tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains.

tRNA-encoding genes (tDNA) are known hot-spots for the integration of ecto-chromosomal DNA (ECDNA) including genomic islands. However, only a few loci are currently known to be targeted by such insertions in Escherichia coli. A PCR-based screening of tDNA integrity was therefore performed on a collection of E. coli strains in order to identify tDNA loci that are most frequently intact and those that are preferred ECDNA insertion sites. It was shown that only a subset of tDNAs were hot-spots for ECDNA insertions, and that the majority of loci were never targeted by such insertions. Polycistronic tDNAs, highly transcribed tDNAs or tDNAs encoding tRNAs recognizing frequently used codons were generally not targeted by ECDNA insertions. Most interestingly, strains of different ECOR groups showed different patterns of tDNA loci polymorphism. More subtle differences were also observed between strains of different pathotypes.