Gene Regulatory and Metabolic Adaptation Processes of Dinoroseobacter shibae DFL12T during Oxygen Depletion

• Published in: The Journal of biological chemistry Vol. 289; no. 19; pp. 13219 - 13231
• Main Authors: Laass, Sebastian, Kleist, Sarah, Bill, Nelli, Drüppel, Katharina, Kossmehl, Sebastian, Wöhlbrand, Lars, Rabus, Ralf, Klein, Johannes, Rohde, Manfred, Bartsch, Annekathrin, Wittmann, Christoph, Schmidt-Hohagen, Kerstin, Tielen, Petra, Jahn, Dieter, Schomburg, Dietmar
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 09.05.2014; American Society for Biochemistry and Molecular Biology
• Subjects: Adaptation, Physiological - physiology; Bacterial Proteins - biosynthesis; Bacterial Proteins - genetics; Denitrification - physiology; Energy Metabolism; Gene Expression Regulation, Bacterial - physiology; Metabolism; Metabolomics; Oxygen Consumption - physiology; Polyhydroxybutanoate; Proteomics; Respiration; Rhodobacteraceae - genetics; Rhodobacteraceae - metabolism; Roseobacter; Systems Biology; Transcriptomics; Metabolomics; Energy Metabolism; Transcriptomics; Proteomics; Metabolism; Respiration; Systems Biology; Roseobacter; Polyhydroxybutanoate
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M113.545004

Metabolic flexibility is the key to the ecological success of the marine Roseobacter clade bacteria. We investigated the metabolic adaptation and the underlying changes in gene expression of Dinoroseobacter shibae DFL12T to anoxic life by a combination of metabolome, proteome, and transcriptome analyses. Time-resolved studies during continuous oxygen depletion were performed in a chemostat using nitrate as the terminal electron acceptor. Formation of the denitrification machinery was found enhanced on the transcriptional and proteome level, indicating that D. shibae DFL12T established nitrate respiration to compensate for the depletion of the electron acceptor oxygen. In parallel, arginine fermentation was induced. During the transition state, growth and ATP concentration were found to be reduced, as reflected by a decrease of A578 values and viable cell counts. In parallel, the central metabolism, including gluconeogenesis, protein biosynthesis, and purine/pyrimidine synthesis was found transiently reduced in agreement with the decreased demand for cellular building blocks. Surprisingly, an accumulation of poly-3-hydroxybutanoate was observed during prolonged incubation under anoxic conditions. One possible explanation is the storage of accumulated metabolites and the regeneration of NADP+ from NADPH during poly-3-hydroxybutanoate synthesis (NADPH sink). Although D. shibae DFL12T was cultivated in the dark, biosynthesis of bacteriochlorophyll was increased, possibly to prepare for additional energy generation via aerobic anoxygenic photophosphorylation. Overall, oxygen depletion led to a metabolic crisis with partly blocked pathways and the accumulation of metabolites. In response, major energy-consuming processes were reduced until the alternative respiratory denitrification machinery was operative. The bacterium Dinoroseobacter shibae was exposed to environmental anoxia. Systems biology analyses showed the time-resolved cellular adaptation processes of D. shibae during oxygen depletion. Oxygen depletion led to a metabolic crisis due to the missing regeneration of ATP and reduction equivalents, until denitrification was established. Here we have elucidated the adaptation processes of marine bacteria to anoxic respiration.