Comparison of conserved structural and regulatory domains within divergent16S rRNA-23S rRNA spacer sequences of cyanobacteria

PCR amplification of the internal transcribed spacer (ITS) between the 16S rRNA and 23S rRNA genes of the cyanobacterium Nostoc PCC 7120 gave three pr oducts. Two represented true ITS regions of different sizes, while the thir d was a heteroduplex. The longer spacer (ITS-L) contained 512 nucleotides a nd carried tRNA(Ile) and tRNA(Ala) genes, separated by a large stem-loop st ructure (V2) composed of short tandemly repeated repetitive sequences. Both tRNA genes, and the 5' half of the intervening stem, were absent from the shorter spacer (ITS-S), of length 283 nucleotides, which was otherwise almo st completely identical to ITS-L. The two spacer regions of Nostoc PCC 7120 were aligned to published ITS sequences of cyanobacteria, the cyanelle of Cyanophora paradoxa and Escherichia coil. Although the ITS regions of cyano bacteria vary in length from 283 to 545 nucleotides and contain either both tRNA(Ile) and tRNA(Ala) genes, only the tRNA(Ile) gene, or neither, there is no correlation between ITS size and coding capacity for tRNAs. Putative secondary structures were determined for the deduced transcripts of the rm operons of several cyanobacteria and were compared to that of E. coil. High ly conserved motifs important for folding and for maturation of the rRNA tr anscripts were identified, and regions homologous to bacterial antiterminat ors (box B-box A) were located. The conserved and variable regions of the c yanobacterial ITS are potential targets of PCR primers and oligonucleotide probes for detection and identification of cyanobacteria at different taxon omic levels.