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Open Access Research article

Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens

Ching Leang1*, Julia Krushkal2, Toshiyuki Ueki1, Marko Puljic2, Jun Sun3, Katy Juárez14, Cinthia Núñez15, Gemma Reguera7, Raymond DiDonato1, Bradley Postier8, Ronald M Adkins6 and Derek R Lovley1

Author Affiliations

1 Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA

2 Department of Preventive Medicine, the University of Tennessee Health Science Center, Memphis, TN 38163, USA

3 Genomatica, Inc, 10520 Wateridge Circle, San Diego, CA 92121, USA

4 Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, AP 510-3, Cuernavaca, Mor. 62250, México

5 Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, AP 510-3, Cuernavaca, Mor. 62250, México

6 Department of Pediatrics, the University of Tennessee Health Science Center, Memphis, TN 38163, USA

7 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48823, USA

8 Department of Biology, Washington University in St Louis, One Brookings Dr, Campus Box 1137, St Louis, MO 63130, USA

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BMC Genomics 2009, 10:331  doi:10.1186/1471-2164-10-331

Published: 22 July 2009

Abstract

Background

The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production.

Results

An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a taclac promoter. Combining both the microarray transcriptome analysis and the computational prediction revealed that the G. sulfurreducens RpoN controls genes involved in a wide range of cellular functions. Most importantly, RpoN controls the expression of the dcuB gene encoding the fumarate/succinate exchanger, which is essential for cell growth with fumarate as the terminal electron acceptor in G. sulfurreducens. RpoN also controls genes, which encode enzymes for both pathways of ammonia assimilation that is predicted to be essential under all growth conditions in G. sulfurreducens. Other genes that were identified as part of the RpoN regulon using either the computational prediction or the microarray transcriptome analysis included genes involved in flagella biosynthesis, pili biosynthesis and genes involved in central metabolism enzymes and cytochromes involved in extracellular electron transfer to Fe(III), which are known to be important for growth in subsurface environment or electricity production in microbial fuel cells. The consensus sequence for the predicted RpoN-regulated promoter elements is TTGGCACGGTTTTTGCT.

Conclusion

The G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of cellular processes.