Splitting of the ribosomal RNA operon on chloroplast DNA from Chlorella ellipsoidea

Summary

We have found in the chloroplast rRNA genes of the unicellular green alga Chlorella ellipsoidea an extended rearrangement, an inversion of a 5.0 kb region which includes the genes for tRNA ^Ala_UGC , 23 S rRNA and 5S rRNA, that results in the rRNA operon being split into two operons: namely, operon 1, 16S rRNA-tRNA ^Ile_GAU and operon 2, tRNA ^Ala_UGC -23 S rRNA-5 S rRNA. S1 mapping using in vitro transcribed rRNAs showed that transcription of the 16 S rRNA gene initiated at 202 and 204 bp upstream from the 5′ end of the 16 S rRNA gene, where the -10 region and the-35 region corresponded to TATCGT and TTGACG, respectively. On the other hand, the genes for tRNA ^Ala_UGC and 23 S rRNA were transcribed in the opposite direction from a point 593 bp upstream from the 5′ end of the 23 S rRNA gene; the -10 and -35 regions were TATTCT and TTGACG, respectively. Sequences around these two putative promoter regions are very similar to each other; this suggests that the two promoters could potentially be transcribed by the same RNA polymerase at the same efficiency. In addition, the second promoter (operon 2) is fanked by inverted repeat sequences of 45 bp, next to which a 12 bp unique sequence is repeated tandemly, giving a possible secondary structure very similar to that of transposable elements. A mechanism through which one prokaryotic operon consisting of several genes splits into two or more smaller operons is discussed in the light of these observations.