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Using small RNA-Seq to identify differential small RNA content of bacterial outer membrane vesicles (OMVs) secreted by Pseudomonas aeruginosa in response to tobramycin exposure

ABSTRACT: Using small RNA-Seq to identify differential small RNA content of bacterial outer membrane vesicles (OMVs) secreted by Pseudomonas aeruginosa in response to tobramycin exposure

PROVIDER: PRJNA762296 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15838100.fastq.gz	Fastqsanger.gz
	SRR15838101.fastq.gz	Fastqsanger.gz
	SRR15838102.fastq.gz	Fastqsanger.gz
	SRR15838103.fastq.gz	Fastqsanger.gz
	SRR15838104.fastq.gz	Fastqsanger.gz

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Using small RNA-Seq to identify differential small RNA content of bacterial outer membrane vesicles (OMVs) secreted by Pseudomonas aeruginosa in response to tobramycin exposure

Project description:Characterization of the sRNA content of OMVs harvested from Pseudomonas aeruginosa strain PA14 LB cultue with and without tobramycin (1ug/mL)

2021-09-12 | GSE183895 | GEO

mRNA transcript distribution bias between Borrelia burgdorferi bacteria and their outer membrane vesicles

Project description:We performed comparative transcriptomic analysis of the outer membrane vesicles (OMVs) released from B. burgdorferi. We identified a total of ~1200 unique transcripts with at least one mapped read from the bacterial cell and its OMVs.

2018-06-21 | GSE114368 | GEO

Porphyromonas gingivalis outer membrane vesicles promote apoptosis via msRNA-regulated DNA methylation in periodontitis

Project description:The outer membrane vesicles (OMVs) produced by Porphyromonas gingivalis (P. gingivalis) contain a variety of bioactive molecules that may be involved in the progression of periodontitis. However, the participation of P. gingivalis OMVs in the development of periodontitis has not been elucidated. Here we isolated P. gingivalis OMVs and confirmed their participation in periodontitis both in vivo and in vitro. Microcomputed Tomography (micro-CT) and histological analysis showed that under the stimulation of P. gingivalis OMVs, the alveolar bone of rats was significantly resorbed in vivo. We found that P. gingivalis OMVs were taken up by hPDLCs (human Periodontal Ligament Cells, hPDLCs) in vitro, then subsequently resulting in apoptosis and inflammatory cytokines releasing which was accomplished by the microRNA-size small RNAs (msRNAs) sRNA45033 in the P. gingivalis OMVs. Through bioinformatics analysis and screening of target genes, Chromobox 5 (CBX5) was identified as the downstream target of screened-out small RNA s45033. Using dual-luciferase reporter assay, overexpression, and knockdown methods, s45033 was confirmed to target CBX5 to regulate hPDLCs apoptosis. In addition, Cleavage Under Targets and Tagmentation (Cut&Tag) analysis confirmed the mechanism that CBX5 regulates apoptosis through the methylation of p53 DNA. Collectively, these findings indicate that the role of P. gingivalis OMVs is immunologically relevant and related to bacterial virulence in the development of periodontitis.

2022-11-30 | GSE218606 | GEO

Haemophilus influenzae Outer membrane vesicles inhalation contributes to steroid-resistant asthma

Project description:Asthma is the most common chronic respiratory disease. Asthma that cannot be well controlled by steroid treatment is called steroid-resistant asthma. Steroid-resistant asthma accounts for only 5% of all asthma cases, but it accounts for 80% of asthma healthcare costs. Nontypeable Haemophilus influenzae (NTHi), as a Gram-negative bacterium, can release outer membrane vesicles (OMVs) and transfer biomolecules to host cells and the external environment by carrying lipopolysaccharides, proteins, peptidoglycans, outer membrane proteins, cell wall components, proteins, nucleic acids, ion metabolites, and signaling molecules. Thus, it plays a role in obtaining nutrition, stress, toxin delivery, adhesion, host immune surveillance evasion, and host immune response regulation. It becomes an essential way in bacterial pathogenesis. To further clarify whether NTHi OMVs could be inhaled to induce steroid-resistant asthma, we isolated and purified NTHi OMVs. In vivo experiments showed that NTHi OMVs could be inhaled and enter airway epithelial cells. Cosensitization with OVA induces steroid-resistant asthma in mice. Furthermore, through high-throughput sequencing, we found that the NTHi OMVs and OVA co-sensitized mice had significantly enriched inflammatory and immune-related signaling pathways, and the transcription and secretion of IL-1β were increased was the potential cause of SRA.

2023-07-18 | GSE222546 | GEO

Tobramycin Treatment of Planktonic Pseudomonas aeruginosa

Project description:As a comparison to tobramycin-treated P. aeruginosa biofilms, we investigated the response of planktonic P. aeruginosa to tobramycin by microarray. Keywords: Tobramycin Response

2008-06-10 | GSE9991 | GEO

small RNA-Seq showing transfer of bacterial outer membrane vesicle (OMV) sRNA to host airway epithelial cells

Project description:This study is the first to show transfer of regulatory bacterial sRNAs from bacterial OMVs to host cells. Demonstration of transfer of bacterial sRNA from Pseudomonas aeruginosa OMVs to host cells in two cell types. RNA isolated from PA14 OMV exposed primary human bronchial epithelial cells or CFBE41o- bronchial epithelial cells as well as unexposed control cells was analyzed by small RNA-Seq. Primary cell exposures were performed on two donors and exposures of CFBE41o- cells were done in triplicate.

2016-05-13 | E-GEOD-80421 | biostudies-arrayexpress

Identification of potential tobramycin-resistant mutagenesis of Escherichia coli strains after spaceflight

Project description:Background: This study aimed to explore potential tobramycin-resistant mutagenesis of Escherichia coli (E. coli) strains after spaceflight. Methods: A spaceflight-induced mutagenesis of multi-drug resistant E.coli strain (T1_13) on the outer space for 64 days (ST5), and a ground laboratory with the same conditions (GT5) were conducted. Both whole-genome sequencing and RNA-sequencing were performed. Results: A total of 75 SNPs and 20 InDels were found to be associated with the resistance mechanism. Compared to T1_13, 1242 genes were differentially expressed in more than 20 of 38 tobramycin-resistant E. coli isolates while not in GT5. Function annotation of these SNPs/InDels related genes and differentially expressed genes was performed. Conclusion: This study provided clues for potential tobramycin-resistant spaceflight-induced mutagenesis of E. coli.

2019-12-13 | GSE123795 | GEO

Transcriptomic remodeling of gastric cells by Helicobacter pylori Outer Membrane Vesicles

Project description:Helicobacter pylori, a bacterium that colonizes the human stomach, like all Gram-negative bacteria spontaneously shed outer membrane vesicles (OMVs). OMVs, which act as a delivery system for bacterial components, are involved in bacterial-host interactions and thus contribute to pathogenesis. In this study, to understand the gene expression changes that human gastric epithelial cells might undergo when exposed to H. pylori-OMVs, we profiled the transcriptomic changes of the MKN74 gastric cell line induced by OMVs compared to control cells and H. pylori-infected cells, using the Ion AmpliSeq™ Transcriptome Human Gene Expression Panel. The top enriched pathways in the OMVs challenge condition included amino acid-related metabolic pathways, mitogen-activated protein kinase signaling, autophagy, and ferroptosis. The cell cycle, DNA replication, and repair pathways were the top diminished pathways. The transcriptomic changes induced by OMVs were largely consistent with those of the bacteria, although often at low expression levels, suggesting that their effects will mostly reinforce those of the bacterium itself. Our data provide a valuable portrayal of the transcriptomic remodeling of gastric cells by H. pylori-OMVs, which can be further dissected regarding the underlying molecular mediators and explored to understand the pathobiology of the full-spectrum of H. pylori-mediated diseases.

2024-04-03 | GSE229512 | GEO

Proteomic analysis of outer membrane vesicles secreted by Vibrio splendidus

Project description:Proteomic analysis was carried out on the outer membrane vesicles （OMVs）of Vibrio splendidus.The results revealed the protein composition and function of OMVs.

2022-09-21 | PXD036928 |

Using small RNA-Seq to verify that 5' tRNA-fMet1 half is over-expressed in outer membrane vesicles (OMVs)

Project description:5′ tRNA-fMet1 half (5′- CGCGGGGTGGAGCAGTCTGGTAGCTCGTCGGGCTC-3′) was cloned into the arabinose-inducible expression vector pMQ70. PA14 was transformed with the tRNA-fMet1 half expression vector or empty vector via electroporation. Characterization of the sRNA content of OMVs secreted by 5' tRNA-fMet1 half over-expression clone and empty vector control clone.

2021-09-12 | GSE183897 | GEO

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