Ontology highlight
ABSTRACT:
PROVIDER: PRJNA912389 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Integrons are genetic platforms that acquire new genes encoded in integron cassettes (ICs), building arrays of adaptive functions for bacteria. ICs generally encode promoterless genes, whose expression relies on the PC promoter within the integron platform. Cassette arrays are assumed to be operon-like structures in which expression is dependent on the distance to the Pc. This is especially relevant in large sedentary chromosomal integrons (SCIs,) like the ones in Vibrio species. We have identified 29 gene-less cassettes in 4 Vibrio SCIs, and explored whether their function could be related to regulating the transcription of adjacent ICs. We show that most gene-less cassettes have promoter activity on the sense strand, enhancing the expression of downstream cassettes. Accordingly, we found that most of the superintegron in Vibrio cholerae is not silent. These promoter cassettes can trigger the expression of a silent dfrB9 resistance cassette downstream, increasing trimethoprim resistance >512-fold in V. cholerae and Escherichia coli. Additionally, one cassette had an antisense promoter capable of reducing trimethoprim resistance through transcriptional interference. Our findings highlight the regulatory role of gene-less cassettes in the expression of adjacent cassettes, emphasizing their significance in large SCIs and their clinical importance if captured by mobile integrons.
2023-04-17 | GSE229776 | GEO
Project description:Integrons are genetic elements that enable bacterial adaptation by collecting new genes encoded in integron cassettes (ICs) to create a reservoir of adaptive functions. These cassettes typically lack their own promoters and rely on the integron platform for their expression. Integrons, well-known for spreading antibiotic resistance genes in clinically relevant Gram-negative species, include Mobile Integrons (MIs), that transport over 170 resistance genes. In contrast, Sedentary Chromosomal Integrons (SCIs), ubiquitous in Vibrio species, are primarily found within bacterial chromosomes. However, their functions are not related to antimicrobial resistance and are largely unexplored. SCIs, typified by the Superintegron (SI) in Vibrio cholerae, represent ancient and highly variable regions in bacterial genomes. The SI is extensive, housing 179 integron cassettes, mostly with unknown functions. Although 19 cassettes encode toxin-antitoxin (TA) systems, which stabilize the array, the intricacies of the SI are challenging to study due to its size and unique integrase. To investigate the SI's impact on V. cholerae, we developed the SeqDelTA approach, enabling the gradual deletion of the SI. This deletion facilitates the use of standard genetic tools without SI interference. Our in-depth analysis of the resulting ∆SI strain, covering various aspects, demonstrated no significant alterations in V. cholerae's physiology. Despite their extended coevolution, SCIs appear to be genetically isolated from the host genome.
2023-11-23 | GSE247496 | GEO
Project description:The toxin–antitoxin cassettes as selecting forces ensuring accumulation and maintenance of cassette functions in chromosomal integrons
| PRJEB62193 | ENA
Project description:We evaluated the possible mechanisms by which exposures to pulp and paper mill effluents gene expression in the fathead minnow hypothalamus Keywords: Toxicology Sexually mature fathead minnows were exposed to 100% pulp and paper mill effluents for 5 days. Tanks contained 4 females and 2 males. A total 4 tanks per effluents were used in this experiment. TM5, TM6, and KM4 represent different pulp and paper mill effluents from different mills coded for by FPInnovations-Paprican.
2010-07-07 | E-GEOD-17130 | biostudies-arrayexpress
Project description:This study investigates lipotoxic stress responses induced by postoperative pancreatic fistula (CR-POPF) effluents in non-malignant stromal cell types relevant for anastomotic healing. Postoperative drain effluents from patients undergoing pancreatoduodenectomy were characterized by gas chromatography–mass spectrometry to identify lipolysis-derived lipid species. Based on functional cytotoxicity screening, two CR-POPF effluents with reproducible biological effects were selected for transcriptomic profiling. Primary human peritoneal mesothelial cell preparations and human foreskin fibroblasts were exposed in vitro to patient-derived effluents, a defined lipolysis-derived lipid (monopalmitin), or medium control. RNA sequencing was performed to characterize stimulus-specific transcriptional stress responses. The dataset enables comparative analysis of metabolic, inflammatory, and stress-associated gene expression programs induced by distinct lipolytic stimuli in stromal and mesothelial cells.
2026-07-29 | GSE319229 | GEO