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A 102 kb RepABC plasmid of xenologous origin modulates chromosomal gene expression in Dinoroseobacter shibae

ABSTRACT: A 102 kb RepABC plasmid of xenologous origin modulates chromosomal gene expression in Dinoroseobacter shibae

PROVIDER: PRJNA814615 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18290041.fastq.gz	Fastqsanger.gz
	SRR18290042.fastq.gz	Fastqsanger.gz
	SRR18290043.fastq.gz	Fastqsanger.gz
	SRR18290044.fastq.gz	Fastqsanger.gz
	SRR18290045.fastq.gz	Fastqsanger.gz

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Similar Datasets

A 102 kb RepABC plasmid of xenologous origin modulates chromosomal gene expression in Dinoroseobacter shibae

Project description:The model organism Dinoroseobacter shibae and many other marine Rhodobacterales (Roseobacteraceae, Alphaproteobacteria) are characterized by a multipartite genome organization. Here we show that the original isolate (Dshi-6) contained six extrachromosomal replicons (ECRs), whereas the strain deposited at the DSMZ (Dshi-5) lacked a 102 kb plasmid. To determine the role of the sixth plasmid, we investigated the genomic and physiological differences between the two strains. Therefore, both genomes were (re-)sequenced and gene expression, growth and substrate utilization were examined. For comparison, we included additional plasmid-cured strains in the genome analysis. In the Dshi-6 population, the conjugative 102 kb RepABC-9 plasmid was only present in about 50 % of the cells, irrespective of its experimentally validated stability. In the presence of the sixth plasmid, copy number changes of other ECRs, in particular a decrease of the 86 kb plasmid, were observed. The most conspicuous finding was the strong influence of plasmids on the chromosomal gene expression, especially the repression of the CtrA regulon and the activation of the denitrification gene cluster. The expression is inversely controlled either by the presence of the 102 kb or the absence of the 86 kb plasmid. We identified global regulatory genes on both plasmids, i.e. a sigma 70 factor, and a quorum sensing synthase, that might be responsible for these major changes. The tremendous effects challenge the current understanding of the relevance of volatile plasmids not only for the original host, but also for new recipients after conjugation.

2022-03-13 | GSE198318 | GEO

Dinoroseobacter shibae

Project description:Dinoroseobacter shibae overview

| PRJNA35939 | ENA

The Sixth Element: a 102-kb RepABC Plasmid of Xenologous Origin Modulates Chromosomal Gene Expression in Dinoroseobacter shibae.

Project description: Not available

| S-EPMC9426580 | biostudies-literature

Dinoroseobacter shibae

Project description:Adaption of Dinoroseobacter shibae to anaerobic conditions

| PRJNA205826 | ENA

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

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

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

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

Dinoroseobacter shibae strain:DSM 16439 | isolate:DSM 16439

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

| PRJNA426730 | ENA

Dinoroseobacter shibae strain:DFL12

Project description:Dinoroseobacter shibae strain:DFL12 Raw sequence reads

| PRJNA294971 | ENA