Functional characterization of bacterial sRNAs using a network biology approach.

Abstract:

:Small RNAs (sRNAs) are important components of posttranscriptional regulation. These molecules are prevalent in bacterial and eukaryotic organisms, and involved in a variety of responses to environmental stresses. The functional characterization of sRNAs is challenging and requires highly focused and extensive experimental procedures. Here, using a network biology approach and a compendium of gene expression profiles, we predict functional roles and regulatory interactions for sRNAs in Escherichia coli. We experimentally validate predictions for three sRNAs in our inferred network: IsrA, GlmZ, and GcvB. Specifically, we validate a predicted role for IsrA and GlmZ in the SOS response, and we expand on current knowledge of the GcvB sRNA, demonstrating its broad role in the regulation of amino acid metabolism and transport. We also show, using the inferred network coupled with experiments, that GcvB and Lrp, a transcription factor, repress each other in a mutually inhibitory network. This work shows that a network-based approach can be used to identify the cellular function of sRNAs and characterize the relationship between sRNAs and transcription factors.

authors

Modi SR,Camacho DM,Kohanski MA,Walker GC,Collins JJ

doi

10.1073/pnas.1104318108

subject

Has Abstract

pub_date

2011-09-13 00:00:00

pages

15522-7

issue

37

eissn

0027-8424

issn

1091-6490

pii

1104318108

journal_volume

108

pub_type

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