Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a relGsu mutant

Funct Integr Genomics. 2007 Jul;7(3):229-55. doi: 10.1007/s10142-007-0048-5. Epub 2007 Apr 4.


Rel(Gsu) 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 Rel(Gsu) 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 Rel(Gsu)-mediated signaling.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / metabolism*
  • Base Sequence
  • Gene Deletion
  • Gene Expression Profiling
  • Gene Expression Regulation, Bacterial*
  • Genes, Bacterial
  • Genome, Bacterial
  • Geobacter / genetics*
  • Ligases / genetics
  • Ligases / physiology*
  • Mutation
  • Operon / genetics
  • Promoter Regions, Genetic*
  • Regulatory Sequences, Nucleic Acid
  • Repressor Proteins / metabolism*
  • Sigma Factor / metabolism*
  • Transcription, Genetic


  • Bacterial Proteins
  • Repressor Proteins
  • Sigma Factor
  • ferric uptake regulating proteins, bacterial
  • sigma factor KatF protein, Bacteria
  • Ligases
  • guanosine 3',5'-polyphosphate synthetases