Identification of Diverse Carbon Utilization Pathways in Shewanella oneidensis MR-1 via Expression Profiling

Michael E. Driscoll[1] (mdriscol@bu.edu)
Margie F. Romine[2] (margie.romine@pnl.gov)
Frank S. Juhn[3] (frnkjn@bu.edu)
Margrethe H. Serres[4] (mserres@mbl.edu)
Lee Anne Mccue[2] (leeann.mccue@pnl.gov)
Alex S. Beliaev[2] (alex.beliaev@pnl.gov)
James K. Fredrickson[2] (jim.fredrickson@pnl.gov)
Timothy S. Gardner[1][3] (tgardner@bu.edu)

[1]Bioinformatics Program, Boston University, St. Boston, MA 02215, USA
[2]Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
[3]Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
[4]Josephine Bay Paul Center , Marine Biological Laboratory, Woods Hole, MA, USA


Abstract

To identify pathways of carbon utilization in the metal-reducing marine bacterium Shewanella oneidensis MR-1, we assayed the expression of cells grown with various carbon sources using a high-density oligonucleotide Affymetrix microarray. Our expression profiles reveal genes and regulatory mechanisms which govern the sensing, import, and utilization of the nucleoside inosine, the chitin monomer N-acetylglucosamine, and a casein-derived mixture of amino acids. Our analysis suggests a prominent role for the pentose-phosphate and Entner-Doudoroff pathways in energy metabolism, and regulatory coupling between carbon catabolism and electron acceptor pathways. In sum, these results indicate that S. oneidensis possesses a broader capacity for carbon utilization than previously reported, a view with implications for optimizing its role in microbial fuel cell and bioremediative applications.

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Japanese Society for Bioinformatics