Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli

Title{Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli}
Publication TypeJournal Article
Year of Publication2010
AuthorsMarr, Carsten, Theis Fabian J., Liebovitch Larry S., and Hütt Marc-Thorsten
Refereed DesignationRefereed
JournalPLoS Computational Biology
Volume6
Issue7
Paginatione1000836
Date Published06/2010
ISSN1553-734X
Abstract

Bacterial cells can adapt to various genomic mutations and intriguingly many environmental changes. They do this by adjusting their gene expression profile to meet the requirements of a new condition. In this work, we study the interplay of different mechanisms of gene regulatory control driving this adaptation in the bacterium E. coli. We deconstruct the network of all transcription factor mediated regulatory interactions into subnets, topologically defined subgraphs which we expect to act as information processing units. Indeed, we find that many subnets react coordinately to cellular stress, and are used by the cells to account for mutations. In these subnets, we also find many small RNA targets. In contrast, those subnets that do not act in a coordinated fashion are highly enriched with feed-forward loops, a 3-node network motif with important information processing properties. Our approach reveals correlations and anti-correlations of three scales of regulatory control: subnets, feed-forward loops, and small RNA.

URLhttp://dx.doi.org/10.1371%2Fjournal.pcbi.1000836
DOIdoi:10.1371/journal.pcbi.1000836
AttachmentSize
journal.pcbi_.1000836.pdf1.09 MB

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