Genomes of “phiKMV-like viruses” of Pseudomonas aeruginosa contain localized single-strand interruptions

Kulakov, Leonid; Ksenzenko, V. N.; Shlyapnikov, M. G.; Кочетков, В. В.; Casale, Antonio Del; Allen, Christopher C. R.; Larkin, Michael J.; Ceyssens, Pieter‐Jan; Lavigne, Rob

doi:10.1016/j.virol.2009.06.024

Cited by 28 publications

(28 citation statements)

References 21 publications

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“…In HRPV-3 genome, they are preceded by a specific motif GCCCA. Localized single-strand interruptions have been identified before in the tailed ‘phiKMV-like viruses’ of Pseudomonas aeruginosa (53,54) and T5 (55–57). In those viruses, the discontinuities were shown to be nicks that were located in one strand only, and in phage φkF77, they were shown to be located in intergenic regions (54).…”

Section: Discussionmentioning

confidence: 89%

Related haloarchaeal pleomorphic viruses contain different genome types

Senčilo

Paulín

Kellner

et al. 2012

Nucleic Acids Research

107

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Archaeal viruses have been the subject of recent interest due to the diversity discovered in their virion architectures. Recently, a new group of haloarchaeal pleomorphic viruses has been discovered. It is distinctive in terms of the virion morphology and different genome types (ssDNA/dsDNA) harboured by rather closely related representatives. To date there are seven isolated viruses belonging to this group. Most of these share a cluster of five conserved genes, two of which encode major structural proteins. Putative proviruses and proviral remnants containing homologues of the conserved gene cluster were also identified suggesting a long-standing relationship of these viruses with their hosts. Comparative genomic analysis revealed three different ways of the genome organization, which possibly reflect different replication strategies employed by these viruses. The dsDNA genomes of two of these viruses were shown to contain single-strand interruptions. Further studies on one of the genomes suggested that the interruptions are located along the genome in a sequence-specific manner and exhibit polarity in distribution.

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Section: Discussionmentioning

confidence: 89%

Related haloarchaeal pleomorphic viruses contain different genome types

Senčilo

Paulín

Kellner

et al. 2012

Nucleic Acids Research

107

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“…The genus was extended with other Pseudomonas phages (PT2, PT5, phikF77, and LUZ19) (30,31,32), Vibrio phage VP93 (5), and Ralstonia phage RSB1 (25). Recently, Pseudomonas fluorescens phage phi-2 has been proposed as a member of this genus (46).…”

Section: Resultsmentioning

confidence: 99%

“…This recently established phage genus is classified within the Autographivirinae subfamily of the Podoviridae along with the "T7-like viruses" and "SP6-like viruses." It groups phages with a common transcriptional scheme, able to infect a wide range of environmentally important bacteria, such as Vibrio spp., Pseudomonas spp., and Ralstonia solanacearum (5,8,25,30,31,32,33,46).…”

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confidence: 99%

Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans, Belonging to the “phiKMV-Like Viruses”

Adriaenssens

Ceyssens

Dunon

et al. 2011

Appl Environ Microbiol

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Pantoea agglomerans is a common soil bacterium used in the biocontrol of fungi and bacteria but is also an opportunistic human pathogen. It has been described extensively in this context, but knowledge of bacteriophages infecting this species is limited. Bacteriophages LIMEzero and LIMElight of P. agglomerans are lytic phages, isolated from soil samples, belonging to the Podoviridae and are the first Pantoea phages of this family to be described. The double-stranded DNA ( Pantoea agglomerans bacteria are Gram-negative, nonsporulating, facultatively anaerobic rods that belong to the family of the Enterobacteriaceae. Synonyms of this species name are Enterobacter agglomerans, Erwinia herbicola, and Erwinia milletiae (6, 19). The genus name Pantoea is derived from the Greek word pantoios, which means "of all sorts and sources," a descriptor well reflected in the habitat, since species of the genus have been isolated from plant surfaces, seeds, water, soil, and even humans and animals (3,19,41). Pantoea agglomerans is known in plant production as a biocontrol agent. It is used in postharvest control of a number of fungi (for instance, Penicillium expansum, Rhizopus stolonifer, Monilinia laxa, and Botrytis cinerea) on a wide variety of fruits (18,44,45,54).

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“…It was also the first known T7-related phage encoding a single-subunit RNA polymerase gene downstream its DNA metabolism genes instead of in the early genomic region [13]. Up to now, three phages infecting P. aeruginosa (LKD16, ϕKF77 and LUZ19) have been reported to be 83-90% identical to ϕKMV at the nucleotide level [14-16]. In addition, phage LUZ2 was reported to be closely related to ϕKMV based on de novo analysis of structural phage proteins [12].…”

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confidence: 99%

“…All three phages display high nucleotide similarity (94-97% identity) to ϕKMV, except for a 382 bp region located between ORF3 and 4 (Figure 1), which was earlier associated with a localized single-stranded nick on the non-coding strand in the related phages LUZ19 and ϕKF77 [16]. As ϕKMV is the only phage of this species which has lost this nick, it is most probably a more recent representative of this phage species.…”

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confidence: 99%

Phenotypic and genotypic variations within a single bacteriophage species

Ceyssens

Glonti

Kropinski

et al. 2011

Virol J

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BackgroundAlthough horizontal gene transfer plays a pivotal role in bacteriophage evolution, many lytic phage genomes are clearly shaped by vertical evolution. We investigated the influence of minor genomic deletions and insertions on various phage-related phenotypic and serological properties.FindingsWe collected ten different isolates of Pseudomonas aeruginosa bacteriophage ϕKMV. All sequenced genomes (42-43 kb, long direct terminal repeats) are nearly identical, which intuitively implied strongly similar infections cycles. However, their latent periods vary between 21 and 28 minutes and they are able to lyse between 5 and 58% of a collection of 107 clinical P. aeruginosa strains. We also noted that phages with identical tail structures displayed profound differences in host spectra. Moreover, point mutations in tail and spike proteins were sufficient to evade neutralization by two phage-specific antisera, isolated from rabbits.ConclusionAlthough all analyzed phages are 83-97% identical at the genome level, they display a surprisingly large variation in various phenotypic properties. The small overlap in host spectrum and their ability to readily escape immune defences against a nearly identical phage are promising elements for the application of these phages in phage therapy.

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Genomes of “phiKMV-like viruses” of Pseudomonas aeruginosa contain localized single-strand interruptions

Cited by 28 publications

References 21 publications

Related haloarchaeal pleomorphic viruses contain different genome types

Related haloarchaeal pleomorphic viruses contain different genome types

Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans, Belonging to the “phiKMV-Like Viruses”

Phenotypic and genotypic variations within a single bacteriophage species

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