The role of recombination and mutation in 16S-23S rDNA spacer rearrangements

The intragenomic heterogeneity of the bacterial intergenic (16S-23S rDNA) s pacer region (ISR) was analysed from the following species in which sequenc es for the complete rRNA operon (rrn) set have been determined (rrn number) : Enterococcus faecalis (6) and E. faecium (6), Bacillus subtilis (10), Sta phylococcus aureus (9), Vibrio cholerae (4), Haemophilus influenzae (6) and Escherichia coli (7). It was found that some spacer sequence blocks were h ighly conserved between operons of a genome, whereas the presence of others was variable. When these variations were analysed using the program PLATO and partial likelihood phylogenies determined by DNAml for each operon set, three regions showed significant (Z>3.3) spatial variation [Region I was 7 8-184 nt long (2.1<Z<49.4), Region II was 10-60 nt long (3.7<Z<23)] and Reg ion III was 6 nt long (3.4<Z>4.4) possibly due to recombination or selectio n. Within Region I, there was sequence block variation in all operon sets [ some operons contained tRNA genes (tRNA(ala), tRNA(ile) or tRNA(glu)), wher eas others had sequence blocks such as VS2 (S. aureus) or rsl (E. coli)]. Q Analysis of the ISR sequence from E. faecalis and E. faecium showed that t here was more interspecies than intraspecies variation (both in DNA sequenc e and in the presence or absence of blocks). Dot matrix analysis of the seq uence blocks in the nine rrn ISRs from S. aureus showed that there was sign ificant homology between VS2 and VS5/VS6. Furthermore, repeat motifs with o nly A or T were present in higher copy numbers in VS5/VS6 than in VS2. Sinc e these sequence blocks (VS2 and VS5-VS6) are related, intragenic evolution resulting in AT expansion may have occurred between these two regions. A m odel is proposed that postulates a role for recombination and AT-expansion in intra-genomic ISR variations. This process may represent a general mecha nism of concerted evolution for bacterial ISR rearrangements. (C) 1999 Else vier Science B.V. All rights reserved.