Archaebacteria: transcription and processing of ribosomal RNA sequences in Halobacterium cutirubrum

The chromosome of Halobacterium cutirubum contains a single ribosomal RNA gene cluster. The 5′ to 3′ organization of genes within this 6‐kbp region is: 16S, alanine tRNA, 23S, 5S, cysteine tRNA. The entire gene cluster is transcribed as a single long primary transcript; processing of mature RNA sequences from the 5′ region of the transcript begins prior to the completion of synthesis at the 3′ end. There are five conserved octanucleotide direct repeats (TGCGAACG) in the 900‐bp 5′‐flanking sequence in front of the 16S gene. The positions of these repeat sequences correspond to the different 5′ ends of the primary transcript and probably represent the RNA polymerase start sites. The 16S and 23S rRNA genes are surrounded by long nearly perfect inverted repeat sequences. These sequences probably form duplex structures in the primary transcript and are recognized by an RNaseIII‐like endonuclease activity that carries out the initial excision of the precursor 16S and 23S rRNA sequences. These precursors are rapidly trimmed to the mature 16S and 23S molecules and assembled into ribosomal particles. The processing sites for 5S rRNA appear to be at or very near to the mature ends of the 5S molecule. The tRNA sequences are processed with reduced efficiency from the primary transcript. Nuclease cuts have been detected at the ends as well as in the middle of the cysteine tRNA sequence suggesting that there may be alternative processing pathways, one resulting in proper excision of the mature tRNA sequence and the other resulting in improper excision and degradation of the tRNA sequence. The transcription termination sequence is believed to be at or beyond an AT‐rich sequence preceded by a GC‐rich sequence located distal to the cysteine tRNA gene.