Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

σF regulon

ABSTRACT: The Alphaproteobacterium Caulobacter crescentus inhabits low-nutrient environments and can tolerate certain levels of heavy metal in these sites. It has been reported that C. crescentus responds to chromium exposure by altering expression of a large number of genes. In this work, we showed that the ECF sigma factor SigF is one of the regulatory proteins involved in the control of this transcriptional response. Microarray experiments from cells under dichromate stress showed that SigF controls a small regulon consisting of seven genes. Promoter analyses revealed that a conserved SigF-dependent sequence is located upstream of all but one gene of this regulon. Surprisingly, sigF itself was not found to be strongly auto-regulated under dichromate exposure. Furthermore, we showed that the second gene (CC3252) in the sigF operon acts as a negative regulator of SigF function, as overexpression of this putative membrane protein abolishes the transcriptional activation of sigF and its regulon under dichromate stress. Additionally, we found that substitution of one or both the conserved cysteines in the protein encoded by CC3252 (C131 and C181) affects the ability of this protein in maintaining expression of SigF-dependent genes at basal levels. Interestingly, we showed that the activation of SigF is not caused by reactive oxygen species generated as a consequence of dichromate exposure. Therefore, dichromate most probably may lead to conformational changes in the putative anti-sigma factor CC3252, releasing SigF to bind RNA polymerase core and drive transcription of its regulon. Three replicates perfomed with independent biological samples

ORGANISM(S): Caulobacter crescentus NA1000

SUBMITTER: Christian Kohler

PROVIDER: E-GEOD-32406 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

σF regulon

Project description:The Alphaproteobacterium Caulobacter crescentus inhabits low-nutrient environments and can tolerate certain levels of heavy metal in these sites. It has been reported that C. crescentus responds to chromium exposure by altering expression of a large number of genes. In this work, we showed that the ECF sigma factor SigF is one of the regulatory proteins involved in the control of this transcriptional response. Microarray experiments from cells under dichromate stress showed that SigF controls a small regulon consisting of seven genes. Promoter analyses revealed that a conserved SigF-dependent sequence is located upstream of all but one gene of this regulon. Surprisingly, sigF itself was not found to be strongly auto-regulated under dichromate exposure. Furthermore, we showed that the second gene (CC3252) in the sigF operon acts as a negative regulator of SigF function, as overexpression of this putative membrane protein abolishes the transcriptional activation of sigF and its regulon under dichromate stress. Additionally, we found that substitution of one or both the conserved cysteines in the protein encoded by CC3252 (C131 and C181) affects the ability of this protein in maintaining expression of SigF-dependent genes at basal levels. Interestingly, we showed that the activation of SigF is not caused by reactive oxygen species generated as a consequence of dichromate exposure. Therefore, dichromate most probably may lead to conformational changes in the putative anti-sigma factor CC3252, releasing SigF to bind RNA polymerase core and drive transcription of its regulon.

2012-10-02 | GSE32406 | GEO

2-Methylcitrate cycle: a well-regulated controller in Bacillus sporulation

Project description:To understand which gene(s) are affected by 2-methylcitrate to lead to the delayed sporulation in ∆prpD, we extracted the total RNA from BMB171 and ∆prpD at 12 h for whole genome transcription analysis by RNA sequencing (RNA-Seq). Our RNA-seq data showed that transcriptions of almost all of the SigF regulon genes, as concluded from the B. subtilis regulon, were significantly down-regulated in ∆prpD compared with the wild type BMB171. However, almost all the regulon genes of SigH, a sigma factor that functions upstream of SigF, were significantly up-regulated in ∆prpD. Those genes included spo0A, the early-expressed operon spoIIA and sigF itself. These results indicated that dysregulation of genes occurred on various levels. In particular, though, post-transcriptional inhibition of sigF functionality might subsequently lead to down-regulation of SigF regulon genes in the ∆prpD mutant.

2019-11-14 | GSE140317 | GEO

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

Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis

Project description:This SuperSeries is composed of the following subset Series: GSE34919: Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (ChIP-chip) GSE34922: Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (Expression) Refer to individual Series

2012-01-20 | E-GEOD-35080 | biostudies-arrayexpress

PhyK, PhyR, σT and σU regulons

Project description:The extracytoplasmic function sigma factor σT is the master regulator of general stress response in Caulobacter crescentus, and controls the expression of its paralogue σU. This work showed that PhyR and NepR act as positive and negative regulators, respectively, of σT expression and function. Biochemical data also indicated that NepR directly binds σT and the phosphorylated form of PhyR. We also demonstrated the essential role of the histidine kinase gene CC3474, here denominated phyK, for expression of σT-dependent genes and for resistance to stress conditions. Additionally, in vivo evidence of PhyK-dependent phosphorylation of PhyR is presented. This study also identified a conserved cysteine residue (C95) present in the periplasmic portion of PhyK that is crucial for the function of the protein. Furthermore, we showed that PhyK, PhyR and σT regulate the same set of genes and that σT is apparently responsible for the direct control of its complete regulon. In contrast, σU seems to have a very modest contribution for expression of a subset of σT-dependent genes. In conclusion, this work describes the mechanism involved in the control of general stress response in C. crescentus. Five experimetal procedures, each of them performed in three replicates. A total of fifteen independent biological samples were used

2011-12-21 | E-GEOD-26977 | biostudies-arrayexpress

Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (ChIP-chip)

Project description:The genome wide ChIP-on-chip analysis to identify the DNA binding sites for the M.tuberculosis sigma factor Rv3286c (SigF) SigF binding sites were determined by microarray analysis of anti-sigF immunoprecipitated DNA from H37Rv(ΔrsbW/sigF)::pmySigF compared to H37Rv(ΔrsbW/sigF)::pMY769 (both cultured with pristinamycin for 3 days). 4 biological replicates were performed.

2012-01-20 | E-GEOD-34919 | biostudies-arrayexpress

Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (Expression)

Project description:The genome wide transcriptome analysis to identify the M.tuberculosis sigma factor Rv3286c (SigF) dependent transcripts as well as Pristimaycin induced transcripts Pristinamycin induced transcripts were identified by comparing the cDNA extracted from H37Rv::pMY769 with and without pristinamycin (3 biological replicates). SigF controlled transcripts were identified by comparing the cDNA extracted from H37Rv::pMYsigF with and without pristinamycin (4 biological replicates).

2012-01-20 | E-GEOD-34922 | biostudies-arrayexpress

Comparison of the expression profiles of the 630E strain and a sigF mutant after 14h of growth

Project description:Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. A significant fraction of genes in each regulon are of unknown function and we can propose new candidates for spore coat proteins synthesized under the control of sigmaE and sigmaK among proteins previously detected in the spore proteome (Lawley et al., 2009 (PMID 19542279)). Global analysis of developmental gene expression under the control of these sigma factors indicate deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We show that the expression of the sigmaE regulon in the mother cell is not strictly under the control of sigmaF despite the fact that the forespore product SpoIIR is required for the processing of pro-sigmaE. In addition, the sigmaK regulon is not controlled by sigmaG in C. difficile in connection with the lack of pro-sigmaK processing in this bacterium. However, a control of the forespore on sigmaK targets is maintained through a sigmaF-dependent regulation of sigmaK-controlled genes, a process that bypasses sigmaG. Here, transcriptional profiling of the Clostridium difficile 630E strain vs. a sigE mutant after 14h of growth in MS is performed. Two-condition experiment: 630E strain 14h vs. sigF mutant 14h. 4 biological replicates for each condition, including dye-swaps.

2014-02-20 | E-GEOD-43199 | biostudies-arrayexpress

A comprehensive genomic, transcriptomic and proteomic analysis of a hyperosmotic stress sensitive ?-proteobacterium.

Project description:BACKGROUND: With the aim of remaining viable, bacteria must deal with changes in environmental conditions, including increases in external osmolarity. While studies concerning bacterial response to this stress condition have focused on soil, marine and enteric species, this report is about Caulobacter crescentus, a species inhabiting freshwater oligotrophic habitats. RESULTS: A genomic analysis reported in this study shows that most of the classical genes known to be involved in intracellular solute accumulation under osmotic adaptation are missing in C. crescentus. Consistent with this observation, growth assays revealed a restricted capability of the bacterium to propagate under hyperosmotic stress, and addition of the compatible solute glycine betaine did not improve bacterial resistance. A combination of transcriptomic and proteomic analyses indicated quite similar changes triggered by the presence of either salt or sucrose, including down-regulation of many housekeeping processes and up-regulation of functions related to environmental adaptation. Furthermore, a GC-MS analysis revealed some metabolites at slightly increased levels in stressed cells, but none of them corresponding to well-established compatible solutes. CONCLUSION: Despite a clear response to hyperosmotic stress, it seems that the restricted capability of C. crescentus to tolerate this unfavorable condition is probably a consequence of the inability to accumulate intracellular solutes. This finding is consistent with the ecology of the bacterium, which inhabits aquatic environments with low nutrient concentration. Three experimental procedures, each of them performed in three replicates. A total of nine independent biological samples were used

2015-04-21 | E-GEOD-49654 | biostudies-arrayexpress

Streptomyces coelicolor A3(2) strain M600 wild type transcriptome ChIP-chip with the bldC null mutant

Project description:Global regulation by the Streptomyces coelicolor atypical MerR-like transcription factor BldC. BldC is a transcriptional regulator essential for morphological development and antibiotic production in Streptomyces coelicolor. Here we identify the BldC regulon by means of chromatin immunoprecipitation (ChIP) microarray analysis. The BldC regulon encompasses at least 201 transcriptional units, which include many genes that play key roles in Streptomyces development (e.g., bldC itself, bldB, bldM, whiB, whiD, whiI, sigF, smeA-sffA, hupS), antibiotic production (e.g., afsK) and stress response (e.g., clpB, nsrR, sigE, sigF). All BldC-binding sites identified by ChIP-chip are present in the promoters of the target genes. In vitro DNA-binding experiments show that BldC is capable of binding DNA specifically in the absence of other proteins and suggest that BldC is a minor-groove DNA-binding protein. The regulon of BldC partially overlaps with that of the pleiotropic regulator BldD. BldC and BldD bind to distinct sites in the promoter region of smeA, where they simultaneously repress its transcription. ChIP-chip experiment using an anti-BldC antibody and a total DNA control. Comparison of IP in wild-type strain vs. IP in a bldC null mutant strain.

2013-01-01 | E-GEOD-28908 | biostudies-arrayexpress

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