Ontology highlight
ABSTRACT:
PROVIDER: PRJNA906727 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22474177_1.fastq.gz | Fastqsanger.gz | |||
| SRR22474177_2.fastq.gz | Fastqsanger.gz | |||
| SRR22474178_1.fastq.gz | Fastqsanger.gz | |||
| SRR22474178_2.fastq.gz | Fastqsanger.gz | |||
| SRR22474179_1.fastq.gz | Fastqsanger.gz |
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Project description:Bacteriophage lambda is one of the most extensively studied organisms, and has been a primary model for understanding basic modes of genetic regulation. Here we examine the progress of lambda gene expression during phage development by ribosome profiling, and thereby provide a very high resolution view of lambda gene expression. The known genes are expressed in a predictable fashion, authenticating the analysis. But many previously unappreciated potential open reading frames become apparent in the expression analysis, revealing an unexpected complexity in the pattern of lambda gene function. We chose temperature induction of the classic cI857 repressor mutation in a lysogen of E. coli MG1655 in order to synchronize the lytic process, sampling the lysogen and control non-lysogen both before and 2, 5, 10, and 20 minutes after shifting the temperature from 32M-BM-0 to 42M-BM-0. The last sample time was chosen to be before any significant cell lysis, but during the later stages of lytic gene expression. Total protected nucleotides within open reading frames were summed to determine the density of translation of each reading frame. We take this number to indicate the overall rate of translation, although obviously this assumes that pauses in translation do not excessively affect the overall rate. Since the expression level is not normalized for the copy number of the replicating phage DNA, it thus encompasses both the effect of DNA template availability on mRNA synthesis and the efficiency of utilization of messengers by ribosomes.
2013-07-01 | E-GEOD-47509 | biostudies-arrayexpress
Project description:Retrons are bacterial genetic retroelements that encode reverse transcriptase capable of producing multicopy single-stranded DNA (msDNA) and function as antiphage defense systems. Phages employ several strategies to counter the host defense systems, but no mechanisms for evading retrons are known. Here, we show that tRNATyr and Rad (retron anti defense) of T5 phage family inhibit the defense activity of retron 78 and a broad range of retrons, respectively. The effector protein of retron 78, ptuAB, specifically degraded tRNATyr leading abortive infection, but phage countervailed this defense by supplying tRNATyr. Rad inhibited retron function by degrading noncoding RNA, the precursor of msDNA. In summary, we demonstrated that viruses encode at least two independent strategies for overcoming bacterial defense systems: anti-defense, such as Rad, and defense canceler, like tRNA.
2024-10-10 | GSE256078 | GEO
Project description:Retrons are bacterial genetic retroelements that encode reverse transcriptase capable of producing multicopy single-stranded DNA (msDNA) and function as antiphage defense systems. Phages employ several strategies to counter the host defense systems, but no mechanisms for evading retrons are known. Here, we show that tRNATyr and Rad (retron anti defense) of T5 phage family inhibit the defense activity of retron 78 and a broad range of retrons, respectively. The effector protein of retron 78, ptuAB, specifically degraded tRNATyr leading abortive infection, but phage countervailed this defense by supplying tRNATyr. Rad inhibited retron function by degrading noncoding RNA, the precursor of msDNA. In summary, we demonstrated that viruses encode at least two independent strategies for overcoming bacterial defense systems: anti-defense, such as Rad, and defense canceler, like tRNA.
2024-10-10 | GSE256077 | GEO
Project description:Bacteriophages (hereafter “phages”) are ubiquitous predators of bacteria in the natural world, but interest is growing in their development into antibacterial therapy as complement or replacement for antibiotics. However, bacteria have evolved a huge variety of anti-phage defense systems allowing them to resist phage lysis to a greater or lesser extent, and in pathogenic bacteria these inevitably impact phage therapy outcomes. In addition to dedicated phage defense systems, some aspects of the general stress response also impact phage susceptibility, but the details of this are not well known. In order to elucidate these factors in the opportunistic pathogen Pseudomonas aeruginosa, we used the laboratory-conditioned strain PAO1 as host for phage infection experiments as it is naturally poor in dedicated phage defense systems. Screening by transposon insertion sequencing indicated that the uncharacterized operon PA3040-PA3042 was potentially associated with resistance to lytic phages. However, we found that its primary role appeared to be in regulating biofilm formation. Its expression was highly growth-phase dependent and responsive to phage infection and cell envelope stress.
2023-10-30 | GSE246284 | GEO
Project description:Optimality of the spontaneous prophage induction rate.
Cortes MG1, Krog J2, Balázsi G3.
1 Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA.
2 The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA.
3 Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA. Electronic address: gabor.balazsi@stonybrook.edu.
Abstract
Lysogens are bacterial cells that have survived after genomically incorporating the DNA of temperate bacteriophages infecting them. If an infection results in lysogeny, the lysogen continues to grow and divide normally, seemingly unaffected by the integrated viral genome known as a prophage. However, the prophage can still have an impact on the host's phenotype and overall fitness in certain environments. Additionally, the prophage within the lysogen can activate the lytic pathway via spontaneous prophage induction (SPI), killing the lysogen and releasing new progeny phages. These new phages can then lyse or lysogenize other susceptible nonlysogens, thereby impacting the competition between lysogens and nonlysogens. In a scenario with differing growth rates, it is not clear whether SPI would be beneficial or detrimental to the lysogens since it kills the host cell but also attacks nonlysogenic competitors, either lysing or lysogenizing them. Here we study the evolutionary dynamics of a mixture of lysogens and nonlysogens and derive general conditions on SPI rates for lysogens to displace nonlysogens. We show that there exists an optimal SPI rate for bacteriophage λ and explain why it is so low. We also investigate the impact of stochasticity and conclude that even at low cell numbers SPI can still provide an advantage to the lysogens. These results corroborate recent experimental studies showing that lower SPI rates are advantageous for phage-phage competition, and establish theoretical bounds on the SPI rate in terms of ecological and environmental variables associated with lysogens having a competitive advantage over their nonlysogenic counterparts.
Copyright © 2019 The Author(s). Published by Elsevier Ltd.. All rights reserved.
2024-09-02 | BIOMD0000000884 | BioModels
Project description:Multiple immune pathways in humans conjugate ubiquitin-like proteins to virus and host molecules as a means of antiviral defense. Here we studied an anti-phage defense system in bacteria, comprising a ubiquitin-like protein, ubiquitin-conjugating enzymes E1 and E2, and a deubiquitinase. We show that during phage infection, this system specifically conjugates the ubiquitin-like protein to the phage central tail fiber, a protein at the tip of the tail that is essential for tail assembly as well as for recognition of the target host receptor. Following infection, cells encoding this defense system release a mixture of partially assembled, tailless phage particles, and fully assembled phages in which the central tail fiber is obstructed by the covalently attached ubiquitin-like protein. These phages exhibit severely impaired infectivity, explaining how the defense system protects the bacterial population from the spread of phage infection. Our findings demonstrate that conjugation of ubiquitin-like proteins is an antiviral strategy conserved across the tree of life.
2024-05-08 | GSE262579 | GEO
Project description:The gene expression profiles of mycobacteriophage D29 and StarStuff were analyzed 15min, 30min, 60min and 150min post-infection (MOI=3), as well as a StarStuff lysogen. The gene expression profiles of 30min and 150min post-induction of an L5 thermo-inducible lysogen, as well as the L5 lysogen itself.
2017-11-13 | GSE99182 | GEO