Nucleotide sequences of the sites involved in the integration of phage 16-3 of Rhizobium meliloti 41

Temperate phage 16-3 of R. meliloti 41 inserts its genome into the host chromosome by site-specific recombination between two unique sequences (attachment sites, att) that are present in the host (attB) and phage chromosomes (attP), resulting in the integrated prophage bordered by the left (attL) and right (attR) attachment sites. The attB and attP sites had been identified previously and mapped close to the cys46 gene of the host and to the C regulator gene of the phage, respectively. The attP region was subsequently localized on the physical map of phage 16-3cti3, as was the attR on the physical map of the cys46-transducing tr4-2 phage. A cosmid clone carrying the attB region was selected from an R. meliloti 41 genomic bank by complementation of the cys46 super(-) allele. The extensive restriction analysis and Southern hybridization data allowed us to localize the three att regions on short BsuRI fragments which were subcloned and sequenced. attP, attB and attR sequences share a 51-bp long perfect homology (boxed). This identity region (core) indicates the limits within which the strand exchange must take place during recombination. The analysis of the sequences revealed some additional features. The core itself shows similarity to a number of tRNA sequences in the database, a phenomenon first described for phage T4. Inside of the identity region there is a 16-bp long imperfect inverted repeat (indicated by shaded area in the attP sequence).