Genomic characterization of Ralstonia solanacearum phage φRSA1 and its related prophage (φRSX) in strain GMI1000

phi RSA1 is a wide-host-range bacteriophage isolated from Ralstonia solanacearum. In this study, the complete nucleotide sequence of the phi RSA1 genomic DNA was determined. The genome was 38,760 bp of doublestranded DNA (65.3% G + C) with 19-bp 5'-extruding cohesive ends (cos) and contained 51 open reading frames (ORFs). Two-thirds of the phi RSA1 genomic region encodes the phage structural modules, and they are very similar to those reported for coliphage P2 and P2-like phages. A phi RSA1 minireplicon with an 8.2-kbp early-expressing region was constructed. A late-expression promoter sequence motif was predicted for these phi RSA1 genes as 5' TGTTGT-(X)(13)-ACAACA. The genomic sequence similarity between phi RSA1 and related phages phi 52237 and phi CTX was interrupted by three AT islands, one of which contained an insertion sequence element, suggesting that they were recombinational hot spots. phi RSA1 was found to be integrated into at least three different strains of R. solanacearum, and the chromosomal integration site (attB) was identified as the 3' portion of the arginine tRNA(CCG) gene. In the light of the phi RSA1 gene arrangement, one possible prophage sequence previously detected on the chromosome of R. solanacearum strain GMI1000 was characterized as a phi RSA1-related prophage (designated phi RSX). phi RSX was found to be integrated at the serine tRNA (GGA) gene as an att site, and its size was determined to be 40,713 bp. phi RSX ORFs shared very high amino acid identity with their phi RSA1 counterparts. The relationships and evolution of these P2-like phages are discussed.