Transcriptome analysis of Shewanella oneidensis MR-1 in response to cold shock

This study presents a global transcriptional analysis of the cold shock response of Shewanella oneidensis MR-1 after a temperature downshift from 30 to 8 or 15oC based on time-series microarray experiments. More than 700 genes were found to be significantly affected (p < 0.05) upon cold shock challenge, especially at 8oC. The temporal gene expression patterns of the classical cold-shock genes varied and only some of them, most notably so1648 and so2787, were differentially regulated in response to temperature downshift. The global response of S. oneidensis to cold shock was also characterized by the up-regulation of genes encoding membrane proteins, DNA metabolism and translation apparatus components, metabolic proteins, regulatory proteins, and hypothetical proteins. Most of the metabolic proteins affected are involved in catalytic processes that generate NADH or NADPH. Keywords: time course, stress response To prepare cells for a microarray analysis, a single colony of MR-1 was used to inoculate 3 ml of LB in 10 ml plastic tubes and grown overnight at 30oC (optimal growth temperature) on a rotary platform (200 rpm). 150 ml of LB medium prewarmed to 30oC in a 500-ml flask was inoculated with an aliquot of a fresh overnight culture to an OD600 of 0.01 and then was shaken on a rotary platform (200 rpm) until an OD600 of a mid-log optical density 0.59 was attained. A 25-ml aliquot of cells was transferred to a 250-ml flask pre-cooled to 8 or 15oC and then incubated in an 8 or 15oC shaking water bath. Samples for microarray analysis were taken at 0 (control), 5, 10, 20, 40, 80 and 160 min, pelleted by centrifugation at maximum speed in a 5415R centrifuge (Eppendorf, Germany) for 10 s, and placed in liquid nitrogen.