This article is part of the supplement: The 2007 International Conference on Bioinformatics & Computational Biology (BIOCOMP'07)

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Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response

Yunfeng Yang1*, Daniel P Harris1, Feng Luo2, Liyou Wu13, Andrea B Parsons1, Anthony V Palumbo1 and Jizhong Zhou13

Author affiliations

1 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA

2 School of Computing, Clemson University, Clemson, SC 29634, USA

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

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Citation and License

BMC Genomics 2008, 9(Suppl 1):S11  doi:10.1186/1471-2164-9-S1-S11

Published: 20 March 2008



Iron homeostasis is a key metabolism for most organisms. In many bacterial species, coordinate regulation of iron homeostasis depends on the protein product of a Fur gene. Fur also plays roles in virulence, acid tolerance, redox-stress responses, flagella chemotaxis and metabolic pathways.


We conducted physiological and transcriptomic studies to characterize Fur in Shewanella oneidensis, with regard to its roles in iron and acid tolerance response. A S. oneidensisfur deletion mutant was defective in growth under iron-abundant or acidic environment. However, it coped with iron depletion better than the wild-type strain MR-1. Further gene expression studies by microarray of the fur mutant confirmed previous findings that iron uptake genes were highly de-repressed in the mutant. Intriguingly, a large number of genes involved in energy metabolism were iron-responsive but Fur-independent, suggesting an intimate relationship of energy metabolism to iron response, but not to Fur. Further characterization of these genes in energy metabolism suggested that they might be controlled by transcriptional factor Crp, as shown by an enriched motif searching algorithm in the corresponding cluster of a gene co-expression network.


This work demonstrates that S. oneidensis Fur is involved in iron acquisition and acid tolerance response. In addition, analyzing genome-wide transcriptional profiles provides useful information for the characterization of Fur and iron response in S. oneidensis.