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

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.

Larger Than Life: Isolation and Genomic Characterization of a Jumbo Phage That Infects the Bacterial Plant Pathogen, Agrobacterium tumefaciens

“…Although the genome of Atu_ph07 only shares 33 homologous ORFs with the genome of bacteriophage T4 (Supplementary Table S2 ), core proteins involved in phage morphogenesis and DNA replication, recombination, and repair were identified (Supplementary Table S3 ) (Miller et al, 2003 ). The phylogenetic trees are consistent with the recent characterization of Xanthomonas phage XacN1 (Yoshikawa et al, 2018 ), which suggested that XacN1, Salicola phage SCTP-2 and Atu_ph07 are distantly related to the Rak2-like jumbo phages.…”

“…The genome of phage SCTP-2 has the highest number of conserved genes with 141 genes (19.7% of Atu_ph07 ORFs) in common with the Atu_ph07 genome, perhaps due to the relatively large size of these phage genomes. Overall, the gene composition of Atu_ph07 is not well conserved with the Rak2-like phages (Figure 5 , Supplementary Table S2 ), consistent with proposal that Atu_ph07, together with SCTP-2, may belong to a new clade that comprises a sister group to the Rak2-like phages (Yoshikawa et al, 2018 ).…”

“…Most jumbo phages are members of the Myoviridae family and contain visible tails. The largest known phage genome belongs to Bacillus phage G at 497 kbp (Donelli et al, 1975 ), followed by Salicola phage SCTP-2 at 440 kbp, Xanthomonas phage XacN1 at 384 kbp (Yoshikawa et al, 2018 ), Pectobacterium phage CBB at 378 kbp (Buttimer et al, 2017a ), Cronobacter phage vB_CsaM_GAP32 at 358 kbp (Abbasifar et al, 2014 ), and Serratia phage BF at 357 kbp (Casey et al, 2017 ). Recently, some of these T4-like jumbo phages (CBB, vB_CsaM_GAP32, BF, vB_KleM-Rak2, K64-1, 121Q, vB_Eco_slurp01, PBECO4) were classified into a new phylogenetic clade called “Rak2-like viruses” (Buttimer et al, 2017a ; Yoshikawa et al, 2018 ), named after Enterobacteria phage Rak2 (Simoliunas et al, 2013 ).…”

Multiple evolutionary origins of giant viruses

“…Normally, with the exception of tRNA genes present in some bacteriophages 63 , 64 , viruses lack translation-related genes. Indeed, the reliance on the translation system of the host is one of the defining features of viruses that have been branded “capsid-encoding” organisms as opposed to cellular life forms, the “ribosome-encoding organisms” 65 .…”

Integrative omics analysis ofPseudomonas aeruginosavirus PA5oct highlights the molecular complexity of jumbo phages

“…In comparison, the in silico RAST annotation pipeline(McNair et al, 2018) allowed the identification of 412 CDS. The genome has long direct terminal repeats (DTR) of 39,080 bases, a characteristic also found in previously published jumbo phages(Yoshikawa et al, 2018).Interestingly, the DTR region includes 105 genes, many of which are highly transcribed in the early phase of the infection(Figure 2). Aside from 449 protein coding sequences, the phage genome also contains twelve tRNAs [Met (CAT), Leu (TAA), Asn (GTT), Thr (TGT), Met (CAT), Leu (TAA), Arg (TCT), Met (CAT), Pro (TGG), Gly (TCC), Ser (TGA) and Ser (GCT)] that were identified by tRNAscan-SE(Lowe et al, 2016) and confirmed in the RNA-Seq data.…”