Comparison of Genomes of Three Xanthomonas oryzae Bacteriophages

The strains of Xanthomonas axonopodis pv. citri, the causative agent of citrus canker, are historically classified based on bacteriophage (phage) sensitivity. Nearly all X. axonopodis pv. citri strains isolated from different regions in Japan are lysed by either phage Cp1 or Cp2; Cp1-sensitive (Cp1 s ) strains have been observed to be resistant to Cp2 (Cp2 r ) and vice versa. In this study, genomic and molecular characterization was performed for the typing agents Cp1 and Cp2. Morphologically, Cp1 belongs to the Siphoviridae. Genomic analysis revealed that its genome comprises 43,870-bp double-stranded DNA (dsDNA), with 10-bp 3=-extruding cohesive ends, and contains 48 open reading frames. The genomic organization was similar to that of Xanthomonas phage phiL7, but it lacked a group I intron in the DNA polymerase gene. Cp2 resembles morphologically Escherichia coli T7-like phages of Podoviridae. The 42,963-bp linear dsDNA genome of Cp2 contained terminal repeats. The Cp2 genomic sequence has 40 open reading frames, many of which did not show detectable homologs in the current databases. By proteomic analysis, a gene cluster encoding structural proteins corresponding to the class III module of T7-like phages was identified on the Cp2 genome. Therefore, Cp1 and Cp2 were found to belong to completely different virus groups. In addition, we found that Cp1 and Cp2 use different molecules on the host cell surface as phage receptors and that host selection of X. axonopodis pv. citri strains by Cp1 and Cp2 is not determined at the initial stage by binding to receptors.

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“…YP_002922634). This protein might be involved in determining the host range, as suggested by Lee et al (30,40).…”

Section: Figmentioning

confidence: 84%

Characterization of Bacteriophages Cp1 and Cp2, the Strain-Typing Agents for Xanthomonas axonopodis pv. citri

Ahmad

Ogawa

Kawasaki

et al. 2014

Appl Environ Microbiol

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“…Xanthomonas oryzae pv. oryzae strain 21 and its lytic phage Xop411 have been described previously (24,25). Strains of Xanthomonas and Escherichia coli were grown at 28°C and 37°C, respectively, in TYG (tryptone, 10 g; yeast extract, 6 g; 1 ml of 1 M MgSO 4 ; 25 ml of 20% [wt/vol] glucose in deionized H 2 O to a final volume of 1 liter).…”

Section: Methodsmentioning

confidence: 99%

“…Strains of Xanthomonas and Escherichia coli were grown at 28°C and 37°C, respectively, in TYG (tryptone, 10 g; yeast extract, 6 g; 1 ml of 1 M MgSO 4 ; 25 ml of 20% [wt/vol] glucose in deionized H 2 O to a final volume of 1 liter). Phage propagation, plaque assay, purification of phage particles, isolation of phage DNA, and restriction digestion were performed as described previously (24,25).…”

Section: Methodsmentioning

confidence: 99%

“…oryzae Siphoviridae phages Xop411, Xp10, and OP1; the X. oryzae pv. oryzae Caudoviridae phage OP2 (20,21,24,56); and the X. campestris pv. pelargonii Caudoviridae phage Xp15 (accession no.…”

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confidence: 99%

“…Results of sequence comparison indicate that phiL7 is similar to the X. oryzae pv. oryzae siphophages Xop411, Xp10, and OP1 (20,24,56) in genome organization and having its own single-subunit RNA polymerase (RNAP), characteristic of T7-like phages of the Podoviridae family, but it differs in possessing a group I intron inserted in the DNA polymerase gene. Other important differences were also found and are discussed in this paper.…”

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confidence: 99%

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Genomic Characterization of the Intron-Containing T7-Like Phage phiL7 ofXanthomonas campestris

Lee

Lin

Weng

et al. 2009

Appl Environ Microbiol

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The lytic phage phiL7, which morphologically belongs to the Siphoviridae family, infects Xanthomonas campestris pv. campestris. Nucleotide sequence analysis has revealed that phiL7 contains a linear doublestranded DNA genome (44,080 bp, 56% G؉C) with a 3-protruding cos site (5-TTACCGGAC-3) and 59 possible genes. Among the deduced proteins, 32 have homologs with known functions and 18 show no database similarities; moreover, the genes encoding these 18 proteins mostly have varying G؉C contents and form clusters dispersed along the genome. Only 39 genes have sequences related (27% to 78%) to those of sequenced genes of X. oryzae pv. oryzae phages, although the genome size and architecture of these Xanthomonas phages are similar. These findings suggest that phiL7 acquired genes by horizontal transfer, followed by evolution via various types of mutations. Major differences were found between phiL7 and the X. oryzae pv. oryzae phages: (i) phiL7 has a group I intron inserted in the DNA polymerase gene, the first such intron observed in Xanthomonas phages; (ii) although infection of phiL7 exerted inhibition to the host RNA polymerase, similar to the situations in X. oryzae pv. oryzae phages Xp10 and Xop411, sequence analysis did not identify a homologue of the Xp10 p7 that controls the shift from host RNA polymerase (RNAP) to viral RNAP during transcription; and (iii) phiL7 lacks the tail fiber protein gene that exhibits domain duplications thought to be important for host range determination in OP1, and sequence analysis suggested that p20 (tail protein III) instead has the potential to play this role.The genus Xanthomonas in the gamma subdivision of the Proteobacteria is a diverse and economically important group of bacterial plant pathogens consisting of 27 species (35), causing tremendous loss in agriculture worldwide. Individual species of this genus comprise multiple pathogenic variants (pathovars) and collectively cause diseases on at least 124 monocot species and 268 dicot species: for example, Xanthomonas campestris pv. campestris causes black rot in crucifers, X. campestris pv. vesicatoria causes spot disease in peppers and tomatoes, X. axonopodis pv. citri causes citrus canker, and X. oryzae pv. oryzae causes bacterial leaf blight on rice plants (17). In addition, members of the genus Xanthomonas commonly produce great amounts of an exopolysaccharide (xanthan gum) and X. campestris pv. campestris has been the organism of choice in industry for production of xanthan, which is useful in food, agriculture, industry and cosmetics (55).For controlling bacterial plant diseases, chemical control with antibiotics and copper compounds has been the standard (31, 46). However, many agrochemicals are toxic and may pose significant environmental and health risks (14). Therefore, there has been a resurgence of interest recently in using bacteriophages to replace the currently prevalent chemical measures, in which phages can be used effectively as part of integrated disease management strategies (12,15,16,32). Although pha...

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Isolation, Characterization, and Genome Sequence Analysis of a Novel Lytic Phage, Xoo-sp15 Infecting Xanthomonas oryzae pv. oryzae

et al. 2021

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Xanthomonas oryzae pv. oryzae (X. oryzae) is a bacterial pathovar of rice diseases all over the world. Owing to emerging antibacterial resistance, phage therapies have gained significant attention to treat various bacterial infections. Nevertheless, comprehensive research is needed for their use as a safe biocontrol agent. In this study, isolation and characterization of a novel phage Xoo-sp15, that infects X. oryzae was ascertained through experimental and bioinformatics analyses to determine its virulent potency and reliability. High throughput sequencing demonstrated that Xoo-sp15 has a dsDNA genome with a total size of 157,091 bp and 39.9% GC content lower than its host (63.6%). Morphological and phylogenetic analyses characterized it as a new member of the Bastille-like group within the family Herelleviridae. In silico analysis revealed that it contains 229 open reading frames and 16 tRNAs. Additionally, this novel phage does not contain any resistant determinants and can infect nine X. oryzae strains. Therefore, Xoo-sp15 has the potential to serve as a novel candidate for phage therapy.

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Comparison of Genomes of Three Xanthomonas oryzae Bacteriophages

Abstract: Background: Xp10 and OP1 are phages of Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial leaf blight in rice plants, which were isolated in 1967 in Taiwan and in 1954 in Japan, respectively. We recently isolated the Xoo phage Xop411.

Cited by 26 publications

References 33 publications

Characterization of Bacteriophages Cp1 and Cp2, the Strain-Typing Agents for Xanthomonas axonopodis pv. citri

Characterization of Bacteriophages Cp1 and Cp2, the Strain-Typing Agents for Xanthomonas axonopodis pv. citri

Genomic Characterization of the Intron-Containing T7-Like Phage phiL7 ofXanthomonas campestris

Isolation, Characterization, and Genome Sequence Analysis of a Novel Lytic Phage, Xoo-sp15 Infecting Xanthomonas oryzae pv. oryzae

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