Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli
- 20 May 2005
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 102 (22) , 7841-7846
- https://doi.org/10.1073/pnas.0500365102
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.Keywords
This publication has 34 references indexed in Scilit:
- Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level ConservationGenome Research, 2003
- Network Motifs: Simple Building Blocks of Complex NetworksScience, 2002
- Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response modelMolecular Microbiology, 2002
- Reverse engineering gene networks using singular value decomposition and robust regressionProceedings of the National Academy of Sciences, 2002
- Topological and causal structure of the yeast transcriptional regulatory networkNature Genetics, 2002
- Network motifs in the transcriptional regulation network of Escherichia coliNature Genetics, 2002
- Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA associationNature Genetics, 2001
- Dynamic regulation of the tryptophan operon: A modeling study and comparison with experimental dataProceedings of the National Academy of Sciences, 2001
- Genome-Wide Location and Function of DNA Binding ProteinsScience, 2000
- Fundamental patterns underlying gene expression profiles: Simplicity from complexityProceedings of the National Academy of Sciences, 2000