Shewanella oneidensis MR-1 etrA deletion mutant strain expression profiling determines fine-tuning regulatory role in anaerobic metabolism

Comparisson of expression profiling of a etrA deletion mutant strain (experimental sample) with that of the wild type Shewanella oneidensis MR-1 strain to assess global direct/indirect genetic regulation EtrA in Shewanella oneidensis MR-1 shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulator Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. is complex and not well understood. Whole-genome expression profiling using a etrA gene deletion mutant as the experimental sample and the wild type strain as the reference, determine that EtrA fine-tunes the expression of genes involved in various anaerobic metabolic pathways, including nitrate, fumarate and dimethyl sulfoxide reduction. Moreover, genes involved in prophage activation and and genes implicated in aerobic metabolism were also differentially expressed. In contrast to previous studies that attributed a minor regulatory role to EtrA in Shewanella spp., this study demonstrates that EtrA acts as a global transcriptional regulator and cofers physiological advantages to the strain under certain growth conditions. Total RNA was extracted from three biological replicate cultures of both S. oneidensis etrA deletion mutant and the wild type strain, grown individually on anaerobic minimal medium supplemented with 2 mM nitrate as the electron acceptor and lactate as the electron donor. Total RNA was collected from mid-log phase cultures. cDNA from each sample was prepared and labeled with Cy-dyes. Three biological replicates per treatment were used for the hybridization of six microarray slides including technical replicates (dye-swap) per experiment.