NONRANDOM LOCATION OF IS1 ELEMENTS IN THE GENOMES OF NATURAL ISOLATESOF ESCHERICHIA-COLI

We have studied the spatial distribution of IS1 elements in the genome s of natural isolates comprising the ECOR reference collection of Esch erichia coli. We find evidence for nonrandomness at three levels. Many pairs of IS1 elements are in much closer physical proximity (<10 kb) than can be accounted for by chance. IS1 elements in close proximity w ere identified by long-range PCR amplification of the genomic sequence between them. Each amplified region was sequenced and its map locatio n determined by database screening or DNA hybridization. Among the ECO R strains with at least two IS1 elements, 54% had one or more pairs of elements separated by <10 kb. We propose that this type of clustering is a result of ''local hopping,'' in which we assume that a significa nt proportion of transposition events leads to the insertion of a daug hter IS element in the vicinity of the parental element. A second leve l of nonrandomness is found in strains with a modest number of IS1 ele ments that were mapped through the use of inverse PCR to amplify flank ing genomic sequences: in these strains, the insertion sites tend to b e clustered over a smaller region of chromosome than would be expected by chance. A third level of nonrandomness is observed in the composit e distribution of IS elements across strains: among 20 mapped ISI elem ents, none were found in the region of 48-77 minutes, a significant ga p. One region of the E. coli chromosome, at 98 min, had a cluster of I S1 elements in seven ECOR strains of diverse phylogenetic origin. We d educe from sequence analysis that this pattern of distribution is a re sult of initial insertion in the most recent common ancestor of these strains and therefore not a hot spot of insertion. Analysis using long -range PCR with primers for IS2 and IS3 also yielded pairs of elements in close proximity, suggesting that these elements may also occasiona lly transpose by local hopping.