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Characterization of the ribosomal RNA gene cluster in Halobacterium cutirubrum Hui, Ivy Yuk Chee


A detailed analysis of the structure and organization of a cloned ribosomal RNA gene cluster from the archaebacterial species Halobacterium cutirubrum was undertaken. The DNA sequence of the entire gene cluster with the exception of a region in the middle of the 23S rRNA gene was determined. The gene organization is found to be identical to that of eubacteria with the 16S, 23S and 5S genes occupying proximal, middle and distal positions respectively. No equivalent to the eucaryotic 5.8S gene could be demonstrated. This ribosomal RNA gene cluster also contains two putative tRNA genes, an alanine tRNA gene in the 16S-23S intergenic space and a cysteine tRNA gene distal to the 5S rRNA gene. The 16S and 23S rRNA genes are surrounded by long nearly perfect inverted repeat sequences which are presumably utilized in the processing of a large primary transcript into mature rRNAs. The 5' sequence flanking the gene cluster contains two imperfect copies, followed by three perfect copies, of a bipartite direct repeat unit which contains the hexanucleotide sequence AAGTAA, believed to an important component of the Halobacterium promoter. In the 3' sequence flanking the 5S rRNA gene, there are sequences which may function in transcription termination—an inverted repeat followed by T₅ upstream from the cysteine tRNA, and a G/C rich region followed by an A/T rich region downstream from the cysteine tRNA. Finally, genomic Southern hybridization experiments indicated that the ribosomal RNA genes are unique single copy DNA within the Halobacterium cutirubrum genome.

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