Intraspecific diversity of the 23S rRNA gene and the spacer region downstream in Escherichia coli

The molecular microevolution of the 23S rRNA gene (rrl) plus the spacer dow nstream has been studied by sequencing of different operons from some repre sentative strains of the Escherichia coli ECOR collection. The rrl gene was fully sequenced in six strains showing a total of 67 polymorphic sites, a level of variation per nucleotide similar to that found for the 16S rRNA ge ne (ws) in a previous study. The size of the gene was highly conserved (290 2 to 2905 nucleotides). Most polymorphic sites were clustered in five secon dary-structure helices. Those regions in a large number of operons were seq uenced, and several variations were found. Sequences of the same helix from two different strains were often widely divergent, and no intermediate for ms existed. Intercistronic variability was detected, although it seemed to be lower than for the rrs gene. The presence of two characteristic sequence s was determined by PCR analysis throughout all of the strains of the ECOR collection, and some correlations with the multilocus enzyme electrophoresi s clusters were detected. The mode of variation of the rrl gene seems to be quite similar to that of the rrs gene. Homogenization of the gene families and transfer of sequences from different clonal lines could explain this p attern of variation detected; perhaps these factors are more relevant to ev olution than single mutation. The spacer region between the 23S and 5S rRNA genes exhibited a highly polymorphic region, particularly at the 3' end.