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RNA-Seq analysis of Pseudomonas aeruginosa PAO1 cells infected with PhiKZ phage

ABSTRACT: RNA-Seq analysis of Pseudomonas aeruginosa PAO1 cells infected with PhiKZ phage

PROVIDER: PRJNA252740 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1393880.fastq.gz	Fastqsanger.gz
	SRR1393890.fastq.gz	Fastqsanger.gz
	SRR1393881.fastq.gz	Fastqsanger.gz
	SRR1393891.fastq.gz	Fastqsanger.gz
	SRR1393882.fastq.gz	Fastqsanger.gz

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Similar Datasets

RNA-Seq analysis of Pseudomonas aeruginosa PAO1 cells infected with PhiKZ phage

Project description:Pseudomonas aeruginosa bacteriophage PhiKZ is the type representative of the M-bM-^@M-^XgiantM-bM-^@M-^Y phage genus with unusually large virions and genomes. By unraveling the transcriptional map of the 280 kb genome to single-nucleotide resolution, we show that it encodes 369 genes organized in 134 operons, 20% more than originally annotated. Early transcription is initiated from 28 highly conserved AT-rich promoters distributed over the PhiKZ genome, all located on the same strand. Transcription of middle and late genes is dependent on protein synthesis and mediated by very poorly conserved middle (6) and late (16) promoters. As a result of massive PhiKZ transcription, halfway through infection only 1.5% of all mRNAs in the infected cell remain bacterial. Unique to PhiKZ is its ability to complete its infection in complete absence of bacterial RNA polymerase (RNAP) enzyme activity. Its transcription is performed by the consecutive action of two PhiKZ-encoded, non-canonical RNAPs, one of which is packed within the virion. This unique, rifampicin-resistant transcriptional machinery is conserved among giant viruses, seems to function without auxiliary factors and might have its origin preceding the split between Gram-positive and Gram-negative bacteria. Construction of transcription maps for the PhiKZ phage and analysis of differential expression of host and phage genes using RNA-Seq data from samples taken in duplicate at 0, 5, 10, 15, and 35 minutes into infection.

2014-06-14 | E-GEOD-58494 | biostudies-arrayexpress

RNA-Seq analysis of Pseudomonas aeruginosa PAO1 cells infected with PhiKZ phage

Project description:Pseudomonas aeruginosa bacteriophage PhiKZ is the type representative of the ‘giant’ phage genus with unusually large virions and genomes. By unraveling the transcriptional map of the 280 kb genome to single-nucleotide resolution, we show that it encodes 369 genes organized in 134 operons, 20% more than originally annotated. Early transcription is initiated from 28 highly conserved AT-rich promoters distributed over the PhiKZ genome, all located on the same strand. Transcription of middle and late genes is dependent on protein synthesis and mediated by very poorly conserved middle (6) and late (16) promoters. As a result of massive PhiKZ transcription, halfway through infection only 1.5% of all mRNAs in the infected cell remain bacterial. Unique to PhiKZ is its ability to complete its infection in complete absence of bacterial RNA polymerase (RNAP) enzyme activity. Its transcription is performed by the consecutive action of two PhiKZ-encoded, non-canonical RNAPs, one of which is packed within the virion. This unique, rifampicin-resistant transcriptional machinery is conserved among giant viruses, seems to function without auxiliary factors and might have its origin preceding the split between Gram-positive and Gram-negative bacteria.

2014-06-14 | GSE58494 | GEO

RNA-seq after chmA knockdown in PhiKZ-infected PAO1 cells

Project description:ChmA forms the phage nucleus in PhiKZ-infected PAO1 cells, we aimed to illuminate the effects on the transcriptome upon knockdown (KD) of ChmA translation through anti-sense-based technology. We identified phage transcripts that are affected in level upon KD of ChmA and clustering allowed to group these together that likely are expressed at a similar stage and dependency in the phage replication cycle.

2024-07-31 | GSE269401 | GEO

Proteomic analyses of Pseudomonas infected with giant phage PhiKZ

Project description:Preliminary analyses of Pseudomonas aeruginosa cells infected with phage PhiKZ and a control at 20 minutes post infection.

2018-11-21 | PXD011520 | Pride

RNA-seq after knockdown of PhiKZ genes in PhiKZ-infected Pseudomonas aeruginosa PAO1 cells

Project description:RNA-seq after knockdown of PhiKZ genes in PhiKZ-infected Pseudomonas aeruginosa PAO1 cells

| PRJNA1124112 | ENA

RNA-seq after knockdown of PhiKZ genes in PhiKZ-infected Pseudomonas aeruginosa PAO1 cells

Project description:We aimed to illuminate the effects on the transcriptome upon translation knockdown (KD) of core genes and other characterised genes or early expressed genes in PHIKZ through anti-sense-based technology. We identified phage transcripts that are affected in level upon KD and clustering allowed to group these together that likely are expressed at a similar stage and dependency in the phage replication cycle. The read coverage can point to alterations in transcripts and mode of action for several candidates that were knocked down.

2024-07-31 | GSE269911 | GEO

Grad-MS PHIKZ phage infected Pseudomonas aeruginosa PAO1 cells

Project description:Protein complexes in phage infected cells probed by MS.

2024-02-03 | PXD038771 | Pride

The repressor C protein, Pf4r, controls superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 filamentous phage and regulates host gene expression

Project description:It has been shown that the filamentous phage, Pf4, plays an important role in biofilm development, stress tolerance, genetic variant formation and virulence in Pseudomonas aeruginosa PAO1. These behaviours are linked to the appearance of superinfective phage variants. Here, we have investigated the molecular mechanism of superinfection as well as how the Pf4 phage can control host gene expression to modulate host behaviours. Pf4 exists as a prophage in PAO1 and encodes a homolog of the P2 phage repressor C. Through a combination of molecular techniques, ChIPseq and transcriptomic analyses, we show that repressor C (Pf4r) is the minimal factor for immunity against reinfection by Pf4 possibly through Pf4r binding to its putative promoter region, and that Pf4r also functions as a transcriptional regulator for expression of host genes. A binding motif for Pf4r was also identified. In wild type P. aeruginosa and Pfr4 complemented Pf4 deficient mutant strains, virulence factor related genes including phenazine and type VI secretion system effectors were upregulated, potentially explaining the reduced virulence of Pf4-deficient P. aeruginosa PAO1. X-ray crystal structure analysis shows that Pf4r forms symmetric homo-dimers homologous to the E.coli bacteriophage P2 RepC protein. A mutation associated with the superinfective Pf4r variant, found at the dimer interface, suggests dimer formation may be disrupted, which derepresses phage replication. This is supported by MALS analysis where the Pf4r* protein only shows monomer formation. Collectively, these data suggest the mechanism by which filamentous phages play such an important role in P. aeruginosa biofilm development.

2021-01-31 | GSE154459 | GEO

RNA-seq after chmA knockdown in PhiKZ-infected PAO1 cells

Project description:RNA-seq after chmA knockdown in PhiKZ-infected PAO1 cells

| PRJNA1121384 | ENA

RNA-seq PHIKZ-infected cells - early infection

Project description:The 280-kB giant bacteriophage PHIKZ expresses hundreds of transcripts upon infection of Pseudomonas aeruginosa. To illuminate which transcripts are the very first and abundant ones, we extracted RNA after infection and sequenced the transcripts. The early expressed genes promise to be important for surpassing the host defence systems and to reprogram the host machinery towards phage replication. We discovered a number of transcripts that encode for proteins which we found in an independent study to be associated with large complexes. In essence, early genes represent exciting opportunities to filter for important factors that could also engage in large complexes.

2024-01-16 | GSE223979 | GEO

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