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E-GEOD-62869 - Oxidative stress management in Dinoroseobacter shibae: Role of extrachromosomal elements and the importance of a small chromid during starvation

Status
Released on 1 January 2015, last updated on 11 February 2015
Organism
Dinoroseobacter shibae DFL 12 = DSM 16493
Samples (6)
Array (1)
Protocols (7)
Description
Aerobic anoxygenic phototrophic bacteria (AAPs) of the Roseobacter group are abundant in the photic zone of the marine environment. Dinoroseobacter shibae, a typical representative, converts light into additional energy that enhances its survival under nutrient-depletion. AAPs produce cytotoxic singlet oxygenunder light exposition, but D. shibae developed mechanisms to counteract the lethal effects of illumination. Recent studies documented a pivotal role of extrachromosomal elements (ECRs) for the ecological fitness of roseobacters, and here we investigated their significance for the adaptation to specific environmental stress. D. shibae possessing five ECRs, i.e. three chromids and two plasmids, was starved for four weeks in the dark and light/dark cycles and the survival strategy was evaluated using transcriptomics. Few genes on the chromosome showed differential expression between non-starved and starved cells, in particular those with a role in oxidative stress response and photosynthesis. Extrachromosomal genes in contrast showed a systematic loss of transcriptional activity, especially in the dark starved cells. The observed silencing of gene expression was not due to plasmid loss, because all five ECRs were stably maintained. Exceptionally, the smallest 72-kb replicon was the least downregulated, and one region with genes for singlet oxygen stress response was even strongly activated under light/dark cycle. A ?72-kb curing mutant completely lost the ability to benefit from AAP under starvation, and we could thus document the essential role of the 72-kb chromid to light-stress adaptation. . Our data moreover suggest that the four ECRs of D. shibae without a vital function are transcriptionally silenced under starvation. Loop-design, two biological replicates of D. shibae DFL12T cultivated in artificial salt water medium with succinate as carbon source and 12/12 light-dark cycles. After reaching stationary phase the cells were starved for 4 weeks in the dark or under light-dark cycle.
Experiment type
transcription profiling by array 
Contacts
Juergen Martin Tomasch <jto07@helmholtz-hzi.de>, Bert Engelen, Heribert Cypionka, Hui Wang, Irene Wagner-Döbler, Jörn Petersen, Jürgen Tomasch, Maya Soora
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-62869.idf.txt
Sample and data relationshipE-GEOD-62869.sdrf.txt
Raw data (1)E-GEOD-62869.raw.1.zip
Processed data (1)E-GEOD-62869.processed.1.zip
Array designA-GEOD-11243.adf.txt
Links