GEO DataSets

(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) 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) 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

Download data

(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) Coordination of cell cycle progression with central metabolism is fundamental to all cell types and likely underlies differentiation into dispersal cells in bacteria. How central metabolism is monitored to regulate cell cycle functions is poorly understood. A forward genetic selection for cell cycle regulators in the polarized alpha-proteobacterium Caulobacter crescentus unearthed the uncharacterized CitA citrate synthase, a TCA (tricarboxylic acid) cycle enzyme, as unprecedented checkpoint regulator of the G1→S transition. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26862

3 Samples

Download data: TXT

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

Organism:

Caulobacter vibrioides NA1000; Sinorhizobium meliloti 2011

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL28391 GPL26862

20 Samples

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(Submitter supplied) The regulatory roles of proteins associating with DNA-dependent RNA polymerase (RNAP) during transcription elongation are poorly characterized in bacteria. A forward genetic selection for Caulobacter crescentus cell cycle mutants revealed the uncharacterized DUF1013 protein (TrcR, transcriptional cell cycle regulator). TrcR associates with promoters and coding sequences (CDSs) and tracks with active RNAP. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26862

4 Samples

Download data: XLSX

(Submitter supplied) The regulatory roles of proteins associating with DNA-dependent RNA polymerase (RNAP) during transcription elongation are poorly characterized in bacteria. A forward genetic selection for Caulobacter crescentus cell cycle mutants revealed the uncharacterized DUF1013 protein (TrcR, transcriptional cell cycle regulator). TrcR associates with promoters and coding sequences (CDSs) and tracks with active RNAP. more...

Organism:

Sinorhizobium meliloti 2011; Caulobacter vibrioides NA1000

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26862 GPL28391

16 Samples

Download data: XLSX

(Submitter supplied) We report that ancestral zinc-finger-domain transcriptional regulators, previously reported to control virulence/symbiosis, implement a cell cycle (S→G1) transcriptional switch. To unravel how this G1-phase transcriptional program is reinstated during a primitive cell cycle, we first defined G1-specific promoters in the model bacterium Caulobacter crescentus by comparative ChIP-Seq analysis. We then exploited one such promoter as genetic proxy, to identify two conserved developmental regulator paralogs, MucR1/2, that constitute a quadripartite and homeostatic regulatory module directing the switch from S→G1-phase transcription. more...

Organism:

Caulobacter vibrioides; Sinorhizobium fredii

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18006 GPL18007

11 Samples

Download data: XLS

(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) Investigation of whole genome expression changes in Magnetospririllum magneticum mutants, probing the role of the CtrA regulatory pathway. The mutants are further described in a manuscript submitted for publication at J. Bacteriology. Developmental events across the prokaryotic life cycle are highly regulated at the transcriptional and post-translational levels. Key elements of a few regulatory networks are conserved among phylogenetic groups of bacteria, although the features controlled by these conserved systems are as diverse as the organisms encoding them. more...

Organism:

Paramagnetospirillum magneticum AMB-1

Type:

Expression profiling by array

Platform:

GPL15199

16 Samples

Download data: PAIR

(Submitter supplied) Bacterial growth and division require regulated synthesis of the macromolecules used to expand and replicate components of the cell. Transcription of housekeeping genes required for metabolic homeostasis and cell proliferation is guided by the sigma factor σ70. The conserved CarD-like transcriptional regulator, CdnL, associates with promoter regions where σ70 localizes and stabilizes the open promoter complex. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18006

4 Samples

Download data: XLSX

(Submitter supplied) Investigation of whole genome gene expression level changes in a Caulobacter crescentus NA1000 dcdnL mutant, compared to the wild-type strain. In bacteria, transcription of housekeeping genes required for metabolic homeostasis and cell proliferation is guided by the sigma factor σ70. The conserved CarD-like transcriptional regulator, CdnL, associates with promoter regions where σ70 localizes and stabilizes the open promoter complex. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by array

Platform:

GPL17931

6 Samples

Download data: CALLS, PAIR