A cryptic transcription factor regulates Caulobacter crescentus adhesion [RNA-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA832111 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18920365.fastq.gz | Fastqsanger.gz | |||
| SRR18920366.fastq.gz | Fastqsanger.gz | |||
| SRR18920367.fastq.gz | Fastqsanger.gz | |||
| SRR18920368.fastq.gz | Fastqsanger.gz | |||
| SRR18920369.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:A cryptic transcription factor regulates Caulobacter crescentus adhesion
| PRJNA832104 | ENA
Project description:A cryptic transcription factor regulates Caulobacter crescentus adhesion [ChIP-seq]
| PRJNA832112 | ENA
Project description:Alphaproteobacteria commonly produce a polar adhesin that is anchored to the exterior of the cell envelope. In Caulobacter crescentus, this adhesin enables permanent attachment to solid surfaces and is known as the holdfast. An ensemble of two-component signal transduction (TCS) proteins control C. crescentus holdfast biogenesis by indirectly regulating expression of HfiA, a potent holdfast inhibitor. We designed a genetic screen to identify regulators of hfiA that function downstream of the TCS adhesion regulatory system. This screen identified a hypothetical protein that we have named RtrC. Though the primary structure of RtrC does not match any defined sequence family, we demonstrate that RtrC directly binds and regulates dozens of sites on the C. crescentus chromosome via a pseudo-palindromic motif. Among these binding sites is the hfiA promoter where RtrC functions to repress transcription and thereby activate holdfast biogenesis. RtrC forms an OR-gated type I coherent feedforward loop with the DNA-binding response regulator SpdR and the adhesion regulator RtrB. This type of network motif is known to buffer gene expression against transient loss of regulating signals. We further demonstrate that, in addition to promoting adhesion, RtrC expression influences cell motility in soft agar. We conclude that the formerly hypothetical gene, rtrC, encodes a transcription factor that functions downstream of the C. crescentus TCS adhesion control system to regulate holdfast biogenesis and motility.
2022-04-27 | GSE201497 | GEO
Project description:Alphaproteobacteria commonly produce a polar adhesin that is anchored to the exterior of the cell envelope. In Caulobacter crescentus, this adhesin enables permanent attachment to solid surfaces and is known as the holdfast. An ensemble of two-component signal transduction (TCS) proteins control C. crescentus holdfast biogenesis by indirectly regulating expression of HfiA, a potent holdfast inhibitor. We designed a genetic screen to identify regulators of hfiA that function downstream of the TCS adhesion regulatory system. This screen identified a hypothetical protein that we have named RtrC. Though the primary structure of RtrC does not match any defined sequence family, we demonstrate that RtrC directly binds and regulates dozens of sites on the C. crescentus chromosome via a pseudo-palindromic motif. Among these binding sites is the hfiA promoter where RtrC functions to repress transcription and thereby activate holdfast biogenesis. RtrC forms an OR-gated type I coherent feedforward loop with the DNA-binding response regulator SpdR and the adhesion regulator RtrB. This type of network motif is known to buffer gene expression against transient loss of regulating signals. We further demonstrate that, in addition to promoting adhesion, RtrC expression influences cell motility in soft agar. We conclude that the formerly hypothetical gene, rtrC, encodes a transcription factor that functions downstream of the C. crescentus TCS adhesion control system to regulate holdfast biogenesis and motility.
2022-04-27 | GSE201498 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE25996: Expression data from Caulobacter crescentus starved for carbon GSE25997: Expression data from Caulobacter crescentus (syn. C. vibrioides) swarmer and stalked cells starved for carbon GSE25998: Expression data from WT, DSigT and DSigU Caulobacter crescentus (syn. C. vibrioides) starved for carbon Refer to individual Series
2011-04-20 | E-GEOD-25999 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in a Caulonacter crescentus NA1000 Plac::CCNA_00382 (ccrM) mutant, compared to the wild-type strain. The mutations engineered into this strain cause the CcrM DNA methyltransferase to be overexpressed and the chromosome to be constitutively methylated at the adenine at GANTC motifs. References of strains: CcrMOE: Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716. WT: Marks, M.E., Castro-Rojas, C.M., Teiling, C., Du, L., Kapatral, V., Walunas, T.L. and Crosson, S. (2010) The genetic basis of laboratory adaptation in Caulobacter crescentus. J Bacteriol, 192, 3678-3688; Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716. A six chip study using total RNA recovered from three separate wild-type cultures of Caulonacter crescentus NA1000 and three separate cultures of a triple mutant strain, Caulonacter crescentus NA1000 Plac::CCNA_00382 (ccrM), in which the ccrM gene coding for a DNA methyltransferase methylating the adenine in GANTC motifs is truncated and its product inactive. Each chip measures the expression level of 3933 genes from Caulobacter crescentus NA1000 with 3 probes per gene and with three-fold technical redundancy.
2014-01-08 | E-GEOD-52722 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in a Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM) mutant, compared to the wild-type strain. The mutations engineered into this strain render it incapable of methylating its genome on the adenine at GANTC motifs. References for strains : WT: Marks, M.E., Castro-Rojas, C.M., Teiling, C., Du, L., Kapatral, V., Walunas, T.L. and Crosson, S. (2010) The genetic basis of laboratory adaptation in Caulobacter crescentus. J Bacteriol, 192, 3678-3688; Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716. DccrM: Gonzalez, D. and Collier, J. (2013) DNA methylation by CcrM activates the transcription of two genes required for the division of Caulobacter crescentus. Mol Microbiol, 88, 203-218. A six chip study using total RNA recovered from three separate wild-type cultures of Caulobacter crescentus NA1000 and three separate cultures of a triple mutant strain, Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM), in which the ccrM gene coding for a DNA methyltransferase methylating the adenine in GANTC motifs is truncated and its product inactive. Each chip measures the expression level of 3933 genes from Caulobacter crescentus NA1000 with 3 probes per gene and with three-fold technical redundancy.
2014-01-08 | E-GEOD-52375 | biostudies-arrayexpress
Project description:Caulobacter crescentus is an alphaproteobacterium that divides assymetrically. Each cell cycle results in the production of a motile flagellated cell and a sessile cell called the swamer cell and the stalked cell, respectively. The flagellar filament is composed of thousands polymerized flagellins. We showed that glycosylation of flagellins is required for the assembly of the flagellum. This glycosylation is performed by soluble FlmG glycosyltransferases that transfer nonulosonic acids (pseudaminic acid or legionaminic acid) directly to the flagellins. Such glycosylation system is also present in a close relative of Caulobacter crescentus, Brevundimonas subvibrioides. The project is to identify the site of glycosylation and the potential sugar added on this site.
2023-01-13 | PXD038730 | Pride
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-04-27 | GSE201499 | GEO
Project description: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. Caulobacter crescentus cells lacking CdnL have severe morphological and growth defects. Our microarray experiment demonstrates how cdnL deletion affects the transcriptome of Caulobacter crescentus.
2019-11-05 | GSE139873 | GEO