title: Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion.
abstract: 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 DFL12(T) 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 DFL12(T) 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 DFL12(T) 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.
authors.affiliation: From the Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Laass
authors.forename: Sarah
authors.initials: S
authors.lastname: Kleist
authors.forename: Nelli
authors.initials: N
authors.lastname: Bill
authors.forename: Katharina
authors.initials: K
authors.lastname: Drüppel
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kossmehl
authors.forename: Lars
authors.initials: L
authors.lastname: Wöhlbrand
authors.forename: Ralf
authors.initials: R
authors.lastname: Rabus
authors.forename: Johannes
authors.initials: J
authors.lastname: Klein
authors.forename: Manfred
authors.initials: M
authors.lastname: Rohde
authors.forename: Annekathrin
authors.initials: A
authors.lastname: Bartsch
authors.forename: Christoph
authors.initials: C
authors.lastname: Wittmann
authors.forename: Kerstin
authors.initials: K
authors.lastname: Schmidt-Hohagen
authors.forename: Petra
authors.initials: P
authors.lastname: Tielen
authors.forename: Dieter
authors.initials: D
authors.lastname: Jahn
authors.forename: Dietmar
authors.initials: D
authors.lastname: Schomburg
mesh_terms: D000222:Adaptation, Physiological / Q000502:physiology*; D001426:Bacterial Proteins / Q000096:biosynthesis* / Q000235:genetics; D058440:Denitrification / Q000502:physiology*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D010101:Oxygen Consumption / Q000502:physiology*; D041902:Rhodobacteraceae / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins
keywords: Energy Metabolism; Metabolism; Metabolomics; Polyhydroxybutanoate; Proteomics; Respiration; Roseobacter; Systems Biology; Transcriptomics