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. 2017 Jul 17;9(7):188.
doi: 10.3390/v9070188.

Novel Fri1-like Viruses Infecting Acinetobacter baumannii-vB_AbaP_AS11 and vB_AbaP_AS12-Characterization, Comparative Genomic Analysis, and Host-Recognition Strategy

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Free PMC article

Novel Fri1-like Viruses Infecting Acinetobacter baumannii-vB_AbaP_AS11 and vB_AbaP_AS12-Characterization, Comparative Genomic Analysis, and Host-Recognition Strategy

Anastasia V Popova et al. Viruses. .
Free PMC article

Abstract

Acinetobacter baumannii is a gram-negative, non-fermenting aerobic bacterium which is often associated with hospital-acquired infections and known for its ability to develop resistance to antibiotics, form biofilms, and survive for long periods in hospital environments. In this study, we present two novel viruses, vB_AbaP_AS11 and vB_AbaP_AS12, specifically infecting and lysing distinct multidrug-resistant clinical A. baumannii strains with K19 and K27 capsular polysaccharide structures, respectively. Both phages demonstrate rapid adsorption, short latent periods, and high burst sizes in one-step growth experiments. The AS11 and AS12 linear double-stranded DNA genomes of 41,642 base pairs (bp) and 41,402 bp share 86.3% nucleotide sequence identity with the most variable regions falling in host receptor-recognition genes. These genes encode tail spikes possessing depolymerizing activities towards corresponding capsular polysaccharides which are the primary bacterial receptors. We described AS11 and AS12 genome organization and discuss the possible regulation of transcription. The overall genomic architecture and gene homology analyses showed that the phages are new representatives of the recently designated Fri1virus genus of the Autographivirinae subfamily within the Podoviridae family.

Keywords: Acinetobacter baumannii; Fri1virus; Podoviridae; RNA polymerase; bacteriophage; capsule types; tail spike.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Morphological characteristics of phage AS11: (A) Phage plaques with opaque haloes on the Acinetobacter baumannii 28 (B) Transmission electron micrographs of the bacteriophage. Staining with 1% uranyl acetate. The scale bar is 50 nm.
Figure 2
Figure 2
Infection analysis of phages AS11 and AS12. Adsorption assay and one-step growth curve of phage AS11 on A. baumannii strain 28 (A) and phage AS12 on A. baumannii strain 1432 (B) with indication of estimated burst size (BS) and latent period (L). Results are the means and standard deviations from three independent experiments. PFU: plaque forming units.
Figure 3
Figure 3
Comparison of AS11 and AS12 genomes. The AS11 and AS12 genomes are schematically presented. Open reading frames (ORFs) are indicated as arrows, the direction of an arrow shows the direction of transcription. The ORFs are colored according to functional predictions: green for genes coding enzymes of nucleotide metabolism and proteins involved in DNA replication and repair; red for virion and lysis protein genes. Overrepresented motifs that likely function as putative phage-encoded RNAP promoters are indicated as violet flags. Terminators are shown as hairpins.
Figure 4
Figure 4
Comparative genome analysis of all known to date Fri1-like viruses. Reference: A. baumannii phage vB_AbaP_AS11 genome. Query: complete genome sequences of related A. baumannii podoviruses, listed in the key left. The DNA regions of AS11 genome that differ from other phages are marked. Map includes divider line showing genomes are linear.
Figure 5
Figure 5
Comparison of RNA polymerases (RNAP) proteins. Phylogenetic tree of single-subunit RNAPs from Fri1-like, phiKMV-like, and Kp34-like phages constructed using a neighbor-joining algorithm is shown. Consensus sequences for overrepresented motifs from intergenic regions of indicated A. baumannii phages are shown.
Figure 6
Figure 6
Identification of AS11 and AS12 phage-encoded T7-type RNAP promoters: (A) A logo representation of putative promoter consensus sequence for phages AS11 and AS12; (B) Sequences of phage-encoded promoters validated by primer extension analysis; (C) Example of in vitro promoter mapping. The products of sequencing reactions, performed with the same end-labelled primers and appropriate PCR fragment as a template were run alongside primer extension reactions.

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