Functional & Integrative Genomics

, Volume 7, Issue 3, pp 229–255 | Cite as

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

  • Julia KrushkalEmail author
  • Bin Yan
  • Laurie N. DiDonato
  • Marko Puljic
  • Kelly P. Nevin
  • Trevor L. Woodard
  • Ronald M. Adkins
  • Barbara A. Methé
  • Derek R. Lovley
Original Paper


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.


Guanosine 3′,5′ bispyrophosphate ppGpp RelA Promoter 



We are grateful to Drs. C. Núñez (Instituto de Biotecnología/UNAM, Cuernavaca, Mexico), C. Leang and T. Ueki (both of University of Massachusetts, Amherst) for critical reading of this manuscript and helpful comments. We also thank R. Glaven (University of Massachusetts, Amherst) for helpful discussions and J. Peeples (University of Tennessee, Memphis) for editorial assistance.

This research was supported by the Office of Science (BER), U.S. Department of Energy, Cooperative Agreement No. DE-FC02-02ER63446.

Supplementary material


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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Julia Krushkal
    • 1
    Email author
  • Bin Yan
    • 1
    • 5
  • Laurie N. DiDonato
    • 2
  • Marko Puljic
    • 1
  • Kelly P. Nevin
    • 2
  • Trevor L. Woodard
    • 2
  • Ronald M. Adkins
    • 4
  • Barbara A. Methé
    • 3
  • Derek R. Lovley
    • 2
  1. 1.Department of Preventive MedicineUniversity of Tennessee Health Science CenterMemphisUSA
  2. 2.Department of Microbiology, Morrill Science Center IV NorthUniversity of MassachusettsAmherstUSA
  3. 3.The Institute for Genomic ResearchRockvilleUSA
  4. 4.Department of PediatricsUniversity of Tennessee Health Science CenterMemphisUSA
  5. 5.NIDCD, National Institutes of HealthBethesdaUSA

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