Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli

doi:10.1073/pnas.0500365102

Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli

^†Department of Pathology, Northwestern University, Chicago, IL 60611; ^§Department of Physics and Center for Complex Networks Research, University of Notre Dame, Notre Dame, IN 46556; and ^¶Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15261

Edited by Charles R. Cantor, Sequenom, Inc., San Diego, CA, and approved April 12, 2005 (received for review January 21, 2005)

Abstract

Recent evidence indicates that potential interactions within metabolic, protein–protein interaction, and transcriptional regulatory networks are used differentially according to the environmental conditions in which a cell exists. However, the topological units underlying such differential utilization are not understood. Here we use the transcriptional regulatory network of Escherichia coli to identify such units, called origons, representing regulatory subnetworks that originate at a distinct class of sensor transcription factors. Using microarray data, we find that specific environmental signals affect mRNA expression levels significantly only within the origons responsible for their detection and processing. We also show that small regulatory interaction patterns, called subgraphs and motifs, occupy distinct positions in and between origons, offering insights into their dynamical role in information processing. The identified features are likely to represent a general framework for environmental signal processing in prokaryotes.

Footnotes

↵ ∥ To whom correspondence should be addressed. E-mail: oltvai{at}pitt.edu.
↵ ‡ Present address: Applied Biodynamics Laboratory, Department of Biomedical Engineering, Boston University, Boston, MA 02215.
Author contributions: G.B., A.-L.B., and Z.N.O. designed research; G.B. performed research; G.B. contributed new reagents/analytic tools; G.B. analyzed data; and G.B., A.-L.B., and Z.N.O. wrote the paper.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: TR, transcriptional regulatory; TF, transcription factor; FFL, feed-forward loop; DIV, divergence; CNV, convergence; CAS, cascade; SRI, single regulatory interaction.