Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation

The ionizing radiation (IR) dose that yields 20% survival (D20) of Shewanella oneidensis MR-1 is lower by factors of 20 and 200 than for Escherichia coli and Deinococcus radiodurans, respectively. Transcriptome analysis was used to identify the genes of MR-1 responding to 40 Gy (D20). We observed the induction of 170 genes and repression of 87 genes in MR-1 during a one-hour recovery period after irradiation. The genomic response of MR-1 to IR is very similar to its response to ultraviolet radiation (254 nm), which included induction of systems involved in DNA repair and prophage synthesis, and the absence of differential regulation of tricarboxylic acid cycle activity which occurs in IR-irradiated D. radiodurans. Furthermore, strong induction of genes encoding antioxidant enzymes in MR-1 was observed. DNA damage may not be the principal cause of high sensitivity to IR considering that MR-1 encodes a complex set of DNA repair systems and 40 Gy IR induces less than one double strand break (DSB) in its genome. Instead, a combination of oxidative stress, protein damage and prophage mediated cell lysis during irradiation and recovery might underlie this organism’s great sensitivity to radiation. Keywords: time course, stress response Gene expression profile of S. oneidensis MR-1 was examined over a period of 1h following IR exposure. Briefly, 80 ml of MR-1 culture grown in Davis medium to OD600 of 0.2 was divided in half. Half of the culture (40 ml) was irradiated on ice to a total dose of 40 Gy. The non-irradiated control culture was incubated on ice for the same length of time (about 20 seconds) as the culture being irradiated. After irradiation, the irradiated cell culture (40 ml) and non-irradiated control culture (40 ml) were each transferred to a separate 100-ml flask (without dilution into fresh medium) and incubated at 30 C on a shaker. An aliquot of cells (12 ml) from each flask was collected after 5 (T5), 20 (T20), and 60 min (T60) of incubation for RNA extraction. Three independent cell cultures and irradiation treatments (repA, repB, and repD) were performed and served as biological replicates for gene expression experiments. For each time point, two technical replicates in hybridization (fluorescent-dye reversal) were carried out for each biological replicate. Thus, six data points were available for each time point (a total of eight data points were available for T20) and enabled the use of statistical tests to determine significant changes in gene expression.