Isolation and characterisation of KP34--a novel φKMV-like bacteriophage for Klebsiella pneumoniae - PubMed (original) (raw)

Isolation and characterisation of KP34--a novel φKMV-like bacteriophage for Klebsiella pneumoniae

Zuzanna Drulis-Kawa et al. Appl Microbiol Biotechnol. 2011 May.

Abstract

Bacteriophage KP34 is a novel virus belonging to the subfamily Autographivirinae lytic for extended-spectrum β-lactamase-producing Klebsiella pneumoniae strains. Its biological features, morphology, susceptibility to chemical and physical agents, burst size, host specificity and activity spectrum were determined. As a potential antibacterial agent used in therapy, KP34 molecular features including genome sequence and protein composition were examined. Phylogenetic analyses and clustering of KP34 phage genome sequences revealed its clear relationships with "phiKMV-like viruses". Simultaneously, whole-genome analyses permitted clustering and classification of all phages, with completely sequenced genomes, belonging to the Podoviridae.

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Figures

Fig. 1

Fig. 1

Electron micrograph of phage KP34 negatively stained with uranyl acetate. The bar indicates 100 nm

Fig. 2

Fig. 2

SDS-PAGE analysis of purified KP34 virus particles with Sigma-Aldrich wide-range molecular weight markers in the left lane

Fig. 3

Fig. 3

Graphic layout made in CLANS software for 36 Autographivirinae genome sequences using BLASTN searches. Analysed sequences are represented by vertices connected by edges reflecting attractive forces proportional to the negative logarithm of the HSP’s P value. The greyness intensity of the connections is proportional to these forces. The not shown phages names forming compact clusters are fully listed in Table S2 in electronic supplementary material

Fig. 4

Fig. 4

Phyml tree of tail tubular proteins A (a) and tail tubular proteins B (b). Sequence from Klebsiella phage KP34 indicated in bold font. Sequences from phages are placed in the grey rectangle. Numbers at nodes, in the shown order, correspond to the minimum of support values calculated in Phyml by _χ_2 and Shimodaira–Hasegawa-like procedure (χ 2-SH); support values resulted from bootstrap analysis in Phyml (PH) and posterior probabilities estimated in Phylobayes (PB). Values of the posterior probabilities and bootstrap percentages lower or equal to 0.50 and 50%, respectively, were omitted or indicated by a dash. GenBank identifiers (gi) of sequences are shown in parenthesis

Fig. 4

Fig. 4

Phyml tree of tail tubular proteins A (a) and tail tubular proteins B (b). Sequence from Klebsiella phage KP34 indicated in bold font. Sequences from phages are placed in the grey rectangle. Numbers at nodes, in the shown order, correspond to the minimum of support values calculated in Phyml by _χ_2 and Shimodaira–Hasegawa-like procedure (χ 2-SH); support values resulted from bootstrap analysis in Phyml (PH) and posterior probabilities estimated in Phylobayes (PB). Values of the posterior probabilities and bootstrap percentages lower or equal to 0.50 and 50%, respectively, were omitted or indicated by a dash. GenBank identifiers (gi) of sequences are shown in parenthesis

Fig. 5

Fig. 5

Comparison of 3′-end genomic sequence in four phages classified to “φKMV-like” viruses. ORFs whose products show significant sequence similarity are presented in the same colour. ORFs in grey have their products annotated as hypothetical protein

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