rrn operons in Haemophilus parainfluenzae and mosaicism of conserved and species-specific sequences in the 16S-23S rDNA long spacer

The mosaic organisation of short-sequence boxes was analysed in the cloned and sequenced long ribosomal spacer (547 bp) of Haemophilus parainfluenzae GR. Comparison and alignment of both the long and the short spacer were performed in H. parainfluenzae and H. influenzae Rd. The long spacer contained two tRNA genes (tRNA(Ala) and tRNA(Ile)) which are highly homologous to the corresponding genes found in the spacers of other species, such as Haemophilus spp., Actinobacillus spp., and Plesiomonas shigelloides. At the 3' end of tRNA(Ala) a putative ribosomal spacer loop was found, showing a strong secondary structure. Pulsed field gel electrophoresis (PFGE) analysis after restriction of the genome of H. parainfluenzae GR with I-Ceu I and subsequent polymerase chain reaction (PCR) analysis of PFGE-separated DNA fragments demonstrated that the H. parainfluenzae genome contained six operons and that the long spacer was present in three copies of them. Two short DNA segments were identified as being species-specific, allowing us to design PCR primers which were useful in the molecular identification of H. parainfluenzae isolates.