title: Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks.
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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America. blanchard@microbio.umass.edu
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Blanchard
authors.forename: Wei-Yun
authors.initials: WY
authors.lastname: Wholey
authors.forename: Erin M
authors.initials: EM
authors.lastname: Conlon
authors.forename: Pablo J
authors.initials: PJ
authors.lastname: Pomposiello
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics*; D015870:Gene Expression; D010269:Paraquat / Q000494:pharmacology; D012333:RNA, Messenger / Q000235:genetics; D013481:Superoxides / Q000378:metabolism*; D015534:Trans-Activators / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D012333:RNA, Messenger; D015534:Trans-Activators; D014157:Transcription Factors; D013481:Superoxides; C070724:SoxR protein, Bacteria; C070725:SoxS protein, E coli; D010269:Paraquat