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

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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.

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Acknowledgments

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.

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  1. Bin Yan

    Present address: NIDCD, National Institutes of Health, Building 10, Magnuson CC, Room 5D55, 10 Center Dr., Bethesda, MD, 20892, USA

Authors and Affiliations

  1. Department of Preventive Medicine, University of Tennessee Health Science Center, 66 N. Pauline Ste. 633, Memphis, TN, 38163, USA

    Julia Krushkal, Bin Yan & Marko Puljic

  2. Department of Microbiology, Morrill Science Center IV North, University of Massachusetts, 639 North Pleasant Str., Amherst, MA, 01003, USA

    Laurie N. DiDonato, Kelly P. Nevin, Trevor L. Woodard & Derek R. Lovley

  3. The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD, 20850, USA

    Barbara A. Methé

  4. Department of Pediatrics, University of Tennessee Health Science Center, 308 West Patient Tower, 50 North Dunlap, Le Bonheur Children’s Medical Center, Memphis, TN, 38103, USA

    Ronald M. Adkins

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Julia Krushkal, Bin Yan, and Laurie N. DiDonato contributed equally to this work.

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Krushkal, J., Yan, B., DiDonato, L.N. et al. Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a rel Gsu mutant. Funct Integr Genomics 7, 229–255 (2007). https://doi.org/10.1007/s10142-007-0048-5

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