Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling

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.