Complete Genome Sequences of Three Novel Pseudomonas fluorescens SBW25 Bacteriophages, Noxifer, Phabio, and Skulduggery

Wojtus, Joanna K.; Fitch, Jess L.; Christian, Eli; Dalefield, Tara; Lawes, Jacob K.; Kumar, K. Ashok; Peebles, Craig L.; Altermann, Eric; Hendrickson, Heather

doi:10.1128/genomea.00725-17

Cited by 9 publications

(3 citation statements)

References 11 publications

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“…The genome of jumbo phage AR9 infecting B. subtilis , a close relative of the PBS2 phage, was sequenced and shown to contain genes orthologous to the RNAP genes of phiKZ-like phages [ 18 ], suggesting that the PBS2 RNAP purified a long time ago [ 35 , 36 ] in fact belongs to this new group of non-canonical jumbo phage RNAPs. At the time of this writing, several dozens of jumbo phages encoding distant homologs of the β′ and β subunits are known [ 18 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 ]. They infect diverse bacterial hosts including members of Pseudomonas , Salmonella , Yersinia , Erwinia , Vibrio , Ralstonia , Bacillus , Aeromonas , Serratia , Klebsiella , Escherichia , and other genera [ 18 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , …”

Section: Jumbo Phages Encoding Rna Polymerases and Their Featuresmentioning

confidence: 99%

Multisubunit RNA Polymerases of Jumbo Bacteriophages

Sokolova

Misovetc

Severinov

2020

Viruses

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Prokaryotic viruses with DNA genome longer than 200 kb are collectively referred to as “jumbo phages”. Some representatives of this phylogenetically diverse group encode two DNA-dependent RNA polymerases (RNAPs)—a virion RNAP and a non-virion RNAP. In contrast to most other phage-encoded RNAPs, the jumbo phage RNAPs are multisubunit enzymes related to RNAPs of cellular organisms. Unlike all previously characterized multisubunit enzymes, jumbo phage RNAPs lack the universally conserved alpha subunits required for enzyme assembly. The mechanism of promoter recognition is also different from those used by cellular enzymes. For example, the AR9 phage non-virion RNAP requires uracils in its promoter and is able to initiate promoter-specific transcription from single-stranded DNA. Jumbo phages encoding multisubunit RNAPs likely have a common ancestor allowing making them a separate subgroup within the very diverse group of jumbo phages. In this review, we describe transcriptional strategies used by RNAP-encoding jumbo phages and describe the properties of characterized jumbo phage RNAPs.

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Section: Jumbo Phages Encoding Rna Polymerases and Their Featuresmentioning

confidence: 99%

Multisubunit RNA Polymerases of Jumbo Bacteriophages

Sokolova

Misovetc

Severinov

2020

Viruses

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“…Phage ϕPsa21 also shows general alignment by BLASTN with ϕKZ-like phages, namely, PhiPA3 (GenBank accession number HQ630627) aligns across 20% of the genome (maximum identity [ID], 75.7%) and Phabio (GenBank accession number MF042360) aligns across 17% of the genome (maximum ID, 73.8%). Phabio is a ϕKZ-like jumbo phage also found in New Zealand (26). Altogether, these observations place ϕPsa21in the Myoviridae family and Phikzvirus genus according to the International Committee on Taxonomy of Viruses (ICTV) classification 2018b.…”

Section: Announcementmentioning

confidence: 99%

Genome Sequence of a Jumbo Bacteriophage That Infects the Kiwifruit Phytopathogen Pseudomonas syringae pv. actinidiae

Wojtus

Frampton

Warring

et al. 2019

Microbiol Resour Announc

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“…P. fluorescens -infecting phages had been isolated, characterised, and evaluated to the ability to control bacterial contamination in different environments, including milk and dairy products and biofilms on abiotic surfaces [ 29 , 30 , 31 , 32 , 33 , 34 , 35 ]. In our previous study, phage UFJF_PfDIW6 isolated from dairy industry wastewater could control P. fluorescens growth and reduce casein hydrolysis in raw milk.…”

Section: Introductionmentioning

confidence: 99%

Genomic Characterisation of UFJF_PfDIW6: A Novel Lytic Pseudomonas fluorescens-Phage with Potential for Biocontrol in the Dairy Industry

Húngaro

Vidigal

Nascimento

et al. 2022

Viruses

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In this study, we have presented the genomic characterisation of UFJF_PfDIW6, a novel lytic Pseudomonas fluorescens-phage with potential for biocontrol in the dairy industry. This phage showed a short linear double-stranded DNA genome (~42 kb) with a GC content of 58.3% and more than 50% of the genes encoding proteins with unknown functions. Nevertheless, UFJF_PfDIW6’s genome was organised into five functional modules: DNA packaging, structural proteins, DNA metabolism, lysogenic, and host lysis. Comparative genome analysis revealed that the UFJF_PfDIW6’s genome is distinct from other viral genomes available at NCBI databases, displaying maximum coverages of 5% among all alignments. Curiously, this phage showed higher sequence coverages (38–49%) when aligned with uncharacterised prophages integrated into Pseudomonas genomes. Phages compared in this study share conserved locally collinear blocks comprising genes of the modules’ DNA packing and structural proteins but were primarily differentiated by the composition of the DNA metabolism and lysogeny modules. Strategies for taxonomy assignment showed that UFJF_PfDIW6 was clustered into an unclassified genus in the Podoviridae clade. Therefore, our findings indicate that this phage could represent a novel genus belonging to the Podoviridae family.

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Complete Genome Sequences of Three Novel Pseudomonas fluorescens SBW25 Bacteriophages, Noxifer, Phabio, and Skulduggery

Abstract: Three novel bacteriophages, two of which are jumbophages, were isolated from compost in Auckland, New Zealand. Noxifer, Phabio, and Skulduggery are double-stranded DNA (dsDNA) phages with genome sizes of 278,136 bp (Noxifer), 309,157 bp (Phabio), and 62,978 bp (Skulduggery).

Cited by 9 publications

References 11 publications

Multisubunit RNA Polymerases of Jumbo Bacteriophages

Multisubunit RNA Polymerases of Jumbo Bacteriophages

Genome Sequence of a Jumbo Bacteriophage That Infects the Kiwifruit Phytopathogen Pseudomonas syringae pv. actinidiae

Genomic Characterisation of UFJF_PfDIW6: A Novel Lytic Pseudomonas fluorescens-Phage with Potential for Biocontrol in the Dairy Industry

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