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Open Access Methodology article

Genome-wide expression links the electron transfer pathway of Shewanella oneidensis to chemotaxis

Shang-Kai Tai1, GuanI Wu1, Shinsheng Yuan1 and Ker-Chau Li12*

Author Affiliations

1 Institute of Statistical Science, Academia Sinica, Taipei 115, Taiwan

2 Department of Statistics, University of California, Los Angeles, CA 90095-1554, USA

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BMC Genomics 2010, 11:319  doi:10.1186/1471-2164-11-319

Published: 21 May 2010

Abstract

Background

By coupling the oxidation of organic substrates to a broad range of terminal electron acceptors (such as nitrate, metals and radionuclides), Shewanella oneidensis MR-1 has the ability to produce current in microbial fuel cells (MFCs). omcA, mtrA, omcB (also known as mtrC), mtrB, and gspF are some known genes of S. oneidensis MR-1 that participate in the process of electron transfer. How does the cell coordinate the expression of these genes? To shed light on this problem, we obtain the gene expression datasets of MR-1 that are recently public-accessible in Gene Expression Omnibus. We utilize the novel statistical method, liquid association (LA), to investigate the complex pattern of gene regulation.

Results

Through a web of information obtained by our data analysis, a network of transcriptional regulatory relationship between chemotaxis and electron transfer pathways is revealed, highlighting the important roles of the chemotaxis gene cheA-1, the magnesium transporter gene mgtE-1, and a triheme c-type cytochrome gene SO4572.

Conclusion

We found previously unknown relationship between chemotaxis and electron transfer using LA system. The study has the potential of helping researchers to overcome the intrinsic metabolic limitation of the microorganisms for improving power density output of an MFC.