Ontology highlight
ABSTRACT:
PROVIDER: PRJNA421081 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6354740.fastq.gz | Fastqsanger.gz | |||
| SRR6354741.fastq.gz | Fastqsanger.gz | |||
| SRR6354732.fastq.gz | Fastqsanger.gz | |||
| SRR6354742.fastq.gz | Fastqsanger.gz | |||
| SRR6354733.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
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:Class 1 integron gene cassettes in rivers in Japan
| PRJDB12624 | ENA
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:The use of biofertilizers is becoming an economical and environmentally friendly alternative to promote sustainable agriculture. Biochar from microalgae can be applied to enhance the productivity of food crops through soil improvement, slow nutrient absorption and release, increased water uptake, and long-term mitigation of greenhouse gas sequestration. Therefore, the aim of this study was to evaluate the stimulatory effects of biochar produced from Spirulina platensis biomass on the development and seed production of rice plants. Biochar was produced by slow pyrolysis at 300°C, and characterization was performed through microscopy, chemical, and structural composition analyses. Molecular and physiological analyses were performed in rice plants submitted to different biochar concentrations (0.02, 0.1, and 0.5 mg mL-1) to assess growth and productivity parameters. Morphological and physicochemical characterization revealed a heterogeneous morphology and the presence of K and Mg minerals in the biochar composition. Chemical modification of compounds post-pyrolysis and a highly porous structure with micropores were observed. Rice plants submitted to 0.5 mg mL-1 of biochar presented a decrease in root length, followed by an increase in root dry weight. The same concentration influenced seed production, with an increase of 44% in the number of seeds per plant, 17% in the percentage of full seeds per plant, 12% in the weight of 1,000 full seeds, 53% in the seed weight per plant, and 12% in grain area. Differential proteomic analyses in shoots and roots of rice plants submitted to 0.5 mg mL-1 of biochar for 20 days revealed a fine-tuning of resource allocation towards seed production. These results suggest that biochar derived from Spirulina platensis biomass can stimulate rice seed production.
2024-09-16 | PXD051225 | Pride
Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces.
2013-06-21 | GSE48198 | GEO