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Open Access Research article

Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses

Haichun Gao123, Xiaohu Wang4, Zamin K Yang2, Timothy Palzkill4 and Jizhong Zhou12*

  • * Corresponding author: Jizhong Zhou jzhou@ou.edu

  • † Equal contributors

Author Affiliations

1 Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA

2 Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA

3 Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA

4 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA

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BMC Genomics 2008, 9:42  doi:10.1186/1471-2164-9-42

Published: 25 January 2008

Abstract

Background

The Arc two-component system is a global regulator controlling many genes involved in aerobic/anaerobic respiration and fermentative metabolism in Escherichia coli. Shewanella oneidensis MR-1 contains a gene encoding a putative ArcA homolog with ~81% amino acid sequence identity to the E. coli ArcA protein but not a full-length arcB gene.

Results

To understand the role of ArcA in S. oneidensis, an arcA deletion strain was constructed and subjected to both physiological characterization and microarray analysis. Compared to the wild-type MR-1, the mutant exhibited impaired aerobic growth and a defect in utilizing DMSO in the absence of O2. Microarray analyses on cells grown aerobically and anaerobically on fumarate revealed that expression of 1009 genes was significantly affected (p < 0.05) by the mutation. In contrast to E. coli ArcA, the protein appears to be dispensable in regulation of the TCA cycle in S. oneidensis. To further determine genes regulated by the Arc system, an ArcA recognition weight matrix from DNA-binding data and bioinformatics analysis was generated and used to produce an ArcA sequence affinity map. By combining both techniques, we identified an ArcA regulon of at least 50 operons, of which only 6 were found to be directly controlled by ArcA in E. coli.

Conclusion

These results indicate that the Arc system in S. oneidensis differs from that in E. coli substantially in terms of its physiological function and regulon while their binding motif are strikingly similar.