Characterization of two related Erwinia myoviruses that are distant relatives of the PhiKZ-like Jumbo phages

Abstract

Bacteriophages are a major force in the evolution of bacteria due to their sheer abundance as well as their ability to infect and kill their hosts and to transfer genetic material. Bacteriophages that infect the Enterobacteriaceae family are of particular interest because this bacterial family contains dangerous animal and plant pathogens. Herein we report the isolation and characterization of two jumbo myovirus Erwinia phages, RisingSun and Joad, collected from apple trees. These two genomes are nearly identical with Joad harboring two additional putative gene products. Despite mass spectrometry data that support the putative annotation, 43% of their gene products have no significant BLASTP hit. These phages are also more closely related to Pseudomonas and Vibrio phages than to published Enterobacteriaceae phages. Of the 140 gene products with a BLASTP hit, 81% and 63% of the closest hits correspond to gene products from Pseudomonas and Vibrio phages, respectively. This relatedness may reflect their ecological niche, rather than the evolutionary history of their host. Despite the presence of over 800 Enterobacteriaceae phages on NCBI, the uniqueness of these two phages highlights the diversity of Enterobacteriaceae phages still to be discovered.

Genomics Education in the Era of Personal Genomics: Academic, Professional, and Public Considerations

“…Some universities have modified the Phage Hunters course so that the second semester of gene characterization is included into other biology classes and have demonstrated equal academic value and success [49]. In addition to the benefits of student learning, students often become authors on scientific publications of bacteriophage characterization, thereby improving their academic portfolio as well [6]. These studies demonstrate that Phage Hunters is a valuable CURE which can be implemented in large undergraduate classes and be advantageous for teaching genomics.…”

“…Important advancements in genomics have expanded to other organisms, such as bacteriophages which are currently being characterized and developed for agricultural treatments such as fire blight [5]. The use of genomics to characterize bacteriophages allows their genomes to be analyzed for bacterial specificity and to identify genes that may be beneficial or harmful in targeting specific bacterial populations [6]. In addition, genomics has played a key role in ushering in new fields of research such as the microbiome, providing many important basic science insights as well as potential treatments for a lack of genomic understanding regarding how to interpret genomic test results is an important need for genomic education about what can and cannot be concluded from personal genomic information.…”

A Novel, Highly Related Jumbo Family of Bacteriophages That Were Isolated Against Erwinia

“…Jumbo bacteriophages were also found to be highly diverse, with over 11 clusters and five singleton bacteriophages suggested from 52 complete jumbo bacteriophage genomes analyzed in 2017, many of which are uncharacterized (Yuan and Gao, 2017). Only a few jumbo bacteriophage families have been characterized beyond sequence analysis and EM, including the phiKZ-like bacteriophages 201phi2-1 (Thomas et al, 2008), KTN4 (Danis-Wlodarczyk et al, 2016), phiPA3 (Monson et al, 2011), phiRSL2 (Bhunchoth et al, 2016), phiRSF1 (Bhunchoth et al, 2016), OBP (Shaburova et al, 2006), EL (Sokolova et al, 2014), and phiKZ (Lecoutere et al, 2009), related bacteriophages phiRSL1 (Yamada et al, 2010) and PaBG (Kurochkina et al, 2018), Cronobacter bacteriophage CR5 (Lee et al, 2016), Prochlorococcus bacteriophage P-SSM2 (Sullivan et al, 2005), related bacteriophages KVP40 (Miller et al, 2003) and Aeh1 (Gibb and Edgell, 2007), Aeromonas bacteriophage phiAS5 (Kim et al, 2012), Pectobacterium bacteriophage CBB (Buttimer et al, 2017), Caulobacter bacteriophage phiCbK (Gill et al, 2012), related Erwinia bacteriophages Joad and RisingSun (Arens et al, 2018), related bacteriophage RaK2 (Simoliunas et al, 2013) and GAP32 (Abbasifar et al, 2014), Bacillus bacteriophage 0305phi8-36 (Thomas et al, 2007), related Bacillus bacteriophages BpSp (Yuan and Gao, 2016) and AR9 (Lavysh et al, 2016, 2017). Herein we further analyze the genome, proteome, and host range of our eight Agrican357virus jumbo bacteriophages.…”

Genome Sequences of Nine Erwinia amylovora Bacteriophages

“…Phages were isolated from apple trees along the Wasatch Front in Utah that appeared to harbor fire blight infection. Phages were plaque purified through a minimum of three passages after amplification via enrichment culture ( 11 ). All nine phages reported in this announcement infect the Erwinia amylovora ATCC 29780 strain, as indicated by plaque assays, and their characteristics are summarized in Table 1 .…”

“…The nine phages were grouped into five distinct clusters by genomic dot plot and average nucleotide identity analyses, as previously described ( 11 ), with the first three groups containing jumbo Myoviridae . The first jumbo group included four myoviruses, vB_EamM_Bosolaphorus, vB_EamM_Desertfox, vB_EamM_MadMel, and vB_EamM_Mortimer, which are similar to previously published Erwinia phage Ea35-70 ( 13 ), as well as other phages we have isolated ( 14 ).…”