Abstract
Pectobacterium atrosepticum is a phytopathogen of economic importance as it is the causative agent of potato blackleg and soft rot. Here we describe the Pectobacterium phage vB_PatP_CB5 (abbreviated as CB5), which specifically infects the bacterium. The bacteriophage is characterized in detail and TEM micrographs indicate that it belongs to the Podoviridae family. CB5 shares significant pairwise nucleotide identity (≥80%) with P. atrosepticum phages φM1, Peat1, and PP90 and also shares common genome organization. Phylograms constructed using conserved proteins and whole-genome comparison-based amino acid sequences show that these phages form a distinct clade within the Autographivirinae. They also possess conserved RNA polymerase recognition and specificity loop sequences. Their lysis cassette resembles that of KP34virus, containing in sequential order a U-spanin, a holin, and a signal–arrest–release (SAR) endolysin. However, they share low pairwise nucleotide identity with the type phage of the KP34virus genus, Klebsiella phage KP34. In addition, phage KP34 does not possess several conserved proteins associated with these P. atrosepticum phages. As such, we propose the allocation of phages CB5, Peat1, φM1, and PP90 to a separate new genus designated Phimunavirus.
Highlights
In the post-genomic era, the number of bacteriophage genomes being deposited into public databases such as the NCBI GenBank has substantially increased, due in part to the ever-decreasing cost of DNA sequencing
We propose the formation of the bacteriophage genus ‘Phimunavirus’ to formally classify these phages, with the Pectobacterium phage φM1 designated as the type phage
Spot tests showed that the phage had an inhibitory effect on of the other strains of P. atrosepticum tested with the observation of zones of clearing at high phage titers despite the absence of distinct plaques
Summary
In the post-genomic era, the number of bacteriophage (phage) genomes being deposited into public databases such as the NCBI GenBank has substantially increased, due in part to the ever-decreasing cost of DNA sequencing. This growing quantity of genomic data has led to increasing insights into the evolutionary relationships between phages. Classification has developed to the point where nucleotide and protein homology can be usefully employed to tease out phylogenetic relationships. This has led to the creation of subfamilies within Myoviridae, Siphoviridae, and Podoviridae, such as the subfamily Autographivirinae. Key defining features of the subfamily Autographivirinae include the presence of a single RNA polymerase (RNAP) gene and a Viruses 2018, 10, 394; doi:10.3390/v10080394 www.mdpi.com/journal/viruses
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