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Ribosomal RNA Operons
Chloroplast ribosomal RNA genes are arranged in an operon very similar to the ribosomal RNA operon of bacteria. The bacterial gene order, 168-23S-58, is preserved in chloroplast operons. The "addition" of a gene for 4.58 rRNA may be a rearrangement of DNA rather than an insertion since this RNA is homologous to the 3'-end of the bacterial 238 RNA and can be regarded as the structural equivalent of this portion of the molecule.

An additional point of similarity is the location of tRNA genes for isoleucine and alanine in the spacer between the 16S and 238 rRNA genes. The same two tRNA genes can be found at corresponding positions in several of the RNA operons of both E. coli and B. subtilis. However, in most chloroplasts, these two tRNA genes contain large introns which are not present in bacteria.

The homology between plastid and bacterial rRNA operons is also apparent from DNA sequence. Though intergenic sequences and intron sequences diverge rapidly and large differences are seen between different species of higher plants, there is a high level of homology between corresponding structural genes (exons) of different organisms.

The sequences of bacterial and higher plant plastid rRNA genes show 60% to 80% similarity. A strong homology between plant and bacterial sequences at the 3' end of the 16S gene, which in bacteria is known to be involved in binding the ribosome to the mRNA at the start of translation, provides evidence that this process may be similar in plastids. Supporting this notion is the fact that chloroplast RNAs have often been found to contain sequences similar to the ribosome binding sites of bacterial mRNAs. 

Transcription of the plastid rRNA operon probably produces a single primary transcript containing the 16S, 23S, 4.5S and 5S rRNAs, along with spacer tRNAs.

This is then processed by a series of endonuclease cleavage to produce the mature RNA products. However, details of this scheme are difficult, to define precisely, since the processing is so rapid that the original transcript probably never accumulates to detectable levels.

 

 
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