Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of small RNAs expressed in Caulobacter crescentus in response to DNA damage

ABSTRACT: RNA-based regulation of gene expression is substantially contributing to the ability of bacteria to rapidly adapt to changing environmental conditions. This study employs RNAseq to define the transcriptome of Caulobacter in response to treatment with the DNA-crosslinking agent mitomycin C. We identify a small, regulatory RNA ChvR synthesized under the control of the conserved ChvIG two-component system which represses production of a TonB-dependent receptor, ChvT, in Caulobacter crescentus. ChvR significantly reduces ChvT expression under different physiological conditions, including the response to DNA damage and growth in minimal medium. Full regulation requires the formation of two distinct base-pairs between the sRNA and its cognate mRNA target, and occurs independent of the ubiquitous RNA chaperone, Hfq.

ORGANISM(S): Caulobacter vibrioides NA1000

PROVIDER: GSE104186 | GEO | 2018/08/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-Seq analysis of Caulobacter crescentus wild-type and delta_hfq (CJW5477) strains

Project description:We report the global changes in the gene expression profile of Caulobacter crescentus in the absence of Hfq.

2017-06-21 | GSE98467 | GEO

Caulobacter crescentus starved for carbon

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

Expression analysis of Caulobacter crescentus NA1000 Plac::CCNA_00382 (ccrM) vs Caulobacter crescentus

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

Expression analysis of Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM) [DccrM] vs Caulobacter crescentus NA1000 wild type [WT]

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

Caulobacter crescentus flagellins glycopeptides analyses

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

Expression analysis of Caulobacter crescentus NA1000 bearing a CCNA_00690 (cdnL) deletion [dcdnL] vs Caulobacter crescentus NA1000 wild type [wt]

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

Expression analysis of Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM) [DccrM] vs Caulobacter crescentus NA1000 wild type [WT]

2014-01-08 | GSE52375 | GEO

Expression analysis of Caulobacter crescentus NA1000 Plac::CCNA_00382 (ccrM) vs Caulobacter crescentus

2014-01-08 | GSE52722 | GEO

Caulobacter crescentus GsrN mutants proteome analysis

Project description:In order to elucidate the global regulatory effects of the sRNA, GsrN, in Caulobacter crescentus, we submitted soluble lysates from a gsrN knockout and over-expression stain for analysis, as well as, a wild-type sample for LC-MS/MS

2018-03-26 | PXD008128 | Pride

Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus

Project description:The alpha-proteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. crescentus. Small RNAs (sRNAs) are a prominent class of regulators of bacterial gene expression, and most sRNAs characterized today engage in direct base-pairing interactions to modulate translation and/or stability of target mRNAs. In many cases, the ubiquitous RNA chaperone, Hfq, contributes to the establishment of RNA-RNA interactions. Although the deletion of the hfq gene is associated with a severe loss of fitness in C. crescentus, the RNA ligands of the chaperone have remained largely unexplored. Here we report on the identification of coding and non-coding transcripts associated with Hfq in C. crescentus, and demonstrate Hfq-dependent post-transcriptional regulation in this organism. We show that the conserved, Hfq-bound sRNA RusT is transcriptionally controlled by the conserved NtrYX two-component system and induced in response to iron starvation. By combining RusT pulse expression with whole-genome transcriptome analysis we determine 16 candidate target transcripts, more than half of which encode outer membrane transporters. We hence suggest RusT to support remodeling of the C. crescentus cell surface when iron supplies are limiting.

2023-11-16 | GSE247928 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data