GEO DataSets

(Submitter supplied) Supporting data for Hottes et al., "DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus" The microarray component of this work monitors mRNA expression during the cell cycle of synchronized populations of Caulobacter crescentus cells. Transcription during the normal cell cycle is compared with transcription during a cell cycle where expression of dnaA, which encodes a key DNA replication initiation factor, is delayed. more...

Organism:

Caulobacter vibrioides

Type:

Expression profiling by array

Platforms:

GPL1076 GPL2748 GPL2749

83 Samples

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(Submitter supplied) Supporting data for: Holtzendorff et. al., "Oscillating global regulators." Keywords = gcrA Keywords = global regulator Keywords: repeat sample

Organism:

Caulobacter vibrioides

Type:

Expression profiling by array

Platform:

GPL1076

13 Samples

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(Submitter supplied) Progression through the Caulobacter cell cycle is driven by the master regulator CtrA, an essential two-component signaling protein that regulates the expression of nearly 100 genes. CtrA is abundant throughout the cell cycle except immediately prior to DNA replication. However, the expression of CtrA-activated genes is generally restricted to S-phase. We identify the conserved protein SciP (small CtrA inhibitory protein) and show that it accumulates during G1 where it inhibits CtrA from activating target genes. more...

Organism:

Caulobacter vibrioides CB15

Type:

Expression profiling by array

Platform:

GPL10469

4 Samples

Download data: TXT

(Submitter supplied) mutants in the stalk biogenesis and sigma-54 pathways Keywords: mutant expression patterns

Organism:

Caulobacter vibrioides

Type:

Expression profiling by array

Platform:

GPL2856

13 Samples

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(Submitter supplied) 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. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21016 GPL21015

10 Samples

Download data: WIG

(Submitter supplied) Many bacteria acquire dissemination and virulence traits in G1-phase. CtrA, an essential and conserved cell cycle transcriptional regulator identified in the dimorphic alpha-proteobacterium Caulobacter crescentus, mysteriously switches from activating promoters in late S-phase to a different set in G1-phase. We found that a core and highly conserved determinant in the DNA-binding domain (DBD) of CtrA governs this promoter switch and that it is also required for promoter reprogramming in stationary phase in response to a (p)ppGpp alarmone signal perceived by the RNA polymerase beta subunit. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26896

10 Samples

Download data: XLSX

(Submitter supplied) In the model organism Caulobacter crescentus, a network of two-component systems involving the response regulators CtrA, DivK and PleD coordinate cell cycle progression with differentiation. Active phosphorylated CtrA prevents chromosome replication in G1 cells while simultaneously regulating expression of genes required for morphogenesis and development. At the G1-S transition, phosphorylated DivK (DivK~P) and PleD (PleD~P) accumulate to indirectly inactivate CtrA, which triggers DNA replication initiation and concomitant cellular differentiation. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22063

3 Samples

Download data: XLSX

(Submitter supplied) Cell fate determination in the asymmetric bacterium Caulobacter crescentus (Caulobacter) is triggered by the localization of the developmental regulator SpmX to the old (stalked) cell pole during the G1-S transition. While SpmX is required to localize and activate the cell fate-determining kinase DivJ at the stalked pole in Caulobacter, it is also required for organelle (stalk) positioning in the cousin Asticaccaulis. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21317

5 Samples

Download data: XLSX

(Submitter supplied) We wanted to test the effect on global gene expression of depleting the essential cell cycle regulator CtrA in order to determine the genes both indirectly and directly transcriptionally regulated by CtrA Gene expression changes in S. meliloti 1,2,4 and 6 hours post CtrA depletion

Organism:

Sinorhizobium meliloti 1021; Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL18182

24 Samples

Download data: TXT

(Submitter supplied) The objective of the study was to determine the role of dnaA in regulating gene expression, and the extent to which the effects are mediated by sda and spo0A.

Organism:

Bacillus subtilis; Escherichia coli; Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by array

Platform:

GPL10707

58 Samples

Download data: GPR

(Submitter supplied) We searched for regulators of chromosome replication in the cell cycle model Caulobacter crescentus and found a novel DNA-binding protein that selectively aids both the initiation of chromosome replication and the initial steps of chromosome partitioning. We identified and purified a protein (OpaA) that binds the chromosome origin of replication (Cori) and its higher-affinity binding to mutated Cori-DNA that increases Cori-plasmid replication in vivo. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21693

6 Samples

Download data: XLS

(Submitter supplied) 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.

Organism:

Bacillus subtilis; Escherichia coli; Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by array

Platform:

GPL10707

12 Samples

Download data: GPR

(Submitter supplied) Alphaproteobacteria stand out for their complex cell cycles, which are often regulated by the DivJ/PleC-DivK-DivL-CckA-ChpT-CtrA pathway. DivJ and PleC set up the polarity of the cell, thereby eventually leading to differential activation of the DNA-binding response regulator CtrA in the two nascent daughter cells. CtrA regulates replication and transcription of many genes, thereby ensuring that processes such as motility and cell division take place at the appropriate cell cycle stage. more...

Organism:

Hyphomonas neptunium

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26030

4 Samples

Download data: XLS

(Submitter supplied) Goal: We have discovered and charactherized a new Nucleoid Associated Protein in Caulobacter crescentus, that we named RedN. To determine its global binding on C.crescentus chromosome we have performed a ChIP-seq using a strain with a RedN-Venus fusion expressed at gene loci and as single copy on the chromosome.

Organism:

Caulobacter vibrioides NA1000

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18276

8 Samples

Download data: BEDGRAPH

(Submitter supplied) The bacterial cell cycle has been extensively studied under standard growth conditions. How it is modulated in response to environmental changes remains poorly understood. Here, we demonstrate that the freshwater bacterium Caulobacter crescentus blocks cell division and grows to filamentous cells in response to stress conditions affecting the cell membrane. Our data suggest that stress switches the membrane-bound cell cycle kinase CckA to its phosphatase mode, leading to the rapid dephosphorylation, inactivation and proteolysis of the master cell cycle regulator CtrA. more...

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18006

7 Samples

Download data: XLSX

(Submitter supplied) Supporting data for Chen et al., "Cytokinesis signals truncation of the PodJ polarity factor by a cell cycle-regulated protease" The microarray component of this work seeks to identify genes whose expression is controlled by the Caulobacter crescentus DivJ-PleC-DivK system. Keywords: time course, mutant/wild-type comparisons

Organism:

Caulobacter vibrioides

Type:

Expression profiling by array

Platforms:

GPL2749 GPL1076 GPL2748

39 Samples

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(Submitter supplied) CRISPR interference (CRISPRi) is a powerful new tool used in different organisms that provides a fast, specific, and reliable way to knockdown gene expression. Caulobacter crescentus is a well-studied model bacterium, and although a variety of genetic tools have been developed, it currently takes several weeks to delete or deplete individual genes, which significantly limits genetic studies. Here, we optimized a CRISPRi approach to specifically downregulate the expression of genes in C. more...

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24555

4 Samples

Download data: WIG

(Submitter supplied) In α-proteobacteria, strict regulation of cell cycle progression is necessary for the specific cellular differentiation required for adaptation to diverse environmental niches. The symbiotic lifestyle of Sinorhizobium meliloti requires a drastic cellular differentiation that includes genome amplification. To achieve polyploidy, the S. meliloti cell cycle program must be altered to uncouple DNA replication from cell division. more...

Organism:

Sinorhizobium meliloti; Sinorhizobium meliloti 1021

Type:

Expression profiling by array

Platform:

GPL18182

31 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bacillus subtilis

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL3655 GPL8889

16 Samples

Download data: GPR, XLS

(Submitter supplied) To compare the transcriptional effects of replication arrest that are dependent on YabA we compared the transcriptional profiles of yabA null and yabA+ cells after treatment with the replication inhibitor HPUra. To avoid secondary effects of replication overinitiation that the yabA-null strain exhibits, we did all experiments in oriC-null cells

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL8889

12 Samples

Download data: GPR