Characterization of transcription patterns of bacteriophage fRSL1 genes during infection cycle.
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PROVIDER: PRJNA131521 | ENA |
REPOSITORIES: ENA
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Project description:fRSL1 is a jumbo myovirus stably and lytically infecting the phytopathogenic bacterium Ralstonia solanacearum. In this study, we investigate the infection cycle of fRSL1 and provide a genomic, proteomic and transcriptomic view of this phage. Its 231-kbp genome sequence showed many genes lacking detectable homologs in the current databases and was vastly different from previously studied phage genomes. In addition to these orphan proteins, fRSL1 was found to encode several enzymes that are unique among known viruses. These include enzymes for the salvage pathway of NAD+ and for the biosynthetic pathways of lipid, carbohydrate and homospermidine. A chitinase-like protein was found to be a potential lysis enzyme. Our proteomics analysis suggests that fRSL1 virions contain at least 25 distinct proteins. We identified six of them including a tail sheath protein and a topoisomerase IB by N-terminal sequencing. Based on a DNA microarray analysis, we identified two transcription patterns.
2010-07-21 | GSE23017 | GEO
Project description:fRSL1 is a jumbo myovirus stably and lytically infecting the phytopathogenic bacterium Ralstonia solanacearum. In this study, we investigate the infection cycle of fRSL1 and provide a genomic, proteomic and transcriptomic view of this phage. Its 231-kbp genome sequence showed many genes lacking detectable homologs in the current databases and was vastly different from previously studied phage genomes. In addition to these orphan proteins, fRSL1 was found to encode several enzymes that are unique among known viruses. These include enzymes for the salvage pathway of NAD+ and for the biosynthetic pathways of lipid, carbohydrate and homospermidine. A chitinase-like protein was found to be a potential lysis enzyme. Our proteomics analysis suggests that fRSL1 virions contain at least 25 distinct proteins. We identified six of them including a tail sheath protein and a topoisomerase IB by N-terminal sequencing. Based on a DNA microarray analysis, we identified two transcription patterns. Total RNA was isolated from 3 ml of fRSL1-infected MAFF730138 cells (containing 1 x 108 CFU infected at moi 0.5 ~ 4) at 0, 10, 30, 90 min, and 30 h post infection (p.i.) using an RNAprotect Bacteria Reagent kit (Qiagen K.K., Tokyo, Japan) according to the manufacturer’s protocol. The integrity and concentration of total RNA were measured using a bioanalysis unit (Agilent 2100 Bioanalyser, Aligent Tech. Palo Alto, CA). Fluorescence-labeled antisense RNA was synthesized by direct incorporation of Cy5-UTP (GE Healthcare Bio-Science Corp., Piscataway, NJ), using each RNA sample and an RNA Transcript SureLABEL Core kit (Takara Bio Inc.). The labeled antisense RNAs were hybridized simultaneously to the microarray chip. DNA microarray preparation, hybridization, processing, scanning, and analyses were performed by Filgen Inc. (Nagoya Japan). For each fRSL1 ORF, 1 to 5 coding sequences of 35 to 40 nucleotide-long were synthesized. A total of 1,100 sequences were put in duplicate on a 40 x 55 array chip. The fluorescence images of hybridized microarrays were obtained with a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA). The Array-Pro Analyzer Ver4.5 (Media Cybernetics, Inc., Silver Spring, MD) was used to determine the signal intensity of each spot and its local background. Scan data images were alalyzed using Microarray Data Analysis Tool Ver3.0 software (Filgen Inc.)
2010-07-21 | E-GEOD-23017 | biostudies-arrayexpress
Project description:We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P4 infecting PAK strain of P. aeruginosa.
2017-07-07 | GSE86022 | GEO
Project description:We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P3 infecting PAK strain of P. aeruginosa.
2016-07-20 | GSE76513 | GEO
Project description:We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P3 infecting PAK strain of P. aeruginosa. RNA profile of Host and Phage at 0min, 3.5min and 13 min after infection of Pseudomonas aeruginosa PAK strain with the Pseudomonas phage PAK P3. Three biological replicates for each time point.
2016-07-20 | E-GEOD-76513 | biostudies-arrayexpress
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
2005-11-18 | GSE3590 | GEO
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
Project description:We observed the expression profile of the total mRNA of wild-type Thermus thermophilus HB8 strain during infection of bacteriophage ϕYS40.
2010-10-15 | GSE19759 | GEO
Project description:Programmed cell suicide of infected bacteria, known as abortive infection (Abi), serves as a central immune defense strategy to prevent the spread of bacteriophage viruses and other invasive genetic elements across a population. Many Abi systems utilize bespoke cyclic nucleotide immune messengers generated upon infection to rapidly mobilize cognate death effectors. Here, we identify a large family of bacteriophage nucleotidyltransferases (NTases) which synthesize competitor cyclic dinucleotide (CDN) ligands and inhibit NAD-depleting TIR effectors activated through a linked STING CDN sensor domain (TIR-STING). Through a functional screen of NTase-adjacent phage genes, we uncover candidate inhibitors of host TIR-STING suicide signaling. Among these, we demonstrate that a virus MazG-like nucleotide pyrophosphatase, Atd1, depletes the starvation alarmone (p)ppGpp, revealing a role for the alarmone-activated host toxin MazF as a key executioner of TIR-driven abortive infection. Phage NTases and counter-defenses like Atd1 preserve host viability to ensure virus propagation, and may be exploited as tools to modulate TIR and STING immune responses.
2023-03-27 | GSE222071 | GEO
