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Integrated transcriptional regulatory network of quorum sensing, replication, and SOS response in Dinoroseobacter shibae

ABSTRACT: Integrated transcriptional regulatory network of quorum sensing, replication, and SOS response in Dinoroseobacter shibae

PROVIDER: PRJNA503610 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8147470.fastq.gz	Fastqsanger.gz
	SRR8147480.fastq.gz	Fastqsanger.gz
	SRR8147490.fastq.gz	Fastqsanger.gz
	SRR8147471.fastq.gz	Fastqsanger.gz
	SRR8147481.fastq.gz	Fastqsanger.gz

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Dinoroseobacter shibae

Project description:Dinoroseobacter shibae overview

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Cell-density resolved comparative analysis of D. shibae wild-type vs. delta-luxI1

Project description:A quorum sensing null mutant was compared with D. shibae wild-type in order to identify quorum sensing controlled traits in this organism. Samples were taken at different optical densities in the exponential phase and in the stationary phase in order to clarify if quorum sensing regulation is dependent on cell-densitiy Samples from Dinoroseobacter shibae DFL 12 wild-type and delta-luxI1 (Dshi_0312) are compared during exponential (OD600 0.1, 0.2, 0.4, 0.6, 0.8) and stationary phase (6h post maximum OD600), two biological replicates

2012-11-03 | E-GEOD-42011 | biostudies-arrayexpress

Integrated transcriptional regulatory network of quorum sensing, replication, and SOS response in Dinoroseobacter shibae

Project description:Transcriptional response of the QS-negative D. shibae strain ∆luxI1 towards externally added 500nM autoinducer (AI) 3-oxo-C14-HSL over a time period of 3 hours.

2018-11-03 | GSE122111 | GEO

Effect of changing light regimes on Dinoroseobacter shibae DFL12 growth

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

Transcriptomic analysis of Dinoroseobacter shibae DFL12T in response to phage infection

Project description:Dinoroseobacter shibae DFL12T was cultured with/without phage R2C, and gene expression was analyzed at 60 min and 140 min during the incubation

2018-01-20 | GSE109415 | GEO

Dinoroseobacter shibae

Project description:Adaption of Dinoroseobacter shibae to anaerobic conditions

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Adaption of Dinoroseobacter shibae to anaerobic conditions

Project description:To unravel the adaptation strategies of D. shibae to anaerobic conditions in microaerobic to anaerobic parts of the ocean and to define the underlying regulatory network an anaerobic shift experiment in Salt-Water-Medium in a chemostate was established. Transcriptome analyses were used to investigate the physiological status of D. shibae under this conditions. Dinoroseobacter shibae wild type strain DSM 16493T was grown in a chemostate in saltwater mininmal medium (SWM) mimicking the conditions in the marine habitat under anaerobic conditions. For growth under oxygen depletion the media were supplemented with 50 mM KNO3 to sustain anaerobic respiration. Therefore, D. shibae was grown aerobically in the chemostate until the culture reached the exponential phase, than countinuously cultivaion was started. The dilution rate was 0.1 h-1, establishing the approximate half-maximum growth rate of D. shibae in the exponential phase. The anaerobic shift was initialised after 20 hours by stopping the aeration. The samples were harvested before (as reference) and 30 minutes after stopping the airation. Three biological replica were analyzed. Comparison: Identification of genes induced or repressed under aerobic conditions in the Dinoroseobacter shibae wild type strain DSM 16493T. Here we compared the transcriptome profile of D. shibae wild type strain DSM 16493T grown aerobically in the chemostate in exponential phase with the transcriptome profile of the D. shibae wild type strain DSM 16493T which was grown without aeration for 5, 10, 15, 20, 30, 60 and 120 min.

2013-08-30 | E-GEOD-47445 | biostudies-arrayexpress

Cell-density resolved comparative analysis of D. shibae wild-type vs. delta-luxI1 overexpressing luxI1 in trans

Project description:D. shibae delta-luxI1 overexpressing the luxI1 gene in trans was compared to the wild-type in order to identify quorum sensing controlled traits in this organism. Samples were taken at different optical densities in the exponential phase and in the stationary phase. Samples from Dinoroseobacter shibae DFL 12 wild-type and delta-luxI1pDP1 are compared during exponential (OD600 0.1, 0.2, 0.4, 0.6, 0.8) and stationary phase (6h post maximum OD600), two biological replicates

2012-11-03 | E-GEOD-42012 | biostudies-arrayexpress

Adaptation of Dinoroseobacter shibae to different kinds of oxidative stress

Project description:The Gram-negative photoheterotrophic bacterium Dinoroseobacter shibae is a member of the high abundant marine Roseobacter group. Living in the photic zone environment of marine ecosystems D. shibae is frequently exposed to oxygen. Oxic environments are hazardous and therefore effective defense mechanisms are required. In the present study, the adaptation of D. shibae to different kinds of oxidative stresses was investigated. Hydrogen peroxide, diamide and paraquat were used as agents to trigger peroxide, thiol and superoxide stress. To define and compare the peroxide, superoxide and thiol stress stimulons in D. shibae, GeLC-MS/MS based proteomic data of cytosolic and surface associated proteins were used. Furthermore, a strain deficient in the rhizobial iron regulator (RirA) was used to study the global impact of RirA on peroxide dependent protein expression.

2021-03-12 | PXD013791 | Pride

Dinoroseobacter shibae strain:DSM 16439 | isolate:DSM 16439

Project description:Dinoroseobacter shibae Dinoroseobacter shibae DSM 16439 transcriptome - FEBA_7_MM_RNA

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