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

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.