| Shewanella oneidensis MR-1 is an environmentally ubiquitous, metabolically versatile microbe with a broad capacity for the reduction of metals. Shewanella's ability to shuttle electrons onto metals---including arsenic and uranium---has made it a leading candidate for use in microbial fuel cells and environmental remediation. Though the Shewanella genome has been sequenced and several of its electron transport enzymes have been characterized, little is known about how this respiratory machinery is regulated. To this end, I have designed the first Affymetrix microarray for this organism, and profiled its genome-wide expression across hundreds of conditions with varying carbon sources, metallic species, and physiologically relevant factors. I applied a mutual information algorithm to this expression compendium to infer the first genome-wide regulatory network for Shewanella. The resulting network extends our knowledge of the genes and regulators which underlie Shewanella's unique respiratory system, and the environmental signals to which they respond. Beyond its descriptive power, this network model suggests strategies for optimizing, this microbe for metal reduction in real-world applications. |
