Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus [RNA-seq]

ABSTRACT: Despite the well-known toxicity of uranium (U) to bacteria, little is known about how cells sense and respond to U. The recent finding of a U-specific stress response in Caulobacter crescentus has provided a foundation for studying the mechanisms of U- perception in bacteria. To gain insight into this process, we used a forward genetic screen to identify the regulatory components governing expression of the urcA promoter (PurcA) that is strongly induced by U. This approach unearthed a previously uncharacterized two-component system, UzcRS, which is responsible for U-dependent activation of PurcA. UzcRS is also highly responsive to zinc and copper, revealing a broader specificity than previously thought. Using ChIP-seq, we found that UzcR binds extensively throughout the genome in a metal-dependent manner and recognizes a non-canonical DNA binding site. Coupling the genome-wide occupancy data with RNA-seq analysis revealed that UzcR is a global regulator of transcription, predominately activating genes encoding proteins that are localized to the cell envelope; these include metallopeptidases, multidrug resistant efflux (MDR) pumps, TonB-dependent receptors and many proteins of unknown function. Collectively, our data suggest that UzcRS couples detection of U, Zn and Cu with a novel extracytoplasmic stress response.

ORGANISM(S): Caulobacter vibrioides

PROVIDER: GSE87172 | GEO | 2016/12/21

SECONDARY ACCESSION(S): PRJNA343782

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus [ChIP-seq]

Project description:Despite the well-known toxicity of uranium (U) to bacteria, little is known about how cells sense and respond to U. The recent finding of a U-specific stress response in Caulobacter crescentus has provided a foundation for studying the mechanisms of U- perception in bacteria. To gain insight into this process, we used a forward genetic screen to identify the regulatory components governing expression of the urcA promoter (PurcA) that is strongly induced by U. This approach unearthed a previously uncharacterized two-component system, UzcRS, which is responsible for U-dependent activation of PurcA. UzcRS is also highly responsive to zinc and copper, revealing a broader specificity than previously thought. Using ChIP-seq, we found that UzcR binds extensively throughout the genome in a metal-dependent manner and recognizes a non-canonical DNA binding site. Coupling the genome-wide occupancy data with RNA-seq analysis revealed that UzcR is a global regulator of transcription, predominately activating genes encoding proteins that are localized to the cell envelope; these include metallopeptidases, multidrug resistant efflux (MDR) pumps, TonB-dependent receptors and many proteins of unknown function. Collectively, our data suggest that UzcRS couples detection of U, Zn and Cu with a novel extracytoplasmic stress response.

2016-12-21 | GSE87171 | GEO

Characterization of five novel Pseudomonas aeruginosa cell-surface signaling systems

2007-11-24 | GSE9657 | GEO

Transcription profiling of Pseudomonas aeruginosa overexpressing the ECF sigmas PA0149, PA2050, PA2093 and PA4896 involved in cell-surface signaling systems

Project description:Cell-surface signaling is a sophisticated regulatory mechanism used by gram-negative bacteria to sense signals from outside the cell and transmit them into the cytoplasm. This regulatory system consists of an outer membrane-localized TonB-dependent receptor (TonB-dependent transducer), a cytoplasmic membrane-localized anti-sigma factor and an extracytoplasmic function (ECF) sigma factor. By microarray analysis we have identified the regulons of four novel P. aeruginosa signaling systems. For that, the ECF sigmas PA0149, PA2050, PA2093 and PA4896 have been overexpressed in P. aeruginosa and their target gene candidates have been identified using DNA microarray. Experiment Overall Design: Five different samples are analyzed namely P. aeruginosa (pMMB67EH) (control/reference sample), P. aeruginosa (pMMB-PA4896) (overexpressing the PA4896 ECF sigma factor), P. aeruginosa (pMMB-PA0149) (overexpressing the PA0149 ECF sigma factor), P. aeruginosa (pMMB-PA2050) (overexpressing the PA2050 ECF sigma factor), and P. aeruginosa (pMMB-PA2093) (overexpressing the PA2093 ECF sigma factor). Two different replicates are included for the three first samples and one for the two last samples.

2008-06-16 | E-GEOD-9657 | biostudies-arrayexpress

Characterization of calf liver Cu,Zn-metallothionein: naturally variable Cu and Zn stoichiometries.

Project description:Cu,Zn-metallothioneins were purified from bovine calf liver in order to examine the stoichiometry of metal binding to the protein. Copper and zinc analyses were carried out by atomic absorption spectrophotometry. Consistent quantitative thiolate analyses were obtained spectrophotometrically with Ellman's reagent and amperometrically with phenylmercuric acetate. These were used to define protein concentration. A complementary method to assess the sum of the thiol and Cu(I) content of metallothionein involved titration of the reducing equivalents of the protein with ferricyanide. The stoichiometry of reaction was consistent with the oxidation of all the sulphydryl groups to disulphides and all of the bound Cu from the cuprous to the cupric oxidation state. Accordingly to these methods, total numbers of zinc plus copper ions bound to metallothionein isolated from a number of calf livers centred on about 7, 10-12, or 15 g-atoms of metal per mol of protein. The reactivity of ferricyanide and 4,7-phenylsulphonyl-2,9-dimethyl-1, 10-phenanthroline (BCS) with Cu,Zn-metallothioneins of various metal ratios was assessed. Zinc metallothionein reacted almost entirely in two slow steps with ferricyanide. As the Cu content of the protein increased, the fraction of reaction occurring in the time of mixing increased in parallel. BCS was able to remove 70-80% of metallothionein-bound Cu as Cu(I). The rest was resistant to reaction.

| S-EPMC1217500 | biostudies-other

Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive.

Project description:Amyotrophic lateral sclerosis has been linked to the gain of aberrant function of superoxide dismutase, Cu,Zn-SOD1 upon protein misfolding. The mechanism of SOD1 misfolding is thought to involve mutations leading to the loss of Zn, followed by protein unfolding and aggregation. We show that the removal of Zn from SOD1 may not lead to an immediate unfolding but immediately deactivates the enzyme through a combination of subtle structural and electronic effects. Using quantum mechanics/discrete molecular dynamics, we showed that both Zn-less wild-type (WT)-SOD1 and its D124N mutant that does not bind Zn have at least metastable folded states. In those states, the reduction potential of Cu increases, leading to the presence of detectable amounts of Cu(I) instead of Cu(II) in the active site, as confirmed experimentally. The Cu(I) protein cannot participate in the catalytic Cu(I)-Cu(II) cycle. However, even without the full reduction to Cu(I), the Cu site in the Zn-less variants of SOD1 is shown to be catalytically incompetent: unable to bind superoxide in a way comparable to the WT-SOD1. The changes are more radical and different in the D124N Zn-less mutant than in the Zn-less WT-SOD1, suggesting D124N being perhaps not the most adequate model for Zn-less SOD1. Overall, Zn in SOD1 appears to be influencing the Cu site directly by adjusting its reduction potential and geometry. Thus, the role of Zn in SOD1 is not just structural, as was previously thought; it is a vital part of the catalytic machinery.

| S-EPMC4258539 | biostudies-literature

A novel extracytoplasmic function (ECF) sigma factor regulates virulence in Pseudomonas aeruginosa

Project description:Next to the two-component and quorum sensing systems, cell-surface signaling (CSS) has been recently identified as an important regulatory system in Pseudomonas aeruginosa. CSS senses signals from outside the cell and transmits them into the cytoplasm. It consists of a TonB-dependent outer membrane receptor, a cytoplasmic membrane-localized sigma factor regulator (or anti-sigma factor), and an extracytoplasmic function (ECF) sigma factor. Upon perception of the extracellular signal by the receptor the ECF sigma factor is activated and promotes the transcription of a specific set of gene(s). Although most P. aeruginosa ECF sigma factors are involved in the regulation of iron uptake, we have identified a novel ECF sigma factor (PA0675) involved in the regulation of virulence. By microarray analysis of cells overexpressing PA0675 from the pMUM3 plasmid we have identified the genes regulated by this sigma factor.

2009-04-21 | GSE15697 | GEO

A novel extracytoplasmic function (ECF) sigma factor regulates virulence in Pseudomonas aeruginosa

2009-04-21 | E-GEOD-15697 | biostudies-arrayexpress

A mutagenic screen identifies a TonB-dependent receptor required for the lanthanide metal switch in the Type I methanotroph “Methylotuvimicrobium buryatense” 5GB1C

Project description:Several of the metabolic enzymes in methanotrophic bacteria rely on metals for both their expression and their catalysis. The MxaFI methanol dehydrogenase enzyme complex uses calcium as a cofactor to oxidize methanol, while the alternative methanol dehydrogenase XoxF uses lanthanide metals such as lanthanum and cerium for the same function. Lanthanide metals, abundant in the earth’s crust and widely used in electronic devices, strongly repress the transcription of mxaF yet activate the transcription of xoxF. This phenomenon of mxaF repression and xoxF activation in the presence of lanthanides is called the “lanthanide switch.” To better understand components of the lanthanide switch in the Type I gammaproteobacterial methanotroph “Methylotuvimicrobium buryatense” 5GB1C, we designed a mutagenesis system and selected for mutants unable to repress the mxaF promoter in the presence of lanthanum. Whole genome resequencing for multiple lanthanide switch mutants identified several unique point mutations in a single gene encoding a TonB-dependent receptor, which we have named LanA. While the LanA TonB-dependent receptor is absolutely required for the lanthanide switch, it does not affect lanthanum uptake by the bacterium. Deletion of a separate lanthanide-repressible gene encoding a TonB protein had no effect on the lanthanide switch or on lanthanum uptake. The discovery of this novel component of the lanthanide regulatory system highlights the complexity of this circuit and suggests further components are likely involved.

2019-05-21 | GSE125909 | GEO

Embryonic brass: pseudo two electron Cu/Zn clusters.

Project description:The isoelectronic M7 clusters [Cu3Zn4](Cp*)5 (1) and {[Cu2Zn5](Cp*)5}+ (2) are described. While 1 can be isolated only as a minor side product from the reaction of Cu(CH3CO2) with equimolar amounts of [Zn2Cp*2] with the trigonal cluster [CuZn2](Cp*)3 as the major product, 2 is available in acceptable yields from the reaction of [CuZn2](Cp*)3 with the Cp*Zn2-transfer-reagent [Cp*Zn2(Et2O)3][BAr4 F]. The trigonal bipyramidal Cu/Zn-clusters exhibit exceptional bonding situations: with formally only one skeleton electron pair they can be regarded as highly electron deficient. However, a detailed DFT analysis reveals that the cluster bonding is supported by 3d orbital contributions of the trigonal metal base unit. The data contribute to the development of an advanced tool-box for synthesis of Hume-Rothery intermetallic (e.g. brass) inspired clusters.

| S-EPMC6301272 | biostudies-literature

Preparation of reduced bovine Cu,Zn superoxide dismutase.

Project description:N.m.r. and e.p.r. were used to measure the oxidation state of copper in Cu,Zn superoxide dismutase treated with reducing agents such as NaBH4, K4Fe(CN)6, Na2S2O4 and H2O2. The activity and the electrophoretic pattern of the treated enzyme were also studied. On the basis of the reducing ability and of the absence of inactivating effects, NaBH4 was the most suitable reducer of those tested. Some characteristics of the reduction of superoxide dismutase by NaBH4 were further investigated. The results obtained indicate that NaBH4 can be used to prepare, in a few minutes, solutions of completely reduced enzyme without any apparent change of the activity and of the structure.

| S-EPMC1145153 | biostudies-other

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