Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis

Mojardín, Laura; Salas, Margarita

doi:10.1128/jvi.01245-16

Cited by 45 publications

(47 citation statements)

References 69 publications

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“…fitness in the presence of diverse phages ( Supplementary Table S4). How the down-regulation of host tRNA and tRNA modification genes impact host fitness, phage growth and infection cycle is not clear, although recent studies have shown increased aminoacyl-tRNA synthetase activities in the early phage infection cycle [125,126].…”

Section: A Crispri Screen Provides Deeper View Of Phage Resistance Dementioning

confidence: 99%

High-throughput mapping of the phage resistance landscape inE. coli

Mutalik¹,

Adler²,

Rishi³

et al. 2020

Preprint

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Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and highthroughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phagemediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.3 Introduction:

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Section: A Crispri Screen Provides Deeper View Of Phage Resistance Dementioning

confidence: 99%

High-throughput mapping of the phage resistance landscape inE. coli

Mutalik¹,

Adler²,

Rishi³

et al. 2020

Preprint

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show abstract

“…A few studies have recently reported findings of phage–host interactions using transcriptomic and metabolomic approaches in P. aeruginosa , Yersinia enterocolitica, Bacillus subtilis , and the marine microbe Sulfitobacter sp. 2047 (Lavigne et al, 2013; Ankrah et al, 2014; Chevallereau et al, 2016; De Smet et al, 2016; Leskinen et al, 2016; Mojardin and Salas, 2016). Chevallereau et al (2016) used next-generation “omics” approaches to investigate the interactions between P. aeruginosa and bacteriophage PAK_P3 and found that RNA processing was hijacked by phage infection and that bacterial transcripts were significantly depleted.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic and Metabolomics Profiling of Phage–Host Interactions between Phage PaP1 and Pseudomonas aeruginosa

et al. 2017

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The basic biology of bacteriophage–host interactions has attracted increasing attention due to a renewed interest in the therapeutic potential of bacteriophages. In addition, knowledge of the host pathways inhibited by phage may provide clues to novel drug targets. However, the effect of phage on bacterial gene expression and metabolism is still poorly understood. In this study, we tracked phage–host interactions by combining transcriptomic and metabolomic analyses in Pseudomonas aeruginosa infected with a lytic bacteriophage, PaP1. Compared with the uninfected host, 7.1% (399/5655) of the genes of the phage-infected host were differentially expressed genes (DEGs); of those, 354 DEGs were downregulated at the late infection phase. Many of the downregulated DEGs were found in amino acid and energy metabolism pathways. Using metabolomics approach, we then analyzed the changes in metabolite levels in the PaP1-infected host compared to un-infected controls. Thymidine was significantly increased in the host after PaP1 infection, results that were further supported by increased expression of a PaP1-encoded thymidylate synthase gene. Furthermore, the intracellular betaine concentration was drastically reduced, whereas choline increased, presumably due to downregulation of the choline–glycine betaine pathway. Interestingly, the choline–glycine betaine pathway is a potential antimicrobial target; previous studies have shown that betB inhibition results in the depletion of betaine and the accumulation of betaine aldehyde, the combination of which is toxic to P. aeruginosa. These results present a detailed description of an example of phage-directed metabolism in P. aeruginosa. Both phage-encoded auxiliary metabolic genes and phage-directed host gene expression may contribute to the metabolic changes observed in the host.

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“…Regulatory antisense RNAs have been observed in lambda phage (Krinke et al, 1991), bacteriophage 186 (Dodd and Egan, 2002), P22 (Liao et al, 1987), and T4 (Belin et al, 1987). Antisense RNA has been detected in phage ϕ29 (Mojardín and Salas, 2016) and AR9 (Lavysh et al, 2017) but no definitive function has been yet assigned.…”

Section: Discussionmentioning

confidence: 99%

A high-resolution map of bacteriophage øX174 transcription

Logel

Jaschke

2020

Preprint

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Bacteriophage øX174 is a model virus for studies across the fields of structural biology, genetics, gut microbiome, and synthetic biology, but did not have a high-resolution transcriptome until this work. In this study we used next-generation sequencing to measure the RNA produced from øX174 while infecting its host E. coli C. We broadly confirm the past transcriptome model while revealing several interesting deviations from previous knowledge. Additionally, we measure the strength of canonical øX174 promoters and terminators and discover both a putative new promoter that may be activated by heat shock sigma factors, as well as rediscover a controversial Rho-dependent terminator. We also provide evidence for the first antisense transcription observed in the Microviridae family, identify two promoters that may be involved in generating this transcriptional activity, and discuss possible reasons why this RNA may be produced.

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Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis

Cited by 45 publications

References 69 publications

High-throughput mapping of the phage resistance landscape inE. coli

High-throughput mapping of the phage resistance landscape inE. coli

Transcriptomic and Metabolomics Profiling of Phage–Host Interactions between Phage PaP1 and Pseudomonas aeruginosa

A high-resolution map of bacteriophage øX174 transcription

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