GcrA depletion study (Caulobacter vibrioides)
Ontology highlight
ABSTRACT:
ORGANISM(S): Caulobacter vibrioides
PROVIDER: GSE1135 | GEO | 2004/03/23
SECONDARY ACCESSION(S): PRJNA87253
REPOSITORIES: GEO
Similar Datasets
Project description:Supporting data for: Holtzendorff et. al., "Oscillating global regulators." Keywords = gcrA Keywords = global regulator
2004-03-22 | E-GEOD-1135 | biostudies-arrayexpress
Project description:ChIP-seq analysis of GcrA atypical transcription factor in Brucella abortus
2019-09-03 | GSE136733 | GEO
Project description:Transcriptional rewiring is the regulation of different targets genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. These regulators are well-conserved across Alphaproteobacteria, but the extent to which their regulatory targets are conserved is not known. In this study, the regulatory targets of GcrA and CcrM were analyzed by SMRT-seq, RNA-seq, and ChIP-seq technologies in the Alphaproteobacterium Brevundimonas subvibrioides, and then compared to those of its close relative C. crescentus that inhabits the same environment. Although the regulators themselves are highly conserved, the genes they regulate are vastly different. GcrA directly regulates 204 genes in C. crescentus, and though B. subvibrioides has orthologs to 147 of those genes, only 48 genes retained GcrA binding in their promoter regions. Additionally, only 12 of those 48 genes demonstrated significant transcriptional change in a gcrA mutant, suggesting extensive transcriptional rewiring between these organisms. Similarly, out of hundreds of genes CcrM regulates in each of these organisms, only 2 genes were found in common. When multiple Alphaproteobacterial genomes were analyzed bioinformatically for potential GcrA regulatory targets, the regulation of genes involved in DNA replication and cell division was well conserved across the Caulobacterales but not outside this order. This work suggests that significant transcriptional rewiring can occur in cell cycle regulatory systems even over short evolutionary distances.
2020-02-01 | GSE138845 | GEO
Project description:Transcriptional rewiring is the regulation of different targets genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. These regulators are well-conserved across Alphaproteobacteria, but the extent to which their regulatory targets are conserved is not known. In this study, the regulatory targets of GcrA and CcrM were analyzed by SMRT-seq, RNA-seq, and ChIP-seq technologies in the Alphaproteobacterium Brevundimonas subvibrioides, and then compared to those of its close relative C. crescentus that inhabits the same environment. Although the regulators themselves are highly conserved, the genes they regulate are vastly different. GcrA directly regulates 204 genes in C. crescentus, and though B. subvibrioides has orthologs to 147 of those genes, only 48 genes retained GcrA binding in their promoter regions. Additionally, only 12 of those 48 genes demonstrated significant transcriptional change in a gcrA mutant, suggesting extensive transcriptional rewiring between these organisms. Similarly, out of hundreds of genes CcrM regulates in each of these organisms, only 2 genes were found in common. When multiple Alphaproteobacterial genomes were analyzed bioinformatically for potential GcrA regulatory targets, the regulation of genes involved in DNA replication and cell division was well conserved across the Caulobacterales but not outside this order. This work suggests that significant transcriptional rewiring can occur in cell cycle regulatory systems even over short evolutionary distances.
2020-02-01 | GSE138844 | GEO
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
Project description:GcrA depletion study (Caulobacter vibrioides)
| PRJNA87253 | ENA
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 σ70-dependent promoters in vivo, but activates transcription primarily at promoters harboring certain DNA methylation sites. Whereas most transcription factors that contact σ70 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.
2015-11-10 | GSE73925 | GEO
Project description: Not available
| S-EPMC5887438 | biostudies-literature
Project description:GcrA binding pattern to Brucella abortus genome
| PRJNA563352 | ENA
Project description:The Caulobacter cell cycle includes in an asymmetric cell division that is driven by a core regulatory circuit comprised of 4 transcription factors (DnaA, GcrA, CtrA, and SciP) and a DNA methyltransferase (CcrM). Using a modified global 5M-bM-^@M-^Y RACE protocol we mapped 2,726 transcriptional start sites (TSS) in the 4mb Caulobacter genome and identified 586 cell cycle-regulated TSS. The core cell cycle circuit directly controls about 55% of cell cycle-regulated TSS by integrating multiple regulatory inputs within at least 322 promoters, providing a large number of transcription profiles from a small number of regulatory factors. Here, we identified previously unknown features of the core cell cycle circuit, including antisense TSS within dnaA and ctrA, plus newly identified TSS for ctrA and ccrM. Altogether, we identified 615 antisense TSS plus 241 genes that are transcribed from multiple TSS. The multiple TSS in the same promoter region often exhibit different cell cycle activation timing, These novel features of the global transcript profile add significant insight to the system architecture of the Caulobacter cell cycle regulatory circuit. Global 5' RACE was performed to map Transcription Start Sites in the Caulobacter NA1000 genome
2014-10-16 | E-GEOD-57365 | biostudies-arrayexpress