vB_PaeM_MIJ3, a Novel Jumbo Phage Infecting Pseudomonas aeruginosa, Possesses Unusual Genomic Features

Imam, Mohammed; Alrashid, Bandar; Patel, Faizal; Dowah, Ahmed S. A.; Brown, Nathan; Millard, Andrew; Clokie, Martha R. J.; Galyov, Edouard E.

doi:10.3389/fmicb.2019.02772

Cited by 43 publications

(51 citation statements)

References 82 publications

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“…Contiguous regions with limited amounts of transcripts detected across multiple timepoints are encased in dotted lines. The two host‐like proteins FtshH and TilS reported in Imam and colleagues () are annotated in blue‐colored text. The figure was created using the software Circos (Krzywinski et al ., ).…”

Section: Resultsmentioning

confidence: 99%

“…In terms of annotation, functions could be attributed for a third of PA5oct proteins and a large portion of predicted CDSs are unique, lacking sequence‐based similarity to the genomes available in the public database GenBank (r235) with the notable exception of the same species isolate, Pseudomonas phage MIJ3 (Imam et al ., ). For this reason, the functional characterization of phage orphan genes is an important endeavour to undertake in order to elucidate basic phage biology as well as phage application safety when thinking of therapeutic settings (Yuan and Gao, ).…”

Section: Discussionmentioning

confidence: 97%

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Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Lood

Danis-Wlodarczyk

Blasdel

et al. 2020

Environmental Microbiology

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Pseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage-bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA-Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four noncoding RNAs (ncRNAs) and 93 virion-associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA-Seq revealed a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA-pncB1-nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position our isolate amongst other phages using a gene-sharing network. This integrative omics study illustrates the molecular diversity of jumbo viruses and raises new questions towards cellular regulation and phage-encoded hijacking mechanisms. ; Tel. +32 16 37 95 24; Fax +32 16 3 21965. † These authors contributed equally to this work.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 97%

Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Lood

Danis-Wlodarczyk

Blasdel

et al. 2020

Environmental Microbiology

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“…The genome sequences of many jumbo phages have few homologs when compared to previously annotated phages or other microorganisms and are even highly divergent when compared to each other (e.g. ФKZ and PA5oct, both infecting P. aeruginosa) (14,15,17,(20)(21)(22).…”

Section: Downloaded Frommentioning

confidence: 99%

Intracellular Organization by Jumbo Bacteriophages

Guan

Bondy‐Denomy

2020

J Bacteriol

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Since their discovery over 100 years ago, the viruses that infect bacteria (bacteriophages) have been widely studied as model systems. Largely overlooked however, have been “jumbo phages”, with genome sizes ranging from 200 - 500 kbp. Jumbo phages generally have large virions with complex structures and a broad host spectrum. While the majority of jumbo phage genes are poorly functionally characterized, recent work has discovered many unique biological features, including a conserved tubulin homolog that coordinates a proteinaceous nucleus-like compartment that houses and segregates phage DNA. The tubulin spindle displays dynamic instability and centers the phage nucleus within the bacterial host during phage infection for optimal reproduction. The shell provides robust physical protection for the enclosed phage genomes against attack from bacterial DNA-targeting immune systems, thereby endowing jumbo phages with broad resistance. In this review, we focus on the current knowledge of the cytoskeletal elements and the specialized nuclear compartment derived from jumbo phages and highlight their importance in facilitating spatial and temporal organization over the viral life cycle. Additionally, we discuss the evolutionary relationships between jumbo phages and eukaryotic viruses, as well as the therapeutic potential and drawbacks of jumbo phages as antimicrobial agents in phage therapy.

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“…This phage could not have been isolated by either conventional liquid enrichment culture or single-plaque procedures with 0.5-0.7% agar upper layer gels. It has the longest genome (316.674 Kb [49]) of any of the 15 Pseudomonas jumbo phages [50].…”

Section: Other Advantages Of Using Dilute Agarose Gels For Initial Phmentioning

confidence: 99%

In-Gel Isolation and Characterization of Large (and Other) Phages

Serwer

Wright

2020

Viruses

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We review some aspects of the rapid isolation of, screening for and characterization of jumbo phages, i.e., phages that have dsDNA genomes longer than 200 Kb. The first aspect is that, as plaque-supporting gels become more concentrated, jumbo phage plaques become smaller. Dilute agarose gels are better than conventional agar gels for supporting plaques of both jumbo phages and, prospectively, the even larger (>520 Kb genome), not-yet-isolated mega-phages. Second, dilute agarose gels stimulate propagation of at least some jumbo phages. Third, in-plaque techniques exist for screening for both phage aggregation and high-in-magnitude, negative average electrical surface charge density. The latter is possibly correlated with high phage persistence in blood. Fourth, electron microscopy of a thin section of a phage plaque reveals phage type, size and some phage life cycle information. Fifth, in-gel propagation is an effective preparative technique for at least some jumbo phages. Sixth, centrifugation through sucrose density gradients is a relatively non-destructive jumbo phage purification technique. These basics have ramifications in the development of procedures for (1) use of jumbo phages for phage therapy of infectious disease, (2) exploration of genomic diversity and evolution and (3) obtaining accurate metagenomic analyses.Here, we both review and augment data projected to help answer the above questions. We propose that data of this type are critical to efficient isolation of large phages, which include those with genomes longer than 200 Kb (jumbo phages [4][5][6]19]) and even larger phages with genome longer than 520 Kb (mega-phages [20,21]). The importance of these answers is illustrated by the fact that no mega-phage has ever been isolated [20,21], although even larger eukaryotic viruses have been isolated [22]. The existence of mega-phages is surmised from assembly of metagenomic sequences [20,21]. Host Bacteria In-Gel: Values of P E for Agarose Gels FundamentalsThe following data indicate that Gram-negative and Gram-positive phage hosts do not fit in the spaces of the 0.5-0.7% agar gels typically used to form phage plaques. This conclusion is derived, first, from the measurement of P E for agarose gels. This measurement begins by determining vs. sphere radius the minimal agarose gel concentration that excludes a sphere during electrophoresis [23]. These P E values are then used to anchor P E values determined from the sieving (gel-induced retardation) of spheres during gel electrophoresis. The most advanced study of the latter [24] yields the following relationship for underivatized, low-electro-osmosis agarose gels cast in 0.025 M sodium phosphate, pH 7.4, 0.001 M MgCl 2 at 25 • C: P E = 148A −0.87 nm; A is the weight percentage of agarose.A 0.7% agarose gel, if characterized by this relationship, has a P E of 202 nm, not large enough to admit a bacterial cell, such as the host for phage G. Our phage G host is~500 nm in radius and 2000-5000 nm in length, as is Escherichia coli [25], a representative of the ...

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vB_PaeM_MIJ3, a Novel Jumbo Phage Infecting Pseudomonas aeruginosa, Possesses Unusual Genomic Features

Cited by 43 publications

References 82 publications

Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Intracellular Organization by Jumbo Bacteriophages

In-Gel Isolation and Characterization of Large (and Other) Phages

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