Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CGH of S. meliloti DnaA and Hda overproducing strains

ABSTRACT: Assays 1-4: Effects of DnaA activity on S. meliloti chromosome, pSymA and pSymB replicon bias. Sheared DNA extracts of IPTG-induced vs uninduced cultures of DnaA (Assays 1,2) or Hda (Assays 3,4) overexpressors were labeled with Cy3 or Cy5 and hybridized applying dye-swap replicate design. Assay 5: Hybridization of sheared DNA of logarithmic (Cy3-labeled) vs stationary phase (Cy5-labeled) culture.

ORGANISM(S): Sinorhizobium meliloti

SUBMITTER: Benjamin Frage

PROVIDER: E-MTAB-3924 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of all major organ systems of Medicago truncatula to create a gene expression atlas

Project description:Medicago truncatula, which has a relatively small diploid genome, has been adopted as a model species for legume genomics. To enhance its value as a model, we have generated a gene expression atlas that provides a global view of gene expression in all major organ systems of this species, with special emphasis on nodule and seed development.

2008-03-15 | E-MEXP-1097 | biostudies-arrayexpress

The leader peptide peTrpL forms antibiotic-containing ribonucleoprotein complexes for posttranscriptional regulation of multiresistance genes

Project description:Bacterial ribosome-dependent attenuators are widespread posttranscriptional regulators. They harbour small upstream ORFs (uORFs) encoding leader peptides, for which no functions in trans are known yet. In the soil-dwelling plant symbiont Sinorhizobium meliloti, the tryptophan biosynthesis gene trpE(G) is preceded by the uORF trpL and is regulated by transcription attenuation according to tryptophan availability. However, trpLE(G) transcription is initiated independently of the tryptophan level in S. meliloti, thereby ensuring a largely tryptophan-independent production of the leader peptide peTrpL. Here we provide evidence for a tryptophan-independent role of peTrpL in trans. We found that peTrpL increases the resistance towards tetracycline, erythromycin, chloramphenicol and the flavonoid genistein, which are substrates of the major multidrug efflux pump SmeAB. Coimmunoprecipitation with 3×FLAG-peTrpL suggested smeR mRNA, which encodes the transcription repressor of smeABR, as a peptide target. Indeed, upon antibiotic exposure, smeR mRNA was destabilized and smeA stabilized in a peTrpL-dependent manner, showing that peTrpL acts in the differential regulation of smeABR. Further, smeR mRNA was coimmunoprecipitated with 3×FLAG-peTrpL in antibiotic-dependent ribonucleoprotein (ARNP) complexes, which in addition contained an antibiotic-induced antisense RNA complementary to smeR. In vitro ARNP reconstitution revealed that the above antibiotics and genistein directly support complex formation. A specific region of the antisense RNA was identified as a seed region for ARNP assembly in vitro. Altogether, our data show that peTrpL is involved in a mechanism for direct utilization of antimicrobial compounds in posttranscriptional regulation of multiresistance genes. We also show that the role of peTrpL in resistance is conserved in other Alphaproteobacteria

2020-05-19 | PXD018342 | Pride

Transcriptome profiling of the S. meliloti EcpR1 sRNA overproducing strain and deletion mutant

Project description:To obtain further clues to putative target genes of Sinorhizobium meliloti EcpR1 (SmelC291) sRNA, the cellular responses 15 minutes, 1 hour, and 4 hours post-induction of ecpR1 overexpression and of the ecpR1 deletion mutant (2011ecpR1) during stationary growth were characterized by microarray-based transcriptome profiling.

2015-04-15 | E-MTAB-3389 | biostudies-arrayexpress

Single-nucleotide variant and marker frequency analysis of Sinorhizobium meliloti strains with rearranged genomic DNA.

Project description:S. meliloti strains with a bi- and monopartite genome configuration were constructed by consecutive Cre/lox-mediated site-specific fusions of the secondary replicons. Beside the correct genomic arrangements, these strains and precursors were tested for variations in the nucleotide sequence. Further, a marker frequency analysis was performed to test if replication is initiated at all origins and to determine the replication termination regions of the triple replicon fusion molecule. To gain the sequence data for these analyses, respective strains were applied to whole genome sequencing using an Illumina MiSeq-System.

2022-10-10 | E-MTAB-11878 | biostudies-arrayexpress

Transcriptome of Sinorhizobium meliloti RNase mutants

Project description:The ribonucleases (RNases) E and J are essential in Escherichia coli and Bacillus subtilis, respectively. Sinorhizobium meliloti contains both, the rne gene encoding RNase E and the rnj gene encoding RNase J. The transcriptomes of the S. meliloti Rm2011 wild type, and rne and rnj mutants were compared.

2017-01-21 | E-MTAB-5435 | biostudies-arrayexpress

Transcription profiling of Medicago truncatula mature, nitrogen-fixing root nodules was vs gene expression in uninoculated roots

Project description:Gene expression in mature, nitrogen-fixing root nodules was compared to gene expression in uninoculated roots.

2005-06-30 | E-MEXP-237 | biostudies-arrayexpress

Regulatory elements coordinating initiation of chromosome replication to the Escherichia coli cell cycle

Project description:Escherichia coli coordinates replication and division cycles by initiating replication at a narrow range of cell sizes. By tracking replisomes in individual cells through thousands of division cycles in wild-type and mutant strains, we were able to compare the relative importance of previously described control systems. We found that accurate triggering of initiation does not require synthesis of new DnaA. The initiation size increased only marginally as DnaA was diluted by growth after dnaA expression had been turned off. This suggests that the conversion of DnaA between its active ATP- and inactive ADP-bound states is more important for initiation size control than the total free concentration of DnaA. In addition, we found that the known ATP/ADP-converters DARS and datA compensate for each other, although the removal of them makes the initiation size more sensitive to the concentration of DnaA. Only disruption of the regulatory inactivation of DnaA (RIDA) mechanism had a radical impact on replication initiation. This result was corroborated by the finding that termination of one round of replication correlates with the next initiation at intermediate growth rates, as would be the case if RIDA-mediated conversion from DnaA-ATP to DnaA-ADP abruptly stops at termination and DnaA-ATP starts accumulating.

2023-05-12 | PXD036580 | Pride

Expression profiles of dnaA null, rok null, and dnaA null; rok null mutants

2015-06-13 | GSE69788 | GEO

Expression profiles of dnaA null, rok null, and dnaA null; rok null mutants

Project description:To identify potential targets of co-regulation by DnaA and Rok, we compared the transcriptional profiles of dnaA null, rok null, and dnaA null rok null mutants. Because a dnaA null mutant requires an oriC- strain background, we used an oriC- oriN+ background for all strains, to allow direct comparisons. We compared biological triplicates for each of the following strains: dnaA null (CAL2074), rok null (CAS196), dnaA null rok null (CAS192), and dnaA+ rok+ (CAL2083; control).

2015-06-13 | E-GEOD-69788 | biostudies-arrayexpress

Transcription profiling of Sinorhizobium meliloti strain 1021FDC5 grown in liquid, solid or semi-solid media

Project description:S. meliloti 1021FDC5 was grown at 30ºC in 20 ml of TY broth with shaking to late logarithmic phase (optical density at 600 nm = 1-1.2). After incubation, cells were pelleted, washed twice in MM and resuspended in 2 ml of the latter medium. For time course experiments in liquid, 0.5 ml of the inoculation culture was added to 50 ml of fresh MM. At various times, samples were removed for determining viable cells counts as well as for RNA isolation/preparation (7 and 14 hours). For experiments on plates, 20 ml of MM containing 0.7% (Semisolid) or 1.3% (Solid) agar was dispensed onto each Petri dish and allowed to gel. The plates were air dried at room temperature for 15 min. 0.1 ml of the inoculation culture was plated onto the surface of the plates and allowed to dry for 10 min. The plates were then inverted and incubated at 30ºC.

2009-04-03 | E-MEXP-1953 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data