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 per formed in H. parainfluenzae and H. influenzae Rd. The long spacer contained two tRNA genes (tRNA(Ala) and tRNA(Ile)) which are highly homologous to th e corresponding genes found in the spacers of other species, such as Haemop hilus spp., Actinobacillus spp., and Plesiomonas shigelloides. At the 3 ' e nd of tRNA(Ala) a putative ribosomal spacer loop was found, showing a stron g secondary structure. Pulsed field gel electrophoresis (PFGE) analysis aft er restriction of the genome of H. parainfluenzae GR with I-Cell I and subs equent polymerase chain reaction (PCR) analysis of PFGE-separated DNA fragm ents demonstrated that the H. parainfluenzae genome contained six operons a nd 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 P CR primers which were useful in the molecular identification of H. parainfl uenzae isolates. (C) 2001 Editions scientifiques et medicales Elsevier SAS.