Overall Organization of the Genomes

The nucleotide sequences of N15, PY54 and ^KO2 have been determined (Casjens et al. 2004; Hertwig et al. 2003b; Ravin et al. 2000). Sequence analyses disclosed 59 (N15), 67 (PY54) and 64 (^KO2) putative open reading frames (ORFs). Similarities to known proteins and functional analyses allowed assignments for a number of gene products. The genes of each phage are situated in two arms separated by the tel site and are arranged in a similar order (Fig. 2). Genes coding for head and tail assembly proteins are located in the left arm. In addition, the left arm of the three phages carries genes for partitioning proteins. Close to the tel site, the right arm harbours the pro-telomerase gene tel essential for the generation of the plasmid hairpin ends. Rightward a large gene resides encoding a multifunctional replication protein (RepA). Adjacent to repA the genomes contain the primary immunity region comprising genes for the prophage repressor CB, the Cro repressor and the Q transcription antiterminator. Further to the right genes probably associated with DNA methylation and host cell lysis have been identified. However, for a significant number of genes of each phage a functional prediction could not be made, even though homologous counterparts at similar positions have been detected in the other phage genomes.

Overall the left arm of the PY54 genome is more closely related to ^KO2 than to N15, whereas N15 and ^KO2 show the strongest homologies in the

Fig. 2 Organization of the phage N15, PY54 and 4>KO2 genomes. Putative genes are indicated by arrows. Functional assignments are shown above the genes. The positions of the telomere resolution sites (telRL) and the origin of PY54 are indicated. Grey bars connect homologous regions of the genomes. a Homologies between PY54 and the other two phages. b Relationship between N15 and 4>KO2

Fig. 2 Organization of the phage N15, PY54 and 4>KO2 genomes. Putative genes are indicated by arrows. Functional assignments are shown above the genes. The positions of the telomere resolution sites (telRL) and the origin of PY54 are indicated. Grey bars connect homologous regions of the genomes. a Homologies between PY54 and the other two phages. b Relationship between N15 and 4>KO2

right arm. As the genomes of all three phages are mosaically related to \ and as some of their genes are highly homologous to each other or to those of lambda-like phages, it has been suggested to include N15, PY54 and ^KO2 as a subgroup into the lambdoid phage family (Casjens et al. 2004). This family comprises a number of similar phages (e.g. P22) that are genetic mosaics sharing a common order and organization of genetic functions along their genomes (Juhala et al. 2000). Some members of this family can easily recombine with each other to produce functional hybrids. Horizontal gene exchange is therefore suggested to be a major component of evolution for these viruses (Hendrix et al. 2003).

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