Transcriptomics

Dataset Information

3

Time series analysis of the transition from light to dark growth of Dinoroseobacter shibae DFL12


ABSTRACT: Transcriptional response of the photoheterotrophic marine bacterium D. shibea to changing light regimes. Second part of the study analysing the transition from photoheterotrophic light to heterotrophic dark growth. Bacterial aerobic anoxygenic photosynthesis (AAP) is an important mechanism of energy gain in aquatic habitats, accounting for up to 5% of the surface ocean’s photosynthetic electron transport. The dominant AAP bacteria in marine communities belong to the Roseobacter clade. For this reason we used Dinoroseobacter shibae as a model organism to study the transcriptional response of AAP bacteria to changing light regimes. We used continuous cultivation of D. shibae in a chemostat in combination with time series microarray analysis in order to identify gene regulatory patterns after a change in illumination. 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 cope with the formation of harmful singlet oxygen during photophosphorylation, an immediate downregulation of photosynthesis-related genes, fine-tuning of the expression of electron transport chain components and upregulation of the transcriptional and translational apparatus. Furthermore, our data indicate that D. shibae might use the 3-hydroxypropionate cycle for CO2 fixation. Analysis of the transcriptome dynamics after the switch from light to dark demonstrates that only few genes are directly regulated in response to light and other signals such as singlet oxygen concentration, electron flow, redox status and energy charge of the cell must be involved in the regulation of the processes accompanying AAP. Based on the transcriptome data first hypothesis about transcriptional control of AAP could be formulated. This study provides the first analysis of AAP on the level of transcriptome dynamics. Our data allow the formulation of testable hypotheses about the mechanisms involved in the regulation of this important biological process. Samples from light grown cells were used as a reference, 6 timepoints in the dark, biological replicates: 2

ORGANISM(S): Dinoroseobacter shibae DFL 12 = DSM 16493  

SUBMITTER: Regina Gohl   Irene Wagner-Döbler  Jürgen Tomasch  Boyke Bunk  Juergen Martin Tomasch  Maria Suarez Diez 

PROVIDER: E-GEOD-25581 | ArrayExpress | 2010-12-03

SECONDARY ACCESSION(S): GSE25581PRJNA142417

REPOSITORIES: GEO, ArrayExpress

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E-GEOD-25581.README.txt Txt
E-GEOD-25581.idf.txt Idf
E-GEOD-25581.processed.1.zip Processed
E-GEOD-25581.raw.1.zip Raw
E-GEOD-25581.sdrf.txt Txt
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