COMPUTATIONAL RESEARCH in BOSTON and BEYOND (CRIBB)

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, environmental remediation, and biologically-based sensors. Though the Shewanella genome has been sequenced and many of the enzymes involved in electron transport have been identified, little is known about how this metabolic machinery is regulated. To this end, we have designed the first Affymetrix microarray for this organism, to observe and its model global gene expression. We have profiled gene expression in hundreds of environmental conditions using a fractional factorial experimental design, varying nutrients, metallic species, and other factors within known physiological ranges. We have used this expression data to infer the first genome-wide regulatory model for Shewanella, and make testable predictions about how we might optimize this bacteria for metal reduction in real-world applications.

Research funded by DOE Genomes to Life Project, the Krell Institute, and Boston University Professors T.S. Gardner and J.J. Collins.