Complete Genome Sequence of Escherichia coli Phage Paul

Holt, Ashley; Saldaña, R. R.; Moreland, Russell; Gill, Jason J.; Liu, Mei; Ramsey, Jolene

doi:10.1128/mra.01093-19

Cited by 7 publications

(5 citation statements)

References 19 publications

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“…In more modern approaches, DNA termini are often computed based off raw short-read sequence data via the analysis of starting positive coverage [ 63 ]. With this approach, the termini of only two other group phages have been determined, SU7 and Paul phages, with noted DTRs of 53 bp (cautioned by the authors) and 193 bp, respectively [ 56 , 61 ]. Given the YF01 phage was sequenced with nanopore long-read technology, we curated reads spanning the entire YF01 genome sequence (~78,600 bp; many >Q30 due to duplex strand basecalling) and analyzed the DNA termini.…”

Section: Resultsmentioning

confidence: 99%

“…In the YF01 phage, the extended MCP isoform is substantially larger (892 a.a) than those seen in many other group members (~500–550 a.a) and most similar in size to that seen in the Paul phage (894 a.a.) [ 56 ]. As observed in T3 phage [ 67 ], the extended MCP isoform results in the addition of an immunoglobulin (Ig)-like domain to the C-terminus of the MCP.…”

Section: Resultsmentioning

confidence: 99%

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Expansion of Kuravirus-like Phage Sequences within the Past Decade, including Escherichia Phage YF01 from Japan, Prompt the Creation of Three New Genera

Batinovic

Fujii

Nittami

2023

Viruses

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Bacteriophages, viruses that infect bacteria, are currently receiving significant attention amid an ever-growing global antibiotic resistance crisis. In tandem, a surge in the availability and affordability of next-generation and third-generation sequencing technologies has driven the deposition of a wealth of phage sequence data. Here, we have isolated a novel Escherichia phage, YF01, from a municipal wastewater treatment plant in Yokohama, Japan. We demonstrate that the YF01 phage shares a high similarity to a collection of thirty-five Escherichia and Shigella phages found in public databases, six of which have been previously classified into the Kuravirus genus by the International Committee on Taxonomy of Viruses (ICTV). Using modern phylogenetic approaches, we demonstrate that an expansion and reshaping of the current six-membered Kuravirus genus is required to accommodate all thirty-six member phages. Ultimately, we propose the creation of three additional genera, Vellorevirus, Jinjuvirus, and Yesanvirus, which will allow a more organized approach to the addition of future Kuravirus-like phages.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Expansion of Kuravirus-like Phage Sequences within the Past Decade, including Escherichia Phage YF01 from Japan, Prompt the Creation of Three New Genera

Batinovic

Fujii

Nittami

2023

Viruses

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“…TEM imaging demonstrated that phages 7-11, Lah_6, and Vp_R1 each belong to the C3 podophage morphotype. Privateer also shares similar proteins with phages in the Kuravirus genus, including Escherichia phages phiEco32 (33 similar proteins) ( Savalia et al, 2008 ), Paul (33 proteins) ( Holt et al, 2019 ) and vB_EcoP_SU10 (32 similar proteins) ( Mirzaei et al, 2014 ). The Kuravirus genus is within the Podoviridae family and consists of C3 morphotype (prolate) phages, with phiEco32 as the exemplar.…”

Section: Resultsmentioning

confidence: 99%

Characterization and complete genome sequence of Privateer, a highly prolate Proteus mirabilis podophage

Corban

Ramsey

2021

PeerJ

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The Gram-negative bacterium Proteus mirabilis causes a large proportion of catheter-associated urinary tract infections, which are among the world’s most common nosocomial infections. Here, we characterize P. mirabilis bacteriophage Privateer, a prolate podophage of the C3 morphotype isolated from Texas wastewater treatment plant activated sludge. Basic characterization assays demonstrated Privateer has a latent period of ~40 min and average burst size around 140. In the 90.7 kb Privateer genome, 43 functions were assigned for the 144 predicted protein-coding genes. Genes encoding DNA replication proteins, DNA modification proteins, four tRNAs, lysis proteins, and structural proteins were identified. Cesium-gradient purified Privateer particles analyzed via LC-MS/MS verified the presence of several predicted structural proteins, including a longer, minor capsid protein apparently produced by translational frameshift. Comparative analysis demonstrated Privateer shares 83% nucleotide similarity with Cronobacter phage vB_CsaP_009, but low nucleotide similarity with other known phages. Predicted structural proteins in Privateer appear to have evolutionary relationships with other prolate podophages, in particular the Kuraviruses

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“…It has an elongated head, with a length of 134 nm (134 ± 6 nm) and width of 44 nm (44 ± 2 nm), and a very short non-contractile tail, which could not be measured ( Figure 1 B). Occurring in less than 1% of Podoviridae virions, this rare morphotype has been observed among phages belonging to the Kuravirus genus (previously referred to as PhiEco32viruses) and include the E. coli phages vB_EcoP_SU10, Paul, and phiEco32 [ 47 , 48 , 49 , 50 ]. At an MOI of 0.12, SU7 has a latency period of 30 min (defined as the time from the addition of phages to a significant rise in phage concentration) and a burst size of 12 PFU/cell ( Figure 2 and Supplementary Figure S1 ).…”

Section: Resultsmentioning

confidence: 99%

Complete Genome Sequence of vB_EcoP_SU7, a Podoviridae Coliphage with the Rare C3 Morphotype

2021

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Enterotoxigenic Escherichia coli (ETEC) strains are an important cause of bacterial diarrheal illness in humans and animals. Infections arising from ETEC could potentially be treated through the use of bacteriophage (phage) therapy, as phages encode for enzymes capable of bacterial cell lysis. vB_EcoP_SU7 was isolated from the Käppala wastewater treatment plant in Stockholm, Sweden, and propagated on an ETEC strain exhibiting the O:139 serovar. Transmission electron microscopy confirmed that vB_EcoP_SU7 belongs to the Podoviridae family and has the rare C3 morphotype of an elongated head. Bioinformatic analyses showed that the genome was 76,626 base pairs long and contained 35 genes with predicted functions. A total of 81 open reading frames encoding proteins with hypothetical function and two encoding proteins of no significant similarity were also found. A putative tRNA gene, which may aid in vB_EcoP_SU7’s translation, was also identified. Phylogenetic analyses showed that compared to other Podoviridae, vB_EcoP_SU7 is a rare Kuravirus and is closely related to E. coli phages with the uncommon C3 morphotype, such as ECBP2, EK010, vB_EcoP_EcoN5, and vB_EcoP_SU10. Phage vB_EcoP_SU7 has a narrow host range, infecting 11 out of the 137 E. coli strains tested, a latency period of 30 min, a burst size of 12 PFU/cell, and an adsorption rate of 8.78 × 10−9 mL/min five minutes post infection. With a limited host range and poor infection kinetics, it is unlikely that SU7 can be a standalone phage used for therapeutic purposes; rather, it must be used in combination with other phages for broad-spectrum therapeutic success.

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Complete Genome Sequence of Escherichia coli Phage Paul

Abstract: Escherichia coli is both a commensal and a pathogen in humans and other animals. Here, we describe the isolation of E. coli strain 4s bacteriophage Paul. The complete 79,429-bp genome was annotated and demonstrates similarity with phieco32viruses, as does its prolate podophage morphology.

Cited by 7 publications

References 19 publications

Expansion of Kuravirus-like Phage Sequences within the Past Decade, including Escherichia Phage YF01 from Japan, Prompt the Creation of Three New Genera

Expansion of Kuravirus-like Phage Sequences within the Past Decade, including Escherichia Phage YF01 from Japan, Prompt the Creation of Three New Genera

Characterization and complete genome sequence of Privateer, a highly prolate Proteus mirabilis podophage

Complete Genome Sequence of vB_EcoP_SU7, a Podoviridae Coliphage with the Rare C3 Morphotype

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