Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus.

Colin Buttimer,Rob Lavigne,Hanne Hendrix,Aidan Coffey,Jean-Paul Noben,Caoimhe Lynch,Horst Neve

doi:10.3390/antibiotics9060352

Abstract

To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB_PatM_CB7), which specifically infects P. atrosepticum. Host range, morphology, latent period, burst size and stability at different conditions of temperature and pH were examined. Analysis of its genome (142.8 kbp) shows that the phage forms a new species of Certrevirus, sharing sequence similarity with other members, highlighting conservation within the genus. Conserved elements include a putative early promoter like that of the Escherichia coli sigma70 promoter, which was found to be shared with other genus members. A number of dissimilarities were observed, relating to DNA methylation and nucleotide metabolism. Some members do not have homologues of a cytosine methylase and anaerobic nucleotide reductase subunits NrdD and NrdG, respectively. Furthermore, the genome of CB7 contains one of the largest numbers of homing endonucleases described in a single phage genome in the literature to date, with a total of 23 belonging to the HNH and LAGLIDADG families. Analysis by RT-PCR of the HNH homing endonuclease residing within introns of genes for the large terminase, DNA polymerase, ribonucleotide reductase subunits NrdA and NrdB show that they are splicing competent. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was also performed on the virion of CB7, allowing the identification of 26 structural proteins—20 of which were found to be shared with the type phages of the genera of Vequintavirus and Seunavirus. The results of this study provide greater insights into the phages of the Certrevirus genus as well as the subfamily Vequintavirinae.

Highlights

IntroductionAntibiotics 2020, 9, 352 pectinolytic enzymes upon plant infection [1,2]
Soft rot Enterobacteriaceae (SRE) is a group of economically important phytopathogenic bacteria that consist of the genera of Pectobacterium and Dickeya, both typified by the production of extracellularAntibiotics 2020, 9, 352; doi:10.3390/antibiotics9060352 www.mdpi.com/journal/antibioticsAntibiotics 2020, 9, 352 pectinolytic enzymes upon plant infection [1,2]
The coming years should see the establishment of additional genera, with at least one other phage type known to infect this SRE

Summary

Introduction

Antibiotics 2020, 9, 352 pectinolytic enzymes upon plant infection [1,2] These bacteria cause pre- and post-harvest losses of potato (Solanum tuberosum L.) production globally, with this food crop being one of the most intensively grown worldwide [3,4,5]. Of the SRE, Pectobacterium atrosepticum has traditionally been the most dominant at affecting the potato crop in temperate climates, causing potato blackleg and soft rot disease [1,6], for which there are currently no effective bactericides. The phages of P. atrosepticum have received this attention, with our lab previously demonstrating the capability of a three-component phage mixture to suppress the formation of soft rot caused by this bacterium on potato tubers [11]. Zaczek-Moczydłowska et al have demonstrated the ability of a phage cocktail targeting

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Conclusion