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ONT-cappable-seq for P23-45 bacteriophage 5 min post-infection

ABSTRACT: ONT-cappable-seq for P23-45 bacteriophage 5 min post-infection

PROVIDER: PRJNA890649 | ENA |

REPOSITORIES: ENA

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ONT-cappable-seq for P23-45 bacteriophage 5 min post-infection

Project description:We performed the long-read RNA sequencing technique ONT-cappable-seq on RNA samples of T. thermophilus infected with phage P23-45 5 minutes post-infection. Using this approach, we obtained the primary transcriptome at the early infection stage and sequenced it in full-length. Based on this data, we were able to identify viral transcription start sites and termination sites and uncover distinct promoter motifs.

2023-12-12 | GSE215811 | GEO

Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages

Project description:We developed ONT-cappable-seq, a specialized long-read RNA sequencing technique that allows end-to-end sequencing of primary prokaryotic transcripts using the Nanopore sequencing platform. We applied ONT-cappable-seq to study the transcriptional landscape of Pseudomonas aeruginosa phage LUZ7, leading to a comprehensive genome-wide map of viral transcription start sites, terminators and complex operon structures that fine-regulate gene expression. At the same time, it provides new insights in the RNA biology of LUZ7 and paves the way for more in depth transcription studies that can help unveil the complex layers of phage-host interactions.

2022-06-24 | GSE196845 | GEO

Refining the transcriptional maps of Pseudomonas aeruginosa phages using ONT-cappable-seq

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Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA-polymerases encoded by P23-45 bacteriophage

Project description:By doing ChIP-seq with antibodies against two P23-45 RNA polymerases gp64 and gp96 we showed that both RNA polymerases interact with the phage genome at the early stage of infection. Gp96 interacts with pre-early P23-45 genes, while gp64 interacts with pre-early, early and some middle-stage genes.

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Refining the transcriptional maps of Pseudomonas aeruginosa phages using ONT-cappable-seq

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Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages

Project description:Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages

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T. thermophilus infected with phage P23-45

Project description:T. thermophilus infected with phage P23-45

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Pseudomonas aeruginosa strain:P23 | isolate:P23

Project description:Pseudomonas aeruginosa strain:P23 | isolate:P23 Genome sequencing

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Temporal regulation of gene expression of the Thermus thermophilus bacteriophage P23-45.

Project description:Regulation of gene expression during infection of the thermophilic bacterium Thermus thermophilus HB8 with the bacteriophage P23-45 was investigated. Macroarray analysis revealed host transcription shut-off and identified three temporal classes of phage genes; early, middle and late. Primer extension experiments revealed that the 5' ends of P23-45 early transcripts are preceded by a common sequence motif that likely defines early viral promoters. T. thermophilus HB8 RNA polymerase (RNAP) recognizes middle and late phage promoters in vitro but does not recognize early promoters. In vivo experiments revealed the presence of rifampicin-resistant RNA polymerizing activity in infected cells responsible for early transcription. The product of the P23-45 early gene 64 shows a distant sequence similarity with the largest, catalytic subunits of multisubunit RNAPs and contains the conserved metal-binding motif that is diagnostic of these proteins. We hypothesize that ORF64 encodes rifampicin-resistant phage RNAP that recognizes early phage promoters. Affinity isolation of T. thermophilus HB8 RNAP from P23-45-infected cells identified two phage-encoded proteins, gp39 and gp76, that bind the host RNAP and inhibit in vitro transcription from host promoters, but not from middle or late phage promoters, and may thus control the shift from host to viral gene expression during infection. To our knowledge, gp39 and gp76 are the first characterized bacterial RNAP-binding proteins encoded by a thermophilic phage.

| S-EPMC3018760 | biostudies-literature

Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA-polymerases encoded by P23-45 bacteriophage

Project description:Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA-polymerases encoded by P23-45 bacteriophage

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