Role of the DNR- and FNR- type regulators in regulation of the denitrification genes in Roseobacter denitrificans OCh114

An aerobic photosynthetic bacterium Roseobacter denitrificans OCh114 has two DNR- and one FNR-type transcriptional regulators, which are predicted to sense nitric oxide and oxygen, respectively. To investigate the role of these regulators in regulation of the denitrification genes, transcriptome profiles of mutant strains of R. denitrificans OCh114 deficient in the genes for the DNR- or FNR-type regulators were determined by NimbleGen Prokaryotic Expression array (12x135K). The mutant strains of R. denitrificans OCh114 deficient in the genes for the DNR- (dnr1 and dnr2) or FNR-type (fnrL) regulators were unable to grow anaerobically by denitrification. Therefore, the strains were initially cultivated aerobically in glycerol medium supplemented with 20 mM NaNO3 in baffled Erlenmeyer flasks with rotary shaking at 200 rpm at 30 ºC. When optical density at 600 nm reached 0.4, the cultures were moved to vials. After the vials were sealed with butyl rubber septa, the cultures were made anaerobic by replacing the headspace gas with argon. Total RNA was extracted after the anaerobic cultivation for 3 hours. The experiment was performed in duplicate independent cultures.