Sequence analysis of the genome of OP2, a lytic bacteriophage of Xanthomonas oryzae pv. oryzae

Abstract

We sequenced and analyzed the genome of OP 2 (MAFF 106404), a bacteriophage that lyses Xanthomonas oryzae pv. oryzae (Xoo). It is 46 643 bp, and the average G + C content is 60.9%. The results suggest that the genome sequence of OP 2 is circularly permuted and terminally redundant, like that of coliphages T4 or P22. Sixty-two open reading frames (ORFs) were predicted in the genome. We constructed a circular map of the restriction enzyme sites and a gene map. The genome is clearly divided into four parts according to transcription direction. The directions of 27 ORFs are leftward and those of 35 are rightward. Most leftward ORFs are commonly conserved among many other phages, and some are structure-related or expressionrelated genes. In contrast, most rightward ORFs contain OP 2 -specific genes as well as DNA polymerase, helicase, dUTPase, and HNH family endonuclease genes. Nine rightward and 25 leftward ORFs have homology with the ORFs of bacteriophage Bcep1, which lyses Burkholderia cepacia. The leftward-transcribed OP 2 genes and their orthologs in Bcep1 conserve a neighboring relationship, although the putative tail fiber gene does not have homology with that of Bcep1. Several ORFs have similarity (<e −5 ) to phage-related genes of Xylella fastidiosa and Xanthomonas spp. Exceptionally, the dUTPase gene had 94% identity with Xoo, and no insertions or deletions were detected in it. However, its neighboring regions did not have homology with the Xoo sequence. Although OP 2 is a virulent phage of Xoo, some of the genetic characters have features of temperate phages.

Bacteriophage OP1, lytic for Xanthomonas oryzae pv. oryzae, changes its host range by duplication and deletion of the small domain in the deduced tail fiber gene

“…The methods of preparation, sequencing, and analysis of phage DNA are described by Inoue et al (2006). A total of 288 clones containing an OP 1 genomic DNA fragment were constructed for analysis of the DNA sequence.…”

“…The method of functional annotation is described by Inoue et al (2006). The similarity of a putative gene in OP 1 and a gene in the database was judged using the expectation value (E-value), which indicates the validity of the match.…”

Adsorption of OP1-related bacteriophages requires the gene encoding a TonB-dependent receptor-like protein in Xanthomonas oryzae pv. oryzae

“…Xoo phage OP 2 , however, differs genetically, serologically and morphologically from OP 1 (Yoshimura et al 1960;Inoue et al 2006b). The relationships between the phages and Xoo strains are shown in Table 1.…”

Identification of a Broad-Spectrum Peptidoglycan Hydrolase Associated with the Particle of <b><i>Xanthomonas oryzae</i></b> Phage Xop411

“…campestris phage phiL7 [Lee et al, 2009], the Xo phages OP1 [Inoue et al, 2006a], OP2 [Inoue et al, 2006b], Xop411 [Lee et al, 2007], Xp10 [Yuzenkova et al, 2003], and the X. campestris pv. pelargonii phage Xp15 (NCBI database AY986977).…”