Origin and Evolution of Studiervirinae Bacteriophages Infecting Pectobacterium: Horizontal Transfer Assists Adaptation to New Niches

Abstract

Black leg and soft rot are devastating diseases causing up to 50% loss of potential potato yield. The search for, and characterization of, bacterial viruses (bacteriophages) suitable for the control of these diseases is currently a sought-after task for agricultural microbiology. Isolated lytic Pectobacterium bacteriophages Q19, PP47 and PP81 possess a similar broad host range but differ in their genomic properties. The genomic features of characterized phages have been described and compared to other Studiervirinae bacteriophages. Thorough phylogenetic analysis has clarified the taxonomy of the phages and their positioning relative to other genera of the Autographiviridae family. Pectobacterium phage Q19 seems to represent a new genus not described previously. The genomes of the phages are generally similar to the genome of phage T7 of the Teseptimavirus genus but possess a number of specific features. Examination of the structure of the genes and proteins of the phages, including the tail spike protein, underlines the important role of horizontal gene exchange in the evolution of these phages, assisting their adaptation to Pectobacterium hosts. The results provide the basis for the development of bacteriophage-based biocontrol of potato soft rot as an alternative to the use of antibiotics.

Novel Acinetobacter baumannii Bacteriophage Aristophanes Encoding Structural Polysaccharide Deacetylase

“…This hinders further attribution of Aristophanes to a particular genus. The intergenomic similarity matrix made with the VIRIDIC tool, possibly better estimating the intergenomic similarities [ 40 , 41 ], places the phage Aristophanes near the Beijerinckvirinae Acinetobacter phages of the genera of Daemvirus , Pettyvirus , and Friunavirus with the value of 18.8–22% which is far beyond the genus threshold of 70% ( Figure S1 ).…”

“…The large subunit of terminase appears to be one of the most conserved proteins e The large subunit of terminase appears to be one of the most conserved proteins encoded in bacteriophage genomes, that makes this protein appropriate for the elucidation of phylogenetic relations [41,42]. The phylogenetic tree, constructed with protein sequences including the representatives of all genera of Beijerinckvirinae subfamily places the phage Aristophanes comparatively distantly from other Beijerinckvirinae phages infecting Acinetobacter spp.…”

Combination Therapy of Phage vB_KpnM_P-KP2 and Gentamicin Combats Acute Pneumonia Caused by K47 Serotype Klebsiella pneumoniae

“…In this study, P-KP2 ORF46, a putative tail fiber protein, had been predicted to be RBP of the phage due to its tail spike-like domain (976-1,050 residues, PDB ID: 3VTN_A), indicating that the protein may mediate specific binding of phage to the host outer membrane proteins (Tu et al, 2017). The C-terminus of ORF46 and its homologous proteins have low sequence conservation (Supplementary Figure 3), suggesting that gp46 may be originated from a later evolutionary stage in the process of horizontal gene exchange (Evseev et al, 2020). Besides, the unique C-terminus may determine the huge host spectrum difference between P-KP2 and its homologous phages.…”

Use of a Specific Phage Cocktail for Soft Rot Control on Ware Potatoes: A Case Study

“…All selected phages had their genomes sequenced and presented a strictly lytic behavior with respect to their isolation strains. The detailed properties of some of these were previously reported [8,15,16]. General features of the phages comprising the experimental phage cocktail are presented in Table 2.…”