
L. G. Koch and S. L. Britton
Aerobic metabolism underlies complexity and capacity
J. Physiol., January 1, 2008; 586(1): 83 - 95.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
L. G. Koch and S. L. Britton
Evolution, atmospheric oxygen, and complex disease
Physiol Genomics, August 20, 2007; 30(3): 205 - 208.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Physiol. Cell Physiol.Home page
T. D. Vo and B. O. Palsson
Building the power house: recent advances in mitochondrial studies through proteomics and systems biology
Am J Physiol Cell Physiol, January 1, 2007; 292(1): C164 - C177.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
R. Sanjuan and S. F. Elena
Epistasis correlates to genomic complexity
PNAS, September 26, 2006; 103(39): 14402 - 14405.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. A. Rahman and D. Schomburg
Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks
Bioinformatics, July 15, 2006; 22(14): 1767 - 1774.
[Abstract] [Full Text] [PDF]