Type-specific contributions to chromosome size differences in Escherichia coli

The Escherichia coli genome varies in size from 4.5 to 5.5 Mb. It is unclea r whether this variation may be distributed finely throughout the genome or is concentrated at just a few chromosomal loci or on plasmids. Further, th e functional correlates of size variation in different genome copies are la rgely unexplored, We carried out comparative macrorestriction mapping using rare-restriction-site alleles (made with the Tn10dRCP2 family of elements, containing the NotI, BlnI, I-CeuI, and ultra-rare-cutting I-SceI sites) am ong the chromosomes of laboratory E. coli K-12, newborn-sepsis-associated E . coli RS218, and uropathogenic E, coli J96. These comparisons showed just a few large accessory chromosomal segments accounting for nearly all strain -to-strain size differences. Of 10 sepsis-associated and urovirulence genes , previously isolated from the two pathogens by scoring for function, all w ere colocalized exclusively with one or more of the accessory chromosomal s egments. The accessory chromosomal segments detected in the pathogenic stra ins from physical, macrorestriction comparisons may be a source of new viru lence genes, not yet isolated by function.