Developmental switch within the bacterial cell cycle regulator CtrA
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ABSTRACT:
PROVIDER: PRJNA553466 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9659280.fastq.gz | Fastqsanger.gz | |||
| SRR9659281.fastq.gz | Fastqsanger.gz | |||
| SRR9659282.fastq.gz | Fastqsanger.gz | |||
| SRR9659283.fastq.gz | Fastqsanger.gz | |||
| SRR9659284.fastq.gz | Fastqsanger.gz |
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Project description: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. A simple side chain modification in one critical residue of this DBD confers opposing developmental phenotypes and transcriptional activities. This region is also central to understanding the developmental reprogramming in the obligate intracellular Rickettsiae where replicative cells develop into dispersal cells and a naturally occurring polymorphism in the rickettsial DBD resembles a mutation that drives CtrA towards activation of the dispersal (G1-phase) program in Caulobacter.
2019-11-25 | GSE134017 | GEO
Project description: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. In this work, we probe the role of the CtrA regulatory network, conserved throughout the Alphaproteobacteria, in the magnetotactic bacterium, Magnetospirillum magneticum strain AMB-1, which possesses unique intracellular organization and compartmentalization. While we show that CtrA in AMB-1 is not essential for viability, it is required for motility, and its putative phosphorylation state dictates the ability of CtrA to activate the flagella biosynthesis gene cascade. Gene expression analysis of strains expressing active and inactive CtrA alleles point to the composition of the extended CtrA regulon, including both direct and indirect targets. These results, combined with a bioinformatic study of the AMB-1 genome, enabled the prediction of an AMB-1 specific CtrA binding site. Further, phylogenetic studies comparing CtrA sequences from Alphaproteobacteria in which the role of CtrA has been experimentally examined reveals an ancestral role of CtrA in the regulation of motility and suggests that its essential functions in other Alphaproteobacteria were acquired subsequently. Total RNA was recovered from each of the wild-type and mutant strains, reverse transcribed to cDNA, fluorescently labeled, and hybridized to whole genome microarrays. The arrays contain 7 probes/gene, with the entire genome duplicated twice. In addition, the arrays contain 7 probes for 22 unannotated ORFs and tiling of a genomic region from coordinates 977403-1097027.
2012-02-17 | E-GEOD-35625 | biostudies-arrayexpress
Project description: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 Log-phase S. meliloti cultures carrying an IPTG-inducible allele of CtrA were split and transferred to growth media lacking IPTG (depletion) and with 1mM IPTG (control). Samples for RNA extraction were taken 1,2,4, and 6 hours after the start of the depletion experiment to monitor gene expression changes in the population after different periods of CtrA depletion.
2015-04-24 | E-GEOD-68218 | biostudies-arrayexpress
Project description: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
2015-04-24 | GSE68218 | GEO
Project description: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, first activates promoters in late S-phase and then mysteriously switches to different target promoters in G1-phase. We uncovered a highly conserved determinant in the DNA-binding domain (DBD) of CtrA uncoupling this promoter switch. We also show that it reprograms CtrA occupancy in stationary cells inducing a (p)ppGpp alarmone signal perceived by the RNA polymerase beta subunit. A simple side chain modification in a critical residue within the core DBD imposes opposing developmental phenotypes and transcriptional activities of CtrA and a proximal residue can direct CtrA towards activation of the dispersal (G1-phase) program. Hence, we propose that this conserved determinant in the CtrA primary structure dictates promoter reprogramming during the growth transition in other alpha-proteobacteria that differentiate from replicative cells into dispersal cells.
| S-EPMC6847485 | biostudies-literature
Project description: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. The cell cycle of the stalked budding alphaproteobacterium Hyphomonas neptunium culminates in an asymmetric cell division at the stalk-bud junction. Here, we investigate the role of the pathway from DivJ and PleC down to CtrA in this recently established model organism. Even though DivJ and PleC are localized to opposite poles, suggesting they are involved in polarity establishment inH. neptunium, DivJ, PleC and the other components of the upstream pathway (DivK and PleD) are not essential for cell cycle regulation. In contrast, the downstream part of the pathway starting from DivL is essential and involved in the regulation of important functions such as replication inhibition, cell division and motility, as shown by the identification of the (direct) regulon of CtrA. The overlap between the regulons of DivJ and PleC, DivK and CtrA is only partial, demonstrating that additional factors feeding into the pathway must be present in H. neptunium. Furthermore, unlike in other alphaproteobacteria, the regulation of CtrA throughout the cell cycle does not take place at the level of CtrA abundance in H. neptunium. All in all, the DivL-CckA-ChpT-CtrA pathway plays an essential role in the regulation of the complicated cell cycle ofH. neptunium, but several proteins feeding into CtrA remain undiscovered. The in-depth analysis of CtrA regulation in this stalked budding organism leads to hypotheses that might also hold in well-established model organisms such as Caulobacter crescentus.
2020-03-29 | GSE124953 | GEO
Project description:We show the role of CckA kinase in controlling the differential DNA binding activity of CtrA
2018-08-31 | GSE113724 | GEO
Project description: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. In this work, we probe the role of the CtrA regulatory network, conserved throughout the Alphaproteobacteria, in the magnetotactic bacterium, Magnetospirillum magneticum strain AMB-1, which possesses unique intracellular organization and compartmentalization. While we show that CtrA in AMB-1 is not essential for viability, it is required for motility, and its putative phosphorylation state dictates the ability of CtrA to activate the flagella biosynthesis gene cascade. Gene expression analysis of strains expressing active and inactive CtrA alleles point to the composition of the extended CtrA regulon, including both direct and indirect targets. These results, combined with a bioinformatic study of the AMB-1 genome, enabled the prediction of an AMB-1 specific CtrA binding site. Further, phylogenetic studies comparing CtrA sequences from Alphaproteobacteria in which the role of CtrA has been experimentally examined reveals an ancestral role of CtrA in the regulation of motility and suggests that its essential functions in other Alphaproteobacteria were acquired subsequently.
2012-02-17 | GSE35625 | GEO
Project description: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. The clearance of CtrA results in downregulation of division and morphogenesis genes and consequently a cell division block. Upon shift to non-stress conditions, cells quickly restart cell division and return to normal cell size. Our data indicate that the temporary inhibition of cell division through the regulated inactivation of CtrA constitutes a growth advantage under stress. Taken together, our work reveals a new mechanism that allows bacteria to alter their mode of proliferation in response to environmental cues by controlling the activity of a master cell cycle transcription factor. Furthermore, our results highlight the role of a bifunctional kinase in this process that integrates the cell cycle with environmental information.
2016-12-13 | GSE90030 | GEO
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 measure Transcription Start Site activity at time points of the Caulobacter NA1000 cell cycle
2014-10-16 | E-GEOD-57364 | biostudies-arrayexpress