Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity

ABSTRACT: Gene expression plasticity allows bacteria to adapt to diverse environments, tie their metabolism to available nutrients, and cope with stress. This is particularly relevant in a niche as dynamic and hostile as the human intestinal tract, yet transcriptional networks remain largely unknown in gut Bacteroides spp. Here, we map transcriptional units and profile their expression levels in Bacteroides thetaiotaomicron over a suite of 15 defined experimental conditions that are relevant in vivo, such as variation of temperature, pH, and oxygen tension, exposure to antibiotic stress, and growth on simple carbohydrates or on host mucin-derived glycans. Thereby, we infer stress- and carbon source-specific transcriptional regulons, including conditional expression of capsular polysaccharides and polysaccharide utilization loci, and expand the annotation of small regulatory RNAs (sRNAs) in this organism. Integrating this comprehensive expression atlas with transposon mutant fitness data, we identify conditionally important sRNAs. One example is MasB, whose inactivation led to increased bacterial tolerance of tetracyclines. Using MS2 affinity purification coupled with RNA sequencing, we predict targets of this sRNA and discuss their potential role in the context of the MasB-associated phenotype. Together, this transcriptomic compendium in combination with functional sRNA genomics—publicly available through a new iteration of the ‘Theta-Base’ web browser (www.helmholtz-hiri.de/en/datasets/bacteroides-v2)—constitutes a valuable resource for the microbiome and sRNA research communities alike.

ORGANISM(S): Bacteroides thetaiotaomicron

PROVIDER: GSE234958 | GEO | 2024/01/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Tetracycline-induced mitohormesis mediates disease tolerance against influenza

Project description:Mitohormesis defines the increase in fitness mediated by adaptive responses to a mild mitochondrial stress. Tetracyclines inhibit not only bacterial but also mitochondrial translation, thus imposing a low level of mitochondrial stress to eukaryotic cells. We show here that the mitochondrial stress response induced by 2 tetracyclins (Tet1, Tet2) improves survival and disease tolerance against lethal influenza virus (IFV) infection. Tolerance to IFV infection is associated with the induction of genes involved in lung epithelial cell and cilia function and with the down-regulation of inflammatory and immune related gene sets in the lung, liver, and kidney.

2022-09-14 | GSE174124 | GEO

Small RNAs from sweet potato upon wounding

Project description:Small RNAs (sRNAs) play important roles in plants encountering stress environments. However, limited research has been conducted on the sRNAs involved in plant wound responses. To identify potential roles for the wounding-related sRNAs, sRNA deep sequencing was used. After leaves were wounded for 0.5 hour, total RNAs from unwounded and wounded leaves were isolated for sRNA library construction. The Illumina platform was used to sequence sRNA libraries. About 12 million sequence reads were obtained for each sample.

2016-04-26 | GSE46457 | GEO

Proteome profiling of Bacillus subtilis stressed with the antibiotics tetracycline and chelocardin

Project description:Chelocardin is an atypical tetracycline and its mechanism of action is discussed controversially in literature. Therefore, we analyzed the bacterial response of Bacillus subtilis to chelocardin and as a control for classical tetracyclines to tetracycline by proteomic profiling. The induced marker proteins mirror the damage in the cell due the antibiotic stress. Proteomic profiling was carried out by 2D-PAGE and spot identification by nUPLC-ESI-MS/MS. The proteomic profile of chelocardin demonstrates a dual mechanism of action with protein biosynthesis inhibition and membrane damage.

2016-03-14 | PXD003439 | Pride

Neisseria meningitides small RNA's regulate Citric acid cycle activity under Feast and Famine conditions

Project description:We identified twin small non-coding RNAs regulating tricarboxylic acid (TCA) cycle activity in Neisseria meningitidis. Expression of TCA cycle enzymes was elevated in sRNA deletion mutants. Direct interaction between sRNAs and the ribosomal entry sites on target mRNAs was demonstrated. Expression of the sRNAs was down-regulated in cells grown in poor medium with glucose as the sole carbon source but not without lrp, indicating that sRNA expression is controlled by the stringent response. N. meningitidis, over-expressing the sRNAs replicated in blood, but not in human cerebrospinal fluid. In addition, Lrp synthesis was inhibited by direct interaction between the sRNA and the 5’ UTR of lrp. sRNAs control adaptation of N. meningitidis to variation in nutrient supply in different niches of its host.

2017-03-22 | PXD000891 | Pride

RNA sequencing of single blastocyst-stage embryos (E3.5) from zygotes which were injected with sperm sRNAs from normal or depressive male mice.

Project description:We demonstrated that sperm sRNAs contribute to paternal transmission of depression-like symptoms.To further investigated the mechanism by which sperm sRNAs contribute to depression inheritance. Since the early embryonic period represents a window of plasticity important for adult phenotypes, we injected sperm sRNAs from mice of normal(F0-Ctl) or stress induced depressive(F0-Dep)into zygotes and assessed transcriptional changes when the embryos developed to the E3.5 blastocyst stage (sRNA-Dep-E3.5 vs sRNA-Ctl-E3.5).

2020-11-06 | GSE160894 | GEO

RNase III CLASH uncovers sRNA regulatory networks coupling metabolism to production of cytolytic toxins in methicillin resistant Staphylococcus aureus

Project description:Methicillin resistant Staphylococcus aureus (MRSA) is an infectious pathogen that poses a significant threat to human health. MRSA is renowned for its ability to adapt to and even thrive in hostile environment within its host. By expressing a battery of virulence factors and toxins, MRSA is able to scavenge effectively essential nutrients and evade the immune system within the host. Post-transcriptional regulation by sRNAs contributes significantly to regulating the expression of virulence factors and toxins. However, the roles of the vast majority of sRNAs during host adaptation remain unknown. To challenge this gap, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) in S. aureus to unravel sRNA-RNA interactions with the double stranded ribonuclease III (RNase III) as a bait under conditions that mimic the host environment. Here we report a global analysis of RNA-RNA interactions in MRSA in vivo, which uncovered hundreds of novel sRNA-RNA pairs. Strikingly, our results indicate that the production of small membrane-permeabilizing toxins is under extensive sRNA-mediated regulation and that their expression is intimately connected to metabolism. We show that at least two sRNAs, RNAIII and RsaE, enhance the production of five clinically relevant cytolytic toxins that are important for survival within the host. Taken together, our data greatly expands the repertoire of sRNA-target interactions in S. aureus and provide detail on how these contribute to adjusting virulence in response to changes in metabolism.

2022-06-16 | PXD025122 | Pride

Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii

Project description:We demonstrate here the transcriptional landscape and functional roles of sRNAs specifically in the regulation of the oxidative stress response of the model haloarchaeon Haloferax volcanii. We sequenced 5 biological replicates of H. volcanii strain H53 under no challenge and oxidative stress (H2O2) conditions at mid-exponential phase (OD 0.4). Thousands of sRNAs, both intergenic and antisense, were discovered using strand-specific sRNA-seq, comprising around 30% of the transcriptome during non-challenged and oxidative stress conditions. Antisense sRNAs were found to overlap both 5’ and 3’ UTRs of mRNAs revealing a hybrid system between Eukarya (3’ UTR) and Bacteria (5’ UTR) sRNA-silencing systems, as well as targeting the coding sequence (CDS) of mRNAs, a unique system to Archaea. We identified hundreds of differentially expressed sRNAs in response to hydrogen peroxide induced oxidative stress in H. volcanii. A majority of these sRNAs are lowly expressed compared to mRNAs. The sRNAs could be classified in two populations based on expression patterns: those that are up-regulated and those that are down-regulated during oxidative stress. Targets of antisense sRNAs decreased in expression when sRNAs were up-regulated indicating that sRNAs are likely playing a negative regulatory role on mRNA targets at the transcript level. Target enrichment of sRNAs included mRNAs involved in transposons, chemotaxis signaling, peptidase activity, transcription factors, and secondary metabolite regulation.

2018-02-20 | GSE103893 | GEO

Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus

Project description:In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome anno- tation in S. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in S. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions. Four RNAseq data sets in total. Each sample was generated by pooling three independent biological replicate RNA preps

2016-01-05 | E-GEOD-74936 | biostudies-arrayexpress

RNA-seq of human melanoma cell line A375 treated with the tetracycline analogs Col-3 or doxycycline against untreated controls

Project description:Apart from their antibacterial activity, tetracyclines have demonstrated diverse and beneficial “off-target” biological activities in human disease, spurring interest in their development as non-antimicrobial therapeutics in diseases such as cancer. To better define biological pathways modified by the tetracyclines in human cancer, we sought to determine differential gene expression in the A375 cancer cell line treated with the tetracyclines, Col-3 and doxycycline, relative to control (vehicle-treated) cells. A375 cells were treated with either 10 μM Col-3, 10 μM doxycycline, or vehicle (DMSO) for 6 h, and changes to gene expression were assessed by RNA-Seq.

2018-09-01 | E-MTAB-7126 | biostudies-arrayexpress

Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum

Project description:Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within the adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress response. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 63 sRNAs were differentially expressed with 57 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST (e-value < 0.001) showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. A large number of these sRNAs is starvation-induced, suggesting their role in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens.

2016-01-26 | GSE68547 | 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