Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes

Genki Yoshikawa,Hiroyuki Ogata,Miyako Nakano,Yanze Li,Romain Blanc-Mathieu,Takeru Kawasaki,Takashi Yamada,Ahmed Askora

doi:10.1038/s41598-018-22239-3

Genki Yoshikawa, Hiroyuki Ogata + Show 6 more

Open Access

https://doi.org/10.1038/s41598-018-22239-3

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Abstract

Xanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins and presents the longest (66 kbp) direct terminal repeats (DTRs) among sequenced viral genomes. The DTRs harbor 56 tRNA genes, which correspond to all 20 amino acids and represent the largest number of tRNA genes reported in a viral genome. Codon usage analysis revealed a propensity for the phage encoded tRNAs to target codons that are highly used by the phage but less frequently by its host. The existence of these tRNA genes and seven additional translation-related genes as well as a chaperonin gene found in the XacN1 genome suggests a relative independence of phage replication on host molecular machinery, leading to a prediction of a wide host range for this jumbo phage. We confirmed the prediction by showing a wider host range of XacN1 than other X. citri phages in an infection test against a panel of host strains. Phylogenetic analyses revealed a clade of phages composed of XacN1 and ten other jumbo phages, indicating an evolutionary stable large genome size for this group of phages.

Highlights

Tailed bacteriophages with genomes larger than 200 kbp are commonly named “jumbo phages”[1]
XacN1 was isolated from a soil sample collected from orange groves in Akitsu, Japan, by plaque assay with X. citri strain MAFF 301080 as the host
In pulsed-field gel electrophoresis (PFGE) analyses, the genomic DNA of XacN1 gave a band at approximately 390 kbp (Supplementary Fig. S2)

Summary

Introduction

Tailed bacteriophages (phages) with genomes larger than 200 kbp are commonly named “jumbo phages”[1]. They usually show large virions, being capable of enclosing a larger genome than those of other smaller phages[2]. A new group of jumbo phages has been recognized[5] This group, named Rak2-like phages, is composed of phages with a genome longer than 300 kbp including Klebsiella phage vB_KleM-RaK26, Escherichia phage PBECO 47, Cronobacter phage vB_CsaM_GAP325, Escherichia phage 121Q (accession number: NC_025447), Klebsiella phage K64-18, Enterobacteria phage vB_PcaM_CBB9, and Serratia phage BF10. We report the genome sequence of a newly isolated Xanthomonas jumbo virus (phage) XacN1

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Conclusion