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Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a rel Gsu mutant
Functional & Integrative Genomics (2007)
  • Julia Krushkal
  • Bin Yan
  • Laurie N DiDonato
  • Marko Puljic
  • Kelly P Nevin
  • Trevor L woodard
  • Ronald M Adkins
  • Barbara A Methѐ
  • Derek Lovley, University of Massachusetts - Amherst
Abstract

RelGsu is the single Geobacter sulfurreducens homolog of RelA and SpoT proteins found in many organisms. These proteins are involved in the regulation of levels of guanosine 3′, 5′ bispyrophosphate, ppGpp, a molecule that signals slow growth and stress response under nutrient limitation in bacteria. We used information obtained from genome-wide expression profiling of the rel Gsu deletion mutant to identify putative regulatory sites involved in transcription networks modulated by RelGsu or ppGpp. Differential gene expression in the rel Gsu deletion mutant, as compared to the wild type, was available from two growth conditions, steady state chemostat cultures and stationary phase batch cultures. Hierarchical clustering analysis of these two datasets identified several groups of operons that are likely co-regulated. Using a search for conserved motifs in the upstream regions of these co-regulated operons, we identified sequences similar to Fur- and RpoS-regulated sites. These findings suggest that Fur- and RpoS-dependent gene expression in G. sulfurreducens is affected by RelGsu-mediated signaling.

Disciplines
Publication Date
July, 2007
Publisher Statement
DOI: 10.1007/s10142-007-0048-5
Citation Information
Julia Krushkal, Bin Yan, Laurie N DiDonato, Marko Puljic, et al.. "Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a rel Gsu mutant" Functional & Integrative Genomics Vol. 7 Iss. 3 (2007)
Available at: http://works.bepress.com/derek_lovley/116/