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Article
Rapid Changes in Gene Expression Dynamics in Response to Superoxide Reveal SoxRS-Dependent and Independent Transcriptional Networks
PLoS ONE (2007)
  • Jeffrey L. Blanchard
  • Wei-Yun Wholey
  • Erin M. Conlon, University of Massachusetts - Amherst
  • Pablo J. Pomposiello
Abstract

Background

SoxR and SoxS constitute an intracellular signal response system that rapidly detects changes in superoxide levels and modulates gene expression in E. coli. A time series microarray design was used to identify co-regulated SoxRS-dependent and independent genes modulated by superoxide minutes after exposure to stress.

Methodology/Principal Findings

soxS mRNA levels surged to near maximal levels within the first few minutes of exposure to paraquat, a superoxide-producing compound, followed by a rise in mRNA levels of known SoxS-regulated genes. Based on a new method for determining the biological significance of clustering results, a total of 138 genic regions, including several transcription factors and putative sRNAs were identified as being regulated through the SoxRS signaling pathway within 10 minutes of paraquat treatment. A statistically significant two-block SoxS motif was identified through analysis of the SoxS-regulated genes. The SoxRS-independent response included members of the OxyR, CysB, IscR, BirA and Fur regulons. Finally, the relative sensitivity to superoxide was measured in 94 strains carrying deletions in individual, superoxide-regulated genes.

Conclusions/Significance

By integrating our microarray time series results with other microarray data, E. coli databases and the primary literature, we propose a model of the primary transcriptional response containing 226 protein-coding and sRNA sequences. From the SoxS dependent network the first statistically significant SoxS-related motif was identified.

Disciplines
Publication Date
November 13, 2007
Publisher Statement

DOI: 10.1371/journal.pone.0001186


This work is licensed under a Creative Commons Attribution 3.0 Unported License.

Citation Information
Jeffrey L. Blanchard, Wei-Yun Wholey, Erin M. Conlon and Pablo J. Pomposiello. "Rapid Changes in Gene Expression Dynamics in Response to Superoxide Reveal SoxRS-Dependent and Independent Transcriptional Networks" PLoS ONE Vol. 2 Iss. 11 (2007)
Available at: http://works.bepress.com/erin_conlon/4/