Conservation and variation of nucleotide sequences within related bacterial genomes: Escherichia coli strains

Abstract

Changes in the patterns produced by annealing restriction endonuclease digests of bacterial genomes with probe DNA containing small portions of a bacterial genome provide sensitive indicators of the degree of nucleotide sequence relatedness that exists in localized regions of the genomes of closely related bacteria. Five probe DNA were used to explore the relatedness of parts of the genomes of 6 laboratory E. coli strains. A range in the amount of variability in the positions of restriction enzyme cleavage sites in the selected portions of the genomes was found. Portions of the genome that are believed to be inactive were more variable than portions that contained functional genes: the sites in and near regions of homology to phage .lambda. DNA in the genome showed the greatest variability. These regions probably represent remnants of cryptic prophages. Variability was assessed pairwise among 4 of the E. coli strains and ranged from 5 to > 25% base pair substitutions in the .lambda.-related regions. In contrast, the endonuclease cleavage sites in the trp, tna, lac, thy regions, and 1 other as-yet-unidentified segment of the genome were more highly conserved. It seems likely that these sites lie in genetic locations that are subject to functional constraints.