Sequence Diversity in the 16S–23S Intergenic Spacer Region (ISR) of the rRNA Operons in Representatives of the Escherichia coli ECOR Collection

Abstract

The ribosomal RNA multigene family in Escherichia coli comprises seven rrn operons of similar, but not identical, sequence. Four operons (rrnC, B, G, and E) contain genes in the 16S-23S intergenic spacer region (ISR) for tRNA(Glu-2) and three (rrnA, D, and H) contain genes for tRNA(Ile-1) and tRNA(Ala-1B). To increase our understanding of their molecular evolution, we have determined the ISR sequence of the seven operons in a set of 12 strains from the ECOR collection. Each operon was specifically amplified using polymerase chain reaction primers designed from genes or open reading frames located upstream of the 16S rRNA genes in E. coli K12. With a single exception (ECOR 40), ISRs containing one or two tRNA genes were found at the same respective loci as those of strain K12. Intercistronic heterogeneity already found in K12 was representative of most variation among the strains studied and the location of polymorphic sites was the same. Dispersed nucleotide substitutions were very few but 21 variable sites were found grouped in a stem-loop, although the secondary structure was conserved. Some regions were found in which a stretch of nucleotides was substituted in block by one alternative, apparently unrelated, sequence (as illustrated by the known putative insertion of rsl in K12). Except for substitutions of different sizes and insertions/deletions found in the ISR, the pattern of nucleotide variation is very similar to that found for the 16S rRNA gene in E. coli. Strains K12 and ECOR 40 showed the highest intercistronic heterogeneity. Most strains showed a strong tendency to homogenization. Concerted evolution could explain the notorious conservation of this region that is supposed to have low functional restrictions.

Patterns of sequence variation in two regions of the 16S rRNA multigene family of Escherichia coli

“…3). However, all strains of MLEE group B2 had only V6-I, indicating that this is a homogeneous group with a highly clonal structure, as previously described by sequencing of the 16s-23s intergenic spacer region (ISR) (Anton et al, 1998 ;Garcia-Martinez et al, 1996), RAPD and RFLP of total DNA (Desjardins et al, 1995), and electrophoretic patterns of carboxylesterase B (Picard et al, 1993). This uniformity was also demonstrated by six strains of a subcluster of MLEE group D, which had only V6-11, and this correlates with the finding of a unique sequence in the ISR limited to only these six strains (Garcia-Martinez et al, 1996).…”

Genotypic Analyses of Escherichia coli Isolated from Chickens with Colibacillosis and Apparently Healthy Chickens in Japan

“…The purity and the amount of DNA in each preparation were estimated colorimetrically and stored at 4 C until use. Amplified ribosomal restriction analysis (ARDRA) was performed on the DNA preparations by the method described by Anton et al (2). The analysis is based on variations of the 16S-23S rRNA intergenic spacer region (ISR) sequence and has been reported to be useful for revealing phylogenic divergence within E. coli (3).…”

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

“…A subset of tDNA loci likely to be associated with ECDNA was selected out of the 85 tDNAs located in the E. coli core genome (except for ileY all the other 85 tDNA loci of strain MG1655 were also present in the genome of strains CFT073, Sakai and EDL933). Because of their stability and because their disruption might adversely affect the growth of strains or their adaptation to changing physiological conditions, tDNAs located inside rDNA (DNA corresponding to rRNA) operons were not studied further (Anton et al, 1998;Asai et al, 1999;Condon et al, 1995). Similarly, insertion inside polycistronic tDNA was considered unlikely since it might disturb the processing of the transcribed RNA into tRNA (King et al, 1986;Li & Deutscher, 1996, 2002Morl & Marchfelder, 2001).…”