Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stationary phase stimulon and CspC regulon

ABSTRACT: The cold shock proteins belong to a family of RNA binding proteins presenting a highly conserved domain, called cold shock domain (CSD). They are involved in various cellular processes, including adaptation to low temperature, nutritional stress, cell growth and stationary phase. Here we investigate the role of CspC in C. crescentus stationary phase and the molecular mechanisms underlying gene regulation by this protein. A global transcriptional profiling experiment comparing cspC and the wild type strain both at exponential and stationary phases was carried out. The results showed that the absence of cspC affected the transcription of 20 genes at exponential phase and 65 genes at stationary phase. Genes encoding enzymes of the glyoxylate cycle were severely downregulated in the mutant at stationary phase. The stationary phase-induced RNA binding protein CspC has an important role in gene expression at this phase. It is required for the expression of the essential gene sciP, the ECF sigma factor sigU, as well as of the genes for the glyoxylate cycle enzymes and for oxidative stress response.

ORGANISM(S): Caulobacter vibrioides NA1000 Caulobacter vibrioides CB15

PROVIDER: GSE61726 | GEO | 2015/08/24

SECONDARY ACCESSION(S): PRJNA261960

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Stationary phase stimulon and CspC regulon

Project description:The cold shock proteins belong to a family of RNA binding proteins presenting a highly conserved domain, called cold shock domain (CSD). They are involved in various cellular processes, including adaptation to low temperature, nutritional stress, cell growth and stationary phase. Here we investigate the role of CspC in C. crescentus stationary phase and the molecular mechanisms underlying gene regulation by this protein. A global transcriptional profiling experiment comparing cspC and the wild type strain both at exponential and stationary phases was carried out. The results showed that the absence of cspC affected the transcription of 20 genes at exponential phase and 65 genes at stationary phase. Genes encoding enzymes of the glyoxylate cycle were severely downregulated in the mutant at stationary phase. The stationary phase-induced RNA binding protein CspC has an important role in gene expression at this phase. It is required for the expression of the essential gene sciP, the ECF sigma factor sigU, as well as of the genes for the glyoxylate cycle enzymes and for oxidative stress response. Two and three replicates were performed to determine the stationary phase stimulon and CspC regulon, respectively. Each replicate was conducted with an independent biological sample.

2015-08-24 | E-GEOD-61726 | biostudies-arrayexpress

Transcriptomic analysis of cspC deficient Acinetobacter baumannii

Project description:This study examined the response of A. baumannii to cspC disruption via transposon mutagenesis. The goal was to gain insight into how a cold shock protein highly expressed within A. baumannii biofilms, CspC, functioned and identify pathways in which it may be involved.

2021-05-12 | GSE164290 | GEO

ChIP-chip analysis of CspC binding in Salmonella enterica serovar Typhimurium strain SL1344

Project description:We performed Chromatin Immunoprecipitation (ChIP) and microarray hybridization analysis of CspC binding in Salmonella Typhimurium strain SL1344 which has been genetically engineered to express a 3xFLAG tagged CspC protein. Chromatin samples were prepared from SL1344 CspC 3xFLAG grown to exponential phase (OD600nm = 0.2). CspC FLAG ChIP and mock normal mouse IgG ChIP reactions were carried out. The purified ChIP DNA samples were hybridized to SL1344 tiling microarrays.

2015-02-26 | E-GEOD-66288 | biostudies-arrayexpress

RNA association patterns of Salmonella cold shock proteins direct discovery of essential virulence function of CspC and CspE

Project description:The functions of many bacterial RNA-binding proteins remain obscure due to a lack of knowledge of their cellular ligands. While well-studied cold-shock protein A (CspA) family members are induced and function at low temperature, other are highly expressed in infection-relevant conditions. Here, RNA ligand profiling of all CspA-family members linked CspC and CspE with Salmonella virulence pathways. Phenotypic assays in vitro demonstrated a crucial role for these proteins in membrane stress, motility, and biofilm formation. Moreover, deletion of cspC and cspE fully attenuates Salmonella in systemic mouse infection. Our results highlight RNA-binding proteins as regulators of pathogenicity and potential targets of antimicrobial therapy.

2017-06-12 | GSE91086 | GEO

Caulobacter vibrioides NA1000

Project description:Stationary phase stimulon and CspC regulon

| PRJNA261960 | ENA

MeRIP sequencing for CSPC vs CRPC samples

Project description:To investigate if there is a difference of N6-methyladenosine(m6A) modification between castration-resistant prostate cancer (CRPC) and castration-sensitive prostate cancer (CSPC), we collected 30 specimens, including 15 CRPC and 15 CSPC, to perform RNA-seq and MeRIP-seq. All specimens were postoperative tissues and each 5 CRPC or CSPC specimens were mixed into 1 sample to meet the RNA dosage of RNA-seq and MeRIP-seq.

2023-01-03 | GSE221961 | GEO

Bifidobacterium longum mutants and resistance to Heat-Shock

Project description:Transcriptional profiling of Bifidobacterium longum mutants versus wt strain in exponentional phase, with or without heat-shock treatment, and in stationary phase Keywords: Characterization of natural mutants Two B. longum mutants (NCC2912 and NCC2913) were analysed versus the wt strain NCC2705 in three conditions : exponential phase 37Â°, exponential phase with 7 min 50Â° heat shock, stationary phase. Two biologic replicates and 2 technical replicates

2010-05-17 | E-GEOD-14628 | biostudies-arrayexpress

Defining the impact of exoribonucleases in the shift between exponential and stationary phases

Project description:The transition between exponential and stationary phase is a natural phenomenon for all bacteria and requires a massive readjustment of the bacterial transcriptome. Exoribonucleases are key enzymes in the transition between the two growth phases. PNPase, RNase R and RNase II are the major degradative exoribonucleases in Escherichia coli. We analysed the whole transcriptome of exponential and stationary phases from the WT and mutants lacking these exoribonucleases (Δpnp, Δrnr, Δrnb, and ΔrnbΔrnr). When comparing the cells from exponential phase with the cells from stationary phase more than 1000 transcripts were differentially expressed, but only 491 core transcripts were common to all strains. There were some differences in the number and transcripts affected depending on the strain, suggesting that exoribonucleases influence the transition between these two growth phases differently. Interestingly, we found that the double mutant RNase II/RNase R is similar to the RNase R single mutant in exponential phase while in stationary phase it seems to be closer to the RNase II single mutant. This is the first global transcriptomic work comparing the roles of exoribonucleases in the transition between exponential and stationary phase.

2019-11-13 | GSE117635 | GEO

Transcriptomic response of Dickeya dadantii to DNA relaxation by novobiocin

Project description:We analyze the transcriptomic response of the phytopathogenic enterobacterium Dickeya dadantii to a DNA supercoiling relaxation shock using the gyrase inhibitor novobiocin. The shock was applied to Dickeya cells grown in minimal medium supplemented with sucrose, in exponential or transition to stationary phase, and in minimal medium with sucrose + PGA (a pectin derivative) in transition to stationary phase.

2019-04-16 | E-MTAB-7650 | biostudies-arrayexpress

ChIP-chip analysis of CspC binding in Salmonella enterica serovar Typhimurium strain SL1344

2015-02-26 | GSE66288 | GEO