Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-sequencing of bicyclomycin treated Escherichia coli str. O157:H7 str. Sakai

ABSTRACT: Enterohaemorrhagic E. coli (EHEC) is a significant human pathogens that cause outbreaks of haemorrhagic colitis and haemolytic uremic syndrome. During infection, pathogens compete for iron with the host, and one mechanism by which EHEC obtains iron is through haem uptake and utilitisation which is encoded by the chu operon. We have demonstrated that the haem receptor chuA is regulated by the Crp-cAMP-dependent sRNA CyaR. We further demonstrate that activation of chuA by CyaR is independent of the chuA RNA-thermometer and termination by Rho. These results highlight the ability of regulatory sRNAs to integrate multiple environmental signals into a layered hierarchy of signal input.

ORGANISM(S): Escherichia coli

PROVIDER: GSE197379 | GEO | 2022/03/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Cell Surface Proteome during Enterohaemorrhagic E. coli infection

Project description:Proteins on the cell surface are crucial for the interaction of a cell with its surrounding environment. Viral infection is known to remodel to the host cell surface to the benefit of the pathogen, but relatively little is known about how bacterial pathogens alter the host cell surface. Enterohaemorrhagic E. coli(EHEC) infects the apical surface of gut epithelium, and maniplates multiple aspects of host physiology. Here we used quantitative cell surface proteomics to investigate EHEC-induced changes to the host cell surface and show that the complement regulatory protein CD55 is cleaved from epithelial surfaces by the EHEC metalloprotease StcE. As a consequence of this, neutrophil attachment to the apical surface of epithelial cells is increased. This study is the first to apply quantitaive cell surface proteomics to EHEC infection and reveals a novel mechanism by which EHEC manipulates the host immune system.

2018-09-10 | PXD010361 | Pride

Transcriptomic analysis for response of EHEC to short chain fatty acids

2008-11-01 | GSE12903 | GEO

The E. coli type III secreted effectors NleB and EspL interact with the microtubule associated protein ensconsin to disrupt vesicle trafficking, part 1

Project description:Enteropathogenic and enterohaemorrhagic E. coli (EPEC and EHEC) translocate a set of type III effector proteins into host cells that are critical for bacterial virulence. These effectors subvert normal host pathways by interacting with a variety of targets within the cell, but the binding partners and mechanism of action of the majority of effectors are not understood. We identified the microtubule associated protein, ensconsin, as a novel target for two EPEC/EHEC effectors. We found that the secreted effectors NleB and EspL bind host ensconsin and work synergistically to paralyze kinesin-based intracellular vesicular transport. Our findings demonstrate that EPEC/EHEC encode multiple effectors that control intracellular vesicle movement and suggest a simple strategy for broad-based immobilization of host cells by pathogens.

2016-12-22 | PXD002933 | Pride

Transcriptomic analysis for response of EHEC to short chain fatty acids

Project description:Enterohaemorrhagic Escherichia coli (EHEC) is an emerging pathogen that causes diarrhea and heamolytic uremic syndrome. Expression of genes associated to pathogenicity is strictly regulated by environmental factors. Since short chian fatty acids (SCFAs) are present in intestinal tract which is a target of EHEC infection, we investigated the response of EHEC genes to SCFAs, such as acetate, propionate and butyrate. Keywords: Culture condition 3 sets of comparison between transcription profiles in EHEC growing in the presence of acetate, propionate or butyrate against EHEC growing in the presence of NaCl. Labelling of cDNA and hybridization were performed twice with independently prepared RNAs.

2010-05-17 | E-GEOD-12903 | biostudies-arrayexpress

Double-kill mechanism of artemisinin against Plasmodium

Project description:The mechanism by which artemisinin and its derivatives (ARTs) kill malaria parasites remains unclear. Haem or iron activates ARTs to produce free radicals that kill malaria parasites. However, adding iron or haem supply did not enhance, but instead attenuated, the antimalarial effect of ARTs, suggesting that the free-radical effect (FRE) is not the only antimalarial mechanism of ARTs. Here, through the single-cell RNA sequencing analysis of Plasmodium yoelii 17XNL and P. falciparum 3D7 in vivo and in vitro, we found that the sensitive stages to ARTs were associated with the expression of genes related to haem and iron (HI), DNA synthesis, antioxidation and the pentose-phosphate-pathway (PPP). Furthermore, the stages included an ART-sensitive cycle crucial for DNA synthesis that encompassed the release of iron through haem degradation to the activation of the PPP by iron. Additionally, the mechanism of haemozoin formation created a unique condition for interaction between ARTs and HI. In particular, HI can attenuate the antimalarial action of ARTs, strongly suggesting the existence of a HI-use-disturbance effect that combined with FRE to confer ARTs with a double-kill antimalarial mechanism different from the effect of iron chelators.

2024-06-08 | GSE234872 | GEO

Small RNA interactome revealed through crosslinking of the degradosome

Project description:UV-crosslining of protein-RNA complexes was employed to capture sRNA-mRNA interactions occuring on the RNA degradosome protein, RNase E, in enterohaemorhaggic E. coli. Abstract from associated mansucript: In many organisms small regulatory RNAs (sRNA) play important roles in the regulation of gene expression by base-pairing to specific target mRNAs. In enterohaemorrhagic E. coli (EHEC), sRNAs are encoded by both the “core” genome and in numerous horizontally acquired pathogenicity islands. To identify functionally important sRNA-target RNA interactions we applied crosslinking and sequencing of hybrids (CLASH) to the core degradosome component RNase E in EHEC. RNase E was shown to bind to many classes of RNA, confirming the wide distribution of degradosome targets. These included several hundred sRNA-mRNA duplexes, and the distribution of non-templated oligo(A) tails indicated that the sRNA target RNase E-mediated cleavage at these interaction sites. Functional repression of target mRNAs was confirmed for the core sRNA RyhB, and the pathogenicity-associated sRNA Esr41. In the case of Esr41, three confirmed target mRNAs participate in iron accumulation and the ∆esr41 strain showed increased growth under conditions of iron limitation. We conclude that CLASH can be used to identify functional targets for bacterial sRNAs.

2017-02-14 | GSE77463 | GEO

Early termination of the Shiga toxin transcript generates a regulatory small RNA

Project description:Enterohaemorrhagic E. coli is significant human pathogen that causes disease ranging from haemorrhagic colitis to haemolytic uremic syndrome. The later can lead to potentially fatal renal failure and is caused by the release of Shiga toxins that are encoded within lambdoid bacteriophages. The toxins are encoded within the late transcript of the phage and are regulated by anti-termination of the PR’ late promoter during lytic induction of the phage. During lysogeny, the late transcript is prematurely terminated at tR’ immediately downstream of PR’, generating a short RNA that is a by-product of anti-termination regulation. We demonstrate that this short transcript binds the small RNA chaperone Hfq, and is processed into a stable 74 nt regulatory small RNA that we have termed, StxS. StxS activates expression of the general stress response sigma factor, RpoS, through direct interactions with an activating seed sequence within the 5’ UTR. StxS represses expression of Shiga toxin 1 and activation of RpoS promotes high cell density growth under nutrient limiting conditions. Many phages utilise anti-termination to regulate the lytic/lysogenic switch and our results demonstrate that short RNAs generated as a by-product of this regulation can acquire regulatory small RNA features and modulate host fitness.

2020-09-16 | GSE143631 | GEO

VS94 SAPI AI-2 Temporal study

Project description:VS94 gene expression at different time-points in SAPI medium in absence and presence of AI-2 was studied. Autoinducer-2 (AI-2) is produced by many species of bacteria, including various commensal bacteria and is involved in inter-species communication. Since, pathogens encounter AI-2 once they enter the human gastro-intestinal tract; we studied the effects of presence of AI-2 on various phenotypes associated with infection and colonization of enterohemorrhagic Escherichia coli (EHEC) namely, chemotaxis, motility and attachment to HeLa cells. AI-2 attracted EHEC when observed in agarose plug assays and also increased EHEC motility by 1.44-fold. AI-2 also increased EHEC attachment to HeLa cells by 1.6-fold; hence, suggesting that exposure to AI-2 inside the gastro-intestinal tract can play an important role in EHEC colonization. We then investigated the global effects of AI-2 on EHEC gene expression using DNA microarrays at various time-points. We found that AI-2 controls virulence gene expression and several other groups of genes (flagellar genes, iron related genes, biofilm genes etc.) associated with virulence in a time-dependent manner. Hence, through these studies we have shown that AI-2 may be a key component in EHEC infection of human gastro-intestinal tract. Keywords: Time course

2008-03-21 | GSE9388 | GEO

Esherichia coli O157:H7 F9 fimbriae recognize plant xyloglucan and elicit a response in Arabidopsis thaliana

Project description:Fresh produce are often a source of enterohaemorrhagic Escherichia coli (EHEC) outbreaks. Fimbriae are extracellular structures involved in cell-to-cell attachment and surface colonisation. F9 (fml) fimbriae have been shown to be expressed at temperatures lower than 37°C, implying a function outwith the mammalian host. As fimbriae are multimeric structures with a molecular pattern, we investigated whether F9 fimbriae could induce a transcriptional response in model plant Arabidopsis thaliana, compared to flagella (H7) and another fimbrial type (Mat3), using DNA microarrays. F9 induced the differential expression of 435 genes, including genes involved in the plant defence response.

2021-02-01 | E-MTAB-9732 | biostudies-arrayexpress

Transcriptomic analysis for Pch/ Ler regulon in enterohaemorrhagic Escherichia coli O157:H7

Project description:Enterohaemorrhagic Escherichia coli (EHEC) is an emerging pathogen that causes diarrhea and heamolytic uremic syndrome. Much of the genomic information that affects virulence is acquired via horizontal transfer. Genes necessary for attaching and effacing lesions are located in the LEE pathogenicity island. LEE gene transcription is positively regulated by Ler, which is also encoded by the LEE, and by Pch regulators, which are encoded at other loci. We identified genes whose transcription profiles were similar to those of the LEE genes, by comparing the effects of altering ler and pch transcript levels. We assigned these genes into two classes, according to their transcription profiles. Keywords: Genetic modification

2008-02-01 | GSE9752 | 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