Effect of changing light regimes on Dinoroseobacter shibae DFL12 growth
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ABSTRACT:
ORGANISM(S): Dinoroseobacter shibae DFL 12 = DSM 16493
PROVIDER: GSE25591 | GEO | 2010/12/03
SECONDARY ACCESSION(S): PRJNA134231
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE25579: Time series analysis of the transition from dark to light growth of Dinoroseobacter shibae DFL12 GSE25581: Time series analysis of the transition from light to dark growth of Dinoroseobacter shibae DFL12 Refer to individual Series
2010-12-03 | E-GEOD-25591 | biostudies-arrayexpress
Project description:Bacterial aerobic anoxygenic photosynthesis (AAP) is an important mechanism of energy generation in aquatic habitats, accounting for up to 5% of the surface ocean's photosynthetic electron transport. We used Dinoroseobacter shibae, a representative of the globally abundant marine Roseobacter clade, as a model organism to study the transcriptional response of a photoheterotrophic bacterium to changing light regimes. Continuous cultivation of D. shibae in a chemostat in combination with time series microarray analysis was used in order to identify gene-regulatory patterns after switching from dark to light and vice versa. The change from heterotrophic growth in the dark to photoheterotrophic growth in the light was accompanied by a strong but transient activation of a broad stress response to the formation of singlet oxygen, an immediate downregulation of photosynthesis-related genes, fine-tuning of the expression of ETC components, as well as upregulation of the transcriptional and translational apparatus. Furthermore, our data suggest that D. shibae might use the 3-hydroxypropionate cycle for CO(2) fixation. Analysis of the transcriptome dynamics after switching from light to dark showed relatively small changes and a delayed activation of photosynthesis gene expression, indicating that, except for light other signals must be involved in their regulation. Providing the first analysis of AAP on the level of transcriptome dynamics, our data allow the formulation of testable hypotheses on the cellular processes affected by AAP and the mechanisms involved in light- and stress-related gene regulation.
| S-EPMC3223308 | biostudies-literature
Project description:D. shibae was cultivated under changing light regimes and samples for transcriptome and metabolome were taken.
2014-07-01 | GSE57164 | GEO
Project description:D. shibae was cultivated under changing light regimes and samples for transcriptome and metabolome were taken. Two independent cultivations in a Chemostat have been performed. Each reactor was run for 3 light/dark-cycles of 12h/12h. Sampling started from the second cycle and continued to the third cycle.
2014-07-01 | E-GEOD-57164 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-02-01 | E-GEOD-53967 | biostudies-arrayexpress
Project description:Aerobic anoxygenic phototrophs (AAPs) as being photoheterotrophs require organic substrates for growth and use light as a supplementary energy source under oxic conditions. We hypothesized that AAPs benefit from light particularly under carbon and electron donor limitation. The effect of light was determined in long-term starvation experiments with Dinoroseobacter shibae DFL 12(T) in both complex marine broth and defined minimal medium with succinate as the sole carbon source. The cells were starved over six months under three conditions: continuous darkness (DD), continuous light (LL), and light/dark cycle (LD, 12 h/12 h, 12 µmol photons m(-2) s(-1)). LD starvation at low light intensity resulted in 10-fold higher total cell and viable counts, and higher bacteriochlorophyll a and polyhydroxyalkanoate contents. This coincided with better physiological fitness as determined by respiration rates, proton translocation and ATP concentrations. In contrast, LD starvation at high light intensity (>22 µmol photons m(-2) s(-1), LD conditions) resulted in decreasing cell survival rates but increasing carotenoid concentrations, indicating a photo-protective response. Cells grown in complex medium survived longer starvation (more than 20 weeks) than those grown in minimal medium. Our experiments show that D. shibae benefits from the light and dark cycle, particularly during starvation.
| S-EPMC3875502 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2014-02-01 | GSE53967 | GEO
Project description:In the present study we have investigated the influence of light and anoxia on the energetic state of the aerobic anoxygenic phototroph (AAP) Dinoroseobacter shibae. Respiration, chemiosmotic proton translocation and the adenylate energy charge (AEC) of the cells were measured comparing light versus dark and oxic versus anoxic conditions. Light caused a decrease of the respiration rates of washed cells. This might be a substitution rather than a direct inhibitory effect, because both photosynthesis and respiration contribute to the proton-motive force. As known from other AAPs, light alone did not induce proton translocation if applied to anoxic cell suspensions. However, additions of small oxygen pulses to anoxic cell suspensions caused two times more proton translocation in the light than in the dark. The AEC of the cells was measured by means of a modified luciferin-luciferase method. Growing cells of D. shibae kept an AEC of 0.93, indicating that the adenylate pool was highly phosphorylated. After harvesting and storing the cells under anoxic conditions for 2 h, the AEC dropped to 0.12. However, the cells remained reactive. Upon addition of oxygen, the AEC increased to its original value within 40 s by the formation of about 12 mM of intracellular ATP. There were no differences whether this recovery experiment was carried out in the dark or in the light. We conclude that D. shibae is able to change its energetic state not only in response to the light regime but also during oxic-anoxic transitions. Both responses appear suited to save in situ organic substrates and endogenous electron donors, thus enhancing the role of photosynthetic energy conservation.
| S-EPMC3064978 | biostudies-literature
Project description:The Roseobacter clade is a ubiquitous group of marine α-proteobacteria. To gain insight into the versatile metabolism of this clade, we took a constraint-based approach and created a genome-scale metabolic model (iDsh827) of Dinoroseobacter shibae DFL12T. Our model is the first accounting for the energy demand of motility, the light-driven ATP generation and experimentally determined specific biomass composition. To cover a large variety of environmental conditions, as well as plasmid and single gene knock-out mutants, we simulated 391,560 different physiological states using flux balance analysis. We analyzed our results with regard to energy metabolism, validated them experimentally, and revealed a pronounced metabolic response to the availability of light. Furthermore, we introduced the energy demand of motility as an important parameter in genome-scale metabolic models. The results of our simulations also gave insight into the changing usage of the two degradation routes for dimethylsulfoniopropionate, an abundant compound in the ocean. A side product of dimethylsulfoniopropionate degradation is dimethyl sulfide, which seeds cloud formation and thus enhances the reflection of sunlight. By our exhaustive simulations, we were able to identify single-gene knock-out mutants, which show an increased production of dimethyl sulfide. In addition to the single-gene knock-out simulations we studied the effect of plasmid loss on the metabolism. Moreover, we explored the possible use of a functioning phosphofructokinase for D. shibae.
| S-EPMC3789786 | biostudies-literature
Project description:Expression dynamics for all genes significantly regulated after the transition from dark to light and vice versa.
2023-11-01 | GSE245756 | GEO