Unequal access of chromosomal regions to each other in Salmonella: probing chromosome structure with phage λ integrase-mediated long-range rearrangements

Summary We have investigated the fluidity of the Salmonella chromosome architecture using the phage lambda site-specific recombination system as a probe. We determined how chromosome position affects the extent of integrase-mediated recombination between pairs of inversely oriented att sites at various loci. We also investigated the accessibility of each chromo- somal att site to an extrachromosomal partner carried on a low-copy plasmid. Recombination events were assayed by semi-quantitative polymerase chain reac- tion of the attP product. The extent of recombination between the chromosome and the plasmid was gen- erally higher than intrachromosomal recombination except for two loci, araA :: attL and galT :: attL , which gave no detectable recombination with any other locus. Based on 20 intervals, we found that chromo- somal locations are not equally accessible to each other. Although multiple factors probably affect accessibility, the most important is the specific com- bination of the end-points used. Neither the size of the intervals nor the accessibility of individual end- points to extrachromosomal sequences is as impor- tant. These results suggest that the chromosome is not completely fluid but rather organized in some way, with barriers that limit the movement of DNA within the cell. The nature of the barriers involved in chro- mosomal organization remains to be determined.