Characterization of the ribosomal RNA gene clusters in Halobacterium cutirubrum

We present a comprehensive and detailed analysis of the structure and organization of a cloned ribosomal RNA gene cluster from the archaebacterial species Halobacterium cutirubrum. With the exception of a region in the middle of the 23 S rRNA gene, the DNA sequence of the entire gene cluster has been determined. The gene organization is similar to that found in typical eubacteria with the 16, 23, and 5 S genes occupying the proximal, middle, and distal positions, respectively. There appears to be no equivalent to the eucaryotic 5.8 S gene in H. cutirubrum. The cluster also contains two putative tRNA genes, an alanine tRNA gene in the 16-23 S intergenic space, and a cysteine tRNA gene distal to the 5 S rRNA gene. The 16 and 23 S rRNA genes are surrounded by long nearly perfect inverted repeat sequences which are presumably utilized along with other structural features of the RNA for the processing of 16 and 23 S rRNA from a large precursor transcript. The 5' sequence flanking the 16 S rRNA gene contains two imperfect copies, followed by three perfect copies of a bipartite direct-repeat unit. The sequence AAGTAA, believed to be an important component of the Halobacterium promotor, is present in the highly conserved portion of the direct repeat unit. In the 3' region flanking the 5 S rRNA gene there are sequences, a short inverted repeat followed by T5, and a G/C-rich region followed by an A/T-rich region, which may function in transcription termination. Genomic southern hybridization experiments clearly indicate that the ribosomal RNA genes are unique single-copy DNA in H. cutirubrum.