Prediction, identification, and artificial selection of DNA rearrangements in Rhizobium: Toward a natural genomic design

Based on the DNA sequence of the symbiotic plasmid of Rhizobium strain NGR234, we predicted potential rearrangements generated by homologous recombination. All predicted rearrangements were identified experimentally by using a PCR-based methodology. Thus, the predicted and the actual dynamic maps of the replicon coincide. By using an approach that does not involve the introduction of exogenous genetic elements, derivative populations that are pure for specific rearrangements were obtained. We propose that knowledge of the DNA sequence of a genome offers the possibility of designing pathways of sequential rearrangements leading to alternative genomic structures. An experimental strategy to isolate bacterial populations containing the desired structures is discussed.