Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of SocB toxin on genome-wide expression in Caulobacter crescentus

ABSTRACT: Caulobacter cells were grown to exponential phase in rich PYE medium. At time zero, expression of socB-M2 was induced by the addition of 0.3% xylose. A reference sample was also collected at this time point. Atter 1.5 hours, the experimental sample was then collected. RNA was extracted from the reference and experimental samples, reverse transcribed into Cy3- or Cy5-labeled cDNA, and then hybridized to Agilent 4x44K Caulobacter arrays.

ORGANISM(S): Caulobacter crescentus

SUBMITTER: Christopher Aakre

PROVIDER: E-MEXP-3990 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The bacterial cell-cycle regulator GcrA is a Ï70 co-factor that drives gene expression from a subset of methylated promoters.

Project description:Cell cycle progression in most organisms requires tightly regulated programs of gene expression. The transcription factors involved typically stimulate gene expression by binding specific DNA sequences in promoters and recruiting RNA polymerase. Here, we find that the essential cell cycle regulator GcrA in Caulobacter crescentus activates the transcription of target genes in a fundamentally different manner. GcrA forms a stable complex with RNA polymerase and localizes to almost all active Ï70-dependent promoters in vivo, but activates transcription primarily at promoters harboring certain DNA methylation sites. Whereas most transcription factors that contact Ï70 interact with domain 4, GcrA interfaces with domain 2, the region that binds the -10 element during strand separation. Using kinetic analyses and a reconstituted in vitro transcription assay, we demonstrate that GcrA can stabilize RNA polymerase binding and directly stimulate open complex formation to activate transcription. Guided by these studies, we identify a regulon of ~200 genes, providing new insight into the essential functions of GcrA. Collectively, our work reveals a new mechanism for transcriptional regulation, and we discuss the potential benefits of activating transcription by promoting RNA polymerase isomerization rather than exclusively recruitment. Examination of GcrA, RNAP, Sigma70 ChIP in PYE and in PYE + rifampicin-treated for 30 min; sigma32 and sigma54 in PYE + rifampicin-treated for 30 min

2015-11-10 | E-GEOD-73925 | biostudies-arrayexpress

Testing the effects of nitric oxide (oxidative) stress on Caulobacter transcription

Project description:The goal of this study was to measure the effects of nitric oxide exposure (using DETA NONOate as a nitric oxide donor) on transcription in Caulobacter. Untreated Caulobacter crescentus were grown to a density of 0.3 (at OD660) in PYE medium (pH 7) in rolled culture tubes. DETA-NONOate treated Caulobacter crescentus were grown to a density of 0.3 (at OD660), and then treated with 100 mM DETA NONOate for 30 minutes.

2010-06-20 | E-GEOD-21139 | biostudies-arrayexpress

HipBA toxin-antitoxin system Caulobacter crescentus.

Project description:Antibiotic persistence is a transient phenotypic state during which a bacterium can withstand otherwise lethal antibiotic exposure or environmental stresses. In Escherichia coli, persistence is promoted by the HipBA toxin-antitoxin system. The HipA toxin functions as a serine/threonine kinase that inhibits cell growth, while the HipB antitoxin neutralizes the toxin. E. coli HipA inactivates the glutamyl-tRNA synthetase GltX, which inhibits translation and triggers the highly conserved stringent response. Although hipBA operons are widespread in bacterial genomes, it is unknown if this mechanism is conserved in other species. Here we describe the functions of three hipBA modules in the alpha-proteobacterium Caulobacter crescentus. The HipA toxins have different effects on growth and macromolecular syntheses, and they phosphorylate distinct substrates. HipA1 and HipA2 contribute to antibiotic persistence during stationary phase by phosphorylating the aminoacyl-tRNA synthetases GltX and TrpS. The stringent response regulator SpoT is required for HipA-mediated antibiotic persistence, but persister cells can form in the absence of all hipBA operons or spoT, indicating that multiple pathways lead to persister cell formation in C. crescentus.

2020-02-06 | PXD015525 | Pride

High-resolution mapping of the spatial organization of Caulobacter crescentus chromosome by chromosome conformation capture in conjunction with next-generation sequencing (Hi-C)

Project description:Chromosomes must be highly compacted and organized within cells, but how this is achieved in vivo remains poorly understood. We report the first use of Hi-C to map the structure of bacterial chromosomes at a high, unprecedented resolution. Analysis of Hi-C data and polymer modeling indicates that the Caulobacter crescentus chromosome consists of multiple, largely independent spatial domains likely comprised of supercoiled plectonemes arrayed into a bottlebrush-like fiber. These domains are stable throughout the cell cycle and re-established concomitantly with DNA replication. We provide strong evidence that domain boundaries are established by highly-expressed genes and the formation of plectoneme-free regions. Additionally, we use Hi-C to demonstrate that supercoiling, the histone-like protein HU, and SMC act at different length-scales and in complementary ways to organize and structure chromosomes within cells. Hi-C experiments were performed on untreated wild type swarmer cells and drug-treated swarmer cells (Novobiocin or Rifampicin) of Caulobacter crescentus CB15N. Hi-C were also performed on swarmer cells of smc knock-out and hup1hup2 knock-out mutants of Caulobacter crescentus. Time-course Hi-C were performed on a synchronous population of Caulobacter crescentus at 5, 10, 30, 45, 60 and 75 minutes after synchronization. The progression of DNA replication during the cell cycle was followed by total genomic DNA sequencing.

2013-10-30 | E-GEOD-45966 | biostudies-arrayexpress

Identification of the PhoB regulon and role of PhoU in the phosphate-starvation response of Caulobacter crescentus (expression)

Project description:An ability to sense and respond to changes in extracellular phosphate is critical to the survival of most bacteria. For Caulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria, Caulobacter responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here, we use ChIP-Seq to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB in both phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes in phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help Caulobacter scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in Caulobacter as depleting PhoU has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit a striking accumulation of large polyphosphate granules suggesting that PhoU participates in controlling intracellular phosphate metabolism. RNA was collected from cultures grown to mid-exponential phase in rich medium (PYE) at 30 degrees C. The strain grown in the presence of 50 mM vanillate was compared to the same strain grown in the absence of vanillate.

2016-08-06 | E-GEOD-71857 | biostudies-arrayexpress

The novel transcription factor, POPEYE, regulates response to iron deficiency in Arabidopsis roots

Project description:ChIP-chip analysis was used to identify direct targets of the transcription factor POPEYE (PYE) ChIP was performed on ProPYE:PYE:GFP plants and on wt plants as a control. The two samples were amplified and hybridized on Agilent arrays. Dye swap was performed for two biological replicates.

2010-11-22 | E-GEOD-21625 | biostudies-arrayexpress

Rhythmic diel pattern of gene expression in maize

Project description:Here we studied the leaf transcriptome in maize, throughout a cycle of 10 h darkness and 14 h light to look for rhythmic patterns of gene expression.

2011-08-19 | E-MEXP-3212 | biostudies-arrayexpress

The coding and noncoding architecture of the Caulobacter crescentus genome

Project description:Caulobacter crescentus undergoes an asymmetric cell division controlled by a genetic circuit that cycles in space and time. We provide a universal strategy for defining the coding potential of bacterial genomes by applying ribosome profiling, RNA-seq, global 5’-RACE, and liquid chromatography coupled with tandem mass spectrometry (LC-MS) data to the 4-megabase C. crescentus genome. We mapped transcript units at single base-pair resolution using RNA-seq together with global 5’ RACE. Additionally, using ribosome profiling and LC-MS, we mapped translation start sites and coding regions with near complete coverage. We found most start codons lacked corresponding Shine-Dalgarno sites although ribosomes were observed to pause at internal Shine-Dalgarno sites within the ORF. These data suggest a more prevalent use of the Shine-Dalgarno sequence for ribosome pausing rather than translation initiation in C. crescentus. Overall 19% of the transcribed and translated genomic elements were newly identified or significantly improved by this approach providing a valuable genomic resource to elucidate the complete C. crescentus genetic circuitry that controls asymmetric cell division. Ribosome profiling and RNA-seq data were collected in Caulobacter crescentus NA1000 cells grown in M2G and PYE media to map transcript and ORF features in the genome.

2014-05-29 | E-GEOD-54883 | biostudies-arrayexpress

Measuring transcriptional differences between Caulobacter crescentus cultured in nitrate versus ammonium as the sole nitrogen source

Project description:This study is measuring the steady-state levels of mRNA in wild-type Caulobacter crescentus grown in M2 defined medium containing either ammonium or nitrate as the sole nitrogen source. Four independent cultures of Caulobacter crecentus were grown in each of two medium conditions: M2(nitrate)glucose and M2(ammonium)glucose. Cultures in each medium type were grown to OD660=0.3 and RNA was isolated from each.

2010-06-20 | E-GEOD-21203 | biostudies-arrayexpress

Transcript profiling of the wild type Arabidopsis grown under different photoperiods

Project description:Arabidopsis rosette leaves were harvested from plants grown under different photoperiods under 100 M-5mol photons m-2 s-1 at 20 M-0C. In the first experiment plants grown under short day conditions 8L/16D (8 h light / 16 h dark) for 4 weeks were compared with plants grown under long day (16L/8D) for 3 weeks. In the second experiment plants grown under 12L/12D for 2 weeks were compared with plants grown first 2 weeks under 12L/12D and then two days under short day (8L/16D) conditions.

2012-07-27 | E-MEXP-3331 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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