Genomic Instability in Regions Adjacent to a Highly ConservedpchProphage inEscherichia coliO157:H7 Generates Diversity in Expression Patterns of the LEE Pathogenicity Island
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ABSTRACTThe LEE pathogenicity island has been acquired on multiple occasions within the different lineages of enteropathogenic and enterohemorrhagicEscherichia coli. In each lineage, LEE expression is regulated by complex networks of pathways, including core pathways shared by all lineages and lineage-specific pathways. Within the O157:H7 lineage of enterohemorrhagicE. coli, strain-to-strain variation in LEE expression has been observed, implying that expression patterns can diversify even within highly related subpopulations. Using comparative genomics ofE. coliO157:H7 subpopulations, we have identified one source of strain-level variation affecting LEE expression. The variation occurs in prophage-dense regions of the genome that lie immediately adjacent to the late regions of thepchprophage carryingpchA, pchB, pchC, and a newly identifiedpchgene,pchX. Genomic segments extending from the holin S region to thepchA, pchB, pchC, andpchXgenes of their respective prophage are highly conserved but are nonetheless embedded within adjacent genomic segments that are extraordinarily variable, termedpchadjacent genomic regions (pchAGR). Despite the remarkable degree of variation, the pattern of variation inpchAGR is highly correlated with the distribution of phylogenetic markers on the backbone of the genome. Quantitative analysis of transcription from theLEE1promoter further revealed that variation in thepchAGR has substantial effects on absolute levels and patterns of LEE1 transcription. Variation in thepchAGR therefore serves as a mechanism to diversify LEE expression patterns, and the lineage-specific pattern ofpchAGR variation could ultimately influence ecological or virulence characteristics of subpopulations within each lineage.
