Dinoroseobacter shibae is a marine bacterium and belongs to the ubiquitously found Roseobacter clade. Investigation of the genome sequence identified genes encoding enzymes of the anaerobic metabolism. 7 Crp/Fnr like regulators were annotated, which leads to the question for the gene regulatory network, proteomic and metabolomic networks controlling the transition between aerobic and anaerobic growth. To answer this question, an aerobic continuously cultivation of D. shibae in a chemostate in

more »

... nimal media supplemented with was established. Time resolved shift experiments from oxic to anoxic growth conditions were performed to characterize the transcriptomic, proteomic and metabolomic adaptation of D. shibae. The transcriptome and proteome data revealed a strong expression of operons encoding proteins for the formation of the denitrification machinery. Furthermore, the expression of the genes encoding the Crp/Fnr like regulators dnrD, dnrE and dnrF was also found increased, which leads to the assumption of involvement in the regulatory network for the establishment of nitrate respiratory conditions. Moreover, the synthesis of PHB was observed under these conditions and verified by transmission electronic microscopy and HPLC analyses. Using a bioinformatics approach the phylogenetic affiliation of DnrE, DnrD and DnrF into the various subfamily of Crp/Fnr like regulators was achieved. Furthermore, comparative transcriptome analyses of wildtype and dnrF deletion mutant revealed the mainly repressing influence of DnrF on several genes encoding for enzymes of the energy generation machinery, transcription factors and iron-sulfur cluster proteins under oxic and anoxic conditions. This leads to the consumption of DnrF acts mainly as a oxygen independent repressor. To identify the essential genes of D. shibae for growth under nitrate respiratory conditions a transposon mutagenesis approach was established. Over 4500 mutants were screened for a growth failure under these conditions. Finally, 53 strains showed a growth def [...]