Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a rel Gsu mutant
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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.
KeywordsGuanosine 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.
- Anderson RT, Vrionis HA, Ortiz-Bernad I, Resch CT, Long PE, Dayvault R, Karp K, Marutzky S, Metzler DR, Peacock A, White DC, Lowe M, Lovley DR (2003) Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl Environ Microbiol 69:5884–5891PubMedCrossRefGoogle Scholar
- Cashel M, Gentry DR, Hernandez VJ, Vinella D (1996) The stringent response. In: Neidhardt C, Curtiss R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology. ASM, Washington, DC, pp 1458–1496Google Scholar
- Drăghici S (2003a) 11.2.1. Euclidian distance, data analysis tools for DNA microarrays. Chapman & Hall/CRC, Washington, DC, pp 265–266Google Scholar
- Drăghici S (2003b) 13.3. Fold change, data analysis tools for DNA microarrays. Chapman & Hall/CRC, Washington, DC, pp 343–347Google Scholar
- Koonin EV, Aravind L, Galperin MY (2000) A comparative-genomic view of the microbial stress response. In: Storz G, Hengge-Aronis R (eds) Bacterial stress responses. ASM, Washington, DC, pp 417–444Google Scholar
- Liu X, Brutlag DL, Liu JS (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 6:127–138Google Scholar
- Methé BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM (2003) The genome of Geobacter sulfurreducens: insights into metal reduction in subsurface environments. Science 302:1967–1969PubMedCrossRefGoogle Scholar
- Wan XF, Verberkmoes NC, McCue LA, Stanek D, Connelly H, Hauser LJ, Wu L, Liu X, Yan T, Leaphart A, Hettich RL, Zhou J, Thompson DK (2004) Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis. J Bacteriol 186:8385–8400PubMedCrossRefGoogle Scholar
- Yan B, Lovley D, Krushkal J (2006a) Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens. Biosystems (in press): DOI 10.1016/j.biosystems.2006.1010.1006