Interestingly, a prophage element found in the identical spot (between mutS and cinA) in the genome of P. fluorescens SBW25 http://​www.​sanger.​ac.​uk/​Projects/​P_​fluorescens has a similar overall organization but contains a P2-like bacteriophage tail cluster (orf5 through orf18) similar to that in phage CTX (Fig. 1), thus resembling another class of phage tail-like bacteriocins, the R-type pyocins of P. aeruginosa [19]. Furthermore, a homologous region from P. fluorescens Pf0-1 (CP000094) contains

both the lambda-like and P2-like tail clusters (Fig. 1), making it similar to the hybrid R2/F2 pyocin locus from P. aeruginosa PAO1 [19]. The differences in organization of the putative phage tail-like pyocins among these prophages clearly indicate that the corresponding loci are subject to extensive recombination, with a possible recombination hotspot between two highly conserved DNA segments comprised of the phage repressor (prtR) and holin Selleckchem Nutlin-3a (hol) genes, and the endolysin (lys) gene (Fig. 1). In strains Pf-5 and Q8r1-96, the putative prophage 01-like pyocins are integrated between mutS and the cinA-recA-recX genes (Fig. 1), which suggests that these elements might be activated click here during the SOS response, as is the putative prophage gene cluster integrated into the mutS/cinA region of P. fluorescens DC206 [21]. The mutS/cinA region

is syntenic in several Gram-negative bacteria [22], and comparisons reveal that prophage 01-like elements occupy the same site in the genomes of P. fluorescens Pf0-1, P. fluorescens SBW25, and P. entomophila L48 [23], whereas unrelated prophages reside upstream of cinA in P. putida F1 (GenBank CP000712) and P. syringae pv. tomato DC3000 [24]. The latter strain, as well as P. putida KT2440 [25], carry SfV-like bacteriophage tail assembly clusters elsewhere in the genome. The putative F- and R-pyocins appear to be ubiquitously distributed among

strains of P. fluorescens as illustrated by a screening experiment Mannose-binding protein-associated serine protease (Fig. 4) in which genomic DNA of different biocontrol strains was hybridized to probes targeting the lambda-like and P2-like bacteriophage tail gene clusters of Q8r1-96 and SBW25, respectively. The F- and R-pyocin-specific probes each strongly hybridized to DNA from 12 of 34 P. fluorescens strains, while the remaining 22 strains tested positive with both probes. Figure 4 Southern hybridization of DNA from 34 strains of P. fluorescens with probes targeting F-pyocin- and R-pyocin-like bacteriophage tail assembly genes. Total genomic DNA from each strain was digested with EcoRI and PstI restriction endonucleases, separated by electrophoresis in a 0.8% agarose gel, and transferred onto a BrightStar-Plus nylon membrane. The blots were hybridized with biotin-labeled probes prepared from P. fluorescens strains Q8r1-96 (A) and SBW25 (B) targeting the SfV-like (A) and CTX-like (B) bacteriophage tail assembly genes, respectively.