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ABSTRACT: Bacteriophage Genomics

PROVIDER: PRJNA754193 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15435530.fastq.gz	Fastqsanger.gz
	SRR15435531.fastq.gz	Fastqsanger.gz
	SRR15435532.fastq.gz	Fastqsanger.gz
	SRR15435533.fastq.gz	Fastqsanger.gz
	SRR15435534.fastq.gz	Fastqsanger.gz

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Project description:Bacteriophage Genomics

| PRJNA646767 | ENA

Time course of the mRNA expression after bacteriophage ϕYS40 infection in wild-type Thermus thermophilus HB8 strain.

Project description:We observed the expression profile of the total mRNA of wild-type Thermus thermophilus HB8 strain during infection of bacteriophage ϕYS40. Keywords: time course, bacteriophage, infection, wild type

2009-11-03 | GSE16954 | GEO

Time course of the mRNA expression after phage ϕYS40 infection in crp deletion mutant of Thermus thermophilus HB8.

Project description:We observed the expression profile of the total mRNA in crp (TTHA1437) deletion mutant strain of Thermus thermophilus HB8 during infection of bacteriophage ϕYS40. Keywords: time course, bacteriophage, infection, CRP, cAMP receptor protein, deletion mutant

2009-11-03 | GSE16955 | GEO

Characterization of attB and core-attP recombination sites of the integrase from Lactobacilus delbrueckii subsp. bulgaricus bacteriophage mv4

Project description:Different attB or attP DNA libraries containing 7-bp random nucleotides were used for in vitro recombination mediated by the purified integrase from mv4 bacteriophage against their cognate wild-type attB or attP recombination site.

2023-12-10 | E-MTAB-13571 | biostudies-arrayexpress

Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome

Project description:We use Illumina sequencing to monitor mutations in the bacteriophage T7 genome in the presence of T7 DNA polymerase that has an altered exonuclease active site. These alterations include mutation of key residues in the exonuclease active site.

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Microarray Analysis of Gene Expression during Bacteriophage T4 Infection

Project description:Genomic microarrays were used to examine the complex temporal program of gene expression exhibited by bacteriophage T4 during the course of development.The microarray data confirm the existence of distinct early, middle, and late transcriptional classes during the bacteriophage replicative cycle.This approach allows assignment of previously uncharacterized genes to specific temporal classes.The genomic expression data verify many promoter assignments and predict the existence of previously unidentified promoters. Keywords: time course

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A Grad-seq resource of RNA and protein complexes of Pseudomonas aeruginosa including transcripts of phage ΦKZ

Project description:Grad-seq of Pseudomonas aerugionosa PAO1 at OD 0.3 with and without infection with ΦKZ bacteriophage

2021-01-06 | GSE157708 | GEO

HOPE-Genomics Intervention for the Improvement of Cancer Patient Knowledge of Genomics

Project description:This clinical trial studies the effectiveness of a web-based cancer education tool called Helping Oncology Patients Explore Genomics (HOPE-Genomics) in improving patient knowledge of personal genomic testing results and cancer and genomics in general. HOPE-Genomics is a web-based education tool that teaches cancer/leukemia patients, and patients who may be at high-risk for developing cancer, about genomic testing and provide patients with information about their own genomic test results. The HOPE-Genomics tool may improve patient’s genomic knowledge and quality of patient-centered care. In addition, it may also improve education and care quality for future patients.

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Pseudomonas aeruginosa two-component regulator BfmR controls bacteriophage lysis and DNA release during biofilm development through PhdA

Project description:Biofilms are surface-adhered bacterial communities encased in an extracellular matrix composed of polysaccharides, proteins, and extracelluar (e)DNA, with eDNA being required for the formation and integrity of biofilms. Here we demonstrate that the spatial and temporal release of eDNA is regulated by BfmR, a regulator essential for Pseudomonas aeruginosa biofilm development. The expression of bfmR coincided with localized cell death and DNA release, with high eDNA concentrations localized to the outer part of microcolonies in the form of a ring and as a cap on small clusters. Additionally, eDNA release and cell lysis increased significantly following bfmR inactivation. Genome-wide transcriptional profiling indicated that bfmR was required for repression of genes associated with bacteriophage assembly and bacteriophage-mediated lysis. In order to determine which of these genes were directly regulated by BfmR, we utilized chromatin immunoprecipitation (ChIP) analysis to identify the promoter of PA0691, termed here phdA, encoding a previously undescribed homologue of the prevent-host-death (Phd) family of proteins. Lack of phdA expression coincided with impaired biofilm development, increased cell death and bacteriophage release, a phenotype comparable to ΔbfmR. Expression of phdA in ΔbfmR biofilms restored eDNA release, cell lysis, release of bacteriophages, and biofilm formation to wild type levels. Moreover, overexpression of phdA rendered P. aeruginosa resistant to lysis mediated by superinfective bacteriophage Pf4 which was only detected in biofilms. The expression of bfmR was stimulated by conditions resulting in membrane perturbation and cell lysis. Thus, we propose that BfmR regulates biofilm development by controlling bacteriophage-mediated lysis and thus, cell death and eDNA release, via PhdA.

2011-06-01 | GSE28953 | GEO

A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.

Project description:One key concept in the evolution of new functions is the ability of enzymes to perform promiscuous side-reactions that serve as a source of novelty that may become beneficial under certain conditions. Here, we identify a mechanism where a bacteriophage-encoded enzyme introduces novelty by inducing expression of a promiscuous bacterial enzyme. By screening for bacteriophage DNA that rescued an auxotrophic E. coli mutant carrying a deletion of the ilvA gene, we show that bacteriophage-encoded S-adenosylmethionine (SAM) hydrolases reduce SAM levels. Via this perturbation of bacterial metabolism, expression of the promiscuous bacterial enzyme MetB is increased, which in turn complements the absence of IlvA. These results demonstrate how foreign DNA can increase the metabolic capacity of bacteria, not only by transfer of bona fide new genes, but also by bringing cryptic bacterial functions to light via perturbations of cellular physiology.

2018-04-11 | GSE92601 | GEO

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