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The toxin–antitoxin cassettes as selecting forces ensuring accumulation and maintenance of cassette functions in chromosomal integrons

ABSTRACT: The toxin–antitoxin cassettes as selecting forces ensuring accumulation and maintenance of cassette functions in chromosomal integrons

PROVIDER: PRJEB62193 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR11475402.fastq.gz	Fastqsanger.gz
	ERR11475403.fastq.gz	Fastqsanger.gz
	ERR11475404.fastq.gz	Fastqsanger.gz
	ERR11475405.fastq.gz	Fastqsanger.gz
	ERR11475422_1.fastq.gz	Fastqsanger.gz

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Chromosomal integrons are genetically and functionally isolated units of genomes

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

Identification of promoter activity in gene-less cassettes from Vibrionaceae superintegrons

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.

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Novel gene cassettes and integrons.

Project description:An increase in multiresistant Enterobacteriaceae was observed at one of the departments of the University Medical Center Utrecht. Nine different integrons and 17 gene cassettes were found, including the new gene cassette aadA8. This cassette was highly related to aadA3 and aadA2. In addition, an unknown promoter sequence was found for two integrons.

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Project description:Integrons gene cassettes in effluents: from integrons to cassettomics

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Integrons and gene cassettes in the enterobacteriaceae.

Project description:Integrons were detected in 59 of 120 (49%) urinary isolates of Enterobacteriaceae by PCR using degenerate primers targeted to conserved regions of class 1, 2, and 3 integrase genes. PCR sequencing analysis of the cassette arrays revealed a predominance of cassettes that confer resistance to the aminoglycosides and trimethoprim.

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Detection of gene cassettes in Tn402-like class 1 integrons.

Project description: Not available

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Belt and braces: two escape ways to maintain the cassette reservoir of large chromosomal integrons

Project description:Belt and braces: two escape ways to maintain the cassette reservoir of large chromosomal integrons

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Project description:Our study found that insertion of commonly used selection cassettes in yeast can drive aberrant transcription events and disrupt expression of neighboring genes. We performed ribosome profiling and mRNA-seq on yeast strains where ORFs had been replaced with common selection cassettes and observed aberrant transcripts. Aberrant transcripts positioned near adjacent genomic loci repressed protein synthesis of those genes by transcription interference (ablating normal length transcript production) coincident with translation of competitive uORFs on the long transcript which prevented translation of the main ORF seen by ribosome profiling.

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Project description:BackgroundGene discovery algorithms typically examine sequence data for low level patterns. A novel method to computationally discover higher order DNA structures is presented, using a context sensitive grammar. The algorithm was applied to the discovery of gene cassettes associated with integrons. The discovery and annotation of antibiotic resistance genes in such cassettes is essential for effective monitoring of antibiotic resistance patterns and formulation of public health antibiotic prescription policies.ResultsWe discovered two new putative gene cassettes using the method, from 276 integron features and 978 GenBank sequences. The system achieved kappa = 0.972 annotation agreement with an expert gold standard of 300 sequences. In rediscovery experiments, we deleted 789,196 cassette instances over 2030 experiments and correctly relabelled 85.6% (alpha > or = 95%, E < or = 1%, mean sensitivity = 0.86, specificity = 1, F-score = 0.93), with no false positives.Error analysis demonstrated that for 72,338 missed deletions, two adjacent deleted cassettes were labeled as a single cassette, increasing performance to 94.8% (mean sensitivity = 0.92, specificity = 1, F-score = 0.96).ConclusionUsing grammars we were able to represent heuristic background knowledge about large and complex structures in DNA. Importantly, we were also able to use the context embedded in the model to discover new putative antibiotic resistance gene cassettes. The method is complementary to existing automatic annotation systems which operate at the sequence level.

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